Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1763500 original size:15 final size:15
Alignment explanation
Indices: 1763480--1763516 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1763470 CTTGAAGAAT
1763480 AAAAAAAT-AATAAGA
1 AAAAAAATGAA-AAGA
1763495 AAAAAAATGAAAAGA
1 AAAAAAATGAAAAGA
1763510 AAAAAAA
1 AAAAAAA
1763517 AACAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (15 bp):
AAAAAAATGAAAAGA
Found at i:1763895 original size:18 final size:18
Alignment explanation
Indices: 1763872--1763909 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1763862 CAAGTTTATC
1763872 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
1763890 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
1763908 TT
1 TT
1763910 CTTTTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:1764195 original size:54 final size:54
Alignment explanation
Indices: 1764113--1764220 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1764103 AGAGAATAAA
*
1764113 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
1 ATCTGTGCAGAAGCCACAGGAAAGGATGAATATGTTGTCAAATATTTTACGAAC
* *
1764167 ATCTGTGCAGAAGCCACATGAAAGGATGAATATGTTGTCAAATGTTTTACGAAC
1 ATCTGTGCAGAAGCCACAGGAAAGGATGAATATGTTGTCAAATATTTTACGAAC
1764221 CAGCGATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (54 bp):
ATCTGTGCAGAAGCCACAGGAAAGGATGAATATGTTGTCAAATATTTTACGAAC
Found at i:1764650 original size:20 final size:22
Alignment explanation
Indices: 1764583--1764667 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
1764573 ACATCTACAT
1764583 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
1764605 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
1764627 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
* * *
1764649 TTTTCAAAGAAGAAAAATT
1 TCTTCAAAGATGATAAATT
1764668 TATTGGATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:1765271 original size:123 final size:123
Alignment explanation
Indices: 1765052--1765384 Score: 490
Period size: 123 Copynumber: 2.7 Consensus size: 123
1765042 CATTCGATGG
* * *
1765052 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTCCATAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* ** *
1765117 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTTTATCACAAAAGGATATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAAC
* *
1765175 ATCAACATTTCCATAGAAAGTTCATAATAAGAAGAAATTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCATAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1765240 ATGAGAAGAACTTGTTCAACCTTTTGTATGACGCTATCACAGAAGGAGATAGATCATC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAAC
* ** *
1765298 ATAAACATTTCCATA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCCATAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
*
1765361 AATGAGAAGAATTTGTTCAACCTT
65 AATGAGAAGAACTTGTTCAACCTT
1765385 GCCTTAATTC
Statistics
Matches: 190, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
122 62 0.33
123 128 0.67
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (123 bp):
ATCAACATTTCCATAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAAC
Found at i:1765507 original size:39 final size:39
Alignment explanation
Indices: 1765448--1765549 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 39
1765438 CAGCATTTCC
* * *
1765448 AGAAGGAGTTCATAATGAGAAGAAGTCATATGAAAAAGA
1 AGAATGAGTTCATAATGAGAAGAACTCATATAAAAAAGA
* * *
1765487 GGAATGAGTTCATAATGAGAAGATCTCATCTAAAAAAGA
1 AGAATGAGTTCATAATGAGAAGAACTCATATAAAAAAGA
*
1765526 AGAATAAGTTCATAATGAGAAGAA
1 AGAATGAGTTCATAATGAGAAGAA
1765550 TTTGTTCAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.21
Consensus pattern (39 bp):
AGAATGAGTTCATAATGAGAAGAACTCATATAAAAAAGA
Found at i:1765789 original size:3 final size:3
Alignment explanation
Indices: 1765781--1765844 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
1765771 TGTTTGTTTT
*
1765781 TTA TTA TTA TTA TAA TTA TT- TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1765827 ATA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1765845 AATAATAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.08
3 49 0.92
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1765802 original size:22 final size:22
Alignment explanation
Indices: 1765777--1765843 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1765767 CATTTGTTTG
1765777 TTTT-TTATTATTATTATAATTA
1 TTTTATTA-TATTATTATAATTA
*
1765799 TTTTATTATATTATTATTATTA
1 TTTTATTATATTATTATAATTA
* *
1765821 --TTATTAATATTAATATTATTA
1 TTTTATT-ATATTATTATAATTA
1765842 TT
1 TT
1765844 AAATAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 5 0.13
21 14 0.36
22 17 0.44
23 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATATTATTATAATTA
Found at i:1767219 original size:13 final size:14
Alignment explanation
Indices: 1767201--1767251 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
1767191 CACAGTTTAG
1767201 TTATAT-TTTAATT
1 TTATATATTTAATT
1767214 TTATATATTT-ATT
1 TTATATATTTAATT
1767227 TTCAATATATTTAATT
1 TT--ATATATTTAATT
1767243 ATTAT-TATT
1 -TTATATATT
1767252 ATTATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.33
14 7 0.21
15 10 0.30
16 3 0.09
17 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:1767248 original size:3 final size:3
Alignment explanation
Indices: 1767240--1767283 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1767230 AATATATTTA
1767240 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1767284 AAATATAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1767703 original size:2 final size:2
Alignment explanation
Indices: 1767660--1767690 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1767650 ATTTATAAAA
*
1767660 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1767691 AAAGTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1767707 original size:151 final size:148
Alignment explanation
Indices: 1767407--1767693 Score: 345
Period size: 151 Copynumber: 2.0 Consensus size: 148
1767397 AATAATCATA
* *
1767407 TTTTAATATTTATTTTTTTTAATATTAAGAAAATAGTTGTCTTAAAGCAACTAGAAGTCCTTTTC
1 TTTTAATATTTATTTTTTTTAATATTAAGAAAATAGCTGTCTTAAAGCAACTAGAAGTACTTTTC
* * * * * * *
1767472 TGATATTTTTAAATAACTAAATATCCTATTTTGATAAATTATATATATATTAATTTAATTTAATT
66 TGATATTTGTAAATAAATAAATATCCTATTTTGATAAAATATAAATATATTAATATAATATAATA
* * *
1767537 TATTTTTAGAAAAATTTT
131 TATATATAAAAAAATTTT
*
1767555 TTATTAATATTTATTAATTTTTTAATATTAAGAAAAT-GACTGTCTTAAAGCAACTAGAAGTATT
1 TT-TTAATATTTATT--TTTTTTAATATTAAGAAAATAG-CTGTCTTAAAGCAACTAGAAGTACT
* *
1767619 TTTCTGATATTTGTAAGTAAATAAATATCTTA-TTT-ATAAAAATATAAATATA-T-ATAT-ATA
62 TTTCTGATATTTGTAAATAAATAAATATCCTATTTTGAT-AAAATATAAATATATTAATATAATA
1767679 T-ATATATATATAAAA
126 TAATATATATATAAAA
1767694 GTTAATATAT
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
146 10 0.08
147 3 0.03
148 5 0.04
149 15 0.13
150 16 0.13
151 70 0.59
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (148 bp):
TTTTAATATTTATTTTTTTTAATATTAAGAAAATAGCTGTCTTAAAGCAACTAGAAGTACTTTTC
TGATATTTGTAAATAAATAAATATCCTATTTTGATAAAATATAAATATATTAATATAATATAATA
TATATATAAAAAAATTTT
Found at i:1772801 original size:17 final size:17
Alignment explanation
Indices: 1772779--1772814 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1772769 CCTCACTTTA
* *
1772779 AATATATCATTTTCCCT
1 AATATATCAGTTACCCT
1772796 AATATATCAGTTACCCT
1 AATATATCAGTTACCCT
1772813 AA
1 AA
1772815 CATGTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATATCAGTTACCCT
Found at i:1777840 original size:18 final size:18
Alignment explanation
Indices: 1777817--1777861 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1777807 ACTATGTAAA
1777817 GTAGTATCGATAACGGTC
1 GTAGTATCGATAACGGTC
*
1777835 GTAGTATCGATAATGGTC
1 GTAGTATCGATAACGGTC
*
1777853 ATAGTATCG
1 GTAGTATCG
1777862 GTACCCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (18 bp):
GTAGTATCGATAACGGTC
Found at i:1782016 original size:17 final size:18
Alignment explanation
Indices: 1781983--1782018 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1781973 TAACTTTCCT
1781983 TTTTGAAAAACCTTTTTC
1 TTTTGAAAAACCTTTTTC
1782001 TTTTGAAAAACCTTTTTC
1 TTTTGAAAAACCTTTTTC
1782019 AATTAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTGAAAAACCTTTTTC
Found at i:1782026 original size:17 final size:18
Alignment explanation
Indices: 1781985--1782026 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1781975 ACTTTCCTTT
**
1781985 TTGAAAAACCTTTTTCTT
1 TTGAAAAACCTTTTTCAA
1782003 TTGAAAAACCTTTTTCAA
1 TTGAAAAACCTTTTTCAA
1782021 TT-AAAA
1 TTGAAAA
1782027 CAAATTGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
TTGAAAAACCTTTTTCAA
Found at i:1788577 original size:2 final size:2
Alignment explanation
Indices: 1788570--1788604 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1788560 GTACTTTCTA
1788570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1788605 TTGTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1788660 original size:26 final size:27
Alignment explanation
Indices: 1788599--1788661 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
1788589 TATATATATA
* * *
1788599 TTATATTTGTTATTTTTTTATTTGATTT
1 TTAT-TTTATTATTCTTTTACTTGATTT
*
1788627 TT-GTTTATTATTCTTTTACTT-ATTT
1 TTATTTTATTATTCTTTTACTTGATTT
1788652 TTATTTTATT
1 TTATTTTATT
1788662 TCGCATGTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 6 0.21
26 21 0.72
28 2 0.07
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (27 bp):
TTATTTTATTATTCTTTTACTTGATTT
Found at i:1793328 original size:19 final size:19
Alignment explanation
Indices: 1793298--1793346 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1793288 TCGTTATAAG
1793298 TATTATA-A-TAATATTAT
1 TATTATATATTAATATTAT
*
1793315 TATTGTATATTAATATTAT
1 TATTATATATTAATATTAT
1793334 TATTAT-TATTAAT
1 TATTATATATTAAT
1793347 TGTTACAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTATATATTAATATTAT
Found at i:1795981 original size:203 final size:203
Alignment explanation
Indices: 1795651--1796038 Score: 670
Period size: 203 Copynumber: 1.9 Consensus size: 203
1795641 CAACTGTAGG
1795651 TTTTTTAAAAGAAAACCGAAGGTTCAAGATATTAAACTCTGAGATGTGAGTAATAAACTCAAGAT
1 TTTTTTAAAAGAAAACCGAAGGTTCAAGATATTAAACTCTGAGATGTGAGTAATAAACTCAAGAT
* * *
1795716 TCGAGGGATATCCAAAGATCGCATGAGTCTAGTATCCATGGAAGAGTAGTGGAACGAGTTATTTC
66 CCGAGGGATATCCAAAGATCACATGAGTCTAGTATCCATGGAAGAGTAGTGGAACAAGTTATTTC
* * * *
1795781 CAATATTGCATATTTGTTCTCCACAAAAGAGTAGTGGAAGCAAATCAACCTTGAACAATGTCAAT
131 CAATATTACAGATTTGGTCTCCACAAAAGAGTAGTGGAAGAAAATCAACCTTGAACAATGTCAAT
1795846 CTGCATGT
196 CTGCATGT
*
1795854 TTTTTTAAAAGAAAGA-CGAAGGTTCAAGATATTAAACTCTGAGATGTGAGTAATCAACTCAAGA
1 TTTTTTAAAAGAAA-ACCGAAGGTTCAAGATATTAAACTCTGAGATGTGAGTAATAAACTCAAGA
1795918 TCCGAGGGATATCCAAAGATCACATGAGTCTAGTATCCATGGAAGAGTAGTGGAACAAGTTATTT
65 TCCGAGGGATATCCAAAGATCACATGAGTCTAGTATCCATGGAAGAGTAGTGGAACAAGTTATTT
* *
1795983 CCAATATTACAGATTTGGTCTCCACAGAAGAGTGGTGGAAGAAAATCAACCTTGAA
130 CCAATATTACAGATTTGGTCTCCACAAAAGAGTAGTGGAAGAAAATCAACCTTGAA
1796039 TCTGATCTTC
Statistics
Matches: 174, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
203 173 0.99
204 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (203 bp):
TTTTTTAAAAGAAAACCGAAGGTTCAAGATATTAAACTCTGAGATGTGAGTAATAAACTCAAGAT
CCGAGGGATATCCAAAGATCACATGAGTCTAGTATCCATGGAAGAGTAGTGGAACAAGTTATTTC
CAATATTACAGATTTGGTCTCCACAAAAGAGTAGTGGAAGAAAATCAACCTTGAACAATGTCAAT
CTGCATGT
Found at i:1796127 original size:36 final size:36
Alignment explanation
Indices: 1796080--1796219 Score: 208
Period size: 36 Copynumber: 3.9 Consensus size: 36
1796070 TTCTTTTCAA
* *
1796080 GCAAATCCAGCCTTCACAAAAGAGTAGTGAAGTAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
* *
1796116 GCAAATCCAGCCTTCACAAAAAAGTAGTGAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
** *
1796152 GCAAATCAAGCCTTCTTAAAAGAGTAGTTAAGCAAT
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
*
1796188 GCAAATAAAGCCTTCACAAAAGAGTAGTGAAG
1 GCAAATCAAGCCTTCACAAAAGAGTAGTGAAG
1796220 TAGGAACATA
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (36 bp):
GCAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
Found at i:1796432 original size:13 final size:13
Alignment explanation
Indices: 1796414--1796438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1796404 GTATTAAAAT
1796414 ATTATTATTATAA
1 ATTATTATTATAA
1796427 ATTATTATTATA
1 ATTATTATTATA
1796439 TTAATATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTATTATAA
Found at i:1801430 original size:9 final size:8
Alignment explanation
Indices: 1801414--1801472 Score: 59
Period size: 8 Copynumber: 7.5 Consensus size: 8
1801404 TAATTTAGCC
1801414 TTTTATTA
1 TTTTATTA
1801422 TTATTATTA
1 TT-TTATTA
*
1801431 TTATA-TA
1 TTTTATTA
*
1801438 TTTTTTTA
1 TTTTATTA
*
1801446 TTTTTTTA
1 TTTTATTA
1801454 TTTTATT-
1 TTTTATTA
*
1801461 TTTTACTA
1 TTTTATTA
1801469 TTTT
1 TTTT
1801473 CCCTTTTTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
7 11 0.26
8 24 0.56
9 8 0.19
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATTA
Found at i:1801555 original size:53 final size:50
Alignment explanation
Indices: 1801489--1801610 Score: 124
Period size: 52 Copynumber: 2.3 Consensus size: 50
1801479 TTGGTTTTTT
1801489 TTTATTTATTTTTTTCCT-CCTAACATTATATATA-TATATATATTATTTATTTA
1 TTTATTTATTTTTTT--TACCTAACATTAT-TA-AGTATATATATT-TTTATTTA
* *
1801542 TTTATTTGA-TTTTTTTAGCTAACATTATTAAGTATATATATTTTTATTTT
1 TTTATTT-ATTTTTTTTACCTAACATTATTAAGTATATATATTTTTATTTA
*
1801592 TTTATAATTATTGTTTTTA
1 TTTAT--TTATTTTTTTTA
1801611 TATTTATTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
50 13 0.22
51 14 0.23
52 19 0.32
53 13 0.22
54 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (50 bp):
TTTATTTATTTTTTTTACCTAACATTATTAAGTATATATATTTTTATTTA
Found at i:1801610 original size:15 final size:14
Alignment explanation
Indices: 1801585--1801626 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1801575 ATATATATTT
1801585 TTATTTTTTTATAA
1 TTATTTTTTTATAA
*
1801599 TTATTGTTTTTATAT
1 TTATT-TTTTTATAA
1801614 TTATTTATTTTAT
1 TTATTT-TTTTAT
1801627 TTGTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTATTTTTTTATAA
Found at i:1801678 original size:21 final size:20
Alignment explanation
Indices: 1801654--1801706 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1801644 ATATATATAT
*
1801654 TATTTTATTTTTATTTTTTTC
1 TATTTTATTTTT-TTGTTTTC
*
1801675 TATTCTATTCTTTTTGTTTTC
1 TATTTTATT-TTTTTGTTTTC
*
1801696 TTTTTTATTTT
1 TATTTTATTTT
1801707 GTTTCTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.07
21 22 0.81
22 3 0.11
ACGTcount: A:0.11, C:0.08, G:0.02, T:0.79
Consensus pattern (20 bp):
TATTTTATTTTTTTGTTTTC
Found at i:1801706 original size:18 final size:18
Alignment explanation
Indices: 1801686--1801720 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1801676 ATTCTATTCT
1801686 TTTTGTTT-TCTTTTTTA
1 TTTTGTTTCTCTTTTTTA
*
1801703 TTTTGTTTCTGTTTTTTA
1 TTTTGTTTCTCTTTTTTA
1801721 ATCTTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTTGTTTCTCTTTTTTA
Found at i:1801768 original size:10 final size:10
Alignment explanation
Indices: 1801750--1801799 Score: 63
Period size: 9 Copynumber: 5.4 Consensus size: 10
1801740 TTATTTTTAT
1801750 TTTTATCTTA
1 TTTTATCTTA
*
1801760 TTATATCTTA
1 TTTTATCTTA
1801770 TTTTAT-TTA
1 TTTTATCTTA
1801779 TTTTA-CTTA
1 TTTTATCTTA
1801788 TTTT-T-TTA
1 TTTTATCTTA
1801796 TTTT
1 TTTT
1801800 TTATTGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 7 0.19
9 15 0.42
10 14 0.39
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATCTTA
Found at i:1801800 original size:18 final size:18
Alignment explanation
Indices: 1801750--1801799 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
1801740 TTATTTTTAT
*
1801750 TTTTATCTTATTATATCTTA
1 TTTTAT-TTATTTTA-CTTA
1801770 TTTTATTTATTTTACTTA
1 TTTTATTTATTTTACTTA
1801788 TTTT-TTTATTTT
1 TTTTATTTATTTT
1801800 TTATTGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 8 0.28
18 8 0.28
19 7 0.24
20 6 0.21
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTATTTTACTTA
Found at i:1801801 original size:28 final size:29
Alignment explanation
Indices: 1801765--1801830 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1801755 TCTTATTATA
*
1801765 TCTTATTTTATT-TATTTTACT-TATTTT
1 TCTTTTTTTATTGTATTTTACTGTATTTT
* * *
1801792 TTTATTTTTTATTGTGTTTTATTGTATTTT
1 TCT-TTTTTTATTGTATTTTACTGTATTTT
1801822 TCTTTTTTT
1 TCTTTTTTT
1801831 CTTTTTTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 2 0.06
28 8 0.26
29 13 0.42
30 8 0.26
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (29 bp):
TCTTTTTTTATTGTATTTTACTGTATTTT
Found at i:1814651 original size:18 final size:17
Alignment explanation
Indices: 1814628--1814661 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1814618 TCCTAAGTCG
1814628 AAAAAGAAAAAGAAAAGA
1 AAAAAGAAAAA-AAAAGA
*
1814646 AAAAAGAGAAAAAAAG
1 AAAAAGAAAAAAAAAG
1814662 TTTAGGGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAGA
Found at i:1817190 original size:22 final size:23
Alignment explanation
Indices: 1817162--1817214 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
1817152 AGCATTCGGT
* *
1817162 TCGTTTATA-TTCATGAACTAGC
1 TCGTTTATAGTTCATAAACAAGC
1817184 TCGTTTATATGTTCATAAACAAGC
1 TCGTTTATA-GTTCATAAACAAGC
1817208 TCGTTTA
1 TCGTTTA
1817215 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 9 0.33
24 18 0.67
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (23 bp):
TCGTTTATAGTTCATAAACAAGC
Found at i:1817994 original size:11 final size:11
Alignment explanation
Indices: 1817978--1818037 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
1817968 GACATGTTCG
1817978 CGAACGTTAAA
1 CGAACGTTAAA
1817989 CGAACGTTAAA
1 CGAACGTTAAA
*
1818000 TGAACGCTT-AA
1 CGAACG-TTAAA
1818011 CGAACGTTAAA
1 CGAACGTTAAA
* *
1818022 TGAACGCTAAA
1 CGAACGTTAAA
*
1818033 TGAAC
1 CGAAC
1818038 ATGTTCTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 2 0.05
11 39 0.91
12 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (11 bp):
CGAACGTTAAA
Found at i:1818012 original size:22 final size:23
Alignment explanation
Indices: 1817979--1818037 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 23
1817969 ACATGTTCGC
1817979 GAACG-TTAAACGAACGTTAAAT
1 GAACGCTTAAACGAACGTTAAAT
1818001 GAACGCTT-AACGAACGTTAAAT
1 GAACGCTTAAACGAACGTTAAAT
*
1818023 GAACGC-TAAATGAAC
1 GAACGCTTAAACGAAC
1818038 ATGTTCTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.91
23 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (23 bp):
GAACGCTTAAACGAACGTTAAAT
Found at i:1818270 original size:49 final size:49
Alignment explanation
Indices: 1818214--1818334 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 49
1818204 CCCTAATTTT
* *
1818214 CATTAAAAGAA-TGCACTTAAAACTATGTCGTTTTCATTAGAGAAAATGA
1 CATTAAAA-AAGTGCACTTAAAACTATATCGTTTTCATCAGAGAAAATGA
* * *
1818263 CATTAAAAAAAAGTGCACTTAGAACTATATCGTTTTCATCAGGGAAAATGG
1 CATT--AAAAAAGTGCACTTAAAACTATATCGTTTTCATCAGAGAAAATGA
*
1818314 CATTAAAAAAGGGCACTTAAA
1 CATTAAAAAAGTGCACTTAAA
1818335 TTCATCAGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
49 19 0.31
50 2 0.03
51 41 0.66
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (49 bp):
CATTAAAAAAGTGCACTTAAAACTATATCGTTTTCATCAGAGAAAATGA
Found at i:1823532 original size:16 final size:16
Alignment explanation
Indices: 1823508--1823542 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1823498 ATATGAGAAA
1823508 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
* *
1823524 AAATTAATTTAATTTT
1 AAATCAATTTAAATTT
1823540 AAA
1 AAA
1823543 ATAACGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:1824392 original size:34 final size:34
Alignment explanation
Indices: 1824349--1824414 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
1824339 AAATTTTCAA
1824349 AGGAAATAATACAACTTACCCATAGAGAAAGCTG
1 AGGAAATAATACAACTTACCCATAGAGAAAGCTG
* *
1824383 AGGAAATAATACAACTTCCCCATAGAGGAAGC
1 AGGAAATAATACAACTTACCCATAGAGAAAGC
1824415 GTAATTACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (34 bp):
AGGAAATAATACAACTTACCCATAGAGAAAGCTG
Found at i:1827396 original size:30 final size:30
Alignment explanation
Indices: 1827305--1827397 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
1827295 TAATAGCAAG
* * *
1827305 TTAGCCTTTTAACTTTATATTTTTGTTATT
1 TTAGCCTTTTAAATTTATGTTTTTGATATT
* * *
1827335 TTAGCCTTTTAAGTTTATG-TTTGGACCATT
1 TTAGCCTTTTAAATTTATGTTTTTGA-TATT
* *
1827365 TTAGCCCTTTAAATTTCTGTTTTTGATATT
1 TTAGCCTTTTAAATTTATGTTTTTGATATT
1827395 TTA
1 TTA
1827398 ATTCTTTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
29 4 0.08
30 42 0.82
31 5 0.10
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.57
Consensus pattern (30 bp):
TTAGCCTTTTAAATTTATGTTTTTGATATT
Found at i:1827431 original size:27 final size:26
Alignment explanation
Indices: 1827382--1827433 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1827372 TTTAAATTTC
*
1827382 TGTTTTTGATATTTTAATTCTTTAAA
1 TGTTTTTGATATTTTAATCCTTTAAA
* *
1827408 TGTTTTCTGTTATTTTAGTCCTTTAA
1 TGTTTT-TGATATTTTAATCCTTTAA
1827434 GTTTCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62
Consensus pattern (26 bp):
TGTTTTTGATATTTTAATCCTTTAAA
Found at i:1831589 original size:16 final size:16
Alignment explanation
Indices: 1831548--1831602 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1831538 ACACACACTT
*
1831548 ATACACACACGCACTC
1 ATACACACACGCACAC
* * *
1831564 ACACAAACACGCAGAC
1 ATACACACACGCACAC
*
1831580 ATGCACACACGCACAC
1 ATACACACACGCACAC
1831596 ATACACA
1 ATACACA
1831603 TGCAAGCACA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.44, C:0.40, G:0.09, T:0.07
Consensus pattern (16 bp):
ATACACACACGCACAC
Found at i:1848922 original size:19 final size:21
Alignment explanation
Indices: 1848900--1848942 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1848890 AAAATATATG
1848900 TTGAAAAC-AAAA-AAAAACT
1 TTGAAAACGAAAAGAAAAACT
1848919 TTGAAAACGAAAAGGAAAAACT
1 TTGAAAACGAAAA-GAAAAACT
1848941 TT
1 TT
1848943 TATTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
22 9 0.43
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (21 bp):
TTGAAAACGAAAAGAAAAACT
Found at i:1855934 original size:31 final size:31
Alignment explanation
Indices: 1855896--1855972 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
1855886 TAAGTCGAGC
* *
1855896 CTTGGGTAGGCTCTGCGA-CCCCGAGATTTTT
1 CTTGGGTAGGCTCTG-GAGCCCCGAGAATTGT
* *
1855927 CTTGGGTAAGCCTCTGTAGCCCCGAGAATTGT
1 CTTGGGT-AGGCTCTGGAGCCCCGAGAATTGT
*
1855959 CGTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
1855973 CAGGCCCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.30
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGGAGCCCCGAGAATTGT
Found at i:1856666 original size:14 final size:14
Alignment explanation
Indices: 1856647--1856678 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1856637 AAAGTGTCTC
1856647 TTTTTTTCATTTCT
1 TTTTTTTCATTTCT
*
1856661 TTTTTTTCTTTTCT
1 TTTTTTTCATTTCT
1856675 TTTT
1 TTTT
1856679 CTGCTATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTCATTTCT
Found at i:1864435 original size:24 final size:25
Alignment explanation
Indices: 1864408--1864459 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1864398 TAGGATGTTT
* * *
1864408 AAAAATAAAACTT-AAAATAAAATA
1 AAAAAGAAAACTTGAAAAGAAAAGA
*
1864432 AAAACGAAAACTTGAAAAGAAAAGA
1 AAAAAGAAAACTTGAAAAGAAAAGA
1864457 AAA
1 AAA
1864460 GAAATAACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (25 bp):
AAAAAGAAAACTTGAAAAGAAAAGA
Found at i:1871490 original size:14 final size:15
Alignment explanation
Indices: 1871471--1871499 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1871461 AACATTGTAT
1871471 CAAAAT-TAAATAAA
1 CAAAATGTAAATAAA
1871485 CAAAATGTAAATAAA
1 CAAAATGTAAATAAA
1871500 AGGGTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (15 bp):
CAAAATGTAAATAAA
Found at i:1872692 original size:221 final size:221
Alignment explanation
Indices: 1872238--1872678 Score: 875
Period size: 221 Copynumber: 2.0 Consensus size: 221
1872228 ATACAATGAC
1872238 CACAACAAAATAGCTGTCGCTTTTTCCCATTTCTATGGGATAAGGGGAAAGTAAGATAGTAGGCT
1 CACAACAAAATAGCTGTCGCTTTTTCCCATTTCTATGGGATAAGGGGAAAGTAAGATAGTAGGCT
1872303 ACCAACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTTTGAATTATGAAATGCCCTCCGTGGGA
66 ACCAACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTTTGAATTATGAAATGCCCTCCGTGGGA
1872368 CTCGATCCCACGACCTCAAGGTTAAGAACATTGTGCTCTACCAACTGAGCTGGATGGTCATTTCT
131 CTCGATCCCACGACCTCAAGGTTAAGAACATTGTGCTCTACCAACTGAGCTGGATGGTCATTTCT
1872433 AATTTCTAATACAATGACCACAACAA
196 AATTTCTAATACAATGACCACAACAA
1872459 CACAACAAAATAGCTGTCGCTTTTTCCCATTTCTATGGGATAAGGGGAAAGTAAGATAGTAGGCT
1 CACAACAAAATAGCTGTCGCTTTTTCCCATTTCTATGGGATAAGGGGAAAGTAAGATAGTAGGCT
1872524 ACCAACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTTTGAATTATGAAATGCCCTCCGT-GGA
66 ACCAACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTTTGAATTATGAAATGCCCTCCGTGGGA
1872588 CTCGATCCCACGACCTCAAGGTTAAGAACATTGTGCTCTACCAACTGAGCTGGATGGTCATTTCT
131 CTCGATCCCACGACCTCAAGGTTAAGAACATTGTGCTCTACCAACTGAGCTGGATGGTCATTTCT
1872653 AATTTCTAATACAATGACCACAACAA
196 AATTTCTAATACAATGACCACAACAA
1872679 AGTTATTAAA
Statistics
Matches: 220, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
220 94 0.43
221 126 0.57
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (221 bp):
CACAACAAAATAGCTGTCGCTTTTTCCCATTTCTATGGGATAAGGGGAAAGTAAGATAGTAGGCT
ACCAACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTTTGAATTATGAAATGCCCTCCGTGGGA
CTCGATCCCACGACCTCAAGGTTAAGAACATTGTGCTCTACCAACTGAGCTGGATGGTCATTTCT
AATTTCTAATACAATGACCACAACAA
Found at i:1874023 original size:29 final size:29
Alignment explanation
Indices: 1873988--1874069 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1873978 AAACTAAATT
*
1873988 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1874017 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1874046 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1874070 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1878766 original size:29 final size:29
Alignment explanation
Indices: 1878731--1878812 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1878721 AAACTAAATT
*
1878731 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1878760 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1878789 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1878813 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1880360 original size:37 final size:37
Alignment explanation
Indices: 1880316--1880389 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1880306 CGCAATTTAA
1880316 CGGGAAACAAATGATTGCACCGATAACAGGACGCAAC
1 CGGGAAACAAATGATTGCACCGATAACAGGACGCAAC
1880353 CGGGAAACAAATGATTGCACCGATAACAGGACGCAAC
1 CGGGAAACAAATGATTGCACCGATAACAGGACGCAAC
1880390 AACCGTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (37 bp):
CGGGAAACAAATGATTGCACCGATAACAGGACGCAAC
Found at i:1880665 original size:23 final size:24
Alignment explanation
Indices: 1880639--1880724 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
1880629 TATAGATCAA
1880639 TCTTG-ATTAGTGCATTCATGCAC
1 TCTTGTATTAGTGCATTCATGCAC
* *
1880662 TCTTGTATTAATGCTTTCA-GCAC
1 TCTTGTATTAGTGCATTCATGCAC
* *
1880685 TCATGTATTAGTGCA-TCTGTGCAC
1 TCTTGTATTAGTGCATTC-ATGCAC
*
1880709 TCCTGTATTAGTGCAT
1 TCTTGTATTAGTGCAT
1880725 CTGTGCATCC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.04
23 21 0.40
24 29 0.56
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (24 bp):
TCTTGTATTAGTGCATTCATGCAC
Found at i:1880715 original size:24 final size:24
Alignment explanation
Indices: 1880681--1880835 Score: 142
Period size: 24 Copynumber: 6.6 Consensus size: 24
1880671 AATGCTTTCA
*
1880681 GCACTCATGTATTAGTGCATCTGT
1 GCACTCCTGTATTAGTGCATCTGT
1880705 GCACTCCTGTATTAGTGCATCTGT
1 GCACTCCTGTATTAGTGCATCTGT
* ** *
1880729 GCA-TCCTGTATTAATATTAT-TGG
1 GCACTCCTGTATTAGT-GCATCTGT
* * * *
1880752 GTACTTCTATATTTAGTACAT-TCGT
1 GCACTCCTGTA-TTAGTGCATCT-GT
**
1880777 G---TAATGTATTAGTGCATCTGT
1 GCACTCCTGTATTAGTGCATCTGT
1880798 GCACTCCTGTATTAGTGCATCTGT
1 GCACTCCTGTATTAGTGCATCTGT
1880822 GCACTCCTGTATTA
1 GCACTCCTGTATTA
1880836 ATATTATTGG
Statistics
Matches: 105, Mismatches: 18, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
21 11 0.10
22 5 0.05
23 15 0.14
24 68 0.65
25 6 0.06
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
GCACTCCTGTATTAGTGCATCTGT
Found at i:1880870 original size:94 final size:93
Alignment explanation
Indices: 1880687--1880873 Score: 365
Period size: 94 Copynumber: 2.0 Consensus size: 93
1880677 TTCAGCACTC
1880687 ATGTATTAGTGCATCTGTGCACTCCTGTATTAGTGCATCTGTGCATCCTGTATTAATATTATTGG
1 ATGTATTAGTGCATCTGTGCACTCCTGTATTAGTGCATCTGTGCATCCTGTATTAATATTATTGG
1880752 GTACTTCTATATTTAGTACATTCGTGTA
66 GTACTTCTATATTTAGTACATTCGTGTA
1880780 ATGTATTAGTGCATCTGTGCACTCCTGTATTAGTGCATCTGTGCACTCCTGTATTAATATTATTG
1 ATGTATTAGTGCATCTGTGCACTCCTGTATTAGTGCATCTGTGCA-TCCTGTATTAATATTATTG
1880845 GGTACTTCTATATTTAGTACATTCGTGTA
65 GGTACTTCTATATTTAGTACATTCGTGTA
1880874 CTCATGGCAC
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 45 0.48
94 48 0.52
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (93 bp):
ATGTATTAGTGCATCTGTGCACTCCTGTATTAGTGCATCTGTGCATCCTGTATTAATATTATTGG
GTACTTCTATATTTAGTACATTCGTGTA
Found at i:1881637 original size:67 final size:67
Alignment explanation
Indices: 1881560--1881762 Score: 379
Period size: 67 Copynumber: 3.0 Consensus size: 67
1881550 ACCAGTTTTC
* *
1881560 AGATAGTAAATATTTTATATGAAATAGGTAACATTTTTAACTTGTATACGGGTATAAGTATGTGT
1 AGATAGTAAATATTTTATACGAAATAGGTAACATTTTTAACTCGTATACGGGTATAAGTATGTGT
1881625 TA
66 TA
*
1881627 AGATAGTAAATATTTTATACAAAATAGGTAACATTTTTAACTCGTATACGGGTATAAGTATGTGT
1 AGATAGTAAATATTTTATACGAAATAGGTAACATTTTTAACTCGTATACGGGTATAAGTATGTGT
1881692 TA
66 TA
1881694 AGATAGTAAATATTTTATACGAAATAGGTAACATTTTTAACTCGTATACGGGTATAAGTATGTGT
1 AGATAGTAAATATTTTATACGAAATAGGTAACATTTTTAACTCGTATACGGGTATAAGTATGTGT
1881759 TA
66 TA
1881761 AG
1 AG
1881763 GGTATATAAG
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 132 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (67 bp):
AGATAGTAAATATTTTATACGAAATAGGTAACATTTTTAACTCGTATACGGGTATAAGTATGTGT
TA
Found at i:1883171 original size:7 final size:7
Alignment explanation
Indices: 1883159--1883183 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1883149 CCCTAAATTA
1883159 AAAACTC
1 AAAACTC
1883166 AAAACTC
1 AAAACTC
1883173 AAAACTC
1 AAAACTC
1883180 AAAA
1 AAAA
1883184 GGCAACTTTT
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:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAACTC
Found at i:1887782 original size:3 final size:3
Alignment explanation
Indices: 1887762--1887807 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
1887752 TTAAAAAATA
*
1887762 TAT TAT TAAT TAT T-T TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1887807 T
1 T
1887808 TAATTTACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1887788 original size:21 final size:21
Alignment explanation
Indices: 1887762--1887807 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1887752 TTAAAAAATA
1887762 TATTATTAATTATT-TTATTAT
1 TATTATTAA-TATTATTATTAT
1887783 TATTATTAATATTATTATTAT
1 TATTATTAATATTATTATTAT
1887804 TATT
1 TATT
1887808 TAATTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTATTAATATTATTATTAT
Found at i:1895510 original size:28 final size:26
Alignment explanation
Indices: 1895481--1895533 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
1895471 TTCGATCTAT
1895481 TTTTTGGTGAAGCTATTAGATAGAGAA
1 TTTTT-GTGAAGCTATTAGATAGAGAA
1895508 --TTTGTGAAGCTATTAGATAGAGAA
1 TTTTTGTGAAGCTATTAGATAGAGAA
1895532 TT
1 TT
1895534 AATCTACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (26 bp):
TTTTTGTGAAGCTATTAGATAGAGAA
Found at i:1895518 original size:24 final size:24
Alignment explanation
Indices: 1895487--1895533 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1895477 CTATTTTTTG
1895487 GTGAAGCTATTAGATAGAGAATTT
1 GTGAAGCTATTAGATAGAGAATTT
1895511 GTGAAGCTATTAGATAGAGAATT
1 GTGAAGCTATTAGATAGAGAATT
1895534 AATCTACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (24 bp):
GTGAAGCTATTAGATAGAGAATTT
Found at i:1906135 original size:70 final size:70
Alignment explanation
Indices: 1906032--1906227 Score: 241
Period size: 70 Copynumber: 2.8 Consensus size: 70
1906022 CTGTAATGCT
* * * * * *
1906032 AGGATATGAATTATACATGTATATAGTTATACCTAGTTAGCAGGGTATGGTTCGATCAACCTGTA
1 AGGATATGGATTATACAGGAATATAGATGTACCTAATTAGCAGGGTATGGTTCGATCAACCTGTA
*
1906097 GTGTC
66 CTGTC
* * * * *
1906102 AGGATATGGATTATGCAGGGATATAGATGTACCTAATTAGTAGGGTATGGTTGGATCAACTTGTA
1 AGGATATGGATTATACAGGAATATAGATGTACCTAATTAGCAGGGTATGGTTCGATCAACCTGTA
1906167 CTGTC
66 CTGTC
* * *
1906172 AGGATATGGATTACACAGGAATATA-ATTGTACCTAATAAGCAGGGCATGGTTCGAT
1 AGGATATGGATTATACAGGAATATAGA-TGTACCTAATTAGCAGGGTATGGTTCGAT
1906228 TCGTGATTGC
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
69 1 0.01
70 106 0.99
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (70 bp):
AGGATATGGATTATACAGGAATATAGATGTACCTAATTAGCAGGGTATGGTTCGATCAACCTGTA
CTGTC
Found at i:1906804 original size:24 final size:22
Alignment explanation
Indices: 1906777--1906856 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 22
1906767 GTATAAATAC
* *
1906777 TTAAATTCACAATATTTTTATATA
1 TTAAATTAAAAATATTTTT-T-TA
*
1906801 TTAACTTAAAAATATTTTTTTA
1 TTAAATTAAAAATATTTTTTTA
* *
1906823 TTAACTTATTAAATATATTTTATTA
1 TTAA---ATTAAAAATATTTTTTTA
1906848 TTAAATTAA
1 TTAAATTAA
1906857 TTTAAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 11 0.23
23 1 0.02
24 16 0.34
25 19 0.40
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAATTAAAAATATTTTTTTA
Found at i:1906827 original size:22 final size:22
Alignment explanation
Indices: 1906787--1906856 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 22
1906777 TTAAATTCAC
1906787 AATATTTTTATATATTAACTTAAA
1 AATATTTTT-T-TATTAACTTAAA
1906811 AATATTTTTTTATTAACTTATTAA
1 AATATTTTTTTATTAACTTA--AA
* *
1906835 ATATATTTTATTATTAAATTAA
1 A-ATATTTTTTTATTAACTTAA
1906857 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 10 0.24
23 2 0.05
24 12 0.29
25 17 0.41
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTTTTTATTAACTTAAA
Found at i:1906834 original size:25 final size:27
Alignment explanation
Indices: 1906800--1906873 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 27
1906790 ATTTTTATAT
* *
1906800 ATTAACTTAAAAATATTTTTTTATTAA
1 ATTAATTTAAAAATATTTTATTATTAA
* *
1906827 CTT-A-TTAAATATATTTTATTATTAA
1 ATTAATTTAAAAATATTTTATTATTAA
1906852 ATTAATTTAAAAATATTTTATT
1 ATTAATTTAAAAATATTTTATT
1906874 TTTATTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 21 0.52
26 2 0.05
27 17 0.43
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTAATTTAAAAATATTTTATTATTAA
Found at i:1906886 original size:27 final size:26
Alignment explanation
Indices: 1906806--1906925 Score: 91
Period size: 27 Copynumber: 4.4 Consensus size: 26
1906796 ATATATTAAC
*
1906806 TTAAAAATATTTT-TTTATTAACTTA-
1 TTAAAAATATTTTATTT-TTAAATTAT
* *
1906831 TTAAATATATTTTATTATTAAATTAAT
1 TTAAAAATATTTTATTTTTAAATT-AT
**
1906858 TTAAAAATATTTTATTTTTATTTTCAT
1 TTAAAAATATTTTATTTTTAAATT-AT
* *
1906885 TTAGAAATATATATTTTATGTTAAAATTTAT
1 TT--AAA-A-ATATTTTATTTTTAAA-TTAT
1906916 TTAAAAATAT
1 TTAAAAATAT
1906926 GACTAAATTG
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
25 18 0.24
26 3 0.04
27 28 0.37
28 1 0.01
29 6 0.08
30 1 0.01
31 16 0.21
32 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTAAAAATATTTTATTTTTAAATTAT
Found at i:1907148 original size:3 final size:3
Alignment explanation
Indices: 1907140--1907230 Score: 155
Period size: 3 Copynumber: 29.3 Consensus size: 3
1907130 TAGTTAACCC
1907140 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1907188 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA GTTCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TT-A TTA TTA T
1907231 AAACACTTTA
Statistics
Matches: 85, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
3 78 0.92
4 5 0.06
5 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1908009 original size:44 final size:45
Alignment explanation
Indices: 1907928--1908084 Score: 162
Period size: 44 Copynumber: 3.6 Consensus size: 45
1907918 TGAGAACAAA
* * * *
1907928 AAACGCCGTAAAAGGTCGAGCTCTATAGCGACATTTTTT-TATAC
1 AAACGCCGTAAAAGGTCAAGATCTATAGCGACGTTTTTTGGATAC
*
1907972 AAACGCCGTAAAAGGTC-AGATATATAGCGACGTTTTTTGGATAC
1 AAACGCCGTAAAAGGTCAAGATCTATAGCGACGTTTTTTGGATAC
* * * *
1908016 AAACACCGCAAAAGG-CAAGATCTATAGCGGCG-TTTTTGGA-AT
1 AAACGCCGTAAAAGGTCAAGATCTATAGCGACGTTTTTTGGATAC
* ** *
1908058 AAATGCCACAAAAGGTCGAGATCTATA
1 AAACGCCGTAAAAGGTCAAGATCTATA
1908085 CCGGCATTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 13 0.13
43 37 0.38
44 47 0.48
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (45 bp):
AAACGCCGTAAAAGGTCAAGATCTATAGCGACGTTTTTTGGATAC
Found at i:1908080 original size:43 final size:42
Alignment explanation
Indices: 1907981--1908107 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 42
1907971 CAAACGCCGT
* * * ** *
1907981 AAAAGGTCAGATATATAGCGACGTTTTTTGGATACAAACACCGC
1 AAAAGGTCAGATCTATAGCGGCG-TTTTTGGA-ATAAATGCCAC
1908025 AAAAGG-CAAGATCTATAGCGGCGTTTTTGGAATAAATGCCAC
1 AAAAGGTC-AGATCTATAGCGGCGTTTTTGGAATAAATGCCAC
* * *
1908067 AAAAGGTCGAGATCTATACCGGCATTTTCGGAATAAATGCC
1 AAAAGGTC-AGATCTATAGCGGCGTTTTTGGAATAAATGCC
1908108 GCAATTATCT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
42 13 0.18
43 39 0.55
44 19 0.27
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAGGTCAGATCTATAGCGGCGTTTTTGGAATAAATGCCAC
Found at i:1911339 original size:45 final size:45
Alignment explanation
Indices: 1911265--1911504 Score: 308
Period size: 45 Copynumber: 5.3 Consensus size: 45
1911255 TGGTATATGG
* * * ***
1911265 TTATGGAAT-AATGGAAAGTGTATTGGTAAACCCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGC
* *
1911309 TTATGGAACAAATGGTAAGTATATTTGTAAAATCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGC
*
1911354 TTATGGAATAAATGGTAAGTATA-TTGATAAAATAAGCTTATGAGC
1 TTATGGAATAAATGGTAAGTATATTTG-TAAAATAAGCTTACGAGC
*
1911399 TTATGGAATAAATGGTAAGTAT-TTTGGTAAAATAAGCTTACTAGC
1 TTATGGAATAAATGGTAAGTATATTT-GTAAAATAAGCTTACGAGC
*
1911444 TTATGGGATTAAATGGTAAGTAT-TTTGGTAAAATAAGCTTACGAGC
1 TTAT-GGAATAAATGGTAAGTATATTT-GTAAAATAAGCTTACGAGC
*
1911490 TTATGGGATAAATGG
1 TTATGGAATAAATGG
1911505 CAAGAGATTT
Statistics
Matches: 176, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
44 11 0.06
45 121 0.69
46 44 0.25
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGC
Found at i:1914292 original size:23 final size:22
Alignment explanation
Indices: 1914262--1914309 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
1914252 CATAAGAGCT
**
1914262 AAAAAATATTAAAAGAAAAAGAA
1 AAAAAATAGAAAAAG-AAAAGAA
1914285 AAAAAATAGAAAAAGAAAAGAA
1 AAAAAATAGAAAAAGAAAAGAA
1914307 AAA
1 AAA
1914310 GAGAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAATAGAAAAAGAAAAGAA
Found at i:1914295 original size:11 final size:10
Alignment explanation
Indices: 1914272--1914326 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 10
1914262 AAAAAATATT
1914272 AAAAGAAAAAG
1 AAAA-AAAAAG
1914283 AAAAAAAATAG
1 AAAAAAAA-AG
1914294 AAAAAGAAAAG
1 AAAAA-AAAAG
1914305 AAAAAGAGAAAG
1 AAAAA-A-AAAG
1914317 AGAAAAAAAA
1 A-AAAAAAAA
1914327 AATGATAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.10
11 23 0.57
12 9 0.22
13 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1914297 original size:7 final size:6
Alignment explanation
Indices: 1914272--1914328 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
1914262 AAAAAATATT
*
1914272 AAAAGA AAAAGA AAAA-A AATAGA AAAAG- AAAAGA AAAAGA GAAAGAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAA-AGA
1914320 AAAA-A AAAA
1 AAAAGA AAAA
1914329 TGATAGATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
5 14 0.31
6 22 0.49
7 6 0.13
8 3 0.07
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:1914297 original size:17 final size:16
Alignment explanation
Indices: 1914272--1914327 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 16
1914262 AAAAAATATT
1914272 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
1914288 AAATAGAAAAAGAAAAGA
1 AAA-AGAAAAAGAAAA-A
1914306 AAAAGAGAAAGAGAAAAA
1 AAAAGA-AAA-AGAAAAA
1914324 AAAA
1 AAAA
1914328 ATGATAGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.08
17 15 0.42
18 12 0.33
19 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAA
Found at i:1917015 original size:21 final size:22
Alignment explanation
Indices: 1916991--1917031 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1916981 TGATTGTTGC
1916991 ATATG-ATGTTATCATGAATAT
1 ATATGAATGTTATCATGAATAT
*
1917012 ATATGAATTTTATCATGAAT
1 ATATGAATGTTATCATGAAT
1917032 GTCATTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ATATGAATGTTATCATGAATAT
Found at i:1917395 original size:45 final size:45
Alignment explanation
Indices: 1917326--1917565 Score: 358
Period size: 45 Copynumber: 5.3 Consensus size: 45
1917316 TGGTATATGG
* * * *
1917326 TTATGGAAT-AATGGCAAGTGTATTGGGAAAATCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
1917370 TTATGGAACAAATGGTAAGTATATTGGTAAAATCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1917415 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
1917460 TTATGGAATAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAAC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
1917505 TTATGGGATTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTAT-GGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1917551 TTAT-GAGATAAATGG
1 TTATGGA-ATAAATGG
1917566 CAAGAGATTT
Statistics
Matches: 182, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
44 10 0.05
45 129 0.71
46 43 0.24
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:1918038 original size:20 final size:21
Alignment explanation
Indices: 1918005--1918046 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1917995 ATTTCCAGAA
1918005 TGCTACAGGGTACCGATACCC
1 TGCTACAGGGTACCGATACCC
1918026 TGCTACA-GGTACCGATACCC
1 TGCTACAGGGTACCGATACCC
1918046 T
1 T
1918047 CACTATTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
TGCTACAGGGTACCGATACCC
Found at i:1925604 original size:41 final size:40
Alignment explanation
Indices: 1925480--1925604 Score: 110
Period size: 41 Copynumber: 3.0 Consensus size: 40
1925470 GCGTTTGTGA
* *
1925480 TTAAAAAGATGTCACTAAAGTACGAGTTTATAGCGGCG-TTT
1 TTAAAAA-ATGCCACTAAAGTACGAGTTT-TAGCAGCGTTTT
* * * *
1925521 ATATAAAAACGCCACTAAAGTATGAGTATTTA-CAGACTTTTT
1 TTA-AAAAATGCCACTAAAGTACGAGT-TTTAGCAG-CGTTTT
* *
1925563 TTAAAAAATGCCACTAAAATACGGGTGTTTAGCAGCGTTTT
1 TTAAAAAATGCCACTAAAGTACGAGT-TTTAGCAGCGTTTT
1925604 T
1 T
1925605 AGAATAAACG
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.03
41 50 0.76
42 14 0.21
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (40 bp):
TTAAAAAATGCCACTAAAGTACGAGTTTTAGCAGCGTTTT
Found at i:1928392 original size:42 final size:41
Alignment explanation
Indices: 1928344--1928480 Score: 136
Period size: 42 Copynumber: 3.3 Consensus size: 41
1928334 TATACAAACA
1928344 CCACTAAAGTACAAGTATTTAGCGGCATTTATGTTAAAAATG
1 CCACTAAAGTACAAGTATTTAGCGGCATTT-TGTTAAAAATG
* *
1928386 CCACTAATA-TACGAGTCTTTAGCGGCA-TTTGTATAAAAATG
1 CCACTAA-AGTACAAGTATTTAGCGGCATTTTGT-TAAAAATG
* * * * * *
1928427 CCACTAAAATACAGGTATGTAGTGGCGTTTGTGCTT-AAAACG
1 CCACTAAAGTACAAGTATTTAGCGGCATTT-TG-TTAAAAATG
1928469 CCACTAAAGTAC
1 CCACTAAAGTAC
1928481 GACCGTTACC
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.05
41 29 0.37
42 41 0.52
43 4 0.05
44 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (41 bp):
CCACTAAAGTACAAGTATTTAGCGGCATTTTGTTAAAAATG
Found at i:1928409 original size:83 final size:82
Alignment explanation
Indices: 1928261--1928537 Score: 229
Period size: 83 Copynumber: 3.4 Consensus size: 82
1928251 AGAAGAAAAT
* * * *
1928261 CCACTAAAGTACGAGTCTTTCGCGGCGTTTATGCTTAAAACGCCACTACAGCACGAATCTATAGC
1 CCACTAAAGTACAAGTATTTAGCGGCGTTTATGCTTAAAACGCCACTA-AACACGAATCTATAGC
* * *
1928326 GGCGTTTTTATACAAACA
65 GGCATTTGTATAAAAACA
* * * * *
1928344 CCACTAAAGTACAAGTATTTAGCGGCATTTATG-TTAAAAATGCCACTAATATACGAGTCTTTAG
1 CCACTAAAGTACAAGTATTTAGCGGCGTTTATGCTT-AAAACGCCACTAA-ACACGAATCTATAG
**
1928408 CGGCATTTGTATAAAAATG
64 CGGCATTTGTATAAAAACA
* * * * * * * *
1928427 CCACTAAAATACAGGTATGTAGTGGCGTTTGTGCTTAAAACGCCACTAAAGTACG-ACCGT-TAC
1 CCACTAAAGTACAAGTATTTAGCGGCGTTTATGCTTAAAACGCCACTAAA-CACGAATC-TATAG
** *
1928490 CGGTGTTTGTACAAAAACA
64 CGGCATTTGTATAAAAACA
* * *
1928509 ACACTAAAATACAA-TATTTACCGGCGTTT
1 CCACTAAAGTACAAGTATTTAGCGGCGTTT
1928538 GTTAAAAAAA
Statistics
Matches: 155, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
81 12 0.08
82 33 0.21
83 108 0.70
84 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (82 bp):
CCACTAAAGTACAAGTATTTAGCGGCGTTTATGCTTAAAACGCCACTAAACACGAATCTATAGCG
GCATTTGTATAAAAACA
Found at i:1934953 original size:2 final size:2
Alignment explanation
Indices: 1934936--1934978 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1934926 TAATAATTAA
* *
1934936 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1934977 AT
1 AT
1934979 TTTATACAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1937844 original size:4 final size:4
Alignment explanation
Indices: 1937827--1937932 Score: 60
Period size: 4 Copynumber: 26.5 Consensus size: 4
1937817 ATTACTAAAA
* * * * *
1937827 TTAT TATAT ATAT TTAT TAAT TTAAT TTA- ATAT TTAT ATAT ATAT TTAT
1 TTAT T-TAT TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT
* * *
1937876 TTA- TTAT CTACT TT-T TTCT TT-T GTT-T TTCTT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTA-T TTAT TTAT TTAT -TTAT TT-AT TTAT TTAT TTAT TTAT
1937923 TTAT TTAT TT
1 TTAT TTAT TT
1937933 TTGTTTCTGT
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
3 11 0.13
4 59 0.72
5 12 0.15
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1937940 original size:35 final size:37
Alignment explanation
Indices: 1937871--1937949 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 37
1937861 TATATATATA
* *
1937871 TTTATTTA-TTATCTACTTTTTTCTTTTGTTTTTCT-
1 TTTATTTATTTATCTACTTTTTTATTTTGTGTTTCTG
*
1937906 TTTATTTATTTATTTA-TTTATTTATTTT-TGTTTCTG
1 TTTATTTATTTATCTACTTT-TTTATTTTGTGTTTCTG
1937942 TTT-TTTAT
1 TTTATTTAT
1937950 CCCATCACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
35 22 0.58
36 16 0.42
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (37 bp):
TTTATTTATTTATCTACTTTTTTATTTTGTGTTTCTG
Found at i:1938006 original size:5 final size:5
Alignment explanation
Indices: 1937958--1938072 Score: 60
Period size: 5 Copynumber: 23.4 Consensus size: 5
1937948 ATCCCATCAC
* * * * * *
1937958 TTTTT TTTTC TTTTT TTTTA TTTAA TTTTG TTTTA -TTAA TTTTTA TTTT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
** * * *
1938007 TATTCG TTTTG TTTTA TCTCA TCTTTA -TTTA TTTTA --TTA TTTTA TTTTA
1 T-TTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
1938056 TTTTA TCTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
1938073 ATTTTTCCTT
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
3 3 0.04
4 8 0.10
5 67 0.80
6 6 0.07
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:1938094 original size:28 final size:29
Alignment explanation
Indices: 1938034--1938105 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
1938024 CTCATCTTTA
**
1938034 TTTATTTTATTATTTTATTTTATTTTATC
1 TTTATTTTATTATTTTATCCTATTTTATC
1938063 -TTATTTTATTATTTT-TCCT-TTTTATC
1 TTTATTTTATTATTTTATCCTATTTTATC
* *
1938089 TTTTATTATGTTATTTT
1 -TTTATTTTATTATTTT
1938106 CATTCTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 7 0.19
27 2 0.05
28 28 0.76
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (29 bp):
TTTATTTTATTATTTTATCCTATTTTATC
Found at i:1939255 original size:15 final size:15
Alignment explanation
Indices: 1939235--1939273 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1939225 ATGCAGTTTA
1939235 TTTTTCTTTATACTT
1 TTTTTCTTTATACTT
*
1939250 TTTTTCTTTCTACTT
1 TTTTTCTTTATACTT
1939265 TTTTTCTTT
1 TTTTTCTTT
1939274 TTTTCTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTATACTT
Found at i:1944942 original size:65 final size:62
Alignment explanation
Indices: 1944873--1945048 Score: 185
Period size: 65 Copynumber: 2.7 Consensus size: 62
1944863 TGGAACACTT
* *
1944873 AGTGCATCGGTGCACTAAGGGTGCATCGATGCATAAAATGCATTCGATGTTT-TA-AACAAGCCT
1 AGTGCATCGATGCA-T--GGGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCCT
1944936 GG
62 -G
* * * *
1944938 AGTGCATCGATGCATGTTCTGTGCATCGATTCATAAAATGCAATCGATGTTTCCATAAAATCCTG
1 AGTGCATCGATGCATG---GGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTG
*
1945003 AGTGCTTCGATGCATGGAAGTGCATCGATGCATAAAATGCATTCGA
1 AGTGCATCGATGCATGG--GTGCATCGATGCATAAAATGCATTCGA
1945049 AATGGGGTGT
Statistics
Matches: 94, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
64 26 0.28
65 59 0.63
66 6 0.06
67 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (62 bp):
AGTGCATCGATGCATGGGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTG
Found at i:1945048 original size:18 final size:19
Alignment explanation
Indices: 1945008--1945048 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1944998 TCCTGAGTGC
* *
1945008 TTCGATGCATGGAAGTGCA
1 TTCGATGCATGAAAATGCA
1945027 -TCGATGCAT-AAAATGCA
1 TTCGATGCATGAAAATGCA
1945044 TTCGA
1 TTCGA
1945049 AATGGGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (19 bp):
TTCGATGCATGAAAATGCA
Found at i:1945677 original size:27 final size:27
Alignment explanation
Indices: 1945647--1945703 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1945637 CTAAATGATG
* * *
1945647 CAAAAATCTAATAAACCAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
* *
1945674 CAAAAACCAAATATATAAATATAAGTT
1 CAAAAACCAAATAAACAAATATAAGTT
1945701 CAA
1 CAA
1945704 GCATTCAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.25
Consensus pattern (27 bp):
CAAAAACCAAATAAACAAATATAAGTT
Found at i:1947719 original size:23 final size:23
Alignment explanation
Indices: 1947687--1947751 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1947677 ATGCACTGCT
*
1947687 GAGTGCATCGATGCACATTCAAG
1 GAGTGTATCGATGCACATTCAAG
* * *
1947710 GAGTGTATCGGTGCACCTT-AAT
1 GAGTGTATCGATGCACATTCAAG
1947732 G-GTGTATCGATGCACATTCA
1 GAGTGTATCGATGCACATTCA
1947752 TAAGATTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 15 0.43
22 4 0.11
23 16 0.46
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (23 bp):
GAGTGTATCGATGCACATTCAAG
Found at i:1947789 original size:21 final size:21
Alignment explanation
Indices: 1947711--1947790 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 21
1947701 ACATTCAAGG
* * *
1947711 AGTGTATCGGTGCACCTTAAT
1 AGTGTATCGATGCATCTTCAT
*
1947732 GGTGTATCGATGCA-CATTCAT
1 AGTGTATCGATGCATC-TTCAT
*
1947753 AAGAT-TCATTGATGCATCTTCAT
1 -AG-TGT-ATCGATGCATCTTCAT
1947776 AGTGTATCGATGCAT
1 AGTGTATCGATGCAT
1947791 TATGCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 26 0.55
22 5 0.11
23 14 0.30
24 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (21 bp):
AGTGTATCGATGCATCTTCAT
Found at i:1951519 original size:21 final size:22
Alignment explanation
Indices: 1951495--1951537 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1951485 AAGACTATTT
1951495 TCATTTTTCAATTTT-AAAATA
1 TCATTTTTCAATTTTGAAAATA
**
1951516 TCATTTTTGTATTTTGAAAATA
1 TCATTTTTCAATTTTGAAAATA
1951538 GAGTCTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
TCATTTTTCAATTTTGAAAATA
Found at i:1953232 original size:7 final size:7
Alignment explanation
Indices: 1953220--1953244 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1953210 TTTGATTCTA
1953220 TCTTGAT
1 TCTTGAT
1953227 TCTTGAT
1 TCTTGAT
1953234 TCTTGAT
1 TCTTGAT
1953241 TCTT
1 TCTT
1953245 TTTGTTGATC
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:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (7 bp):
TCTTGAT
Found at i:1958388 original size:5 final size:5
Alignment explanation
Indices: 1958375--1958465 Score: 55
Period size: 5 Copynumber: 17.8 Consensus size: 5
1958365 TAAAAAGATA
* * ** *
1958375 AAAAT AAAAG AAAAAG AAAAAG AAAAG AAAAG AAAA- ATAA- AAATT AAAAT
1 AAAAG AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1958425 AAAAG AAAAAG AAACGAG AAAAG AAAA- AAGAA- AAAAG AAAA
1 AAAAG -AAAAG AAA--AG AAAAG AAAAG AA-AAG AAAAG AAAA
1958466 AAGAGGAAAG
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
4 9 0.12
5 43 0.59
6 16 0.22
7 5 0.07
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:1958416 original size:39 final size:39
Alignment explanation
Indices: 1958359--1958452 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 39
1958349 CTAAATTGAA
* *
1958359 AAAAGATAA-AAAGATAAAAA-TAAAAGAAAAAGAAAAAG
1 AAAAGAAAAGAAAAATAAAAATTAAAA-AAAAAGAAAAAG
*
1958397 AAAAGAAAAGAAAAATAAAAATTAAAATAAAAGAAAAAG
1 AAAAGAAAAGAAAAATAAAAATTAAAAAAAAAGAAAAAG
1958436 AAACGAGAAAAGAAAAA
1 AAA--AGAAAAGAAAAA
1958453 AGAAAAAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 8 0.16
39 24 0.49
40 5 0.10
41 12 0.24
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.07
Consensus pattern (39 bp):
AAAAGAAAAGAAAAATAAAAATTAAAAAAAAAGAAAAAG
Found at i:1958434 original size:6 final size:6
Alignment explanation
Indices: 1958366--1958486 Score: 81
Period size: 6 Copynumber: 19.5 Consensus size: 6
1958356 GAAAAAAGAT
*
1958366 AAAAAG ATAAAA- ATAAAAG AAAAAG AAAAAG -AAAAG -AAAAG AAAAAT
1 AAAAAG A-AAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * *
1958413 AAAAAT TAAAA- TAAAAG AAAAAG -AAACG AGAAAAG AAAAAAG AAAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG -AAAAAG -AAAAAG
1958462 AAAAAAG AGGAAAGAG AAAAAG AAA
1 -AAAAAG A--AAA-AG AAAAAG AAA
1958487 TAAGGTGGGT
Statistics
Matches: 100, Mismatches: 5, Indels: 20
0.80 0.04 0.16
Matches are distributed among these distances:
5 19 0.19
6 43 0.43
7 31 0.31
8 4 0.04
9 3 0.03
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:1958468 original size:39 final size:36
Alignment explanation
Indices: 1958367--1958469 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 36
1958357 AAAAAAGATA
* *
1958367 AAAAGATAAAAATAAAAG-AAAAAGAAAAAGAAAAG
1 AAAAGAAAAAAAAAAAAGAAAAAAGAAAAAGAAAAG
1958402 AAAAGAAAAATAAAAATTAA-AATAAAAGAAAAAGAAACGAG
1 AAAAGAAAAA-AAAAA--AAGAA-AAAAGAAAAAGAAA--AG
1958443 AAAAGAAAAAAGAAAAAAGAAAAAAGA
1 AAAAGAAAAAA-AAAAAAGAAAAAAGA
1958470 GGAAAGAGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
35 9 0.16
36 4 0.07
38 3 0.05
39 22 0.39
40 3 0.05
41 16 0.28
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.06
Consensus pattern (36 bp):
AAAAGAAAAAAAAAAAAGAAAAAAGAAAAAGAAAAG
Found at i:1961386 original size:11 final size:11
Alignment explanation
Indices: 1961362--1961433 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
1961352 TTAATAATAG
*
1961362 TATTTTT-ATA
1 TATTTTTAATT
1961372 TATTTTTAATT
1 TATTTTTAATT
*
1961383 TATTATCTAA--
1 TATT-TTTAATT
*
1961393 T-TTTTTATTT
1 TATTTTTAATT
*
1961403 TATTTTTTATT
1 TATTTTTAATT
*
1961414 TATTTTTATTT
1 TATTTTTAATT
1961425 CTATTTTTA
1 -TATTTTTA
1961434 TCATATCACT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 3 0.06
9 2 0.04
10 9 0.19
11 22 0.46
12 12 0.25
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTTAATT
Found at i:1961403 original size:5 final size:5
Alignment explanation
Indices: 1961395--1961559 Score: 60
Period size: 5 Copynumber: 33.4 Consensus size: 5
1961385 TTATCTAATT
* * * * *
1961395 TTTTA TTTTA TTTTT TATTTA TTTTTA TTTCTA TTTT- TATCA TATCA
1 TTTTA TTTTA TTTTA T-TTTA -TTTTA TTT-TA TTTTA TTTTA TTTTA
* * * *
1961442 CTTTT- TTTCT- TTTTG TTTTA TTTAA TTTTG TTTTA -TTAA TTTTA -TTTA
1 -TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
** * **
1961490 TTTT- TATTCG TTTTG TTTTA TTTCC TCTTTA -TTTA TTTTA TTTTA --TTA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA
* *
1961538 TTTTA CTTTA TCTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TT
1961560 ATTTTTCCTT
Statistics
Matches: 121, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
3 3 0.02
4 18 0.15
5 82 0.68
6 17 0.14
7 1 0.01
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:1961409 original size:6 final size:6
Alignment explanation
Indices: 1961394--1961434 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1961384 ATTATCTAAT
* *
1961394 TTTTTA -TTTTA TTTTT- TATTTA TTTTTA TTTCTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
1961435 CATATCACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:1961412 original size:24 final size:22
Alignment explanation
Indices: 1961375--1961432 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1961365 TTTTATATAT
*
1961375 TTTTAATTTATTATCTAATTTTTTA
1 TTTT-ATTTTTTAT-TAA-TTTTTA
*
1961400 TTTTATTTTTTATTTATTTTTA
1 TTTTATTTTTTATTAATTTTTA
1961422 TTTCTATTTTT
1 TTT-TATTTTT
1961433 ATCATATCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 9 0.30
23 9 0.30
24 8 0.27
25 4 0.13
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATTTTTTATTAATTTTTA
Found at i:1961470 original size:24 final size:23
Alignment explanation
Indices: 1961443--1961512 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
1961433 ATCATATCAC
1961443 TTTTTTTCTTTTTGTTTTATTTAA
1 TTTTTTTCTTTTTGTTTTATTT-A
* **
1961467 TTTTGTTT-TATTAATTTTATTTA
1 TTTT-TTTCTTTTTGTTTTATTTA
*
1961490 TTTTTATTCGTTTTGTTTTATTT
1 TTTTT-TTCTTTTTGTTTTATTT
1961513 CCTCTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
22 1 0.03
23 7 0.19
24 25 0.69
25 3 0.08
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (23 bp):
TTTTTTTCTTTTTGTTTTATTTA
Found at i:1961525 original size:48 final size:47
Alignment explanation
Indices: 1961443--1961541 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 47
1961433 ATCATATCAC
* *
1961443 TTTTTTTCTTTTTGTTTTATTTAATTTTGTTTTA-TTAATTTTATTTA
1 TTTTTTTCGTTTTGTTTTATTTAATTTTGATTTATTTAATTTTA-TTA
** *
1961490 TTTTTATTCGTTTTGTTTTATTTCCTCTTT-ATTTATTTTATTTTATTA
1 TTTTT-TTCGTTTTGTTTTATTTAAT-TTTGATTTATTTAATTTTATTA
1961538 TTTT
1 TTTT
1961542 ACTTTATCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
47 5 0.11
48 28 0.64
49 11 0.25
ACGTcount: A:0.15, C:0.05, G:0.04, T:0.76
Consensus pattern (47 bp):
TTTTTTTCGTTTTGTTTTATTTAATTTTGATTTATTTAATTTTATTA
Found at i:1961553 original size:23 final size:22
Alignment explanation
Indices: 1961517--1961564 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
1961507 TTATTTCCTC
*
1961517 TTTATTTATTTTATTTTATTAT
1 TTTATTTATCTTATTTTATTAT
1961539 TTTACTTTATCTTATTTTATTAT
1 TTTA-TTTATCTTATTTTATTAT
1961562 TTT
1 TTT
1961565 TCCTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTATCTTATTTTATTAT
Found at i:1962784 original size:24 final size:23
Alignment explanation
Indices: 1962752--1962803 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
1962742 ATAAGGATCG
1962752 TGTCACAAGAGCAGAGAAAACACA
1 TGTCACAAGAGCAGAGAAAA-ACA
*
1962776 TGTCACAAGAGCAGAGAAAAACG
1 TGTCACAAGAGCAGAGAAAAACA
1962799 TGTCA
1 TGTCA
1962804 TAAGGACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (23 bp):
TGTCACAAGAGCAGAGAAAAACA
Found at i:1964687 original size:31 final size:31
Alignment explanation
Indices: 1964644--1964713 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1964634 CTTTTAAAAC
1964644 TTGCAATACAGTCCCCCAACATTTAATCCGT
1 TTGCAATACAGTCCCCCAACATTTAATCCGT
* *
1964675 TTGCAATGCAGTCCCCCAACATTTAGTCCGT
1 TTGCAATACAGTCCCCCAACATTTAATCCGT
1964706 TTGCAATA
1 TTGCAATA
1964714 TGGTCTCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACATTTAATCCGT
Found at i:1970063 original size:11 final size:11
Alignment explanation
Indices: 1970047--1970109 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1970037 AAATTTACAT
1970047 TATTAAAAATA
1 TATTAAAAATA
1970058 TATTAAAAATA
1 TATTAAAAATA
* ***
1970069 CATTATTGATA
1 TATTAAAAATA
1970080 -ATTATAAAAT-
1 TATTA-AAAATA
1970090 T-TTAAAAATA
1 TATTAAAAATA
1970100 TATTAAAAAT
1 TATTAAAAAT
1970110 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1970236 original size:7 final size:7
Alignment explanation
Indices: 1970216--1970315 Score: 83
Period size: 7 Copynumber: 14.3 Consensus size: 7
1970206 ATTTGTAATT
1970216 AACCCTA
1 AACCCTA
**
1970223 AGGCCTA
1 AACCCTA
1970230 AACCCTA
1 AACCCTA
**
1970237 AAATCTA
1 AACCCTA
*
1970244 AATCCTA
1 AACCCTA
1970251 AACCCTA
1 AACCCTA
* *
1970258 AACCTTG
1 AACCCTA
*
1970265 AATCCTA
1 AACCCTA
*
1970272 AATCCTA
1 AACCCTA
* *
1970279 AACCTTT
1 AACCCTA
*
1970286 AATCCTA
1 AACCCTA
1970293 AACCCTA
1 AACCCTA
*
1970300 AACCATA
1 AACCCTA
1970307 AACCCTA
1 AACCCTA
1970314 AA
1 AA
1970316 TCTAATTATA
Statistics
Matches: 70, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 70 1.00
ACGTcount: A:0.43, C:0.32, G:0.03, T:0.22
Consensus pattern (7 bp):
AACCCTA
Found at i:1970250 original size:21 final size:21
Alignment explanation
Indices: 1970226--1970315 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
1970216 AACCCTAAGG
*
1970226 CCTAAACCCTAAA-ATCTAAAT
1 CCTAAACCCTAAACCT-TAAAT
*
1970247 CCTAAACCCTAAACCTTGAAT
1 CCTAAACCCTAAACCTTAAAT
* *
1970268 CCTAAATCCTAAACCTTTAAT
1 CCTAAACCCTAAACCTTAAAT
* *
1970289 CCTAAACCCTAAACCATAAAC
1 CCTAAACCCTAAACCTTAAAT
1970310 CCTAAA
1 CCTAAA
1970316 TCTAATTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 59 0.98
22 1 0.02
ACGTcount: A:0.43, C:0.32, G:0.01, T:0.23
Consensus pattern (21 bp):
CCTAAACCCTAAACCTTAAAT
Found at i:1971477 original size:13 final size:13
Alignment explanation
Indices: 1971459--1971488 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1971449 AACATCTTGA
*
1971459 AAATGTTGGCAGT
1 AAATGTTGGCAAT
1971472 AAATGTTGGCAAT
1 AAATGTTGGCAAT
1971485 AAAT
1 AAAT
1971489 AAGCAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (13 bp):
AAATGTTGGCAAT
Found at i:1972271 original size:11 final size:11
Alignment explanation
Indices: 1972251--1972316 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
1972241 CGCGTGGTGA
*
1972251 TGAATTGAGCT
1 TGAATCGAGCT
1972262 TGAATCGAGCT
1 TGAATCGAGCT
* **
1972273 TGAATTGAATT
1 TGAATCGAGCT
1972284 TGAATCGAGCT
1 TGAATCGAGCT
*
1972295 TGAGTCTTGAGCT
1 TGAATC--GAGCT
*
1972308 TAAATCGAG
1 TGAATCGAG
1972317 TCTCGAGTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 34 0.79
13 9 0.21
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (11 bp):
TGAATCGAGCT
Found at i:1972276 original size:22 final size:22
Alignment explanation
Indices: 1972251--1972316 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
1972241 CGCGTGGTGA
1972251 TGAATTGAGCTTGAATCGAGCT
1 TGAATTGAGCTTGAATCGAGCT
**
1972273 TGAATTGAATTTGAATCGAGCT
1 TGAATTGAGCTTGAATCGAGCT
* *
1972295 TGAGTCTTGAGCTTAAATCGAG
1 TGA--ATTGAGCTTGAATCGAG
1972317 TCTCGAGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 23 0.64
24 13 0.36
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (22 bp):
TGAATTGAGCTTGAATCGAGCT
Found at i:1974180 original size:22 final size:23
Alignment explanation
Indices: 1974152--1974196 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1974142 TTTACAACTT
1974152 AAATTTCTTCCTC-TCAAATTTG
1 AAATTTCTTCCTCTTCAAATTTG
*
1974174 AAATTTCTTCCTCTTTAAATTTG
1 AAATTTCTTCCTCTTCAAATTTG
1974197 CTTTACAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (23 bp):
AAATTTCTTCCTCTTCAAATTTG
Found at i:1974565 original size:33 final size:32
Alignment explanation
Indices: 1974528--1974601 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 32
1974518 ATCGGATTTA
*
1974528 GGTCGGGTCGAGTTTTTTAAAGTTTGATATTCG
1 GGTCGGGTCGAGTTTTTT-AAGTGTGATATTCG
*
1974561 GGTCGGGTC-AGGTTTTTGTAAGTGTGATATTCT
1 GGTCGGGTCGA-GTTTTT-TAAGTGTGATATTCG
1974594 GGTCGGGT
1 GGTCGGGT
1974602 TCGGGTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 1 0.03
33 35 0.95
34 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.35, T:0.41
Consensus pattern (32 bp):
GGTCGGGTCGAGTTTTTTAAGTGTGATATTCG
Found at i:1974620 original size:45 final size:45
Alignment explanation
Indices: 1974557--1974653 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
1974547 AAGTTTGATA
* *
1974557 TTCGGG-TCGGGTCAGGTTTTTGTAAGTGTGATATTCTGGTCGGG
1 TTCGGGTTTGGGTCAGGTTTTTGTAAGTGTGATATTCGGGTCGGG
* * *
1974601 TTCGGGTTTGGGTCGGGTTTTTTTAAGTTTGATATTCGGGTCGGG
1 TTCGGGTTTGGGTCAGGTTTTTGTAAGTGTGATATTCGGGTCGGG
1974646 -TCGGGTTT
1 TTCGGGTTT
1974654 TTTAAGTGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 14 0.30
45 33 0.70
ACGTcount: A:0.09, C:0.10, G:0.38, T:0.42
Consensus pattern (45 bp):
TTCGGGTTTGGGTCAGGTTTTTGTAAGTGTGATATTCGGGTCGGG
Found at i:1974623 original size:78 final size:76
Alignment explanation
Indices: 1974532--1974683 Score: 250
Period size: 78 Copynumber: 2.0 Consensus size: 76
1974522 GATTTAGGTC
*
1974532 GGGTCGAGTTTTTTAAAGTTTGATATTCGGGTCGGGTCAGGTTTTTGTAAGTGTGATATTCTGGT
1 GGGTCGAGTTTTTTAAAGTTTGATATTCGGGTCGGGTCAGGTTTTT-TAAGTGTGATATTCGGGT
1974597 CGGGTTCGGGTTT
65 CGGG-TCGGGTTT
* * *
1974610 GGGTCGGGTTTTTTTAAGTTTGATATTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC
1 GGGTCGAGTTTTTTAAAGTTTGATATTCGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCGGGTC
1974675 GGGTCGGGT
66 GGGTCGGGT
1974684 CGGGTTTAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
76 6 0.09
77 21 0.30
78 43 0.61
ACGTcount: A:0.12, C:0.09, G:0.37, T:0.41
Consensus pattern (76 bp):
GGGTCGAGTTTTTTAAAGTTTGATATTCGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCGGGTC
GGGTCGGGTTT
Found at i:1974649 original size:33 final size:33
Alignment explanation
Indices: 1974601--1974683 Score: 132
Period size: 32 Copynumber: 2.5 Consensus size: 33
1974591 TCTGGTCGGG
* *
1974601 TTCGGGTTTGGGTCGGGTTTTTTTAAGTTTGATA
1 TTCGGG-TCGGGTCGGGTTTTTTTAAGTGTGATA
1974635 TTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
1974667 TTCGGGTCGGGTCGGGT
1 TTCGGGTCGGGTCGGGT
1974684 CGGGTTTAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 31 0.67
33 9 0.20
34 6 0.13
ACGTcount: A:0.10, C:0.10, G:0.39, T:0.42
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:1975293 original size:18 final size:16
Alignment explanation
Indices: 1975251--1975297 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1975241 GTTTCAAATT
*
1975251 CAGATTTCAATTCCTA
1 CAGATTCCAATTCCTA
1975267 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCC-T-A
*
1975285 CATATTCCAATTC
1 CAGATTCCAATTC
1975298 TCTCAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 13 0.48
17 1 0.04
18 13 0.48
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (16 bp):
CAGATTCCAATTCCTA
Found at i:1976344 original size:27 final size:26
Alignment explanation
Indices: 1976296--1976346 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1976286 AACTGACATG
*
1976296 GCAGTTTCTAGAAGGTTCAGTCAGTA
1 GCAGTTTCTAGAAGATTCAGTCAGTA
1976322 GCAGTTTTCTAGAAGA-TCTAGTCAG
1 GCAG-TTTCTAGAAGATTC-AGTCAG
1976347 CGCCTTCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (26 bp):
GCAGTTTCTAGAAGATTCAGTCAGTA
Found at i:1988678 original size:35 final size:35
Alignment explanation
Indices: 1988610--1988684 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
1988600 AAAATACTTC
* *
1988610 AATTTAGGGTTTATAATGTAATTAAAGTATTTTGT
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
*
1988645 AATTTAGGGTTTAGAATGTAATTAACA-TGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTAA-AGTATTTTGG
1988680 AATTT
1 AATTT
1988685 TGAACACGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
Found at i:1992748 original size:20 final size:22
Alignment explanation
Indices: 1992729--1992837 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 22
1992719 AAAAATTTTA
1992729 ATATTATAATAATATATTTAATT
1 ATATTATAATAATATATTTAA-T
** *
1992752 ATATTATAATAATATAGAATATT
1 ATATTATAATAATATA-TTTAAT
*
1992775 ATATTAT-ATTATAT-TTTAAT
1 ATATTATAATAATATATTTAAT
* *
1992795 TTAATT-TAATAA-ATAATTAAT
1 AT-ATTATAATAATATATTTAAT
*
1992816 ATAATT-T-ATAATATTTTTAAT
1 AT-ATTATAATAATATATTTAAT
1992837 A
1 A
1992838 AAGTATATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
20 11 0.16
21 25 0.37
22 6 0.09
23 24 0.35
24 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATTATAATAATATATTTAAT
Found at i:1992780 original size:28 final size:23
Alignment explanation
Indices: 1992729--1992836 Score: 81
Period size: 23 Copynumber: 5.0 Consensus size: 23
1992719 AAAAATTTTA
1992729 ATATTATAATAATATATTTAATT
1 ATATTATAATAATATATTTAATT
**
1992752 ATATTATAATAATATA-GAATATT
1 ATATTATAATAATATATTTA-ATT
*
1992775 ATATTAT-ATTATAT-TTTAATT
1 ATATTATAATAATATATTTAATT
*
1992796 -TAATT-TAATAA-ATAATTAA-T
1 AT-ATTATAATAATATATTTAATT
*
1992816 ATAATT-T-ATAATATTTTTAAT
1 AT-ATTATAATAATATATTTAAT
1992837 AAAGTATATT
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
20 9 0.13
21 25 0.37
22 8 0.12
23 26 0.38
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATTATAATAATATATTTAATT
Found at i:2003678 original size:22 final size:22
Alignment explanation
Indices: 2003653--2003709 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
2003643 ACATTTCATG
* *
2003653 GCACATATATGATATGTTGTTT
1 GCACGTATATGATATGTTGTCT
2003675 GCACGTATATGATATGTTGTCT
1 GCACGTATATGATATGTTGTCT
2003697 GCACGTATATGAT
1 GCACGTATATGAT
2003710 GCTGGTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (22 bp):
GCACGTATATGATATGTTGTCT
Done.