Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1744034 original size:25 final size:25
Alignment explanation
Indices: 1743996--1744119 Score: 214
Period size: 25 Copynumber: 5.0 Consensus size: 25
1743986 AGTTAAGGGA
*
1743996 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1744020 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1744045 TTAGGGTTTAAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1744070 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1744095 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1744120 GGGTTGTCGG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
24 6 0.06
25 89 0.94
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:1744257 original size:3 final size:3
Alignment explanation
Indices: 1744249--1744304 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
1744239 GCAAAAATTG
* **
1744249 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1744293 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1744305 CGGAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1744661 original size:90 final size:89
Alignment explanation
Indices: 1744549--1744718 Score: 288
Period size: 90 Copynumber: 1.9 Consensus size: 89
1744539 CTTTAGGAAG
* *
1744549 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTAC
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATAC
1744613 ATGATGAAGAGATCTGGCCATCTAAA
64 ATGATGAAGAGATCTGGCCATCTAAA
*
1744639 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
1744704 GATGAAGAGATCTGG
66 GATGAAGAGATCTGG
1744719 TCTAGGGATG
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 2 0.03
89 34 0.45
90 40 0.53
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (89 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
GATGAAGAGATCTGGCCATCTAAA
Found at i:1744682 original size:46 final size:46
Alignment explanation
Indices: 1744549--1744682 Score: 132
Period size: 46 Copynumber: 3.0 Consensus size: 46
1744539 CTTTAGGAAG
*
1744549 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * * **
1744595 --TGTTGACACGGCTCTTACATGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAA
1744639 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1744683 TGGTTGACAC
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
46 31 0.48
47 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAA
Found at i:1744703 original size:43 final size:44
Alignment explanation
Indices: 1744566--1744708 Score: 139
Period size: 46 Copynumber: 3.2 Consensus size: 44
1744556 ACTCGGTTCC
*
1744566 TACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTAT-CTAATGGTTGACACGGCTCA
* * * ** * * * *
1744610 TACATGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATCTAATGGT--TGACACGGCTCA
1744656 TACGTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCA
1 TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
1744699 TACGTGATGA
1 TACGTGATGA
1744709 AGAGATCTGG
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
43 24 0.32
44 19 0.25
45 4 0.05
46 28 0.37
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
Found at i:1744719 original size:43 final size:44
Alignment explanation
Indices: 1744582--1744749 Score: 125
Period size: 43 Copynumber: 3.9 Consensus size: 44
1744572 ATGAGGACGG
*
1744582 CTGGTTATCCTAAT-GTTGACACGGCTCTTACATGATGAAGAGAT
1 CTGGTTAT-CTAATGGTTGACACGGCTCATACATGATGAAGAGAT
** * * * * * * *
1744626 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCTAATGGT--TGACACGGCTCATACATGATGAAGA-GAT
*
1744672 CTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAATGGTTGACACGGCTCATACATGATGAAGAGAT
* * *
1744715 CTGG---TCT-AGGGATGACACGGTTCATACATGATGAA
1 CTGGTTATCTAATGGTTGACACGGCTCATACATGATGAA
1744750 AAACTCTGGC
Statistics
Matches: 98, Mismatches: 21, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
40 27 0.28
42 1 0.01
43 29 0.30
44 8 0.08
45 4 0.04
46 28 0.29
47 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (44 bp):
CTGGTTATCTAATGGTTGACACGGCTCATACATGATGAAGAGAT
Found at i:1758891 original size:13 final size:12
Alignment explanation
Indices: 1758866--1758903 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1758856 TCCTCTCTCC
*
1758866 TTTTTTCTGTTT
1 TTTTTTTTGTTT
1758878 TTTTCTTTTGTTT
1 TTTT-TTTTGTTT
1758891 TTTTTTTTGTTT
1 TTTTTTTTGTTT
1758903 T
1 T
1758904 CAATTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:1759275 original size:25 final size:25
Alignment explanation
Indices: 1759237--1759360 Score: 223
Period size: 25 Copynumber: 5.0 Consensus size: 25
1759227 AGTTAAGGGA
*
1759237 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1759261 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1759286 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1759311 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
1759336 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
1759361 GGGTTGTCGG
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 6 0.06
25 91 0.94
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:1759498 original size:3 final size:3
Alignment explanation
Indices: 1759490--1759545 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
1759480 GCAAAAATTG
* **
1759490 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1759534 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1759546 CGGGAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1763902 original size:17 final size:17
Alignment explanation
Indices: 1763880--1763920 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1763870 CATAAAAACA
*
1763880 ATTAAAT-TGAATAAATT
1 ATTAAATAT-AATAAAAT
1763897 ATTAAATATAATAAAAT
1 ATTAAATATAATAAAAT
1763914 ATTAAAT
1 ATTAAAT
1763921 GAGTAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTAAATATAATAAAAT
Found at i:1768417 original size:15 final size:15
Alignment explanation
Indices: 1768399--1768431 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1768389 ATCAACAAAT
1768399 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
1768414 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
1768429 ATA
1 ATA
1768432 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:1768458 original size:125 final size:125
Alignment explanation
Indices: 1768320--1768578 Score: 502
Period size: 125 Copynumber: 2.1 Consensus size: 125
1768310 TTACATAAAT
1768320 TATGTAAAATTTAATATTAATTAAAATAAAAATAATATGTGATATATTTAAATACGTAAATAATA
1 TATGTAAAATTTAATATTAATTAAAATAAAAATAATATGTGATATATTTAAATACGTAAATAATA
1768385 TATTATCAACAAATATAATTTTTATATAAATAATTTTTATTTAAATATTTAGAATTTTAC
66 TATTATCAACAAATATAATTTTTATATAAATAATTTTTATTTAAATATTTAGAATTTTAC
1768445 TATGTAAAATTTAATATTAATTAAAATAAAAATAATATGTGATATATTTAAATACGTAAATAATA
1 TATGTAAAATTTAATATTAATTAAAATAAAAATAATATGTGATATATTTAAATACGTAAATAATA
1768510 TATTATCAACAAATATAATTTTTATATAAATAATTTTTATTTAAATATTTAGAATTTTAC
66 TATTATCAACAAATATAATTTTTATATAAATAATTTTTATTTAAATATTTAGAATTTTAC
1768570 T-TGTTAAAA
1 TATG-TAAAA
1768579 AATATAAAAC
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
124 2 0.02
125 131 0.98
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (125 bp):
TATGTAAAATTTAATATTAATTAAAATAAAAATAATATGTGATATATTTAAATACGTAAATAATA
TATTATCAACAAATATAATTTTTATATAAATAATTTTTATTTAAATATTTAGAATTTTAC
Found at i:1768542 original size:15 final size:15
Alignment explanation
Indices: 1768524--1768556 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1768514 ATCAACAAAT
1768524 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
1768539 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
1768554 ATA
1 ATA
1768557 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:1772838 original size:16 final size:16
Alignment explanation
Indices: 1772817--1772860 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1772807 CTTAATATCA
1772817 TCTCAAAACCTAAAAT
1 TCTCAAAACCTAAAAT
* *
1772833 TCTCAAATCCTTAAAT
1 TCTCAAAACCTAAAAT
*
1772849 T-TCAATACCTAA
1 TCTCAAAACCTAA
1772861 CCCTTAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (16 bp):
TCTCAAAACCTAAAAT
Found at i:1774581 original size:29 final size:28
Alignment explanation
Indices: 1774534--1774589 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1774524 TTTTTATTAC
1774534 GTATGTGTTTGATTCATGTTTTATTTTTG
1 GTATGTGTTTGATTCATG-TTTATTTTTG
*
1774563 GTATGTTGTTTTATT-ATGTTTATTTTT
1 GTATG-TGTTTGATTCATGTTTATTTTT
1774590 AATATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 8 0.32
30 8 0.32
ACGTcount: A:0.14, C:0.02, G:0.18, T:0.66
Consensus pattern (28 bp):
GTATGTGTTTGATTCATGTTTATTTTTG
Found at i:1777958 original size:16 final size:16
Alignment explanation
Indices: 1777937--1777977 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1777927 AAAAGTGAAA
1777937 AACTTAAAATTGATAT
1 AACTTAAAATTGATAT
*
1777953 AACTTAAAATTTATAT
1 AACTTAAAATTGATAT
*
1777969 AAATTAAAA
1 AACTTAAAA
1777978 AAAGAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (16 bp):
AACTTAAAATTGATAT
Found at i:1778070 original size:2 final size:2
Alignment explanation
Indices: 1778065--1778289 Score: 62
Period size: 2 Copynumber: 112.0 Consensus size: 2
1778055 GAAAAAAATA
* * *
1778065 AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* *
1778107 ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T AT A- AGT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
* * * *
1778145 -T AT AT AT AT AA AT -T AT GT TT AT AT GA- ACT AT AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT A-T
* * * * * *
1778187 AT AT AT GT AA ACT AT AT AT GT AT AA ACT AT AA AA AGT AT AT AGT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T
* * * *
1778231 TT AT AA ACT AT A- AT TT AT AT -T A- AT AT AGT AT AA AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
1778272 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1778290 TATTCAAAGT
Statistics
Matches: 161, Mismatches: 35, Indels: 54
0.64 0.14 0.22
Matches are distributed among these distances:
1 13 0.08
2 135 0.84
3 13 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1778101 original size:13 final size:13
Alignment explanation
Indices: 1778085--1778217 Score: 96
Period size: 13 Copynumber: 10.2 Consensus size: 13
1778075 AATATAAGTT
1778085 TATATATAAACTA
1 TATATATAAACTA
1778098 TATATATAAACTA
1 TATATATAAACTA
* *
1778111 TAT-T-TATATTA
1 TATATATAAACTA
*
1778122 TAAACTATATAA-T-
1 TATA-TATA-AACTA
**
1778135 TAT-TATAAGTTA
1 TATATATAAACTA
*
1778147 TATATATAAATTA
1 TATATATAAACTA
* *
1778160 TGTTTATATGAACTA
1 --TATATATAAACTA
1778175 TATATATAAACTA
1 TATATATAAACTA
*
1778188 TATATGTAAACTA
1 TATATATAAACTA
1778201 TATATGTATAAACTA
1 TATA--TATAAACTA
1778216 TA
1 TA
1778218 AAAAGTATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 20
0.74 0.11 0.16
Matches are distributed among these distances:
10 1 0.01
11 12 0.13
12 4 0.04
13 54 0.57
14 3 0.03
15 21 0.22
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1778268 original size:90 final size:89
Alignment explanation
Indices: 1778085--1778292 Score: 205
Period size: 87 Copynumber: 2.4 Consensus size: 89
1778075 AATATAAGTT
* * * *
1778085 TATATATAAACTATATATATAAACTATATTTATATTATAAACTATATAATTATTATAAGTTATAT
1 TATATATAAACTATATATATAAACTATA-TTATAGTATAAACTATAAAAGTATTATAAGTTATAA
* * *
1778150 ATATAAATTATGTTTATATGAACTA
65 ATATAAATTATATTAATATGAACAA
*
1778175 TATATATAAACTATATATGTAAACTATA-TAT-GTATAAACTATAAAAAGTA-TAT-AGTTTATA
1 TATATATAAACTATATATATAAACTATATTATAGTATAAACTAT-AAAAGTATTATAAG-TTATA
* * *
1778236 AACTATAATTTATATTAATATAGTATAA
64 AA-TATAAATTATATTAATAT-GAACAA
* *
1778264 -ATATATATA-TATATATATATA-TATATTAT
1 TATATATAAACTATATATATAAACTATATTAT
1778293 TCAAAGTGAG
Statistics
Matches: 99, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
86 6 0.06
87 32 0.32
88 31 0.31
89 3 0.03
90 27 0.27
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (89 bp):
TATATATAAACTATATATATAAACTATATTATAGTATAAACTATAAAAGTATTATAAGTTATAAA
TATAAATTATATTAATATGAACAA
Found at i:1778607 original size:10 final size:11
Alignment explanation
Indices: 1778549--1778653 Score: 50
Period size: 11 Copynumber: 10.2 Consensus size: 11
1778539 AATTGTAGAT
1778549 TATATAT-GTA
1 TATATATAGTA
*
1778559 TA-ATATAAGTT
1 TATATAT-AGTA
*
1778570 TATATATA-AA
1 TATATATAGTA
*
1778580 CTTTATATAGTA
1 -TATATATAGTA
1778592 TATATAT-GTA
1 TATATATAGTA
* *
1778602 TGTATA-ACTA
1 TATATATAGTA
1778612 -ATATA-AGTA
1 TATATATAGTA
*
1778621 -ATCTATAG-A
1 TATATATAGTA
1778630 TTATATATA-TA
1 -TATATATAGTA
*
1778641 TATATATATTA
1 TATATATAGTA
1778652 TA
1 TA
1778654 GAAACACTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
9 16 0.22
10 22 0.31
11 29 0.40
12 5 0.07
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (11 bp):
TATATATAGTA
Found at i:1778960 original size:15 final size:15
Alignment explanation
Indices: 1778940--1778988 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
1778930 CCATGAATAG
1778940 TATATATAAACTATA
1 TATATATAAACTATA
*
1778955 TATATATAACCTATATA
1 TATATATAAAC--TATA
1778972 TATATATAAACTATA
1 TATATATAAACTATA
1778987 TA
1 TA
1778989 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 16 0.53
17 14 0.47
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:1778962 original size:17 final size:17
Alignment explanation
Indices: 1778940--1778988 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1778930 CCATGAATAG
1778940 TATATATAAAC--TATA
1 TATATATAAACTATATA
*
1778955 TATATATAACCTATATA
1 TATATATAAACTATATA
1778972 TATATATAAACTATATA
1 TATATATAAACTATATA
1778989 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 10 0.33
17 20 0.67
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TATATATAAACTATATA
Found at i:1779093 original size:14 final size:14
Alignment explanation
Indices: 1779074--1779124 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
1779064 ACCTTAAACC
*
1779074 TAAACCCTAAATTT
1 TAAACCCTAAATAT
*
1779088 TAAACCATAAATAT
1 TAAACCCTAAATAT
*
1779102 TAAACCCTAAACA-
1 TAAACCCTAAATAT
1779115 TAAACCCTAA
1 TAAACCCTAA
1779125 TACATGTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
13 10 0.30
14 23 0.70
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAATAT
Found at i:1779120 original size:13 final size:13
Alignment explanation
Indices: 1779060--1779129 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
1779050 TATAGTTTAT
*
1779060 ATAAACCTTAAAC
1 ATAAACCCTAAAC
* *
1779073 CTAAACCCTAAATT
1 ATAAACCCTAAA-C
* * *
1779087 TTAAACCATAAAT
1 ATAAACCCTAAAC
1779100 ATTAAACCCTAAAC
1 A-TAAACCCTAAAC
1779114 ATAAACCCTAATAC
1 ATAAACCCTAA-AC
1779128 AT
1 AT
1779130 GTATTACATG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
13 21 0.46
14 25 0.54
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAACCCTAAAC
Found at i:1779271 original size:4 final size:4
Alignment explanation
Indices: 1779232--1779284 Score: 70
Period size: 4 Copynumber: 13.0 Consensus size: 4
1779222 AATTTCATTT
* * *
1779232 TATG ATATG TATG CATG TATG CATG TATG CATG TATG TATG TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1779281 TATG
1 TATG
1779285 ATGCATACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
4 38 0.90
5 4 0.10
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:1779443 original size:23 final size:22
Alignment explanation
Indices: 1779395--1779444 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1779385 TATGATACAT
* *
1779395 ATGTTATATGCATATATTATGT
1 ATGTTATATGCATATATGATGA
* *
1779417 ATGTATATATGTATGTATGATGA
1 ATGT-TATATGCATATATGATGA
1779440 ATGTT
1 ATGTT
1779445 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (22 bp):
ATGTTATATGCATATATGATGA
Found at i:1780574 original size:23 final size:23
Alignment explanation
Indices: 1780542--1780593 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1780532 GTACGATACA
*
1780542 TATGT-TATATGCATATATTATG
1 TATGTATATATGCATATATGATG
*
1780564 TATGTATATATGCATGTATGATG
1 TATGTATATATGCATATATGATG
*
1780587 CATGTAT
1 TATGTAT
1780594 TGAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (23 bp):
TATGTATATATGCATATATGATG
Found at i:1780589 original size:11 final size:11
Alignment explanation
Indices: 1780549--1780594 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1780539 ACATATGTTA
*
1780549 TATGCATATAT
1 TATGCATGTAT
*
1780560 TATGTATGTAT
1 TATGCATGTAT
1780571 ATATGCATGTAT
1 -TATGCATGTAT
*
1780583 GATGCATGTAT
1 TATGCATGTAT
1780594 T
1 T
1780595 GAAATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (11 bp):
TATGCATGTAT
Found at i:1791641 original size:25 final size:23
Alignment explanation
Indices: 1791590--1791636 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1791580 TTTGATTTGA
1791590 TCTTTGGAAAGGAAAAACTGACC
1 TCTTTGGAAAGGAAAAACTGACC
* *
1791613 TCTTTGGAAAGGAGAAATTGACC
1 TCTTTGGAAAGGAAAAACTGACC
1791636 T
1 T
1791637 GTCTTGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (23 bp):
TCTTTGGAAAGGAAAAACTGACC
Found at i:1792221 original size:32 final size:32
Alignment explanation
Indices: 1792080--1792366 Score: 410
Period size: 32 Copynumber: 9.1 Consensus size: 32
1792070 ACTCGTATAA
1792080 TAAT-CTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
1792111 TAA-ACTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
*
1792142 TAA-ACTGTTCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
1792173 TAA-ACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
1792204 TAATATTATCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
1792236 TAATCCTGTCCATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
1792268 TAAT-CATGTCCATATGTCCCGAAAGACATAGG
1 TAATAC-TGTCCATATGTCCCGAAAGACATAGG
*
1792300 TAATCCTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
1792332 TAATACTGTCCATATGTCTCGAAAGATATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
1792364 TAA
1 TAA
1792367 CCCTCGACTC
Statistics
Matches: 239, Mismatches: 12, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
31 90 0.38
32 148 0.62
33 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:1797245 original size:30 final size:30
Alignment explanation
Indices: 1797183--1797258 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
1797173 ATAGTTATTA
*
1797183 TATTTTATATTAATATAATAATATAAATAT
1 TATTTTATATTAAAATAATAATATAAATAT
* * *
1797213 TATTTTTTATTAAAATAAT-ATTTATATGAT
1 TATTTTATATTAAAATAATAATATAAAT-AT
* *
1797243 TATTATATATTTAAAT
1 TATTTTATATTAAAAT
1797259 TTATTAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 6 0.16
30 32 0.84
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TATTTTATATTAAAATAATAATATAAATAT
Found at i:1797401 original size:23 final size:24
Alignment explanation
Indices: 1797374--1797430 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
1797364 AGCGATATGG
1797374 TAATATTT-TT-TTATAATTAATGT
1 TAATATTTATTGTTATAATTAAT-T
*
1797397 TAATATTTATTGTTATATTTAATT
1 TAATATTTATTGTTATAATTAATT
1797421 TAA-ATTTATT
1 TAATATTTATT
1797431 ATGAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 15 0.48
24 6 0.19
25 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TAATATTTATTGTTATAATTAATT
Found at i:1798331 original size:127 final size:127
Alignment explanation
Indices: 1797959--1798489 Score: 897
Period size: 126 Copynumber: 4.2 Consensus size: 127
1797949 TCCCCAAGAA
1797959 CGCG-CCCTCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC
1 CGCGCCCCT-GGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC
* *
1798023 CCGGGGGACATAAGTAACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGAAAGG
65 CCGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
* * * * *
1798086 TGCGCCCCCGGGAACGCGCCTTCACTGCCCCCTAAGGAATAATAGATATT-ACATGAATAGTTCC
1 CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
* * *
1798150 TGGGGGACATAAGTGACATAATAGTGTAATGATAACATATTCTCTGACAAAATAATAGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
1798212 CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
1 CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
1798277 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
*
1798339 CGC-CCCCTGGGAACGAGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
1 CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
*
1798403 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACACAATAATGGAAGG
66 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
* * *
1798465 CGCACCCCCGGGAACGCGTCTTCAC
1 CGCGCCCCTGGGAACGCGCCTTCAC
1798490 ATGAATAGTA
Statistics
Matches: 378, Mismatches: 23, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
126 240 0.63
127 135 0.36
128 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (127 bp):
CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGG
Found at i:1798410 original size:253 final size:253
Alignment explanation
Indices: 1797959--1798489 Score: 897
Period size: 253 Copynumber: 2.1 Consensus size: 253
1797949 TCCCCAAGAA
1797959 CGCG-CCCTCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC
1 CGCGCCCCT-GGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC
1798023 CCGGGGGACATAAGTAACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGAAAGGTG
65 CCGGGGGACATAAGTAACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGAAAGGTG
* * *
1798088 CGCCCCCGGGAACGCGCCTTCACTGCCCCCTAAGGAATAATAGATATTACATGAATAGTTCCTGG
130 CGCCCCCGGGAACGAGCCTTCACGGCCCCCTAAGGAATAATAGATATTACATGAATAGTTCCCGG
*
1798153 GGGACATAAGTGACATAATAGTGTAATGATAACATATTCTCTGACAAAATAATAGAAGG
195 GGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATAGAAGG
1798212 CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
1 CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
* *
1798277 CGGGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAA-G-GC
66 CGGGGGACATAAGTAACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGAAAGGTGC
* *
1798340 GCCCCCTGGGAACGAGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCG
131 GCCCCC-GGGAACGAGCCTTCACGGCCCCCTAAGGAATAATAGATATT-ACATGAATAGTTCCCG
* *
1798405 GGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACACAATAATGGAAGG
194 GGGGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATAGAAGG
* * *
1798465 CGCACCCCCGGGAACGCGTCTTCAC
1 CGCGCCCCTGGGAACGCGCCTTCAC
1798490 ATGAATAGTA
Statistics
Matches: 262, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
251 8 0.03
252 38 0.15
253 212 0.81
254 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (253 bp):
CGCGCCCCTGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCC
CGGGGGACATAAGTAACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGAAAGGTGC
GCCCCCGGGAACGAGCCTTCACGGCCCCCTAAGGAATAATAGATATTACATGAATAGTTCCCGGG
GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATAGAAGG
Found at i:1798689 original size:127 final size:127
Alignment explanation
Indices: 1798530--1798998 Score: 857
Period size: 127 Copynumber: 3.7 Consensus size: 127
1798520 ATATGTAACG
* *
1798530 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATAACTATTATTCCTTAGGGGACCAT
1 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
*
1798595 GAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
66 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1798657 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
1 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
* *
1798722 GAAGGTGCGTTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
66 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1798784 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
1 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
*
1798849 GAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
66 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
1798911 TATTATGTCACTTATGCCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
1 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
* *
1798976 GAAAGCGCATTCCCGGGGGCGCG
66 GAAGGCGCGTTCCCGGGGGCGCG
1798999 TTCTTGGGGA
Statistics
Matches: 330, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 330 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (127 bp):
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
Found at i:1799582 original size:23 final size:23
Alignment explanation
Indices: 1799510--1799582 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
1799500 AAAAATTAAA
* *
1799510 ATTAATATAAATTCAT-AATAAAT
1 ATTAATATTAATT-ATAAAAAAAT
**
1799533 -TTAA-ATTAAACATAACAATAAAT
1 ATTAATATTAATTATAA-AA-AAAT
1799556 ATTAATATTAATTATAAAAAAAT
1 ATTAATATTAATTATAAAAAAAT
1799579 ATTA
1 ATTA
1799583 CCATATCGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 2 0.05
21 5 0.13
22 5 0.13
23 12 0.31
24 6 0.15
25 9 0.23
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTAATATTAATTATAAAAAAAT
Found at i:1799746 original size:31 final size:31
Alignment explanation
Indices: 1799679--1799779 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
1799669 TAATTAGCAC
* * *
1799679 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
1799707 AAATAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
1799738 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
*
1799769 TAAAATATAAT
1 -AAAAAATAAT
1799780 AACTATTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 14 0.24
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:1804905 original size:14 final size:14
Alignment explanation
Indices: 1804886--1804913 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1804876 TAATTCATAT
1804886 CAAGGTATAAATCC
1 CAAGGTATAAATCC
1804900 CAAGGTATAAATCC
1 CAAGGTATAAATCC
1804914 TCTCACGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
CAAGGTATAAATCC
Found at i:1806451 original size:15 final size:15
Alignment explanation
Indices: 1806431--1806459 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1806421 ATTAACATCA
1806431 TTATTTAATAATTTG
1 TTATTTAATAATTTG
1806446 TTATTTAATAATTT
1 TTATTTAATAATTT
1806460 ATTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTATTTAATAATTTG
Found at i:1809485 original size:16 final size:18
Alignment explanation
Indices: 1809464--1809515 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1809454 GTTTCAGATT
1809464 CAGATTCTAATTC-CT-A
1 CAGATTCTAATTCTCTCA
*
1809480 CAGATT-TCAATTCTTTCA
1 CAGATTCT-AATTCTCTCA
*
1809498 CAGATTCTAATTATCTCA
1 CAGATTCTAATTCTCTCA
1809516 TAAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.03
16 11 0.38
17 1 0.03
18 15 0.52
19 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (18 bp):
CAGATTCTAATTCTCTCA
Found at i:1817892 original size:17 final size:17
Alignment explanation
Indices: 1817865--1817897 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1817855 CCTCATTTTT
1817865 TCATAAAAATCTTAAAAG
1 TCATAAAAATC-TAAAAG
1817883 TCAT-AAAATCTAAAA
1 TCATAAAAATCTAAAA
1817898 TGTTCCTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (17 bp):
TCATAAAAATCTAAAAG
Found at i:1820966 original size:20 final size:19
Alignment explanation
Indices: 1820938--1821021 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 19
1820928 CGCGAACTCC
1820938 AATTCCGCAACACAATAGTCA
1 AATT-CGCAACACAA-AGTCA
1820959 AATTCGCAACACAAAAGTCA
1 AATTCGCAACAC-AAAGTCA
* *
1820979 AATTAGCAATACAGAAGTCA
1 AATTCGCAACACA-AAGTCA
**
1820999 AATTCGCAATGCGAAAGTCA
1 AATTCGCAACAC-AAAGTCA
1821019 AAT
1 AAT
1821022 GTTTTTACGC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.02
20 48 0.86
21 7 0.12
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.19
Consensus pattern (19 bp):
AATTCGCAACACAAAGTCA
Found at i:1821550 original size:20 final size:20
Alignment explanation
Indices: 1821500--1821550 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1821490 TCGCAACGTG
*
1821500 ATTTTAGTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
* * *
1821520 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
1821540 ATTTAAGTTTC
1 ATTTAAGTTTC
1821551 AGAAACTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:1825153 original size:61 final size:63
Alignment explanation
Indices: 1825088--1825207 Score: 163
Period size: 66 Copynumber: 1.9 Consensus size: 63
1825078 TGAAAGTTGA
1825088 TTGATGAGGAAATAAG-ATTTATTT-TTTGATTAATTGATTTGTAAAAGTTGATTTGTTTAAT
1 TTGATGAGGAAATAAGAATTTATTTGTTTGATTAATTGATTTGTAAAAGTTGATTTGTTTAAT
* * * *
1825149 TTGATGTGTAAATAAGAATTATTTTTTTGTTTGTTTAATTGATTTGTAAAAGTTGATTT
1 TTGATGAGGAAATAAG-A--ATTTATTTGTTTGATTAATTGATTTGTAAAAGTTGATTT
1825208 TTTGGTTCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 14 0.28
65 7 0.14
66 29 0.58
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (63 bp):
TTGATGAGGAAATAAGAATTTATTTGTTTGATTAATTGATTTGTAAAAGTTGATTTGTTTAAT
Found at i:1825545 original size:39 final size:39
Alignment explanation
Indices: 1825491--1825578 Score: 167
Period size: 39 Copynumber: 2.3 Consensus size: 39
1825481 GCAAGTTGTA
1825491 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1825530 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1825569 GATTTTGATT
1 GATTTTGATT
1825579 AGCATCAGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1825910 original size:18 final size:18
Alignment explanation
Indices: 1825887--1825923 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1825877 CGAAATTTAT
1825887 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1825905 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1825923 A
1 A
1825924 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1826398 original size:20 final size:20
Alignment explanation
Indices: 1826375--1826433 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
1826365 GCATTGCGAT
1826375 AGTCAAATTCGCAACG-AGAA
1 AGTCAAATTCGCAACGCA-AA
1826395 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACGCAAA
1826415 AGTCAAATTCGCAACGCAA
1 AGTCAAATTCGCAACGCAA
1826434 TTTTCGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 37 0.97
21 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.15
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAA
Found at i:1834731 original size:6 final size:6
Alignment explanation
Indices: 1834712--1834750 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1834702 GTGAAGCCGG
** *
1834712 TTTTGA TTGGGA TTTTGA TTTTGA TTGTGA TTTTGA TTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTT
1834751 CCTTTTTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (6 bp):
TTTTGA
Found at i:1834735 original size:18 final size:18
Alignment explanation
Indices: 1834712--1834750 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1834702 GTGAAGCCGG
1834712 TTTTGATTGGGATTTTGA
1 TTTTGATTGGGATTTTGA
*
1834730 TTTTGATTGTGATTTTGA
1 TTTTGATTGGGATTTTGA
1834748 TTT
1 TTT
1834751 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (18 bp):
TTTTGATTGGGATTTTGA
Found at i:1836826 original size:3 final size:3
Alignment explanation
Indices: 1836818--1836860 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1836808 TCTTCGGGGA
*
1836818 CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1836861 AGGGTTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1837059 original size:24 final size:24
Alignment explanation
Indices: 1837032--1837085 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1837022 CCATCACATC
*
1837032 ATCAAAATCCGAGTATTCCCCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* * *
1837056 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
1837080 ATCAAA
1 ATCAAA
1837086 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:1837924 original size:19 final size:19
Alignment explanation
Indices: 1837900--1837971 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
1837890 AAAAATTTGT
1837900 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1837919 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
1837938 GTTGCGAATTTGAAATTCC
1 GTTGCGAATTTGAAATTCA
1837957 GTATTGCGAATTTGA
1 G--TTGCGAATTTGA
1837972 CTATCGCTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 38 0.76
21 12 0.24
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1838062 original size:20 final size:20
Alignment explanation
Indices: 1838039--1838083 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1838029 TGGAAACTGG
1838039 GTTGCAAAATTGGAGTTCAC
1 GTTGCAAAATTGGAGTTCAC
* *
1838059 GTTGCGAAATTGGAGTTCGC
1 GTTGCAAAATTGGAGTTCAC
1838079 GTTGC
1 GTTGC
1838084 GAATTTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (20 bp):
GTTGCAAAATTGGAGTTCAC
Found at i:1838084 original size:20 final size:19
Alignment explanation
Indices: 1838046--1838126 Score: 99
Period size: 19 Copynumber: 4.2 Consensus size: 19
1838036 TGGGTTGCAA
* *
1838046 AATTGGAGTTCACGTTGCG
1 AATTGGAGATCGCGTTGCG
*
1838065 AAATTGGAGTTCGCGTTGCG
1 -AATTGGAGATCGCGTTGCG
*
1838085 AATTTGAGATCGCGTTGCG
1 AATTGGAGATCGCGTTGCG
* *
1838104 AATTTGAGATCGCGTTGCT
1 AATTGGAGATCGCGTTGCG
1838123 AATT
1 AATT
1838127 TGTTGGTCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 39 0.68
20 18 0.32
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (19 bp):
AATTGGAGATCGCGTTGCG
Found at i:1838097 original size:19 final size:19
Alignment explanation
Indices: 1838058--1838128 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
1838048 TTGGAGTTCA
* *
1838058 CGTTGCGAAATTGGAGTTCG
1 CGTTGCG-AATTTGAGATCG
1838078 CGTTGCGAATTTGAGATCG
1 CGTTGCGAATTTGAGATCG
1838097 CGTTGCGAATTTGAGATCG
1 CGTTGCGAATTTGAGATCG
*
1838116 CGTTGCTAATTTG
1 CGTTGCGAATTTG
1838129 TTGGTCATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 41 0.85
20 7 0.15
ACGTcount: A:0.20, C:0.15, G:0.31, T:0.34
Consensus pattern (19 bp):
CGTTGCGAATTTGAGATCG
Found at i:1840245 original size:30 final size:30
Alignment explanation
Indices: 1840206--1840267 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1840196 ACCTATGGAC
* *
1840206 AGTTGCCGAGGATCTTTATGACCTCTAGAT
1 AGTTACCGAGGATCCTTATGACCTCTAGAT
* * *
1840236 AGTTACCGAGGTTCCTTGTGACCTCTGGAT
1 AGTTACCGAGGATCCTTATGACCTCTAGAT
1840266 AG
1 AG
1840268 GTCCTTCGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCCTTATGACCTCTAGAT
Found at i:1845333 original size:31 final size:31
Alignment explanation
Indices: 1845263--1845386 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
1845253 GTCGAGGGTT
*
1845263 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
1845294 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* *
1845326 TACCTATGTTCTAAGGAATATATGGACAGTA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
1845357 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
1845387 TGCCGAGGAT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
31 49 0.65
32 26 0.35
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:1845423 original size:30 final size:30
Alignment explanation
Indices: 1845373--1845445 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1845363 GGTTCTTCGG
* * * *
1845373 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
* *
1845403 GACCTCTGGATAGTTACCGAGGTTCCTTGT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
1845433 GACCTCTGGATAG
1 GACCTCTGGATAG
1845446 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCCTTAT
Found at i:1848012 original size:6 final size:6
Alignment explanation
Indices: 1847976--1848003 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1847966 AATAATATTA
1847976 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1848004 TTATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:1849227 original size:27 final size:27
Alignment explanation
Indices: 1849197--1849278 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 27
1849187 AATTTTATTG
1849197 AGGACCAAATATATAATAATACAAATT-
1 AGGACCAAATATATAATAATA-AAATTA
* * *
1849224 AGGACTAAATTGATAGAATATGTAAATATTA
1 AGGACCAAA-T-ATATAATA-ATAAA-ATTA
*
1849255 AGGACCAAATATATAATTATAAAA
1 AGGACCAAATATATAATAATAAAA
1849279 ATTTTATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
27 9 0.21
28 5 0.12
29 15 0.35
30 6 0.14
31 8 0.19
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (27 bp):
AGGACCAAATATATAATAATAAAATTA
Found at i:1849737 original size:20 final size:20
Alignment explanation
Indices: 1849712--1849762 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1849702 GCAATCAGAC
1849712 AGAAGAAGAAACAGGCAAGA
1 AGAAGAAGAAACAGGCAAGA
1849732 AGAAGAAGAAACAGGCAAGA
1 AGAAGAAGAAACAGGCAAGA
1849752 AGAAGAAGAAA
1 AGAAGAAGAAA
1849763 GAAGCTCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.63, C:0.08, G:0.29, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAAACAGGCAAGA
Found at i:1853511 original size:22 final size:22
Alignment explanation
Indices: 1853483--1853524 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1853473 TTTTCAGCTG
*
1853483 TTTGTAACTCATGTAATTACAT
1 TTTGTAACTCATATAATTACAT
*
1853505 TTTGTAACTCTTATAATTAC
1 TTTGTAACTCATATAATTAC
1853525 TCTGTAACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTGTAACTCATATAATTACAT
Found at i:1861386 original size:65 final size:65
Alignment explanation
Indices: 1861276--1861406 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
1861266 AATGTGAAAA
*
1861276 TAGTAATTATATAAAATATTAATATATATTCTTTATATTTTTTCAAACTAAGTTATATAAATGGT
1 TAGTAATTATATAAAATATTAATATATATTCTTTATATTTTTTCAAACTAAGTCATATAAATGGT
* *
1861341 TAGTAATTATATAAAATATTAATATATGTTCTTTCT-TTTTATTCAAACTAAGTCATATAAATGG
1 TAGTAATTATATAAAATATTAATATATATTCTTTATATTTT-TTCAAACTAAGTCATATAAATGG
1861405 T
65 T
1861406 T
1 T
1861407 TTTTTATACA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 4 0.06
65 58 0.94
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (65 bp):
TAGTAATTATATAAAATATTAATATATATTCTTTATATTTTTTCAAACTAAGTCATATAAATGGT
Found at i:1861916 original size:23 final size:22
Alignment explanation
Indices: 1861869--1861957 Score: 72
Period size: 23 Copynumber: 4.0 Consensus size: 22
1861859 CATATGACCA
* *
1861869 AAAATATGTCA-AAAGGCAAACG
1 AAAACATGTCATAAAGACAAA-G
1861891 AAAACATGTCATAAAGACAGAAG
1 AAAACATGTCATAAAGACA-AAG
* * * *
1861914 AAAACGTGCCACAAAGACATATG
1 AAAACATGTCATAAAGACA-AAG
* *
1861937 AAAACATGACATATAGACAAA
1 AAAACATGTCATAAAGACAAA
1861958 CTTATAGAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 11 0.21
23 40 0.75
24 2 0.04
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (22 bp):
AAAACATGTCATAAAGACAAAG
Found at i:1862240 original size:18 final size:18
Alignment explanation
Indices: 1862217--1862262 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1862207 TAGTACCCAC
* *
1862217 TTTATTATATTTTTAATT
1 TTTATTATATATTAAATT
*
1862235 TTTATTTTATATTAAATT
1 TTTATTATATATTAAATT
1862253 TTTATT-TATA
1 TTTATTATATA
1862263 ATTCTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTATATATTAAATT
Found at i:1864280 original size:14 final size:13
Alignment explanation
Indices: 1864258--1864329 Score: 62
Period size: 14 Copynumber: 5.6 Consensus size: 13
1864248 GGTATAATAT
1864258 TTAAATTTTAAGAA
1 TTAAATTTTAA-AA
*
1864272 TTAATTTTTAAAA
1 TTAAATTTTAAAA
*
1864285 TTAAA-ATTAAAA
1 TTAAATTTTAAAA
1864297 TTAAA---TAAAA
1 TTAAATTTTAAAA
*
1864307 TATAAATATTTGAAA
1 T-TAAAT-TTTAAAA
1864322 TTAAATTT
1 TTAAATTT
1864330 ATTACCGCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 11 0.22
13 8 0.16
14 15 0.31
15 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
TTAAATTTTAAAA
Found at i:1870963 original size:12 final size:12
Alignment explanation
Indices: 1870946--1870979 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1870936 GAATTTCCAT
1870946 TGGCTCACCAGC
1 TGGCTCACCAGC
1870958 TGGCTCACCAGC
1 TGGCTCACCAGC
*
1870970 TGGGTCACCA
1 TGGCTCACCA
1870980 TTGAAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (12 bp):
TGGCTCACCAGC
Found at i:1884542 original size:20 final size:19
Alignment explanation
Indices: 1884496--1884550 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1884486 CAATAGTCCA
* *
1884496 AAAAGTTTCAATACTTTTC
1 AAAAGTTTCAAAACTTCTC
**
1884515 AAGTGTTTCAAAACTATCTC
1 AAAAGTTTCAAAACT-TCTC
*
1884535 AAAAGTTTCGAAACTT
1 AAAAGTTTCAAAACTT
1884551 TCCCTAAAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
AAAAGTTTCAAAACTTCTC
Found at i:1885666 original size:75 final size:77
Alignment explanation
Indices: 1885578--1885747 Score: 229
Period size: 75 Copynumber: 2.2 Consensus size: 77
1885568 AACATAACAT
* * * *
1885578 GTTGCACCTAAAATGTTATAAATTG-TAAGAGAATAAGTTACAAATGAT-AATGTTATTAATATT
1 GTTGCACCTAAAATGTTATAAA-CGATAAGAAAATAAGTTACAAACGATGAATGTTATAAATATT
1885641 -TTAACATTTTAG
65 ATTAACATTTTAG
** * * *
1885653 GTTGTGCCTAAAATGATATAAACGATAAGAAAATAAGTTATAAACGGTGAATGTTATAAATATTA
1 GTTGCACCTAAAATGTTATAAACGATAAGAAAATAAGTTACAAACGATGAATGTTATAAATATTA
1885718 TTAACATTTTAG
66 TTAACATTTTAG
1885730 GTTGCACCTAAAATGTTA
1 GTTGCACCTAAAATGTTA
1885748 ATAGATTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
74 1 0.01
75 38 0.47
76 14 0.17
77 27 0.34
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (77 bp):
GTTGCACCTAAAATGTTATAAACGATAAGAAAATAAGTTACAAACGATGAATGTTATAAATATTA
TTAACATTTTAG
Found at i:1886239 original size:70 final size:72
Alignment explanation
Indices: 1886136--1886270 Score: 166
Period size: 70 Copynumber: 1.9 Consensus size: 72
1886126 ATTTGCATAA
*** * * * *
1886136 TCTCATTTTCCATATTATTTTAAATTTGGAAGTATCGATACTTGTGGAAAAGTATTGATA-TTTT
1 TCTCATTTTCCATATTATTTTAAATTCAAAAGTATCAATACTTATAGAAAAGTATCGATACTTTT
1886200 GTAGTCT
66 GTAGTCT
* * *
1886207 TCTCATTTTCC-TTTTTTTTTAAATTCAAAAGTATTAATACTTATAGAAAAGTATCGATACTTTT
1 TCTCATTTTCCATATTATTTTAAATTCAAAAGTATCAATACTTATAGAAAAGTATCGATACTTTT
1886271 AATTTTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 38 0.72
71 15 0.28
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (72 bp):
TCTCATTTTCCATATTATTTTAAATTCAAAAGTATCAATACTTATAGAAAAGTATCGATACTTTT
GTAGTCT
Found at i:1889480 original size:9 final size:8
Alignment explanation
Indices: 1889468--1889525 Score: 50
Period size: 7 Copynumber: 7.2 Consensus size: 8
1889458 ATTTTTACTA
*
1889468 TTTTATCT
1 TTTTATTT
1889476 TTTT-TTT
1 TTTTATTT
1889483 TTTT-TTT
1 TTTTATTT
*
1889490 TTTT-TGT
1 TTTTATTT
1889497 TTTTATTCT
1 TTTTATT-T
1889506 TCTTTATTT
1 T-TTTATTT
1889515 TCTTTATTT
1 T-TTTATTT
1889524 TT
1 TT
1889526 CTATCTTCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
7 19 0.43
8 6 0.14
9 13 0.30
10 6 0.14
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTATTT
Found at i:1900951 original size:105 final size:105
Alignment explanation
Indices: 1900769--1901946 Score: 2014
Period size: 105 Copynumber: 11.4 Consensus size: 105
1900759 AGGTTTTACC
*
1900769 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1900834 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1900874 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1900939 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1900979 CAGAGCCAA--T----TTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1901038 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1901078 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1901143 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1901183 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTGACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1901248 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ***
1901288 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** **
1901353 ACGAAGGGACCGCTGACTGTCAACCGACAATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
*
1901394 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1901459 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1901499 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1901564 ACGAAGGGACCGCTGGTTGTCAACAAACA-TT-TC----T
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1901598 ------CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1901657 ACGAAGGGACCGCTAGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1901697 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1901762 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
1901802 CAGAGTCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1901867 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1901907 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1901947 GAAACAATAC
Statistics
Matches: 1016, Mismatches: 38, Indels: 38
0.93 0.03 0.03
Matches are distributed among these distances:
93 86 0.08
94 2 0.00
95 2 0.00
99 99 0.10
101 1 0.00
103 3 0.00
104 2 0.00
105 725 0.71
106 96 0.09
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1901558 original size:43 final size:43
Alignment explanation
Indices: 1901509--1901663 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
1901499 CAGAGCCAAT
1901509 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
* *** ** * * *
1901552 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTC-TCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACA--ACGT-AAG
*
1901602 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
*
1901645 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
1901664 GACCGCTAGT
Statistics
Matches: 83, Mismatches: 20, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
43 37 0.45
44 3 0.04
45 8 0.10
46 2 0.02
47 2 0.02
48 8 0.10
49 4 0.05
50 19 0.23
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
Found at i:1901740 original size:198 final size:198
Alignment explanation
Indices: 1901189--1901946 Score: 1151
Period size: 198 Copynumber: 3.7 Consensus size: 198
1901179 ATGTCAGAGC
*
1901189 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTGACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1901254 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* **
1901319 ATTGGACTCAAGAC-A-GTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAACCGACA
131 ATTGGACTCCAGACAACGT--AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-C-A-A
*
1901382 ATTTCTCAATTTCAGAGC
191 A-----C-ATTTC----T
*
1901400 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
1901465 GGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
1901530 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
131 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
1901595 TCT
196 TCT
1901598 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
1901663 GGACCGCTAGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* **
1901728 ATTGGGCTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
131 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
1901793 TCT
196 TCT
1901796 CAATTTCAGAGTCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCA-A--C---TTC-A-----CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1901861 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTC
54 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTC
1901926 ACAACGAAGGATATTGGACTC
119 ACAACGAAGGATATTGGACTC
1901947 GAAACAATAC
Statistics
Matches: 516, Mismatches: 17, Indels: 29
0.92 0.03 0.05
Matches are distributed among these distances:
198 199 0.39
199 1 0.00
201 1 0.00
202 5 0.01
203 1 0.00
204 3 0.01
205 1 0.00
208 2 0.00
209 1 0.00
210 123 0.24
211 176 0.34
212 1 0.00
213 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (198 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
TCT
Found at i:1903629 original size:18 final size:18
Alignment explanation
Indices: 1903606--1903650 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1903596 TTATTACCTA
*
1903606 TTTATTATTTTTATTTTT
1 TTTATTATTTTTACTTTT
* *
1903624 TTTATTTTTTTTCCTTTT
1 TTTATTATTTTTACTTTT
*
1903642 ATTATTATT
1 TTTATTATT
1903651 CTATCGTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTATTATTTTTACTTTT
Found at i:1903630 original size:15 final size:16
Alignment explanation
Indices: 1903610--1903650 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1903600 TACCTATTTA
*
1903610 TTATTTTTATTT-TTT
1 TTATTTTTATTTCCTT
1903625 TTATTTTT-TTTCCTT
1 TTATTTTTATTTCCTT
*
1903640 TTATTATTATT
1 TTATTTTTATT
1903651 CTATCGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 17 0.77
16 2 0.09
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTTTATTTCCTT
Found at i:1903641 original size:10 final size:9
Alignment explanation
Indices: 1903606--1903635 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1903596 TTATTACCTA
*
1903606 TTTATTATT
1 TTTATTTTT
1903615 TTTATTTTT
1 TTTATTTTT
1903624 TTTATTTTT
1 TTTATTTTT
1903633 TTT
1 TTT
1903636 CCTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:1903921 original size:10 final size:10
Alignment explanation
Indices: 1903903--1903961 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
1903893 ATTTTTACTA
*
1903903 TTTTATCTTT
1 TTTTTTCTTT
1903913 TTTTTTCTTT
1 TTTTTTCTTT
*
1903923 TTTTTTGTTT
1 TTTTTTCTTT
1903933 TTATTCTTC-TT
1 TT-TT-TTCTTT
*
1903944 TATTTTCTTT
1 TTTTTTCTTT
*
1903954 ATTTTTCT
1 TTTTTTCT
1903962 ATCTTCATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 3 0.08
10 30 0.75
11 5 0.12
12 2 0.05
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1903942 original size:22 final size:20
Alignment explanation
Indices: 1903910--1903949 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1903900 CTATTTTATC
*
1903910 TTTTTTTTTCTTTTTTTTTG
1 TTTTTTTTTCTTTATTTTTG
1903930 TTTTTATTCTTCTTTATTTT
1 TTTTT-TT-TTCTTTATTTT
1903950 CTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.05, C:0.07, G:0.03, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTCTTTATTTTTG
Found at i:1904652 original size:21 final size:20
Alignment explanation
Indices: 1904616--1904672 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1904606 AATTTAATAA
* *
1904616 ATTTGAGATTAAGGTTAGAG
1 ATTTAAGATTAGGGTTAGAG
1904636 ATTTAAGAATTAGGGTTAGAG
1 ATTTAAG-ATTAGGGTTAGAG
*
1904657 ATTTAAGTTTAGGGTT
1 ATTTAAGATTAGGGTT
1904673 TTATGAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (20 bp):
ATTTAAGATTAGGGTTAGAG
Found at i:1906971 original size:8 final size:8
Alignment explanation
Indices: 1906958--1906986 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1906948 TAGTTGTCAT
1906958 TTTTATTA
1 TTTTATTA
1906966 TTTTATTA
1 TTTTATTA
1906974 TTTTATTA
1 TTTTATTA
1906982 TTTTA
1 TTTTA
1906987 ATATGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATTA
Found at i:1907488 original size:2 final size:2
Alignment explanation
Indices: 1907483--1907559 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
1907473 GATATATGTA
1907483 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1907525 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1907560 ATGTATGCAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.01, C:0.00, G:0.48, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1907564 original size:4 final size:4
Alignment explanation
Indices: 1907557--1907619 Score: 87
Period size: 4 Copynumber: 16.2 Consensus size: 4
1907547 TGTGTGTATG
*
1907557 TGTA TGTA TGCA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TAG-A TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA TGTA
1907605 TGTA TG-- TGTA TGTA T
1 TGTA TGTA TGTA TGTA T
1907620 ATATATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 1 0.02
4 49 0.92
5 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:1911908 original size:29 final size:30
Alignment explanation
Indices: 1911875--1911943 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
1911865 ATTATCTTTG
1911875 TTTTTGTTTTAACTTATTAAATAT-TTTTA
1 TTTTTGTTTTAACTTATTAAATATATTTTA
* * *
1911904 TTTTTGTCTTAATTTATTAAATATATTTTG
1 TTTTTGTTTTAACTTATTAAATATATTTTA
*
1911934 TTTTTATTTT
1 TTTTTGTTTT
1911944 TCAGCTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (30 bp):
TTTTTGTTTTAACTTATTAAATATATTTTA
Found at i:1912717 original size:23 final size:23
Alignment explanation
Indices: 1912691--1912739 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1912681 AAAAAAATAT
*
1912691 ATATTTAATAAATTAAGACAAAA
1 ATATTTAATAAATTAAAACAAAA
*
1912714 ATATTTAATAAGTTAAAACAAAA
1 ATATTTAATAAATTAAAACAAAA
1912737 ATA
1 ATA
1912740 AAGATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
ATATTTAATAAATTAAAACAAAA
Found at i:1915513 original size:2 final size:2
Alignment explanation
Indices: 1915502--1915546 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1915492 GTTAAAGTGC
1915502 AT AT -T 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
1915543 -T AT A
1 AT AT A
1915547 ATTATGGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1916669 original size:13 final size:14
Alignment explanation
Indices: 1916651--1916683 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1916641 TTAGAAGGTG
*
1916651 AAAATAAATTA-TT
1 AAAATAAAATAGTT
1916664 AAAATAAAATAGTT
1 AAAATAAAATAGTT
1916678 AAAATA
1 AAAATA
1916684 TATAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AAAATAAAATAGTT
Found at i:1917228 original size:21 final size:20
Alignment explanation
Indices: 1917191--1917231 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1917181 TTATTAAATT
1917191 TTGATCATTTATGTTATTGA
1 TTGATCATTTATGTTATTGA
1917211 TTGATGCATTT-TGATTATTGA
1 TTGAT-CATTTATG-TTATTGA
1917232 ATTGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGATCATTTATGTTATTGA
Found at i:1917426 original size:31 final size:31
Alignment explanation
Indices: 1917350--1917428 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1917340 AATTCAAAGA
* * **
1917350 TTAAATTAATGTTTCATCTAAAGTTTAGAGG
1 TTAAATTAATATTTTATCTAAAACTTAGAGG
*
1917381 TTAAATTAATATTTTATCTAAAACTTATAGG
1 TTAAATTAATATTTTATCTAAAACTTAGAGG
1917412 TTAAATTAATATTTTAT
1 TTAAATTAATATTTTAT
1917429 AAAAAAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (31 bp):
TTAAATTAATATTTTATCTAAAACTTAGAGG
Found at i:1931288 original size:3 final size:3
Alignment explanation
Indices: 1931274--1931436 Score: 254
Period size: 3 Copynumber: 54.3 Consensus size: 3
1931264 TACCCATATC
* *
1931274 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
1931322 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
1931370 ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1931418 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
1931437 AATACATATA
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 146 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1936939 original size:14 final size:15
Alignment explanation
Indices: 1936909--1936941 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1936899 TTATTATTTT
1936909 ATTTATTAAGATAAA
1 ATTTATTAAGATAAA
*
1936924 ATTTATTAA-TTAAA
1 ATTTATTAAGATAAA
1936938 ATTT
1 ATTT
1936942 GAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTATTAAGATAAA
Found at i:1944196 original size:14 final size:14
Alignment explanation
Indices: 1944172--1944212 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1944162 ATATTATGCT
1944172 TGAAG-AAAAAAAA
1 TGAAGAAAAAAAAA
1944185 TGAAGAAAAAAAAA
1 TGAAGAAAAAAAAA
1944199 -GAAGTAAAAAAAAA
1 TGAAG-AAAAAAAAA
1944213 AGGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (14 bp):
TGAAGAAAAAAAAA
Found at i:1944218 original size:26 final size:24
Alignment explanation
Indices: 1944173--1944245 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 24
1944163 TATTATGCTT
1944173 GAAGAAAAAAAATGAAGAAAAAAAAA
1 GAAGAAAAAAAA--AAGAAAAAAAAA
* *
1944199 GAAGTAAAAAAAAAAGGAAAAGAAA
1 GAAG-AAAAAAAAAAGAAAAAAAAA
*
1944224 GAAAAAAAAGAAAAAAGAAAAA
1 G-AAGAAAA-AAAAAAGAAAAA
1944246 GGGGGGTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 15 0.38
26 17 0.43
27 8 0.20
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (24 bp):
GAAGAAAAAAAAAAGAAAAAAAAA
Found at i:1944222 original size:31 final size:32
Alignment explanation
Indices: 1944187--1944247 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
1944177 AAAAAAAATG
*
1944187 AAGAAA-AAAAAAGAAGTAAAAA-AAAAAGGAA
1 AAGAAAGAAAAAA-AAGAAAAAAGAAAAAGGAA
1944218 AAGAAAGAAAAAAAAGAAAAAAGAAAAAGG
1 AAGAAAGAAAAAAAAGAAAAAAGAAAAAGG
1944248 GGGGTCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (32 bp):
AAGAAAGAAAAAAAAGAAAAAAGAAAAAGGAA
Found at i:1944246 original size:13 final size:12
Alignment explanation
Indices: 1944174--1944245 Score: 65
Period size: 13 Copynumber: 5.7 Consensus size: 12
1944164 ATTATGCTTG
*
1944174 AAGAAAAAAAATG
1 AAGAAAAAAAA-A
1944187 AAGAAAAAAAAA
1 AAGAAAAAAAAA
1944199 GAAGTAAAAAAAAA
1 -AAG-AAAAAAAAA
*
1944213 AGGAAAAGAAAGAA
1 AAGAAAA-AAA-AA
*
1944227 AA-AAAAGAAAA
1 AAGAAAAAAAAA
1944238 AAGAAAAA
1 AAGAAAAA
1944246 GGGGGGTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 4 0.08
12 10 0.20
13 23 0.47
14 12 0.24
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:1946675 original size:110 final size:112
Alignment explanation
Indices: 1946328--1946872 Score: 837
Period size: 110 Copynumber: 5.0 Consensus size: 112
1946318 CAAAGATTCA
* ** *
1946328 AATCTATCATTTGAAAGATTAGCTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1946392 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAA-AATTTGTTCAACCTTTTACCTG
1946440 -A---ATCATTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1946500 A-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAA-AATTTGTTCAACCTTTTACCTG
1946547 AATCCATCATTTGA-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1946611 AGGAAGAAGAAGTTCATAATGAG-AAATTTGTTCAACC-TTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAAATTTGTTCAACCTTTTACCTG
* *
1946656 AATCCATCATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
1946720 AGGAAGAAGAAGTTCATAATTAGAAAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAAATTTGTTCAACCTTTTACCTG
* * * * *
1946767 AATTCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1946831 AGAAAGAAGAAGTTCATAAT-AGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAA-AATTTGTTCAACCTTTT
1946873 GCATAATTCT
Statistics
Matches: 408, Mismatches: 13, Indels: 25
0.91 0.03 0.06
Matches are distributed among these distances:
107 46 0.11
108 52 0.13
109 49 0.12
110 127 0.31
111 113 0.28
112 21 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAAATTTGTTCAACCTTTTACCTG
Done.