Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1755777 original size:64 final size:66
Alignment explanation
Indices: 1755621--1755780 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 66
1755611 AAATAAATTG
* * *
1755621 AACATAGAATGCATTTCATGCATCAATGCA-CATACCATGCATCGATGCACTAAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTAAGGATTTTATGA
1755685 A
66 A
* ** *
1755686 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTAAGGAT-TTTATG
1755749 -A
65 AA
*
1755750 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1755781 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 31 0.36
65 49 0.58
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCATCGATGCACTAAGGATTTTATGA
A
Found at i:1760692 original size:22 final size:22
Alignment explanation
Indices: 1760667--1760712 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1760657 TTTTAGAGCC
*
1760667 TTAGGATGAATTTAAACTTAAT
1 TTAGGATGAATATAAACTTAAT
* *
1760689 TTAGGCTGAATATAGACTTAAT
1 TTAGGATGAATATAAACTTAAT
1760711 TT
1 TT
1760713 CGTCCAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (22 bp):
TTAGGATGAATATAAACTTAAT
Found at i:1761419 original size:17 final size:17
Alignment explanation
Indices: 1761394--1761451 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1761384 TGAAACAATT
* * *
1761394 ATGAGCTAGTTTTATTA
1 ATGAACTAGTTTAATCA
* *
1761411 ATGAACTAGTTAAATGA
1 ATGAACTAGTTTAATCA
*
1761428 ATAAACTAGTTTAATCA
1 ATGAACTAGTTTAATCA
1761445 ATGAACT
1 ATGAACT
1761452 CATTTAAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (17 bp):
ATGAACTAGTTTAATCA
Found at i:1761437 original size:34 final size:36
Alignment explanation
Indices: 1761399--1761468 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
1761389 CAATTATGAG
* *
1761399 CTAGTTTTATTAATGAACT-AGTTAAATGAA-TAAA
1 CTAGTTTAATCAATGAACTCAGTTAAATGAACTAAA
*
1761433 CTAGTTTAATCAATGAACTCATTTAAATGAACTAAA
1 CTAGTTTAATCAATGAACTCAGTTAAATGAACTAAA
1761469 TGCATGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 17 0.55
35 10 0.32
36 4 0.13
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (36 bp):
CTAGTTTAATCAATGAACTCAGTTAAATGAACTAAA
Found at i:1765950 original size:29 final size:29
Alignment explanation
Indices: 1765915--1765996 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1765905 AAACTAAATT
*
1765915 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1765944 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1765973 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1765997 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:1767308 original size:15 final size:15
Alignment explanation
Indices: 1767285--1767314 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1767275 AGGAGGCTGG
1767285 AATTACAACAATAAC
1 AATTACAACAATAAC
*
1767300 AATTCCAACAATAAC
1 AATTACAACAATAAC
1767315 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:1770718 original size:29 final size:29
Alignment explanation
Indices: 1770683--1770764 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1770673 AAACTAAATT
*
1770683 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1770712 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1770741 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1770765 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:1778285 original size:2 final size:2
Alignment explanation
Indices: 1778278--1778308 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1778268 CATATTCAAG
1778278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1778309 TAGCAATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1781130 original size:32 final size:32
Alignment explanation
Indices: 1781089--1781177 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
1781079 TATACTAGTT
1781089 AGGTTTTCATTCAGATAATGCACAATATGTTC
1 AGGTTTTCATTCAGATAATGCACAATATGTTC
*
1781121 AGGTTTTCATTCAGATAATGCACAGTATGTTC
1 AGGTTTTCATTCAGATAATGCACAATATGTTC
* * *
1781153 AGATTTGCATTCAGACAATGCACAA
1 AGGTTTTCATTCAGATAATGCACAA
1781178 GAGTATTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (32 bp):
AGGTTTTCATTCAGATAATGCACAATATGTTC
Found at i:1781738 original size:22 final size:22
Alignment explanation
Indices: 1781711--1781762 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1781701 ATTCAATATG
1781711 TTTGAAAAGGAAATGAACATGT
1 TTTGAAAAGGAAATGAACATGT
1781733 TTTGAAAAGGAAATGAACATGT
1 TTTGAAAAGGAAATGAACATGT
1781755 TTTGAAAA
1 TTTGAAAA
1781763 TCAAGGGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (22 bp):
TTTGAAAAGGAAATGAACATGT
Found at i:1782399 original size:20 final size:20
Alignment explanation
Indices: 1782376--1782425 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1782366 TTTGTGTTAA
1782376 TTAAAATATGGTTAAAG-AGC
1 TTAAAATATGGTTAAAGCA-C
* * *
1782396 TTAAAATGTGTTTAAAGCAT
1 TTAAAATATGGTTAAAGCAC
1782416 TTAAAATATG
1 TTAAAATATG
1782426 AAAAATAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (20 bp):
TTAAAATATGGTTAAAGCAC
Found at i:1782653 original size:48 final size:48
Alignment explanation
Indices: 1782590--1782683 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
1782580 TTTAATCAAA
*
1782590 GTTTCAAAACATTCAATTACAGTGAGTTTAAGAGTTTCAAAACTTTTG
1 GTTTCAAAACATTCAATTACAGTGACTTTAAGAGTTTCAAAACTTTTG
* * **
1782638 GTTTCAAAACTTTCAATTATAGTGACTTTAAGAGTTTTGAAACTTT
1 GTTTCAAAACATTCAATTACAGTGACTTTAAGAGTTTCAAAACTTT
1782684 CCAAACATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (48 bp):
GTTTCAAAACATTCAATTACAGTGACTTTAAGAGTTTCAAAACTTTTG
Found at i:1784048 original size:66 final size:66
Alignment explanation
Indices: 1783938--1784304 Score: 355
Period size: 66 Copynumber: 5.9 Consensus size: 66
1783928 TGTGCAATGG
* * * *
1783938 TTATCGATCGATTTTTATTAATGCATAACAATGCATTATTGGCATAAAAGGTGCCATTAATGAAA
1 TTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGAAA
1784003 A
66 A
* *
1784004 TTATCGATCGCTTTTGATTAATGCATAACAGTGCATTATCGGCATAAAATGTGCCACTAATGAAA
1 TTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGAAA
1784069 A
66 A
* * * *
1784070 TCATTGATC-A--TT--TT--TGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAA
1 TTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGAAA
1784128 A
66 A
* * * * *
1784129 TTATCGATCAATTTTGATTAATGCATAACGGTTCATTATCGACATAAAAGGCGCCACTAAT-AAA
1 TTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGAAA
1784193 A
66 A
* ** * * *
1784194 --AT---T--A--TTGATTAATGAATAATGGTACATTATTGGTATAAAA---GCCACTAATGAAA
1 TTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGAAA
1784247 A
66 A
* * *
1784248 -TATCGATCGATTTTGTTTAATACATAAC-GATGCATTATCAGCATAAAAGGTGCCACT
1 TTATCGATCGATTTTGATTAATGCATAACAG-TGCATTATCGGCATAAAAGGTGCCACT
1784305 CATGGTATTC
Statistics
Matches: 249, Mismatches: 32, Indels: 41
0.77 0.10 0.13
Matches are distributed among these distances:
53 9 0.04
54 4 0.02
55 2 0.01
56 30 0.12
58 2 0.01
59 49 0.20
60 3 0.01
61 3 0.01
62 28 0.11
63 4 0.02
64 2 0.01
65 10 0.04
66 103 0.41
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (66 bp):
TTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGAAA
A
Found at i:1784150 original size:125 final size:121
Alignment explanation
Indices: 1783954--1784304 Score: 440
Period size: 125 Copynumber: 2.9 Consensus size: 121
1783944 ATCGATTTTT
** * *
1783954 ATTAATGCATAACAATGCATTATTGGCATAAAAGGTGCCATTAATGAAAATTATCGATCGCTTTT
1 ATTAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTT
* *
1784019 GATTAATGCATAACAGTGCATTATCGGCATAAAATGTGCCACTAATGAAAATCATTG
66 GATTAATGCATAAC-GTGCATTATCGGCATAAAAGGTGCCACTAATAAAAATCATTG
** *
1784076 ATCATTTTTGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAAATTATCGATCAAT
1 ---ATTAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGAT
* * * *
1784141 TTTGATTAATGCATAACGGTTCATTATCGACATAAAAGGCGCCACTAATAAAAATTATTG
63 TTTGATTAATGCATAAC-GTGCATTATCGGCATAAAAGGTGCCACTAATAAAAATCATTG
* * * *
1784201 ATTAATGAATAATGGTACATTATTGGTATAAAA---GCCACTAATGAAAA-TATCGATCGATTTT
1 ATTAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTT
* * *
1784262 GTTTAATACATAACGATGCATTATCAGCATAAAAGGTGCCACT
66 GATTAATGCATAACG-TGCATTATCGGCATAAAAGGTGCCACT
1784305 CATGGTATTC
Statistics
Matches: 198, Mismatches: 27, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
117 1 0.01
118 48 0.24
119 14 0.07
122 27 0.14
125 108 0.55
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (121 bp):
ATTAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTT
GATTAATGCATAACGTGCATTATCGGCATAAAAGGTGCCACTAATAAAAATCATTG
Found at i:1791071 original size:66 final size:66
Alignment explanation
Indices: 1790961--1791274 Score: 374
Period size: 66 Copynumber: 4.9 Consensus size: 66
1790951 GTGCAATGGC
* ** * *
1790961 TATCGATAGATTTTGATTAAAGCATAATAGTGCATTATCAACATAAAAGGTGCCACTATTGAAAA
1 TATCGATAGATTTTGATTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAAAA
1791026 T
66 T
* ** *
1791027 TATCGATAGATTTTGATTAATGAATAATTGTGCATTATCGACATAAAATGTGCCACTAATGAAAA
1 TATCGATAGATTTTGATTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAAAA
1791092 T
66 T
* * * * *
1791093 CATTGATCG---TT--TT--TGCATAACGGTGCATTATTGGCATAAAAGGTGCCACTAATGAAAA
1 TATCGATAGATTTTGATTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAAAA
1791151 T
66 T
* **
1791152 TATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGGTATAAAAGGTGCCACTAATGAAAA
1 TATCGATAGATTTTGATTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAAAA
1791217 T
66 T
* * * *
1791218 TATCAATTGATTTTGTTTAATGTATAACGGTGCATTATC-AGCATAAAAGGTGCCACT
1 TATCGATAGATTTTGATTAATGCATAACGGTGCATTATCGA-CATAAAAGGTGCCACT
1791275 CATGGTATTC
Statistics
Matches: 215, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
59 47 0.22
61 2 0.01
62 2 0.01
63 2 0.01
64 2 0.01
66 160 0.74
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (66 bp):
TATCGATAGATTTTGATTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAAAA
T
Found at i:1791135 original size:125 final size:130
Alignment explanation
Indices: 1790990--1791274 Score: 391
Period size: 125 Copynumber: 2.2 Consensus size: 130
1790980 AAGCATAATA
* * *
1790990 GTGCATTATCAACATAAAAGGTGCCACTATTGAAAATTATCGATAGATTTTGATTAATGAATAAT
1 GTGCATTATCAGCATAAAAGGTGCCACTAATGAAAATTATCGATAGATTTTGATTAATGAATAAC
* * *
1791055 TGTGCATTATCGACATAAAATGTGCCACTAATG-AAA-ATC-ATTGA-TCGTTT-TTGCATAACG
66 GGTGCATTATCGACATAAAAGGTGCCACTAATGAAAATATCAATTGATTCGTTTAATGCATAACG
** * *
1791115 GTGCATTATTGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAAC
1 GTGCATTATCAGCATAAAAGGTGCCACTAATGAAAATTATCGATAGATTTTGATTAATGAATAAC
** * *
1791180 GGTGCATTATCGGTATAAAAGGTGCCACTAATGAAAATTATCAATTGATTTTGTTTAATGTATAA
66 GGTGCATTATCGACATAAAAGGTGCCACTAATGAAAA-TATCAATTGA-TTCGTTTAATGCATAA
1791245 CG
129 CG
1791247 GTGCATTATCAGCATAAAAGGTGCCACT
1 GTGCATTATCAGCATAAAAGGTGCCACT
1791275 CATGGTATTC
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
125 87 0.64
126 3 0.02
128 3 0.02
129 5 0.04
131 5 0.04
132 34 0.25
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (130 bp):
GTGCATTATCAGCATAAAAGGTGCCACTAATGAAAATTATCGATAGATTTTGATTAATGAATAAC
GGTGCATTATCGACATAAAAGGTGCCACTAATGAAAATATCAATTGATTCGTTTAATGCATAACG
Found at i:1796414 original size:20 final size:20
Alignment explanation
Indices: 1796376--1796431 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1796366 GCTCGAAATC
***
1796376 ATTTTTCAAAATTTCATTTT
1 ATTTTTCAAAATCAAATTTT
1796396 ATTTTTCAAAATCAAATTTT
1 ATTTTTCAAAATCAAATTTT
* *
1796416 -GTTTTCAAAAGCAAAT
1 ATTTTTCAAAATCAAAT
1796432 CATTTTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.48
Consensus pattern (20 bp):
ATTTTTCAAAATCAAATTTT
Found at i:1800831 original size:20 final size:20
Alignment explanation
Indices: 1800806--1800854 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1800796 GAGAGAGTTA
1800806 AATAAACCCAATTGACAAAG
1 AATAAACCCAATTGACAAAG
* *
1800826 AATAAACCCAATTGACATAT
1 AATAAACCCAATTGACAAAG
1800846 AATAAACCC
1 AATAAACCC
1800855 TTATCCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.18
Consensus pattern (20 bp):
AATAAACCCAATTGACAAAG
Found at i:1806705 original size:17 final size:19
Alignment explanation
Indices: 1806684--1806724 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 19
1806674 TTATTAGTTT
1806684 ATATTTTAATTAA-TATAC
1 ATATTTTAATTAACTATAC
*
1806702 -TA-TTTATTTAACTATAC
1 ATATTTTAATTAACTATAC
1806719 ATATTT
1 ATATTT
1806725 CAGCTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 2 0.11
19 2 0.11
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTTTAATTAACTATAC
Found at i:1808796 original size:25 final size:25
Alignment explanation
Indices: 1808768--1808850 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 25
1808758 GATATAACTC
*
1808768 AAAAATTAAAAAAACTAAATAATAA
1 AAAAATTAAAAAAAATAAATAATAA
* ** * *
1808793 AAAAAATCGAATAATTAAATAATAA
1 AAAAATTAAAAAAAATAAATAATAA
1808818 AAAACATTAAGAAATAAAATAAATAAATAA
1 AAAA-ATT-A-AAA-AAAATAAAT-AATAA
1808848 AAA
1 AAA
1808851 TATAATAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
25 24 0.56
26 2 0.05
28 2 0.05
29 7 0.16
30 8 0.19
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (25 bp):
AAAAATTAAAAAAAATAAATAATAA
Found at i:1808855 original size:16 final size:16
Alignment explanation
Indices: 1808829--1808866 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1808819 AAACATTAAG
1808829 AAAT-AAAATA-AAT-
1 AAATAAAAATATAATA
1808842 AAATAAAAATATAATA
1 AAATAAAAATATAATA
1808858 AAATAAAAA
1 AAATAAAAA
1808867 CTTTACAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 6 0.27
15 3 0.14
16 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAAATATAATA
Found at i:1808863 original size:20 final size:22
Alignment explanation
Indices: 1808811--1808864 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
1808801 GAATAATTAA
1808811 ATAATAAAA-AACATTAAGAAAT
1 ATAATAAAATAA-ATTAAGAAAT
*
1808833 AAAAT-AAATAAA-TAA-AAAT
1 ATAATAAAATAAATTAAGAAAT
1808852 ATAATAAAATAAA
1 ATAATAAAATAAA
1808865 AACTTTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 8 0.29
20 10 0.36
21 4 0.14
22 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAATAAAATAAATTAAGAAAT
Found at i:1809861 original size:20 final size:20
Alignment explanation
Indices: 1809827--1809878 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1809817 TTCTTATCAA
* *
1809827 AATAATA-TTATAATTATAT
1 AATAATATTTAAAATTAGAT
*
1809846 AATGATATTTAAAATTAGAT
1 AATAATATTTAAAATTAGAT
1809866 AATAATATTTAAA
1 AATAATATTTAAA
1809879 TACATACCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AATAATATTTAAAATTAGAT
Found at i:1811976 original size:20 final size:20
Alignment explanation
Indices: 1811931--1811979 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1811921 TTTGAGTTGA
*
1811931 TTAAAATATGTTTAAAGTGT
1 TTAAAATATGTTTAAACTGT
* *
1811951 TAAAAATGTGTTTAAAACT-T
1 TTAAAATATGTTT-AAACTGT
1811971 TTAAAATAT
1 TTAAAATAT
1811980 TAAAAACACT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (20 bp):
TTAAAATATGTTTAAACTGT
Found at i:1818687 original size:16 final size:16
Alignment explanation
Indices: 1818666--1818710 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
1818656 CGACAAAACT
1818666 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
1818682 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
1818698 TTTACTATTCACG
1 TTTACTATTCACG
1818711 TGAATAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (16 bp):
TTTACTATTCACGAAA
Found at i:1819019 original size:10 final size:10
Alignment explanation
Indices: 1819004--1819032 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1818994 GGAGTAAGAA
1819004 ATGATTTTGG
1 ATGATTTTGG
1819014 ATGATTTTGG
1 ATGATTTTGG
1819024 ATGATTTTG
1 ATGATTTTG
1819033 AAACTAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (10 bp):
ATGATTTTGG
Found at i:1824550 original size:30 final size:29
Alignment explanation
Indices: 1824480--1824551 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
1824470 CAAATAATTT
1824480 TATTAT-AAAATA-TCTAAATTATTTAAA
1 TATTATAAAAATATTCTAAATTATTTAAA
*
1824507 TA-TAGTAATAATATTCATAAATTATTTAAA
1 TATTA-TAAAAATATTC-TAAATTATTTAAA
1824537 TATTATAAAAATATT
1 TATTATAAAAATATT
1824552 TTATTTTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 3 0.08
28 5 0.13
29 2 0.05
30 24 0.63
31 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TATTATAAAAATATTCTAAATTATTTAAA
Found at i:1824551 original size:19 final size:18
Alignment explanation
Indices: 1824480--1824552 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 18
1824470 CAAATAATTT
*
1824480 TATTATAAAATATCTAAA
1 TATTATAAAATATTTAAA
* *
1824498 TTATT-TAAATATAGTAATAA
1 -TATTATAAA-ATATTTA-AA
*
1824518 TATTCATAAATTATTTAAA
1 TATT-ATAAAATATTTAAA
1824537 TATTATAAAAATATTT
1 TATTAT-AAAATATTT
1824553 TATTTTTCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 6 0.14
19 26 0.62
20 6 0.14
21 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (18 bp):
TATTATAAAATATTTAAA
Found at i:1828410 original size:21 final size:21
Alignment explanation
Indices: 1828386--1828426 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1828376 AAAAAATTAC
* *
1828386 TTAAAATATTATTATTTTTAT
1 TTAAAATATAAATATTTTTAT
1828407 TTAAAATATAAATATTTTTA
1 TTAAAATATAAATATTTTTA
1828427 ATATTTACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATATAAATATTTTTAT
Found at i:1828479 original size:20 final size:21
Alignment explanation
Indices: 1828450--1828497 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1828440 AGTACTCAAC
* *
1828450 AATAACAAAATGGGTAAAAA-
1 AATAATAAAATGGATAAAAAT
*
1828470 AATAATAAAATTGATAAAAAT
1 AATAATAAAATGGATAAAAAT
1828491 AATAATA
1 AATAATA
1828498 TTTTTGGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAATAAAATGGATAAAAAT
Found at i:1830795 original size:21 final size:21
Alignment explanation
Indices: 1830764--1830812 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1830754 AAACATCAAA
*
1830764 TAAAATAAATAATATTATTTAT
1 TAAAATAAATAATAATATTT-T
1830786 TAAAA-AAATAATAATATTTT
1 TAAAATAAATAATAATATTTT
1830806 TAAAATA
1 TAAAATA
1830813 TTAGAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATAAATAATAATATTTT
Found at i:1830994 original size:14 final size:14
Alignment explanation
Indices: 1830977--1831035 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
1830967 ATTAATTATT
1830977 TATTAAAATAATAA
1 TATTAAAATAATAA
**
1830991 TATT--GTTAA-AA
1 TATTAAAATAATAA
*
1831002 TATTAAAAAACATAA
1 TATTAAAATA-ATAA
*
1831017 TATTAAAATAAGAA
1 TATTAAAATAATAA
1831031 TATTA
1 TATTA
1831036 TATTATATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 1 0.03
14 13 0.38
15 11 0.32
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:1831185 original size:29 final size:29
Alignment explanation
Indices: 1831129--1831185 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1831119 ATTAATAATT
* *
1831129 TATTATATATCATTAAAATAAAAGTATAA
1 TATTATATATCAATAAAATAAAACTATAA
*
1831158 TATTATATAT-AATAATAATATAACTATA
1 TATTATATATCAATAA-AATAAAACTATA
1831186 TCAATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
TATTATATATCAATAAAATAAAACTATAA
Found at i:1831265 original size:42 final size:46
Alignment explanation
Indices: 1831193--1831291 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 46
1831183 ATATCAATAA
*
1831193 AATATTATATTATTAAAATTATCAATAAAT-ATA-AT-TTAATAATT
1 AATATTATATTATTAAAATTAACAATAAATAATATATATTAAT-ATT
*
1831237 AATATT-T-TTATTAAAA-TAACACTAAAATAATATATATTAATATT
1 AATATTATATTATTAAAATTAACAAT-AAATAATATATATTAATATT
1831281 AAATATATATA
1 -AATAT-TATA
1831292 AAATAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
41 5 0.11
42 13 0.29
43 4 0.09
44 11 0.24
45 10 0.22
46 1 0.02
47 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (46 bp):
AATATTATATTATTAAAATTAACAATAAATAATATATATTAATATT
Found at i:1831274 original size:32 final size:32
Alignment explanation
Indices: 1831230--1831299 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
1831220 AATATAATTT
**
1831230 AATAAT-TAATATTTTTATTAAA-ATAACACTAA
1 AATAATATAATATTAATATTAAATAT-ACA-TAA
*
1831262 AATAATAT-ATATTAATATTAAATATATATAA
1 AATAATATAATATTAATATTAAATATACATAA
1831293 AATAATA
1 AATAATA
1831300 ATGTTGTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 10 0.30
32 20 0.61
33 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAATATAATATTAATATTAAATATACATAA
Found at i:1831298 original size:21 final size:20
Alignment explanation
Indices: 1831261--1831299 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1831251 AATAACACTA
* *
1831261 AAATAATATATATTAATATT
1 AAATAATATAAAATAATATT
1831281 AAATATATATAAAATAATA
1 AAATA-ATATAAAATAATA
1831300 ATGTTGTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAATATAAAATAATATT
Found at i:1833621 original size:18 final size:18
Alignment explanation
Indices: 1833600--1833642 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1833590 TTATGACTTG
1833600 TAATATTTTTATACCTTT
1 TAATATTTTTATACCTTT
1833618 TAATATTTTTATACCTTT
1 TAATATTTTTATACCTTT
1833636 TAATATT
1 TAATATT
1833643 GTAAACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATATTTTTATACCTTT
Found at i:1838120 original size:10 final size:9
Alignment explanation
Indices: 1838100--1838134 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
1838090 ATACTTTCAA
1838100 TTCCATTTT
1 TTCCATTTT
1838109 TTCCATTTTT
1 TTCCA-TTTT
1838119 TTCCATTTT
1 TTCCATTTT
1838128 TTCCATT
1 TTCCATT
1838135 GTGGGAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (9 bp):
TTCCATTTT
Found at i:1841080 original size:44 final size:44
Alignment explanation
Indices: 1840989--1841069 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
1840979 ATTAATAATA
1840989 TTTTATTATTTATGAAAAAATTAATAGATTAGTTAATTTATTAT
1 TTTTATTATTTATGAAAAAATTAATAGATTAGTTAATTTATTAT
* * *
1841033 TTTTATTATTTATTAATAAATTTATA-ATTA-TT-ATTTA
1 TTTTATTATTTATGAAAAAATTAATAGATTAGTTAATTTA
1841070 GATTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 5 0.15
42 2 0.06
43 4 0.12
44 23 0.68
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (44 bp):
TTTTATTATTTATGAAAAAATTAATAGATTAGTTAATTTATTAT
Found at i:1842425 original size:19 final size:20
Alignment explanation
Indices: 1842401--1842452 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
1842391 ATATCAAAAT
*
1842401 GGTATCGGTACCA-GAAGGG
1 GGTATCGGTACCATAAAGGG
*
1842420 GGTATCGATACCATAAAGGG
1 GGTATCGGTACCATAAAGGG
1842440 GAAGTATCGGTAC
1 G--GTATCGGTAC
1842453 TATAGGGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
22 9 0.33
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (20 bp):
GGTATCGGTACCATAAAGGG
Found at i:1842459 original size:20 final size:20
Alignment explanation
Indices: 1842436--1842475 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1842426 GATACCATAA
* *
1842436 AGGGGAAGTATCGGTACTAT
1 AGGGGAAGTACCGATACTAT
*
1842456 AGGGGGAGTACCGATACTAT
1 AGGGGAAGTACCGATACTAT
1842476 TGAACATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (20 bp):
AGGGGAAGTACCGATACTAT
Found at i:1843060 original size:23 final size:23
Alignment explanation
Indices: 1843030--1843097 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
1843020 GACAATTATA
1843030 TGGCACTTCGGTGCAAACCTATG
1 TGGCACTTCGGTGCAAACCTATG
*
1843053 TGGCACTTTGGTGCAAACCTATG
1 TGGCACTTCGGTGCAAACCTATG
*
1843076 TGGCACTTCAGTGCAAACCTAT
1 TGGCACTTCGGTGCAAACCTAT
1843098 ATGGTCATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAAACCTATG
Found at i:1845897 original size:14 final size:14
Alignment explanation
Indices: 1845875--1845910 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1845865 CCATAAAGAA
*
1845875 CAAGTATCCTCTTC
1 CAAGGATCCTCTTC
1845889 CAAGGATCCTCTTC
1 CAAGGATCCTCTTC
1845903 CAAGGATC
1 CAAGGATC
1845911 GATGGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (14 bp):
CAAGGATCCTCTTC
Found at i:1847268 original size:20 final size:20
Alignment explanation
Indices: 1847225--1847278 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1847215 TCCTAATTTT
*
1847225 GGTATCGATACC-GGTAGGG
1 GGTATCGATACCAGGTAGAG
1847244 GGTATCGATACCATGGTA-AG
1 GGTATCGATACCA-GGTAGAG
1847264 GGTATCGATACCAGG
1 GGTATCGATACCAGG
1847279 AAATATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.44
20 14 0.44
21 4 0.12
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCAGGTAGAG
Found at i:1847272 original size:73 final size:73
Alignment explanation
Indices: 1847172--1847330 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 73
1847162 CCATGAGGTA
*
1847172 GTATCGATACCATGGAAAAGGTATCGATACCAAG-AATCATCGATCCTAATTTTGGTATCGATAC
1 GTATCGATACCATGGAAAAGGTATCGATACCAAGAAAT-ATCGAACCTAATTTTGGTATCGATAC
* *
1847236 CGGTAGGGG
65 CCGAAGGGG
* * * * *
1847245 GTATCGATACCATGGTAAGGGTATCGATACCAGGAAATATTGAACCTATTTTTGGTATCGATACC
1 GTATCGATACCATGGAAAAGGTATCGATACCAAGAAATATCGAACCTAATTTTGGTATCGATACC
1847310 CGAAGGGG
66 CGAAGGGG
*
1847318 GTATCGGTACCAT
1 GTATCGATACCAT
1847331 AGAGTAAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
73 73 0.96
74 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (73 bp):
GTATCGATACCATGGAAAAGGTATCGATACCAAGAAATATCGAACCTAATTTTGGTATCGATACC
CGAAGGGG
Found at i:1847760 original size:54 final size:54
Alignment explanation
Indices: 1847695--1847961 Score: 363
Period size: 54 Copynumber: 4.9 Consensus size: 54
1847685 CCAAATCGAT
* * *
1847695 ACTAAGTGTGCATTTCAGGGAATTGATCATATGTGGATGAATAACCGTTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * * *
1847749 ACTAATTGTGCATTTCAAGAAATTCATCCTATGTGGATGAATAACCATTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * * * *
1847803 ACTAAGTGTGCATTTCACAGAATTCATCCTATGGGGATGAAAAATCGTTTCGAC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
** *
1847857 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTATTTTGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * * *
1847911 ACTAATTGTACATTTCACGAAATTCATCCTACGTGGATGAATAACCGTTTC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1847962 AGCATTGTGA
Statistics
Matches: 183, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 183 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (54 bp):
ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
Found at i:1847991 original size:162 final size:161
Alignment explanation
Indices: 1847690--1847991 Score: 408
Period size: 162 Copynumber: 1.9 Consensus size: 161
1847680 AATTACCAAA
* * * *
1847690 TCGATACTAAGTGTGCATTTCAGGGAATTGATCATATGTGGATGAATAACCGTTTCGGCACTAAT
1 TCGACACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCATTTCGGCACTAAT
* * * * **
1847755 TGTGCATTTCAAGAAATTCATCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCA
66 TGTACATTTCAAGAAATTCATCCTACGTGGATGAATAACCATTTCAGCACTAAGAGTGCA-TAAA
1847820 CAGAATTCATCCTATGGGGATGAAAAATCGTT
130 CAGAATTCATCCTATGGGGATGAAAAATCGTT
* * *
1847852 TCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTATTTTGGCACTAAT
1 TCGACACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCATTTCGGCACTAAT
* * * **
1847917 TGTACATTTCACGAAATTCATCCTACGTGGATGAATAACCGTTTCAGCATTGTGAGTGCA-AAAC
66 TGTACATTTCAAGAAATTCATCCTACGTGGATGAATAACCATTTCAGCACTAAGAGTGCATAAAC
1847981 ATGAAATTCAT
131 A-G-AATTCAT
1847992 AATATGTTTA
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
160 3 0.03
161 1 0.01
162 116 0.97
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (161 bp):
TCGACACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCATTTCGGCACTAAT
TGTACATTTCAAGAAATTCATCCTACGTGGATGAATAACCATTTCAGCACTAAGAGTGCATAAAC
AGAATTCATCCTATGGGGATGAAAAATCGTT
Found at i:1847998 original size:108 final size:108
Alignment explanation
Indices: 1847695--1847991 Score: 274
Period size: 108 Copynumber: 2.8 Consensus size: 108
1847685 CCAAATCGAT
* ** * * * * * * **
1847695 ACTAAGTGTGCATTTCAGGGAATTGATCATATGTGGATGAATAACCGTTTCGGCACTAATTGTGC
1 ACTAAGTGTACATTTCACAGAATTCATCCTACGGGGATGAAAAACCGTTTCGACACTAAGAGTGC
*** *
1847760 ATTTCAAGAAATTCATCCTATGTGGATGAATAACCATTTCGGC
66 AAAACACGAAATTCATCCTATGTGGATGAATAACCATTTCGGC
* * * *
1847803 ACTAAGTGTGCATTTCACAGAATTCATCCTATGGGGATGAAAAATCGTTTCGACACTAAGTGTGC
1 ACTAAGTGTACATTTCACAGAATTCATCCTACGGGGATGAAAAACCGTTTCGACACTAAGAGTGC
*** * * *
1847868 ATTTCACGGAATTCATCCTATGTGGATGAATAACTATTTTGGC
66 AAAACACGAAATTCATCCTATGTGGATGAATAACCATTTCGGC
* * * * **
1847911 ACTAATTGTACATTTCAC-GAAATTCATCCTACGTGGATGAATAACCGTTTC-AGCATTGTGAGT
1 ACTAAGTGTACATTTCACAG-AATTCATCCTACGGGGATGAAAAACCGTTTCGA-CACTAAGAGT
*
1847974 GCAAAACATGAAATTCAT
64 GCAAAACACGAAATTCAT
1847992 AATATGTTTA
Statistics
Matches: 159, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
107 2 0.01
108 157 0.99
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (108 bp):
ACTAAGTGTACATTTCACAGAATTCATCCTACGGGGATGAAAAACCGTTTCGACACTAAGAGTGC
AAAACACGAAATTCATCCTATGTGGATGAATAACCATTTCGGC
Found at i:1854111 original size:19 final size:19
Alignment explanation
Indices: 1854071--1854112 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1854061 ATCTAATTTT
*
1854071 GGTATCGATACCGATAGGG
1 GGTATCGATACCGATAGAG
*
1854090 GGTATCGGTACC-ATAGTAG
1 GGTATCGATACCGATAG-AG
1854109 GGTA
1 GGTA
1854113 GTATCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCGATAGAG
Found at i:1854123 original size:22 final size:18
Alignment explanation
Indices: 1854071--1854125 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 18
1854061 ATCTAATTTT
1854071 GGTATCGATACCGATAGGG
1 GGTATCGATACC-ATAGGG
*
1854090 GGTATCGGTACCATAGTAGG
1 GGTATCGATACCATAG--GG
1854110 GTAGTATCGATACCAT
1 G--GTATCGATACCAT
1854126 GGTAAGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 3 0.10
22 12 0.40
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (18 bp):
GGTATCGATACCATAGGG
Found at i:1854188 original size:95 final size:93
Alignment explanation
Indices: 1854015--1854199 Score: 237
Period size: 95 Copynumber: 2.0 Consensus size: 93
1854005 ATGCCAACAA
* * * * *
1854015 GGTAGTATCGATACCATGGAAAGGTATCGATACCAAGAATCATCTAATCTAATTTTGGTATCGAT
1 GGTAGTATCGATACCATGGAAAGGTATCAATACCAAGAAACATCGAACCTAATTTTGGCATCGAT
*
1854080 ACCGATAGGGGGTATCGGTACCATAGTAG
66 ACCGATA-GGGGTATCAGTACCATAGTAG
* * *
1854109 GGTAGTATCGATACCATGGTAAGAGTATCAATACCAGGAAACATCGAACCTATTTTTGGCATCGA
1 GGTAGTATCGATACCATGGAAAG-GTATCAATACCAAGAAACATCGAACCTAATTTTGGCATCGA
*
1854174 TACCCGAATA-GGGTATCATTACCATA
65 TA-CCG-ATAGGGGTATCAGTACCATA
1854200 ATGTAGAAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
94 22 0.28
95 50 0.64
96 3 0.04
97 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (93 bp):
GGTAGTATCGATACCATGGAAAGGTATCAATACCAAGAAACATCGAACCTAATTTTGGCATCGAT
ACCGATAGGGGTATCAGTACCATAGTAG
Found at i:1854844 original size:54 final size:54
Alignment explanation
Indices: 1854560--1854836 Score: 419
Period size: 54 Copynumber: 5.1 Consensus size: 54
1854550 TTACCAAATA
* * * * *
1854560 GGCACTAAGTGTGCATTTTACAGAATTCTTCCTATGTGGATGAATAATCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1854614 TGCACTAAATGTGCATTTCACGTAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1854668 GGCAATAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1854722 GGTACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1854776 GGCAGTAATTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1854830 AGCACTA
1 GGCACTA
1854837 TGGGTGCAAA
Statistics
Matches: 202, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 202 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:1854898 original size:108 final size:108
Alignment explanation
Indices: 1854557--1854900 Score: 388
Period size: 108 Copynumber: 3.2 Consensus size: 108
1854547 TTATTACCAA
* * * **
1854557 ATAGGCACTAAGTGTGCATTTTACAGAATTCTTCCTATGTGGATGAATAATCGTTTTTGCACTAA
1 ATAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAA
*
1854622 ATGTGCATTTCACGT-AATTCATCCTATGTGGATGAATAACCGT
66 GTGTGCA-TTCACGTGAATTCATCCTATGTGGATGAATAACCGT
* * * * * * *
1854665 TTCGGCAATAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGTACTAA
1 ATAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAA
1854730 GTGTGCATTTCACG-GAATTCATCCTATGTGGATGAATAACCGT
66 GTGTGCA-TTCACGTGAATTCATCCTATGTGGATGAATAACCGT
* * * * *
1854773 TTCGGCAGTAATTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAT
1 ATAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAA
* ** ** ** *
1854838 GGGTGCA-AAACGTGCAATTCATAATATGTTTATGAATGACCGT
66 GTGTGCATTCACGTG-AATTCATCCTATGTGGATGAATAACCGT
* *
1854881 ATAGGCACTACGGGTGCATT
1 ATAGGCACTAAGTGTGCATT
1854901 ACATAGAAAA
Statistics
Matches: 200, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
106 3 0.01
107 1 0.00
108 196 0.98
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (108 bp):
ATAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAA
GTGTGCATTCACGTGAATTCATCCTATGTGGATGAATAACCGT
Found at i:1854900 original size:162 final size:162
Alignment explanation
Indices: 1854557--1854900 Score: 418
Period size: 162 Copynumber: 2.1 Consensus size: 162
1854547 TTATTACCAA
* * * **
1854557 ATAGGCACTAAGTGTGCATTTTACAGAATTCTTCCTATGTGGATGAATAATCGTTTTTGCACTAA
1 ATAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* * * ***
1854622 ATGTGCATTTCACGTAATTCATCCTATGTGGATGAATAACCGTTTCGGCAATAAGTGTGCATTTC
66 ATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCAATAAGGGTGCAAAAC
**
1854687 ACGAAATTCATCCTATGTGGATGAATAACCGT
131 ACGAAATTCATAATATGTGGATGAATAACCGT
* * * * *
1854719 TTCGGTACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCAGTAA
1 ATAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* * * *
1854784 TTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTATGGGTGCAAAAC
66 ATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCAATAAGGGTGCAAAAC
** * ** *
1854849 GTGCAATTCATAATATGTTTATGAATGACCGT
131 ACGAAATTCATAATATGTGGATGAATAACCGT
* *
1854881 ATAGGCACTACGGGTGCATT
1 ATAGGCACTAAGTGTGCATT
1854901 ACATAGAAAA
Statistics
Matches: 149, Mismatches: 33, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
162 149 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (162 bp):
ATAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
ATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCAATAAGGGTGCAAAAC
ACGAAATTCATAATATGTGGATGAATAACCGT
Found at i:1856323 original size:18 final size:20
Alignment explanation
Indices: 1856281--1856321 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1856271 AGGAGGAATC
1856281 AAGATGTATCAAGATTTGAAA
1 AAGATGTATCAAGATTT-AAA
1856302 AAGATGTATCAAG-TTTAAA
1 AAGATGTATCAAGATTTAAA
1856321 A
1 A
1856322 GAGAGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 13 0.65
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (20 bp):
AAGATGTATCAAGATTTAAA
Found at i:1858282 original size:20 final size:20
Alignment explanation
Indices: 1858254--1858304 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1858244 ATGGGCATGG
* *
1858254 AGTATCGATATAGGAAGAAC
1 AGTACCGATACAGGAAGAAC
1858274 AGTACCGATACAGGAAGAAC
1 AGTACCGATACAGGAAGAAC
1858294 AGTACCGATAC
1 AGTACCGATAC
1858305 TTAAAGGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
AGTACCGATACAGGAAGAAC
Found at i:1863609 original size:21 final size:21
Alignment explanation
Indices: 1863532--1863611 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
1863522 GTCGAGGGTT
* *
1863532 TTATGTGGTCCTTTGGGATAA
1 TTATGTGGTCCTTCGGGACAA
*
1863553 TTATGTGG-CACTTCGTG-CAAA
1 TTATGTGGTC-CTTCGGGAC-AA
*
1863574 CCTATGTGGTCCTTCGGGACAA
1 -TTATGTGGTCCTTCGGGACAA
1863596 TTATGTGG-CACTTCGG
1 TTATGTGGTC-CTTCGG
1863612 TGTAAATTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
20 2 0.04
21 28 0.60
22 15 0.32
23 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (21 bp):
TTATGTGGTCCTTCGGGACAA
Found at i:1866539 original size:20 final size:20
Alignment explanation
Indices: 1866503--1866541 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1866493 TATTTGAATC
*
1866503 AAATTAATTAGATATTATTT
1 AAATTAATTAGAAATTATTT
*
1866523 AAATTAATTATAAATTATT
1 AAATTAATTAGAAATTATT
1866542 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTT
Found at i:1866856 original size:17 final size:14
Alignment explanation
Indices: 1866821--1866850 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1866811 ATTTTGTTTG
1866821 TATTAAAATAATAT
1 TATTAAAATAATAT
1866835 TATTAATAATAATAT
1 TATTAA-AATAATAT
1866850 T
1 T
1866851 TTATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAAAATAATAT
Found at i:1868703 original size:17 final size:18
Alignment explanation
Indices: 1868681--1868714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1868671 TCAGCCGGTC
1868681 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
1868698 CGGTTCTGATCGGTTCA
1 CGGTTCTGAACGGTTCA
1868715 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:1871867 original size:60 final size:60
Alignment explanation
Indices: 1871767--1871880 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1871757 AAATGGTTAC
* * * *
1871767 TCGACTATAGAATATTAGTTTATTAATTTACTCGATTATTAAAAGTTATAAAATAATCAT
1 TCGACTATAGAATATTAGTTTATTAAGTCACTCGACTATTAAAAGTTACAAAATAATCAT
* * * * *
1871827 TCGATTATAGAGTATTATTTTGTTAAGTCACTTGACTATTAAAAGTTACAAAAT
1 TCGACTATAGAATATTAGTTTATTAAGTCACTCGACTATTAAAAGTTACAAAAT
1871881 GGTCACCCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (60 bp):
TCGACTATAGAATATTAGTTTATTAAGTCACTCGACTATTAAAAGTTACAAAATAATCAT
Found at i:1874193 original size:34 final size:33
Alignment explanation
Indices: 1874117--1874223 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
1874107 GTGGTAAGAA
* *
1874117 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
1874151 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
1874186 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
1874220 ATTT
1 ATTT
1874224 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:1874205 original size:36 final size:34
Alignment explanation
Indices: 1874150--1874228 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
1874140 TTTAAATAGT
*
1874150 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
1874182 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
1874216 TATTATTTATTTA
1 TATTATTTTTTTA
1874229 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:1874389 original size:17 final size:17
Alignment explanation
Indices: 1874367--1874420 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1874357 AATGTTAATA
1874367 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1874384 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1874401 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1874418 TTT
1 TTT
1874421 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1875004 original size:128 final size:128
Alignment explanation
Indices: 1874844--1875081 Score: 440
Period size: 128 Copynumber: 1.9 Consensus size: 128
1874834 TTACCTGATT
1874844 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1874909 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGG
*
1874972 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
** *
1875037 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGT
1875082 CCCCTGAGAA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 106 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGG
Found at i:1876504 original size:24 final size:24
Alignment explanation
Indices: 1876477--1876576 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
1876467 GATATCAAAA
*
1876477 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1876501 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1876525 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* ** * *
1876549 GTTTAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1876573 ATCA
1 ATCA
1876577 GATAAATATT
Statistics
Matches: 54, Mismatches: 20, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
23 2 0.04
24 50 0.93
25 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1877726 original size:17 final size:17
Alignment explanation
Indices: 1877706--1877740 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1877696 CCTTCCATCG
*
1877706 ATCTTATTATTTAATTC
1 ATCTTATCATTTAATTC
*
1877723 ATCTTATCATTTACTTC
1 ATCTTATCATTTAATTC
1877740 A
1 A
1877741 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (17 bp):
ATCTTATCATTTAATTC
Found at i:1879044 original size:7 final size:7
Alignment explanation
Indices: 1879032--1879063 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1879022 TGGTCAACTC
1879032 CGGTCAA
1 CGGTCAA
1879039 CGGTCAA
1 CGGTCAA
1879046 CGGGTCAA
1 C-GGTCAA
1879054 CGGTCAA
1 CGGTCAA
1879061 CGG
1 CGG
1879064 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1879053 original size:8 final size:8
Alignment explanation
Indices: 1879033--1879079 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1879023 GGTCAACTCC
1879033 GGTCAAC-
1 GGTCAACG
1879040 GGTCAACG
1 GGTCAACG
1879048 GGTCAAC-
1 GGTCAACG
1879055 GGTCAACG
1 GGTCAACG
1879063 GGT---CG
1 GGTCAACG
1879068 GGTCAACG
1 GGTCAACG
1879076 GGTC
1 GGTC
1879080 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1879053 original size:15 final size:15
Alignment explanation
Indices: 1879033--1879079 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1879023 GGTCAACTCC
1879033 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1879048 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1879063 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1879076 GGTC
1 GGTC
1879080 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1879084 original size:18 final size:18
Alignment explanation
Indices: 1879061--1879137 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1879051 CAACGGTCAA
1879061 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1879079 CGGGTCGGGTCAA----T
1 CGGGTCGGGTCAACGGGT
*
1879093 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1879110 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1879128 CGGGTCGGGT
1 CGGGTCGGGT
1879138 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.21
14 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.12, C:0.19, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1879097 original size:31 final size:31
Alignment explanation
Indices: 1879055--1879133 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1879045 ACGGGTCAAC
1879055 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
1879086 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1879117 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1879134 GGGTTGTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1879109 original size:13 final size:13
Alignment explanation
Indices: 1879079--1879114 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1879069 GTCAACGGGT
*
1879079 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
1879092 TGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1879105 CGGGTCGGGT
1 CGGGTCGGGT
1879115 CGGGTCAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1879133 original size:13 final size:13
Alignment explanation
Indices: 1879040--1879084 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1879030 TCCGGTCAAC
*
1879040 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1879055 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1879068 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1879081 GGTC
1 GGTC
1879085 GGGTCAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1882525 original size:18 final size:18
Alignment explanation
Indices: 1882504--1882539 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1882494 CTTCCATCCG
*
1882504 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1882522 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1882540 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1883855 original size:7 final size:7
Alignment explanation
Indices: 1883843--1883874 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1883833 TGGTCAACTC
1883843 CGGTCAA
1 CGGTCAA
1883850 CGGTCAA
1 CGGTCAA
1883857 CGGGTCAA
1 C-GGTCAA
1883865 CGGTCAA
1 CGGTCAA
1883872 CGG
1 CGG
1883875 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1883864 original size:8 final size:8
Alignment explanation
Indices: 1883844--1883890 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1883834 GGTCAACTCC
1883844 GGTCAAC-
1 GGTCAACG
1883851 GGTCAACG
1 GGTCAACG
1883859 GGTCAAC-
1 GGTCAACG
1883866 GGTCAACG
1 GGTCAACG
1883874 GGT---CG
1 GGTCAACG
1883879 GGTCAACG
1 GGTCAACG
1883887 GGTC
1 GGTC
1883891 GGGTCAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1883864 original size:15 final size:15
Alignment explanation
Indices: 1883844--1883890 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1883834 GGTCAACTCC
1883844 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1883859 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1883874 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1883887 GGTC
1 GGTC
1883891 GGGTCAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1883895 original size:18 final size:18
Alignment explanation
Indices: 1883872--1883943 Score: 72
Period size: 18 Copynumber: 3.6 Consensus size: 18
1883862 CAACGGTCAA
1883872 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1883890 CGGGTCAATGGGTCGGGTAAACGGGT
1 CGGGTC---GGGTC-----AACGGGT
1883916 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1883934 CGGGTCGGGT
1 CGGGTCGGGT
1883944 TGTGACCGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
18 23 0.50
21 5 0.11
23 5 0.11
26 13 0.28
ACGTcount: A:0.12, C:0.19, G:0.50, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1883902 original size:26 final size:28
Alignment explanation
Indices: 1883869--1883939 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 28
1883859 GGTCAACGGT
1883869 CAACGGGTCGGGTCAA--CGGGTCGGGT
1 CAACGGGTCGGGTCAAGCCGGGTCGGGT
* * *
1883895 CAATGGGTCGGGTAAACGGGTCGGGTCGGGT
1 CAACGGGTCGGGTCAA---GCCGGGTCGGGT
1883926 CAACGGGTCGGGTC
1 CAACGGGTCGGGTC
1883940 GGGTTGTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 14 0.39
31 22 0.61
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.17
Consensus pattern (28 bp):
CAACGGGTCGGGTCAAGCCGGGTCGGGT
Found at i:1883939 original size:13 final size:13
Alignment explanation
Indices: 1883851--1883921 Score: 97
Period size: 13 Copynumber: 5.3 Consensus size: 13
1883841 TCCGGTCAAC
*
1883851 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1883866 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1883879 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1883892 GGTCAATGGGTCG
1 GGTCAACGGGTCG
*
1883905 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1883918 GGTC
1 GGTC
1883922 GGGTCAACGG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
13 39 0.76
15 12 0.24
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1886018 original size:19 final size:18
Alignment explanation
Indices: 1885990--1886046 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1885980 TAAATATATT
1885990 TAATATTTATTTAATATAA
1 TAAT-TTTATTTAATATAA
*
1886009 TAATTATTA-TTAGT-T-A
1 TAATT-TTATTTAATATAA
1886025 TAATTTT-TTTAAATATAA
1 TAATTTTATTT-AATATAA
1886043 TAAT
1 TAAT
1886047 AATTCCACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 2 0.06
18 10 0.32
19 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TAATTTTATTTAATATAA
Found at i:1888383 original size:16 final size:16
Alignment explanation
Indices: 1888360--1888420 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1888350 GGGTTTCCAA
1888360 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
1888376 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1888392 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1888408 CGTTTATGTTCGT
1 CGTTTATGTTCGT
1888421 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:1889038 original size:182 final size:182
Alignment explanation
Indices: 1888829--1889474 Score: 926
Period size: 182 Copynumber: 3.5 Consensus size: 182
1888819 CGATCCAAAT
* * *
1888829 AAAATGTATCGATCCATATCAATATAACAGGTAAAAATATGACAAAACCGGT-T-TAATTATGAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA--ATGAC
* * * *
1888892 AAAATCGGTAAAGCGCTACCGAATATGTTGAAAGTATCGATTAGATTAAAATAAGCATCGACACT
64 AAAATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATTA-ATTAATATAAGTATCGACACT
*
1888957 TTGGGAATTTAAAAGAGAAGCAGTAA-AGCGCCTATAAAGTGTCGATACTTTATA
128 TTGGGAATTTAAAAGAGAAGCAGTAATAGCGCATATAAAGTGTCGATACTTTATA
* ** * *
1889011 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGCCAAAAATGGTCTTGAAAAGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
* * *
1889076 AATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGA-TACTTTAATATAAGTATCGACACTCT
66 AATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATTA-ATTAATATAAGTATCGACACTTT
* *
1889140 GGGAATTTAAAAGAGAAGCAGTAATAGTGCGTATAAAGTGTCGATACTTTATA
130 GGGAATTTAAAAGAGAAGCAGTAATAGCGCATATAAAGTGTCGATACTTTATA
* * *
1889193 AAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGAAAAAACCGGTCTCGAAATGATAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
** * *
1889258 AATCGGTAAAGCGCTACC-AGATATATTTGATTGTGTCG-TTACTTTATATAAGTATCGACACTT
66 AATCGGTAAAGCGCTACCGA-ATATA-TTGAAAGTGTCGATTAATTAATATAAGTATCGACACTT
* *
1889321 TGGGAATTTAAAAGAGAAGCAGTAATAGCACATATAAAGTGTCGATTCTTTATA
129 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCATATAAAGTGTCGATACTTTATA
* *
1889375 AAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
*
1889440 AATCGGTAAAGCGCTACCGGATATATTGAAAGTGT
66 AATCGGTAAAGCGCTACCGAATATATTGAAAGTGT
1889475 AGATACTTTA
Statistics
Matches: 416, Mismatches: 41, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
181 53 0.13
182 348 0.84
183 13 0.03
184 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (182 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
AATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATTAATTAATATAAGTATCGACACTTTG
GGAATTTAAAAGAGAAGCAGTAATAGCGCATATAAAGTGTCGATACTTTATA
Found at i:1891726 original size:9 final size:9
Alignment explanation
Indices: 1891708--1891743 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1891698 GAAGGTTATT
1891708 GGTA-AGGA
1 GGTAGAGGA
1891716 GGTAGAGGA
1 GGTAGAGGA
*
1891725 GGTAGTGGA
1 GGTAGAGGA
1891734 GGTAGAGGA
1 GGTAGAGGA
1891743 G
1 G
1891744 AAGGAAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.31, C:0.00, G:0.56, T:0.14
Consensus pattern (9 bp):
GGTAGAGGA
Found at i:1891978 original size:33 final size:33
Alignment explanation
Indices: 1891941--1892006 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1891931 AATAAATGGT
1891941 GTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAA
1 GTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAA
* *
1891974 GTGGTGAAATAAGTTGAGGTGTTGAGGGGTGAA
1 GTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAA
1892007 CTTAAGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (33 bp):
GTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAA
Found at i:1892212 original size:18 final size:18
Alignment explanation
Indices: 1892191--1892229 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1892181 AAAAAAATAT
1892191 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
*
1892209 GAAGAATAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1892227 GAA
1 GAA
1892230 ATGATGAGGA
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:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1893763 original size:19 final size:19
Alignment explanation
Indices: 1893739--1893787 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1893729 AATGTAGGGT
1893739 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1893758 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1893777 TAATTTTGTAT
1 TAATTTTGTAT
1893788 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1894587 original size:201 final size:201
Alignment explanation
Indices: 1894236--1894631 Score: 632
Period size: 201 Copynumber: 2.0 Consensus size: 201
1894226 AACATATGTT
*
1894236 TCGATACATTTACAAAAAGTATCAATCCCAAAAACATCGAAACCCATTGTTATAATATAATAGGT
1 TCGATACATTTACAAAAAGTATCAATCCCAAAAACATCGAAACCCATTATTATAATATAATAGGT
*
1894301 AATTTTTCAATGTAACCGGTATAAATCTACCGATTTTATGTGAGAATACATCTACATAATATATC
66 AATTTTTCAATGTAACCGGTATAAATCTACCGATTTTATGTGAGAATACATCAACATAATATATC
* *
1894366 GACACCTTTTAAGATTGTGTCGATAGTTTTTG-CCTAGAATGAATGCCCAAACTAGGTGCACGCA
131 GACACCTTTTAAGATTGTGTCAATACTTTTTGTCC-AGAATGAATGCCCAAACTAGGTGCACGCA
1894430 TAAAGTG
195 TAAAGTG
* * * *
1894437 TCGATACATTTACAAAAGGTATCGATCCCAAAAACATCGAAACTCATTATTATAATGTAATAGGT
1 TCGATACATTTACAAAAAGTATCAATCCCAAAAACATCGAAACCCATTATTATAATATAATAGGT
* * ** *
1894502 AATTTTTCAATGTAACCGGTATAATTCTACCGGTTTTATGTGAGAATATGTCAACATAATGTATC
66 AATTTTTCAATGTAACCGGTATAAATCTACCGATTTTATGTGAGAATACATCAACATAATATATC
* * *
1894567 GACACTTTTTAAGTTTGTGTCAATACTTTTTGTCCCGAATGAATGCCCAAACTAGGTGCACGCAT
131 GACACCTTTTAAGATTGTGTCAATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGCAT
1894632 TGGCCATGAA
Statistics
Matches: 178, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
201 176 0.99
202 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (201 bp):
TCGATACATTTACAAAAAGTATCAATCCCAAAAACATCGAAACCCATTATTATAATATAATAGGT
AATTTTTCAATGTAACCGGTATAAATCTACCGATTTTATGTGAGAATACATCAACATAATATATC
GACACCTTTTAAGATTGTGTCAATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGCAT
AAAGTG
Found at i:1896395 original size:24 final size:25
Alignment explanation
Indices: 1896368--1896422 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1896358 TTTCAAGTTC
*
1896368 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
1896392 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
*
1896416 GTTTCAA
1 ATTTCAA
1896423 TATAATAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 4 0.16
24 19 0.76
25 2 0.08
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:1897213 original size:20 final size:20
Alignment explanation
Indices: 1897170--1897213 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1897160 ATAAGATAAT
* *
1897170 TATAATGTAATAGGTAAATT
1 TATAATGTAACAGGTAAATA
* *
1897190 TATAATGTAACCGGTAGATA
1 TATAATGTAACAGGTAAATA
1897210 TATA
1 TATA
1897214 CCGGTTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (20 bp):
TATAATGTAACAGGTAAATA
Found at i:1897426 original size:199 final size:198
Alignment explanation
Indices: 1897082--1898480 Score: 1861
Period size: 199 Copynumber: 7.0 Consensus size: 198
1897072 TCAGTAATCT
*
1897082 CCAGAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATC
1 CCAGAATGAATGACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTA-TAAAAGTATCGATC
* ** *
1897147 CCAGAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTATAATGTAACCGGTAGATATA
64 CCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAATA
* * *
1897212 TACCGGTTAATTAGAAAATAGGTTTACATAATATATCGCCACTTTTTAAA-TTGTGTCGATACTT
129 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
*
1897276 TTTGT
194 TTTGA
* *
1897281 CCACAATGAATGACCAACCGAGGTACACGAATAAAGTGTCGATACATTTATAAAACGTATCGATC
1 CCAGAATGAATGACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAA-GTATCGATC
** * * * *
1897346 CCAAAAACATCGAA-ACTCATAATTACAATATAATAGGTAAATTTACAATGTAACCGGTAGATAT
64 CCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAAT
* *
1897410 ATATCGGTTAATTAGAAAATAGGTCTACATAATATATCGACACTTTTTAAA-TTGTGTCGATACT
128 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACT
*
1897474 TTTTGC
193 TTTTGA
1897480 CCTA-AATGAATGACCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTATCGAT
1 CC-AGAATGAATGACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAA-GTATCGAT
*
1897544 CCCAAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAAT
63 CCCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAAT
* * * * *
1897609 ATATCGATTAATTAGAAAATATGTCTACATAATGTATCGATACTTTTTAAATTTGTGTCGATACG
128 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACT
1897674 TTTTGA
193 TTTTGA
* ** *
1897680 CCAGAATGAATGCCCAACGACATGCACGAATAAAGTGTCGATACATTTATAAAAAGTATTGATCC
1 CCAGAATGAATGACCAACGAGGTGCACGAATAAAGTGTCGATACATTTAT-AAAAGTATCGATCC
* *
1897745 CAAAAACATCGAATAAAATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATAT
65 CAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAATAT
* *
1897810 ACCGGTTAATTAGAAAATAAGTCTACATAATGTATCGACACTTCTTAAATTTGTGTCGATACTTT
130 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
1897875 TTGA
195 TTGA
*
1897879 CCAGAATGACTGAATGAATGCTCAACGAGGTGAACGAATAAAGTGTCGATACATTTATAAAAAGT
1 CCAG-A--A-TGAATG-A--C-CAACGAGGTGCACGAATAAAGTGTCGATACATTTAT-AAAAGT
* * * *
1897944 ATCAATCCCAAAAACATCGAATAAGATAATTATAAAGTAATATGTCAATTTCCAATGTAACCGGT
57 ATCGATCCCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGT
* * * *
1898009 AGAAATATACCGGTTAATTAGAAAATATGTCTACATAATGTATCAATACTTTTTAAATTCGTGTC
122 AGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTC
*
1898074 GATACTTTTTGT
187 GATACTTTTTGA
* * *
1898086 CCAGAATGAATG-CCTAA-AAGAGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGAT
1 CCAGAATGAATGACC-AACGAG-GTGCACGAATAAAGTGTCGATACATTTATAAA-AGTATCGAT
* * *
1898148 CCCAAAAACATCGAA-ACCGATAATTAAAATGTAATAGGTAAATTTCCAATATAACCGGT-GTAA
63 CCCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAG-AA
* * *
1898211 ATATACCGGTT--TTAAGAGAGAATAGGTTTACATAGTGTATCGACACTTTTTAAATTTATGTCG
126 ATATACCGGTTAATT-AGA-A-AATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCG
*
1898274 AT-GTGTTTTGA
188 ATACT-TTTTGA
* * * * **
1898285 CCAGAAAGAATGCCCAACGGGGTGTACGAATAAAGTGTCGATACATTTATAAAAGTATCGATTAC
1 CCAGAATGAATGACCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAGTATCGATCCC
* * * *
1898350 ATAAACATCGAA-ACTGATAAATATAATGTAGTAGGTAAATTTCCAATGTAACCGGTAGAAATAT
66 AAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAATAT
* *
1898414 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAAGTTGTGTCGATACTTT
130 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
1898479 TT
195 TT
1898481 AAAATTATGC
Statistics
Matches: 1076, Mismatches: 93, Indels: 63
0.87 0.08 0.05
Matches are distributed among these distances:
196 2 0.00
197 8 0.01
198 126 0.12
199 699 0.65
200 48 0.04
201 2 0.00
202 1 0.00
203 12 0.01
204 1 0.00
206 2 0.00
207 175 0.16
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
CCAGAATGAATGACCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAGTATCGATCCC
AAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAATATA
CCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTT
TGA
Found at i:1900020 original size:19 final size:19
Alignment explanation
Indices: 1899996--1900039 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1899986 ATGTAGGGGA
*
1899996 AATTTTGTATACGATTCAT
1 AATTTTGTATACAATTCAT
*
1900015 AATTTTGTATACAATTTAT
1 AATTTTGTATACAATTCAT
1900034 AATTTT
1 AATTTT
1900040 TTATGTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACAATTCAT
Found at i:1903191 original size:198 final size:199
Alignment explanation
Indices: 1902724--1903214 Score: 605
Period size: 200 Copynumber: 2.5 Consensus size: 199
1902714 TAAAAAATAC
* * *
1902724 GTCGATACATTTTCTAAAAGTATCAA-CCCTAAAAACATCGAAACCAATAATTTTAATGTAATAG
1 GTCGATACA-TTTATAAAAGTATCAATCCCT-AAAACATCGAAACCGATAATTATAATGTAATAG
* *
1902788 GTAAATTAACAATGTAACCGGTATAAATATACCAGTTAATTACAAAATAGATAAACATATTGTAT
64 GTAAATTTACAATGTAACCGGTATAAATATACCAGTTAATAACAAAATAGATAAACATATTGTAT
* * *
1902853 CGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACACA
129 CGACACTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTACACACA
1902918 TAAAGT
194 TAAAGT
* * * * *
1902924 GTCGATTCATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATGATATAATAGG
1 GTCGATACATTTA-TAAAAGTATCAATCCCTAAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * * * *
1902989 TAAATTTACGATGTAACCGGTATAAATATACCGATTTTATAAGAGAATAGGTCAACAT-TATGTA
65 TAAATTTACAATGTAACCGGTATAAATATACC-AGTTAATAACAAAATAGATAAACATAT-TGTA
* * * ** * *
1903053 TCGACACTTTTTAAATATGTGTCGATACTT-TTTTCCATCATGAATTCCC-AACGAGGTACACGC
128 TCGACACTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTACACAC
1903116 ATAAAGT
193 ATAAAGT
*
1903123 GTCGATACATTTA-AAATTGTATCAATCCCTAAAACATCGAAACCGATAATTATAATGTAATAGG
1 GTCGATACATTTATAAA-AGTATCAATCCCTAAAACATCGAAACCGATAATTATAATGTAATAGG
** * *
1903187 TAAATTTTTAATGTTACTGGTATAAATA
65 TAAATTTACAATGTAACCGGTATAAATA
1903215 AACAGGTTTA
Statistics
Matches: 248, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
197 3 0.01
198 65 0.26
199 34 0.14
200 95 0.38
201 51 0.21
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (199 bp):
GTCGATACATTTATAAAAGTATCAATCCCTAAAACATCGAAACCGATAATTATAATGTAATAGGT
AAATTTACAATGTAACCGGTATAAATATACCAGTTAATAACAAAATAGATAAACATATTGTATCG
ACACTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTACACACATA
AAGT
Found at i:1903288 original size:23 final size:23
Alignment explanation
Indices: 1903232--1903288 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1903222 TTAATTGGAA
*
1903232 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGCGCTACCT
* *
1903256 -ATTTCATTATATAAGCGCTACCT
1 AATAT-GTTATATAAGCGCTACCT
1903279 AATATGTTAT
1 AATATGTTAT
1903289 TGTACTTGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACCT
Found at i:1904416 original size:23 final size:23
Alignment explanation
Indices: 1904390--1904446 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
1904380 AAGAACCATA
*
1904390 TAGATATGTCCCGAAGGACCTCG
1 TAGATATGTCCCGAAGGACCACG
* *
1904413 TAGAAATATCCCGAAGGACCACG
1 TAGATATGTCCCGAAGGACCACG
*
1904436 TAGATTTGTCC
1 TAGATATGTCC
1904447 TAAAGGATCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
TAGATATGTCCCGAAGGACCACG
Found at i:1904574 original size:16 final size:16
Alignment explanation
Indices: 1904540--1904593 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
1904530 TTATACCATT
*
1904540 TCACATAG-CTTAT-A
1 TCACATAGACATATAA
1904554 TCACATAGACATATAA
1 TCACATAGACATATAA
*
1904570 TCACATAGATCATGTAA
1 TCACATAGA-CATATAA
1904587 -CACATAG
1 TCACATAG
1904594 GATAAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 8 0.23
15 4 0.11
16 17 0.49
17 6 0.17
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (16 bp):
TCACATAGACATATAA
Found at i:1905102 original size:19 final size:19
Alignment explanation
Indices: 1905078--1905121 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1905068 ACTATGGTAT
1905078 CGATACTATACTTCAGTAA
1 CGATACTATACTTCAGTAA
*
1905097 CGATACTATACTTCAGTAT
1 CGATACTATACTTCAGTAA
1905116 CGATAC
1 CGATAC
1905122 ACATACTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (19 bp):
CGATACTATACTTCAGTAA
Found at i:1910533 original size:2 final size:2
Alignment explanation
Indices: 1910526--1910646 Score: 214
Period size: 2 Copynumber: 62.5 Consensus size: 2
1910516 GAACCAAAAC
1910526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
1910567 AT AT AT AT AT AT -T AT 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 AT AT AT AT AT AT
1910607 AT AT AT AT AT AT AT AT A- 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 AT AT AT AT AT A
1910647 AATAAATCAT
Statistics
Matches: 115, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
1 4 0.03
2 111 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1910844 original size:23 final size:23
Alignment explanation
Indices: 1910817--1910894 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
1910807 ACCAAAGTAT
*
1910817 CACATAGAAATGTCCCGAATGAC
1 CACATAGAAATGTCCCGAAAGAC
*
1910840 CACATAGATATGTCCCGAAAGAC
1 CACATAGAAATGTCCCGAAAGAC
* *
1910863 CACGTAGAAATGTCCCGAAGGAC
1 CACATAGAAATGTCCCGAAAGAC
*
1910886 CATATAGAA
1 CACATAGAA
1910895 TTATCCGAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (23 bp):
CACATAGAAATGTCCCGAAAGAC
Found at i:1910915 original size:22 final size:23
Alignment explanation
Indices: 1910821--1910916 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 23
1910811 AAGTATCACA
* * *
1910821 TAGAAATGTCCCGAATGACCACA
1 TAGAAATATCCCGAAGGACCACG
* * *
1910844 TAGATATGTCCCGAAAGACCACG
1 TAGAAATATCCCGAAGGACCACG
* **
1910867 TAGAAATGTCCCGAAGGACCATA
1 TAGAAATATCCCGAAGGACCACG
* *
1910890 TAGAATTAT-CCGAAGGACTACG
1 TAGAAATATCCCGAAGGACCACG
1910912 TAGAA
1 TAGAA
1910917 CCCTTGACTC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
22 15 0.25
23 46 0.75
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.19
Consensus pattern (23 bp):
TAGAAATATCCCGAAGGACCACG
Found at i:1915217 original size:21 final size:21
Alignment explanation
Indices: 1915153--1915217 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1915143 GCATTTTCCA
* *
1915153 GAAAAAAGATCGATCCATTTT-
1 GAAAAAGGATCAATCC-TTTTG
*
1915174 GAAAAAGGATCAATCC-CTTG
1 GAAAAAGGATCAATCCTTTTG
* *
1915194 GAAAAGGGATCCATCCTTTTG
1 GAAAAAGGATCAATCCTTTTG
1915215 GAA
1 GAA
1915218 GTTTAAATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.06
20 14 0.39
21 20 0.56
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (21 bp):
GAAAAAGGATCAATCCTTTTG
Found at i:1917947 original size:15 final size:15
Alignment explanation
Indices: 1917923--1917959 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1917913 ATATTTAGCT
* *
1917923 GGGCGAGCGGATATG
1 GGGCGGGCGGATACG
1917938 GGGCGGGCGGATACG
1 GGGCGGGCGGATACG
1917953 GGGCGGG
1 GGGCGGG
1917960 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.62, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATACG
Found at i:1932254 original size:54 final size:55
Alignment explanation
Indices: 1932143--1932260 Score: 184
Period size: 54 Copynumber: 2.2 Consensus size: 55
1932133 AGTAGTGTCG
1932143 TCTCCAGATTGACCGATTTCCTCAGAGAGAGAGGAACACTGTCAACACCAAATTA
1 TCTCCAGATTGACCGATTTCCTCAGAGAGAGAGGAACACTGTCAACACCAAATTA
** * *
1932198 TCTCCAGATTGATTGATTTCCTCAGAGATA-AGGAACAGTGTCAACACCAAATTA
1 TCTCCAGATTGACCGATTTCCTCAGAGAGAGAGGAACACTGTCAACACCAAATTA
*
1932252 TCTCTAGAT
1 TCTCCAGAT
1932261 CTCTTCAATG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
54 31 0.53
55 27 0.47
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (55 bp):
TCTCCAGATTGACCGATTTCCTCAGAGAGAGAGGAACACTGTCAACACCAAATTA
Found at i:1937605 original size:19 final size:19
Alignment explanation
Indices: 1937581--1937618 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1937571 TTTCACTGAA
1937581 AATATTTTCCAGAAAATGT
1 AATATTTTCCAGAAAATGT
1937600 AATATTTTCCAGAAAATGT
1 AATATTTTCCAGAAAATGT
1937619 TTTCGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
AATATTTTCCAGAAAATGT
Found at i:1937970 original size:30 final size:29
Alignment explanation
Indices: 1937936--1938014 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 29
1937926 AATTGAGTAT
1937936 ATTATTATAATATTAA-AAATATAATATTGA
1 ATTATTATAATATTAATAAATAT-AT-TTGA
* *
1937966 ATTATTAAAAATATTAATAAATATATTTTA
1 ATTATT-ATAATATTAATAAATATATTTGA
*
1937996 ATTATTTTAATAATTAATA
1 ATTATTATAAT-ATTAATA
1938015 TTTTGGTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 3 0.07
30 22 0.52
31 11 0.26
32 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
ATTATTATAATATTAATAAATATATTTGA
Found at i:1940950 original size:21 final size:22
Alignment explanation
Indices: 1940926--1940980 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1940916 TTCTCTCACG
1940926 TTTTTATTAAAG-TTCTTTT-C
1 TTTTTATTAAAGTTTCTTTTAC
*
1940946 TTTTTACTTTAAGTTTCTTTTAC
1 TTTTTA-TTAAAGTTTCTTTTAC
*
1940969 TTTCTTTTTAAA
1 TTT-TTATTAAA
1940981 CAAATGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.21
21 5 0.18
22 7 0.25
23 8 0.29
24 2 0.07
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTATTAAAGTTTCTTTTAC
Found at i:1944865 original size:18 final size:19
Alignment explanation
Indices: 1944830--1944866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1944820 CACGGAATGT
1944830 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1944850 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1944867 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1945047 original size:37 final size:37
Alignment explanation
Indices: 1945013--1945082 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1945003 TACAAATTGT
1945013 AAAATATTTATAT-ATTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTTCTTTAAAAAATTAAATTC
* * *
1945049 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTAAAAAATTAAA
1945083 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTAAAAAATTAAATTC
Found at i:1952647 original size:17 final size:17
Alignment explanation
Indices: 1952621--1952660 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1952611 ACTTTAAACT
* * *
1952621 TAAAATATAAAAGTCTA
1 TAAAAAATAAAAATCGA
1952638 TAAAAAATAAAAATCGA
1 TAAAAAATAAAAATCGA
1952655 TAAAAA
1 TAAAAA
1952661 CTTAAGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (17 bp):
TAAAAAATAAAAATCGA
Found at i:1962158 original size:21 final size:21
Alignment explanation
Indices: 1962112--1962166 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1962102 ACAAAACCTG
* *
1962112 CTGAAAATCCTACAGCCCCTA
1 CTGAAAATCCTACAACCACTA
*
1962133 CTGAAAATCCTACAACCACTG
1 CTGAAAATCCTACAACCACTA
* *
1962154 TTGAAATTCCTAC
1 CTGAAAATCCTAC
1962167 CGCCATTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.24
Consensus pattern (21 bp):
CTGAAAATCCTACAACCACTA
Found at i:1966870 original size:41 final size:41
Alignment explanation
Indices: 1966825--1966989 Score: 219
Period size: 41 Copynumber: 4.0 Consensus size: 41
1966815 ATTCGCGTTG
1966825 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1966866 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * ** **
1966907 CATTTCACGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1966947 TATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
1966988 CA
1 CA
1966990 AATTCGTTGT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 34 0.32
41 72 0.67
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1966875 original size:20 final size:20
Alignment explanation
Indices: 1966850--1966962 Score: 154
Period size: 20 Copynumber: 5.6 Consensus size: 20
1966840 TAGTTGAAAA
1966850 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
1966870 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
1966891 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
1966911 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
1966931 TCGCGTTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
1966951 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1966963 AGTCTACAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 64 0.81
21 15 0.19
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1966998 original size:40 final size:41
Alignment explanation
Indices: 1966954--1967046 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
1966944 TTCTATTTCG
*
1966954 CGTTGCGATAGTCTACA-ATGTCGTTGCGATTTTCCAAATT
1 CGTTGAGATAGTCTACAGATGTCGTTGCGATTTTCCAAATT
* *
1966994 CGTTGTGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGAGATAGTCTACAGATGTCGTTGCGATTTTCCAAATT
1967035 CGTTGAGATAGT
1 CGTTGAGATAGT
1967047 TAAAAAAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 16 0.33
41 33 0.67
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGAGATAGTCTACAGATGTCGTTGCGATTTTCCAAATT
Found at i:1967134 original size:6 final size:6
Alignment explanation
Indices: 1967123--1967154 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1967113 GACACGTATT
1967123 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1967155 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1967658 original size:6 final size:6
Alignment explanation
Indices: 1967647--1967673 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1967637 TCTCGTCTCG
1967647 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1967674 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1967800 original size:22 final size:22
Alignment explanation
Indices: 1967773--1967886 Score: 98
Period size: 22 Copynumber: 5.4 Consensus size: 22
1967763 AATTTGGAAA
1967773 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGACAACTGTAAACT
* * *
1967795 ATCGCAACAACAACTATAGACT
1 ATCGCAACGACAACTGTAAACT
* *
1967817 ATCGCAACG--AA-TTTCAAA-A
1 ATCGCAACGACAACTGT-AAACT
*
1967836 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAAACT
*
1967858 ATCGCAACG-CGAACTGGAAA--
1 ATCGCAACGAC-AACTGTAAACT
1967878 ATCGCAACG
1 ATCGCAACG
1967887 CGATTTTCAA
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
19 11 0.15
20 13 0.18
21 5 0.07
22 45 0.61
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAAACT
Found at i:1967883 original size:20 final size:20
Alignment explanation
Indices: 1967858--1967991 Score: 124
Period size: 20 Copynumber: 6.6 Consensus size: 20
1967848 ACTGTAGACT
*
1967858 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1967878 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1967899 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
1967919 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
1967939 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1967960 ATAGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1967980 ATCGCAACGCGA
1 ATCGCAACGCGA
1967992 TTTTCAACTA
Statistics
Matches: 87, Mismatches: 25, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
20 59 0.68
21 28 0.32
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1967895 original size:63 final size:62
Alignment explanation
Indices: 1967770--1967957 Score: 179
Period size: 63 Copynumber: 3.0 Consensus size: 62
1967760 ACGAATTTGG
* * ** *
1967770 AAAATCGCAACGACAACTGTAAACTATCGCAACAAC-AACTATAGACTATCGCAA--CGAATTTC
1 AAAATCGCAACGACAACTGT-AACTATCGCAAC-GCGAAC--TGGAAAATCGCAACGCGATTTTC
1967832 A
62 A
1967833 AAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
1 AAAATCGCAACGACAACTGTA-ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
** * ** * *
1967896 ACTATCGCAACG-CGAAATG-AAAAATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCA
1 AAAATCGCAACGAC-AACTGTAACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
1967957 A
1 A
1967958 CTATAGCAAC
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
61 48 0.44
62 4 0.04
63 56 0.52
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (62 bp):
AAAATCGCAACGACAACTGTAACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
Found at i:1967904 original size:21 final size:21
Alignment explanation
Indices: 1967878--1968033 Score: 129
Period size: 21 Copynumber: 7.6 Consensus size: 21
1967868 GAACTGGAAA
1967878 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
1967899 ATCGCAACGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
** ** *
1967919 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
1967939 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
1967960 ATAGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
1967980 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
1968001 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
1968022 ATCGCAACGCGA
1 ATCGCAACGCGA
1968034 AATGCAACGC
Statistics
Matches: 105, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
20 44 0.42
21 61 0.58
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Done.