Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:2893000 original size:86 final size:86
Alignment explanation
Indices: 2892849--2893101 Score: 427
Period size: 86 Copynumber: 2.9 Consensus size: 86
2892839 TTAAATACAT
* * *
2892849 AAATGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAGAAAGGTTAACTATACACGTGGATTT
1 AAATGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAGAAAAGTTAACTATACATGTGAATTT
2892914 AAGTTGGGATAGAAGTATTTA
66 AAGTTGGGATAGAAGTATTTA
* *
2892935 AAATGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAGAAAAGTTAACCAAACATGTGAATTT
1 AAATGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAGAAAAGTTAACTATACATGTGAATTT
2893000 AAGTTGGGATAGAAGTATTTA
66 AAGTTGGGATAGAAGTATTTA
*
2893021 AAAAGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAG-AAAGCTTAACTATACATGTGAATT
1 AAATGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAGAAAAG-TTAACTATACATGTGAATT
*
2893085 TAAGTTGGGATGGAAGT
65 TAAGTTGGGATAGAAGT
2893102 TGACTGAGAA
Statistics
Matches: 157, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
85 4 0.03
86 153 0.97
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.25
Consensus pattern (86 bp):
AAATGAAGAAAAGAAACTCTAGTCGAAGAAGTTGACTGAGAAAAGTTAACTATACATGTGAATTT
AAGTTGGGATAGAAGTATTTA
Found at i:2893120 original size:49 final size:49
Alignment explanation
Indices: 2893048--2893142 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
2893038 TCTAGTCGAA
2893048 GAAGTTGACTGAGAAAGCTTAACTATACATGTGAATTTAAGTTGGGATG
1 GAAGTTGACTGAGAAAGCTTAACTATACATGTGAATTTAAGTTGGGATG
*
2893097 GAAGTTGACTGAGAAAGGTTAACTATACATGTGAATTTAAGTTGGG
1 GAAGTTGACTGAGAAAGCTTAACTATACATGTGAATTTAAGTTGGG
2893143 GTAGAAGTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (49 bp):
GAAGTTGACTGAGAAAGCTTAACTATACATGTGAATTTAAGTTGGGATG
Found at i:2904594 original size:18 final size:18
Alignment explanation
Indices: 2904567--2904608 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2904557 CTTAGCTCAC
2904567 AGCTCATCTCGGACGTCT
1 AGCTCATCTCGGACGTCT
* *
2904585 AGCTCCTCTCGTACGTCT
1 AGCTCATCTCGGACGTCT
2904603 AGCTCA
1 AGCTCA
2904609 CCACTCTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.36, G:0.19, T:0.29
Consensus pattern (18 bp):
AGCTCATCTCGGACGTCT
Found at i:2905828 original size:5 final size:5
Alignment explanation
Indices: 2905818--2905851 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2905808 ATTTTCCACA
* *
2905818 AAAAT AAAAT AAACT AAAAT AAAAC AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2905852 ATGGAAGGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:2906369 original size:4 final size:4
Alignment explanation
Indices: 2906360--2906385 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2906350 TTAAAGTGCT
2906360 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
2906386 CAGAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2908107 original size:3 final size:3
Alignment explanation
Indices: 2908093--2908175 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
2908083 ATTAGTGTAA
*
2908093 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2908141 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2908176 CGTAATTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2913169 original size:23 final size:22
Alignment explanation
Indices: 2913111--2913197 Score: 120
Period size: 22 Copynumber: 3.9 Consensus size: 22
2913101 TGTTTGAGCT
*
2913111 TTCATAGGGGTATTGATACCCA
1 TTCATAGGGGTATCGATACCCA
* *
2913133 TTTATAGGGGTATCAATACCCA
1 TTCATAGGGGTATCGATACCCA
*
2913155 TTCATAGGGGGTATCGGTACCCA
1 TTCATA-GGGGTATCGATACCCA
*
2913178 TTCATAGGGGTATCGGTACC
1 TTCATAGGGGTATCGATACC
2913198 TCTTAATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 38 0.66
23 20 0.34
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCA
Found at i:2913434 original size:21 final size:21
Alignment explanation
Indices: 2913410--2913450 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2913400 ATGTTTAATG
2913410 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
*
2913431 AAAAGGATACCAATTGTTAA
1 AAAAAGATACCAATTGTTAA
2913451 AAAGATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:2913457 original size:18 final size:18
Alignment explanation
Indices: 2913410--2913467 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 18
2913400 ATGTTTAATG
2913410 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
2913428 AACAAAAGGATACCAATTGTT
1 -A-AAAA-GATACCAATTGTT
* *
2913449 AAAAAGATATCAGTTGTT
1 AAAAAGATACCAATTGTT
2913467 A
1 A
2913468 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 5 0.14
20 5 0.14
21 13 0.37
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:2915119 original size:19 final size:19
Alignment explanation
Indices: 2915095--2915133 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2915085 TCGAATGCAT
2915095 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2915114 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2915133 T
1 T
2915134 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2915150 original size:65 final size:63
Alignment explanation
Indices: 2915032--2915240 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
2915022 TATTCAAAGG
* *
2915032 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
2915094 TTC
61 TTT
2915097 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
2915162 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
2915226 CATGCATCGATGCAC
1 CATGCACCGATGCAC
2915241 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:2915234 original size:64 final size:65
Alignment explanation
Indices: 2915081--2915241 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
2915071 GAATTAATTG
* * *** *
2915081 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
2915146 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
2915209 A
65 A
2915210 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
2915242 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2915256 original size:64 final size:64
Alignment explanation
Indices: 2915032--2915261 Score: 225
Period size: 64 Copynumber: 3.6 Consensus size: 64
2915022 TATTCAAAGG
* * * *
2915032 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
2915094 TTC
62 TTT
* * *
2915097 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
2915162 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
2915226 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
2915262 AGTGTTTCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.50
65 64 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:2921042 original size:20 final size:21
Alignment explanation
Indices: 2921013--2921068 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2921003 TTTGTGCTTC
*
2921013 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
2921033 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
2921055 ATGCATCGATGCAT
1 ATGCATCGATGCAT
2921069 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:2922645 original size:21 final size:21
Alignment explanation
Indices: 2922603--2922646 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2922593 ACCCCGGGAG
*
2922603 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
2922624 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
2922645 CT
1 CT
2922647 CCTTCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:2923700 original size:19 final size:19
Alignment explanation
Indices: 2923676--2923714 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2923666 TCGAATGCAT
2923676 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2923695 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2923714 T
1 T
2923715 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2923731 original size:65 final size:63
Alignment explanation
Indices: 2923613--2923821 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
2923603 TATTCAAAGG
* *
2923613 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
2923675 TTC
61 TTT
2923678 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
2923743 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
2923807 CATGCATCGATGCAC
1 CATGCACCGATGCAC
2923822 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:2923815 original size:64 final size:65
Alignment explanation
Indices: 2923662--2923822 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
2923652 GAATTAATTG
* * *** *
2923662 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
2923727 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
2923790 A
65 A
2923791 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
2923823 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:2923837 original size:64 final size:64
Alignment explanation
Indices: 2923613--2923842 Score: 225
Period size: 64 Copynumber: 3.6 Consensus size: 64
2923603 TATTCAAAGG
* * * *
2923613 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
2923675 TTC
62 TTT
* * *
2923678 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
2923743 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
2923807 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
2923843 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.50
65 64 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:2925938 original size:33 final size:33
Alignment explanation
Indices: 2925893--2925962 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2925883 CTTTACAAAC
* * *
2925893 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACATT
* * *
2925926 TCCCTAGCTTTTCATGGGATCAGCTAGAACATT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACATT
2925959 TCCC
1 TCCC
2925963 CTTTACAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACATT
Found at i:2926367 original size:19 final size:19
Alignment explanation
Indices: 2926343--2926379 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2926333 CACTTTGCAC
*
2926343 TATGGTATCGATACCCTTG
1 TATGGTATCAATACCCTTG
2926362 TATGGTATCAATACCCTT
1 TATGGTATCAATACCCTT
2926380 TTTTCATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (19 bp):
TATGGTATCAATACCCTTG
Found at i:2926443 original size:23 final size:23
Alignment explanation
Indices: 2926417--2926488 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
2926407 GGTGTATTGA
2926417 TACCCATTCATAGGGGGTATCGG
1 TACCCATTCATAGGGGGTATCGG
*
2926440 TACCCATTAATAGGGGGTATC-G
1 TACCCATTCATAGGGGGTATCGG
2926462 TCACCCATTCATA-GGGGTATCGG
1 T-ACCCATTCATAGGGGGTATCGG
2926485 TACC
1 TACC
2926489 TCTTAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
22 13 0.29
23 32 0.71
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (23 bp):
TACCCATTCATAGGGGGTATCGG
Found at i:2931447 original size:148 final size:150
Alignment explanation
Indices: 2930553--2931473 Score: 854
Period size: 149 Copynumber: 6.2 Consensus size: 150
2930543 TAACGTGTTC
* * * *
2930553 TTTAGAGACAAATCACACTCGTAACGACTGTTACACGTTATGTAACGTTTC-TAGTATCCACAAT
1 TTTAGAAACAAATCACACTCCTAACGACCGTTACACGTTATGTAACG-TACGTAGTATCCACAAT
* ** * * *
2930617 CGCGATATTATAATCACATCTGTGACAGTTA-CTATAACCATAATTTGATAATATGAATCAGAAA
65 CGCGATATTGTAATCACATCTGTGACAGACACCT-TAACCATAATTTAATATTATGAATAAGAAA
* *
2930681 ACATTGAATTTGCA-AAATATT
129 ACATTGAATTTGTACAAATTTT
* * * *
2930702 TTTAGAAACAAATCAAACTCCTAATGACCGTTACACTTTATGTAATGT-CTGTAGTATCCACAAT
1 TTTAGAAACAAATCACACTCCTAACGACCGTTACACGTTATGTAACGTAC-GTAGTATCCACAAT
* * * * * * *
2930766 CACGATATTGTAATCACATATGAGACATACA-CTGTAACAATAAATTATAAATATTATGAATCAT
65 CGCGATATTGTAATCACATCTGTGACAGACACCT-TAACCAT-AATT-T-AATATTATGAATAAG
* *
2930830 ATAACATT-ATATTTATAC-AA-TTT
126 AAAACATTGA-ATTTGTACAAATTTT
* * * * * * *
2930853 TTTAGAAATAAAATCACACTCCTAACGACCGTTACGCATTATGTAACATCCGTAGTATCTATAAT
1 TTTAGAAA-CAAATCACACTCCTAACGACCGTTACACGTTATGTAACGTACGTAGTATCCACAAT
* * * *
2930918 CGCGATATTGTAATTACAT-TCGTGACAGACACCATAACTATAATTTAATATAATGAATAA-AAA
65 CGCGATATTGTAATCACATCT-GTGACAGACACCTTAACCATAATTTAATATTATGAATAAGAAA
2930981 A-ATTGAATTTGTAC--ATTTT
129 ACATTGAATTTGTACAAATTTT
* * * * * * * *
2931000 TCTAGAAACAAGTCAAACTCTTAATGATCGTTACA-GATTATGTAACGTATGTAGTATTCACAAT
1 TTTAGAAACAAATCACACTCCTAACGACCGTTACACG-TTATGTAACGTACGTAGTATCCACAAT
* * * * * * *
2931064 CGCGATACTGTAATCACATCCGTGACAAACACCATAACCGTAGTTTAATATTATGAATCAGAAAA
65 CGCGATATTGTAATCACATCTGTGACAGACACCTTAACCATAATTTAATATTATGAATAAGAAAA
* *
2931129 CATTGAATTTGAACAATTTTT
130 CATTGAATTTGTACAAATTTT
* * * * **
2931150 TTTAGAAATATATCACACTCATAACGACCGTTATGA-GTTATGTAACGTTTGTAGTATCCACAAT
1 TTTAGAAACAAATCACACTCCTAACGACCGTTA-CACGTTATGTAACGTACGTAGTATCCACAAT
* * *
2931214 CGTGATATTGTAATCACAT-TCGTGACAGACACCGTAACCGTAATTTAATATTATGAATAAGAAA
65 CGCGATATTGTAATCACATCT-GTGACAGACACCTTAACCATAATTTAATATTATGAATAAGAAA
* * * *
2931278 ACATTAAATTTTTA-TATTTTT
129 ACATTGAATTTGTACAAATTTT
* * * * * *
2931299 TTTA-AAACAAACCACACTCGTAATGACCATTAGACGTTATGTAACGTACGTAGAATCCACAATC
1 TTTAGAAACAAATCACACTCCTAACGACCGTTACACGTTATGTAACGTACGTAGTATCCACAATC
* * * * * *
2931363 GCGATGTTATAATCATATCTATGACACACACCTTAACCGTAATTTAATATTATGAATAAG-AAAC
66 GCGATATTGTAATCACATCTGTGACAGACACCTTAACCATAATTTAATATTATGAATAAGAAAAC
*
2931427 ATCGAATTTGTACAAATTTT
131 ATTGAATTTGTACAAATTTT
* * *
2931447 TTTAAAAACAATTCACACTCATAACGA
1 TTTAGAAACAAATCACACTCCTAACGA
2931474 TTGTTATATC
Statistics
Matches: 632, Mismatches: 115, Indels: 50
0.79 0.14 0.06
Matches are distributed among these distances:
146 92 0.15
147 40 0.06
148 125 0.20
149 126 0.20
150 126 0.20
151 19 0.03
152 102 0.16
153 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (150 bp):
TTTAGAAACAAATCACACTCCTAACGACCGTTACACGTTATGTAACGTACGTAGTATCCACAATC
GCGATATTGTAATCACATCTGTGACAGACACCTTAACCATAATTTAATATTATGAATAAGAAAAC
ATTGAATTTGTACAAATTTT
Found at i:2939967 original size:24 final size:24
Alignment explanation
Indices: 2939938--2939983 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2939928 CTGAATTTTT
2939938 CTCGTTTATTATAAAATTTTAATG
1 CTCGTTTATTATAAAATTTTAATG
2939962 CTCGTTTATTATAAAATTTTAA
1 CTCGTTTATTATAAAATTTTAA
2939984 GGATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.50
Consensus pattern (24 bp):
CTCGTTTATTATAAAATTTTAATG
Found at i:2939999 original size:23 final size:24
Alignment explanation
Indices: 2939942--2939999 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
2939932 ATTTTTCTCG
* * *
2939942 TTTATTATAAAATTTTAATGCTCG
1 TTTATTATAAAATTTTAAGGATCA
2939966 TTTATTATAAAATTTTAAGGAT-A
1 TTTATTATAAAATTTTAAGGATCA
*
2939989 TTTATTTTAAA
1 TTTATTATAAA
2940000 GTTATTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (24 bp):
TTTATTATAAAATTTTAAGGATCA
Found at i:2940866 original size:13 final size:13
Alignment explanation
Indices: 2940802--2940866 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
2940792 GTCATAAATA
*
2940802 TATGATGCGCATT
1 TATGACGCGCATT
**
2940815 TATGACATGCATT
1 TATGACGCGCATT
*
2940828 TATGACGTGCATT
1 TATGACGCGCATT
* *
2940841 TATGGCGCACATT
1 TATGACGCGCATT
2940854 TATGACGCGCATT
1 TATGACGCGCATT
2940867 ACGCGTCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:2954302 original size:19 final size:19
Alignment explanation
Indices: 2954268--2954308 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2954258 TTCTTTTTGA
2954268 TTTATTCCTTTCTTTTA-T
1 TTTATTCCTTTCTTTTACT
2954286 TTTATTTCCTTAT-TTTTACT
1 TTTA-TTCCTT-TCTTTTACT
2954306 TTT
1 TTT
2954309 CTCTCTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTCCTTTCTTTTACT
Found at i:2958846 original size:21 final size:21
Alignment explanation
Indices: 2958791--2958849 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2958781 ACTCGTATAG
* *
2958791 AATGCACCGAAGTACCAGTAGA
1 AATGCA-CGAAGTGCCACTAGA
* *
2958813 AATACACGAAGTGCCCCTAGA
1 AATGCACGAAGTGCCACTAGA
2958834 AATGCACGAAGTGCCA
1 AATGCACGAAGTGCCA
2958850 TATAAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (21 bp):
AATGCACGAAGTGCCACTAGA
Found at i:2960973 original size:35 final size:35
Alignment explanation
Indices: 2960931--2961005 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
2960921 TTCATGTTCA
2960931 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
* * *
2960966 AAATTCCAAAATACTTTAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
2961001 AAATT
1 AAATT
2961006 TAAGTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCC
Found at i:2962393 original size:13 final size:13
Alignment explanation
Indices: 2962375--2962413 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
2962365 GTATTTACAT
2962375 TTTATTTTAATAA
1 TTTATTTTAATAA
2962388 TTTATTACTTAATAA
1 TTTATT--TTAATAA
2962403 TTTATTTTAAT
1 TTTATTTTAAT
2962414 TACTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTTTAATAA
Found at i:2963121 original size:22 final size:25
Alignment explanation
Indices: 2963077--2963132 Score: 82
Period size: 22 Copynumber: 2.4 Consensus size: 25
2963067 AACGTGTTAG
*
2963077 AGAAAAAAAAAGATAATGCAAATAA
1 AGAAAATAAAAGATAATGCAAATAA
2963102 AGAAAATAAAA-A-AATG-AAATAA
1 AGAAAATAAAAGATAATGCAAATAA
2963124 AGAAAATAA
1 AGAAAATAA
2963133 GATAGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 15 0.50
23 4 0.13
24 1 0.03
25 10 0.33
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.12
Consensus pattern (25 bp):
AGAAAATAAAAGATAATGCAAATAA
Found at i:2963210 original size:11 final size:11
Alignment explanation
Indices: 2963192--2963232 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2963182 TAAATAAAAT
2963192 AAATAAAACAA
1 AAATAAAACAA
*
2963203 AGATAAAACAA
1 AAATAAAACAA
*
2963214 AAATAAATAAAA
1 AAATAAA-ACAA
2963226 AAATAAA
1 AAATAAA
2963233 TAAAATAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (11 bp):
AAATAAAACAA
Found at i:2963258 original size:19 final size:19
Alignment explanation
Indices: 2963148--2963366 Score: 137
Period size: 19 Copynumber: 11.3 Consensus size: 19
2963138 AGAAAAGAAT
*
2963148 GATAAAGGAAAAAAATAAA
1 GATAAAGAAAAAAAATAAA
* *
2963167 G-TAAAGATAAGAAAGTAAA
1 GATAAAGA-AAAAAAATAAA
* * * *
2963186 TA-AAATAAATAAAACAAA
1 GATAAAGAAAAAAAATAAA
*
2963204 GATAAAACAAAAATAAATAAA
1 GAT-AAAGAAAAA-AAATAAA
* *
2963225 -A-AAATAAATAAAATAAA
1 GATAAAGAAAAAAAATAAA
2963242 GATAAAGAGAAAAAATATAAA
1 GATAAAGA-AAAAAA-ATAAA
*
2963263 GA-AAATGAAAAAAAAATGAA
1 GATAAA-G-AAAAAAAATAAA
* *
2963283 GATAAAGAAATAAAATAAC
1 GATAAAGAAAAAAAATAAA
*
2963302 TATAAAGAAATAAAAAACTAAA
1 GATAAAG-AA-AAAAAA-TAAA
2963324 GATAAA-AAATAAAAATAAA
1 GATAAAGAAA-AAAAATAAA
**
2963343 -ATAAAGAGGAAAAATAAA
1 GATAAAGAAAAAAAATAAA
*
2963361 AATAAA
1 GATAAA
2963367 ATAAAGGAAA
Statistics
Matches: 156, Mismatches: 26, Indels: 36
0.72 0.12 0.17
Matches are distributed among these distances:
17 7 0.04
18 36 0.23
19 44 0.28
20 32 0.21
21 28 0.18
22 9 0.06
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.15
Consensus pattern (19 bp):
GATAAAGAAAAAAAATAAA
Found at i:2963261 original size:15 final size:13
Alignment explanation
Indices: 2963104--2963382 Score: 79
Period size: 14 Copynumber: 20.5 Consensus size: 13
2963094 GCAAATAAAG
2963104 AAAATAAA-AAAA
1 AAAATAAAGAAAA
*
2963116 TGAAATAAAGAAAA
1 -AAAATAAAGAAAA
* *
2963130 TAAGATAGAGAAAA
1 -AAAATAAAGAAAA
* *
2963144 GAATGATAAAGGAAA
1 -AA-AATAAAGAAAA
*
2963159 AAAATAAAGTAAAG
1 AAAATAAAG-AAAA
* * *
2963173 ATAAGAAAGTAAAT
1 AAAATAAAG-AAAA
*
2963187 AAAATAAATAAAA
1 AAAATAAAGAAAA
*
2963200 CAAAGAT-AA-AACA
1 -AAA-ATAAAGAAAA
*
2963213 AAAATAAA-TAAA
1 AAAATAAAGAAAA
*
2963225 AAAATAAATAAAA
1 AAAATAAAGAAAA
2963238 TAAAGATAAAGAGAAA
1 -AAA-ATAAAGA-AAA
2963254 AAATATAAAGAAAATGA
1 AAA-ATAAAG-AAA--A
* *
2963271 AAAAAAAATGAAGA
1 AAAATAAA-GAAAA
* * *
2963285 TAAAGAAATAAAA
1 AAAATAAAGAAAA
*
2963298 TAACTATAAAGAAATAA
1 -AA-AATAAAG-AA-AA
*
2963315 AAAACTAAAGATAA
1 AAAA-TAAAGAAAA
*
2963329 AAAAT-AA-AAAT
1 AAAATAAAGAAAA
**
2963340 AAAATAAAGAGGA
1 AAAATAAAGAAAA
*
2963353 AAAAT-AA-AAAT
1 AAAATAAAGAAAA
*
2963364 AAAATAAAGGAAA
1 AAAATAAAGAAAA
*
2963377 ATAATA
1 AAAATA
2963383 GTAAAAATAA
Statistics
Matches: 197, Mismatches: 46, Indels: 46
0.68 0.16 0.16
Matches are distributed among these distances:
11 15 0.08
12 23 0.12
13 39 0.20
14 60 0.30
15 34 0.17
16 19 0.10
17 7 0.04
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.15
Consensus pattern (13 bp):
AAAATAAAGAAAA
Found at i:2963285 original size:41 final size:37
Alignment explanation
Indices: 2963156--2963366 Score: 137
Period size: 41 Copynumber: 5.5 Consensus size: 37
2963146 ATGATAAAGG
* *
2963156 AAAAAAATAAAG-TAAAGATAAGAAAGTA-AATAAAATA
1 AAAAAAATAAAGATAAAGA-AA-AAAATATAAAAAAATA
* * *
2963193 AATAAAACAAAGATAAA-ACAAAAATAAATAAAAAAATA
1 AAAAAAATAAAGATAAAGA-AAAAA-ATATAAAAAAATA
*
2963231 AATAAAATAAAGATAAAGAGAAAAAATATAAAGAAAATGAA
1 AAAAAAATAAAGATAAAGA-AAAAAATATAAA-AAAAT--A
*
2963272 AAAAAAATGAAGATAAAGAAATAAAATAACTATAAAGAAAT-
1 AAAAAAATAAAGATAAAGAAA-AAAAT-A-TA-AAA-AAATA
* *
2963313 AAAAAACTAAAGATAAA-AAATAAAA-ATAAAATAAAGA
1 AAAAAAATAAAGATAAAGAAA-AAAATATAAAA-AAATA
** *
2963350 GGAAAAATAAAAATAAA
1 AAAAAAATAAAGATAAA
2963367 ATAAAGGAAA
Statistics
Matches: 142, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
36 9 0.06
37 29 0.20
38 35 0.25
39 11 0.08
40 10 0.07
41 38 0.27
42 1 0.01
43 3 0.02
44 6 0.04
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.15
Consensus pattern (37 bp):
AAAAAAATAAAGATAAAGAAAAAAATATAAAAAAATA
Found at i:2963337 original size:6 final size:6
Alignment explanation
Indices: 2963309--2963460 Score: 51
Period size: 6 Copynumber: 24.0 Consensus size: 6
2963299 AACTATAAAG
* **
2963309 AAATAAA AAACTAA AGATAAA AAATAA AAAT-A AAATAA AGAGGAA AAATAA
1 AAAT-AA AAA-TAA AAAT-AA AAATAA AAATAA AAATAA A-AATAA AAATAA
* * * * * * *
2963360 AAATAA AATAAAGGA AAATAA TAGTAA AAAT-A AGATAT ACATAT AAATAA
1 AAATAA AA-ATA--A AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * *
2963410 AGCATTAA AAATGAAA TAAATAA AAAT-A AAA-AA TAATAA AAATAA TAATAA
1 A--AATAA AAAT--AA -AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
2963461 TAGTGATAGG
Statistics
Matches: 108, Mismatches: 22, Indels: 31
0.67 0.14 0.19
Matches are distributed among these distances:
5 16 0.15
6 55 0.51
7 20 0.19
8 10 0.09
9 7 0.06
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:2963382 original size:24 final size:24
Alignment explanation
Indices: 2963320--2963382 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
2963310 AATAAAAAAC
*
2963320 TAAAGATAAAAAATAAAAATAAAA
1 TAAAGAGAAAAAATAAAAATAAAA
*
2963344 TAAAGAGGAAAAATAAAAATAAAA
1 TAAAGAGAAAAAATAAAAATAAAA
2963368 TAAAG-GAAAATAATA
1 TAAAGAGAAAA-AATA
2963383 GTAAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.16
Consensus pattern (24 bp):
TAAAGAGAAAAAATAAAAATAAAA
Found at i:2963445 original size:13 final size:13
Alignment explanation
Indices: 2963309--2963445 Score: 66
Period size: 13 Copynumber: 10.0 Consensus size: 13
2963299 AACTATAAAG
2963309 AAATAAAAAACTAA
1 AAATAAAAAA-TAA
*
2963323 AGATAAAAAATAA
1 AAATAAAAAATAA
2963336 AAAT--AAAATAA
1 AAATAAAAAATAA
* **
2963347 AGAGGAAAAATAA
1 AAATAAAAAATAA
2963360 AAATAAAATAA-AGGA
1 AAATAAAA-AATA--A
* *
2963375 AAAT-AATAGTAA
1 AAATAAAAAATAA
*
2963387 AAATAAGATATACATAT
1 AAATAA-A-A-A-ATAA
* *
2963404 AAATAAAGCATTAA
1 AAATAAA-AAATAA
2963418 AAATGAAATAAATAA
1 AAAT-AAA-AAATAA
2963433 AAATAAAAAATAA
1 AAATAAAAAATAA
2963446 TAAAAATAAT
Statistics
Matches: 92, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
11 9 0.10
12 5 0.05
13 27 0.29
14 24 0.26
15 17 0.18
16 2 0.02
17 8 0.09
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.18
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:2963447 original size:16 final size:17
Alignment explanation
Indices: 2963423--2963454 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2963413 ATTAAAAATG
2963423 AAATAAATAAAAATAAA
1 AAATAAATAAAAATAAA
2963440 AAAT-AATAAAAATAA
1 AAATAAATAAAAATAA
2963455 TAATAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAAATAAAAATAAA
Found at i:2965378 original size:60 final size:64
Alignment explanation
Indices: 2965304--2965469 Score: 207
Period size: 65 Copynumber: 2.6 Consensus size: 64
2965294 TTGAAGTTGA
*
2965304 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA-GT-A-T-TGTTTAACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAACGTGAGTAAGTTTAACCAAATTG
* ** * *
2965364 GTTTTGAGTTGGATATCCTTCGTCT-TGAAGTTGAAATAAAATCTTGAGTAAGTTTCACCAAATT
1 GCTTTGAGTTGGATATCCTTCGT-TGTGAAGTTGAAATCCAA-CGTGAGTAAGTTTAACCAAATT
2965428 G
64 G
* *
2965429 GCTTTGTGTTGGATATCATTCGTTGTGAAGTTGAAATCCAA
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA
2965470 TCTCGAGTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
60 36 0.41
61 1 0.01
62 1 0.01
63 1 0.01
64 2 0.02
65 47 0.53
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.39
Consensus pattern (64 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAACGTGAGTAAGTTTAACCAAATTG
Found at i:2966372 original size:20 final size:19
Alignment explanation
Indices: 2966343--2966388 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2966333 CCCTAAACAT
*
2966343 TTTTCCTTTTTTCCTTTCTC
1 TTTT-CTTTTTTTCTTTCTC
*
2966363 TTTTCTTTTTTTCTTTTTC
1 TTTTCTTTTTTTCTTTCTC
2966382 TTCTTCT
1 TT-TTCT
2966389 GACTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTTTTTTTCTTTCTC
Found at i:2975695 original size:21 final size:20
Alignment explanation
Indices: 2975671--2975711 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2975661 AAAAGTTAAT
* *
2975671 AAAATAAAAATATAAATGAAG
1 AAAAGAAAAAAATAAA-GAAG
2975692 AAAAGAAAAAAATAAAGAAG
1 AAAAGAAAAAAATAAAGAAG
2975712 GCAAACTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAGAAAAAAATAAAGAAG
Found at i:2976626 original size:17 final size:19
Alignment explanation
Indices: 2976591--2976634 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2976581 TTAGAGAGAG
*
2976591 AAAAAAAGATAATGAAAAT
1 AAAAAAAGAAAATGAAAAT
2976610 AAAAAAA-AAAATG-AAAT
1 AAAAAAAGAAAATGAAAAT
2976627 AAAGAAAA
1 AAA-AAAA
2976635 TAAGATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAAAGAAAATGAAAAT
Found at i:2976642 original size:14 final size:13
Alignment explanation
Indices: 2976589--2976851 Score: 100
Period size: 14 Copynumber: 19.7 Consensus size: 13
2976579 TGTTAGAGAG
*
2976589 AGAAAAAAAGATAA
1 AGAAAATAA-ATAA
*
2976603 TGAAAATAAA-AA
1 AGAAAATAAATAA
*
2976615 AAAAAATGAAATAA
1 AGAAAAT-AAATAA
2976629 AGAAAATAAGATAA
1 AGAAAATAA-ATAA
2976643 AGAAAATAATGATAA
1 AGAAAATAA--ATAA
2976658 AGGAAAA-AAATAA
1 A-GAAAATAAATAA
* **
2976671 AG-TAA-AGGTAA
1 AGAAAATAAATAA
*
2976682 A-AAAGTAAATAA
1 AGAAAATAAATAA
*
2976694 A-ACAAATATAACAA
1 AGA-AAATA-AATAA
2976708 AGATAAATAAAATAA
1 AGA-AAAT-AAATAA
* * *
2976723 ATAAAAAAAAGAA
1 AGAAAATAAATAA
*
2976736 AGAGAAAAAATATAA
1 AGA-AAATAA-ATAA
2976751 AGAAAATGAAA-AA
1 AGAAAAT-AAATAA
* *
2976764 A-ATAA-AGATAA
1 AGAAAATAAATAA
2976775 AGATAAATAAATAA
1 AGA-AAATAAATAA
*
2976789 A-TAAATAACTATAA
1 AGAAAATAA--ATAA
2976803 AG-AAATAAATAA
1 AGAAAATAAATAA
*
2976815 ACTAAAGATAAA-AA
1 A-GAAA-ATAAATAA
* *
2976829 ATAAAAAAAATACA
1 AGAAAATAAATA-A
*
2976843 TGAAAATAA
1 AGAAAATAA
2976852 TAGTAAAAAT
Statistics
Matches: 191, Mismatches: 32, Indels: 52
0.69 0.12 0.19
Matches are distributed among these distances:
10 2 0.01
11 11 0.06
12 33 0.17
13 32 0.17
14 75 0.39
15 32 0.17
16 6 0.03
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (13 bp):
AGAAAATAAATAA
Found at i:2976651 original size:9 final size:9
Alignment explanation
Indices: 2976599--2976822 Score: 63
Period size: 9 Copynumber: 25.8 Consensus size: 9
2976589 AGAAAAAAAG
*
2976599 ATAATGAAA
1 ATAAAGAAA
2976608 ATAAA-AAA
1 ATAAAGAAA
*
2976616 AAAAATG-AA
1 ATAAA-GAAA
2976625 ATAAAGAAA
1 ATAAAGAAA
2976634 AT-AAG---
1 ATAAAGAAA
2976639 ATAAAGAAA
1 ATAAAGAAA
*
2976648 ATAATG---
1 ATAAAGAAA
2976654 ATAAAGGAAA
1 ATAAA-GAAA
*
2976664 A-AAATAAA
1 ATAAAGAAA
* *
2976672 GTAAAGGTAA
1 ATAAA-GAAA
*
2976682 A-AAAGTAA
1 ATAAAGAAA
2976690 ATAAA-ACAA
1 ATAAAGA-AA
*
2976699 ATATAACAAA
1 ATA-AAGAAA
*
2976709 GATAAATAAA
1 -ATAAAGAAA
*
2976719 ATAAATAAA
1 ATAAAGAAA
*
2976728 AAAAAGAAA
1 ATAAAGAAA
*
2976737 GAGAAA-AAA
1 -ATAAAGAAA
2976746 TATAAAGAAA
1 -ATAAAGAAA
2976756 ATGAAA-AAA
1 AT-AAAGAAA
2976765 ATAAAG---
1 ATAAAGAAA
2976771 ATAAAGATAA
1 ATAAAGA-AA
*
2976781 ATAAA-TAA
1 ATAAAGAAA
* *
2976789 ATAAATAACT
1 ATAAAGAA-A
2976799 ATAAAG-AA
1 ATAAAGAAA
*
2976807 ATAAATAAA
1 ATAAAGAAA
*
2976816 CTAAAGA
1 ATAAAGA
2976823 TAAAAAATAA
Statistics
Matches: 161, Mismatches: 25, Indels: 58
0.66 0.10 0.24
Matches are distributed among these distances:
5 2 0.01
6 13 0.08
7 1 0.01
8 34 0.21
9 75 0.47
10 32 0.20
11 4 0.02
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (9 bp):
ATAAAGAAA
Found at i:2976676 original size:18 final size:19
Alignment explanation
Indices: 2976640--2976694 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2976630 GAAAATAAGA
*
2976640 TAAAGAAAATAATGATAAAGG
1 TAAA-AAAATAAAG-TAAAGG
2976661 -AAAAAAATAAAGTAAAGG
1 TAAAAAAATAAAGTAAAGG
*
2976679 TAAAAAAGTAAA-TAAA
1 TAAAAAAATAAAGTAAA
2976695 ACAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 10 0.32
19 18 0.58
20 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.16
Consensus pattern (19 bp):
TAAAAAAATAAAGTAAAGG
Found at i:2976717 original size:24 final size:24
Alignment explanation
Indices: 2976680--2976734 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2976670 AAGTAAAGGT
*
2976680 AAAAAAG-TAAATAAAACAAATAT
1 AAAAAAGATAAATAAAACAAATAA
* *
2976703 AACAAAGATAAATAAAATAAATAA
1 AAAAAAGATAAATAAAACAAATAA
2976727 AAAAAAGA
1 AAAAAAGA
2976735 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (24 bp):
AAAAAAGATAAATAAAACAAATAA
Found at i:2976751 original size:33 final size:34
Alignment explanation
Indices: 2976706--2976793 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
2976696 CAAATATAAC
2976706 AAAGATAAATAAAATAAATAAAAAAAAGAAAGAG
1 AAAGATAAATAAAATAAATAAAAAAAAGAAAGAG
* * *
2976740 AAA-A-AATATAAAGA-AAATGAAAAAAATAAAGAT
1 AAAGATAA-ATAAA-ATAAATAAAAAAAAGAAAGAG
2976773 AAAGATAAAT-AAATAAATAAA
1 AAAGATAAATAAAATAAATAAA
2976794 TAACTATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
32 3 0.07
33 33 0.73
34 7 0.16
35 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (34 bp):
AAAGATAAATAAAATAAATAAAAAAAAGAAAGAG
Found at i:2976754 original size:19 final size:18
Alignment explanation
Indices: 2976710--2976789 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
2976700 TATAACAAAG
*
2976710 ATAAATAAAAT-AAATAAA
1 ATAAAGAAAATGAAA-AAA
*
2976728 AAAAAGAAAGA-GAAAAAA
1 ATAAAGAAA-ATGAAAAAA
2976746 TATAAAGAAAATGAAAAAA
1 -ATAAAGAAAATGAAAAAA
2976765 ATAAAGATAAA-GATAAATAA
1 ATAAAGA-AAATGA-AAA-AA
2976785 ATAAA
1 ATAAA
2976790 TAAATAACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
18 20 0.38
19 25 0.48
20 7 0.13
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (18 bp):
ATAAAGAAAATGAAAAAA
Found at i:2976786 original size:4 final size:4
Alignment explanation
Indices: 2976777--2976833 Score: 53
Period size: 4 Copynumber: 13.2 Consensus size: 4
2976767 AAAGATAAAG
*
2976777 ATAA ATAA ATAA ATAA ATAA CTATAA AGAA ATAA ATAA ACTAAA GATAA
1 ATAA ATAA ATAA ATAA ATAA --ATAA ATAA ATAA ATAA A-T-AA -ATAA
2976826 A-AA ATAA A
1 ATAA ATAA A
2976834 AAAAATACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
3 3 0.07
4 31 0.69
5 3 0.07
6 7 0.16
7 1 0.02
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:2976802 original size:18 final size:18
Alignment explanation
Indices: 2976781--2976832 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2976771 ATAAAGATAA
2976781 ATAAATAAATAAATAACT
1 ATAAATAAATAAATAACT
*
2976799 ATAAAGAAATAAATAAACT
1 ATAAATAAATAAAT-AACT
2976818 A-AAGATAAA-AAATAA
1 ATAA-ATAAATAAATAA
2976833 AAAAAATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.07
18 19 0.63
19 9 0.30
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (18 bp):
ATAAATAAATAAATAACT
Found at i:2976802 original size:22 final size:22
Alignment explanation
Indices: 2976759--2976833 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
2976749 AAAGAAAATG
*
2976759 AAAA-AAATAAAGATAAAGATAA
1 AAAATAAATAAA-CTAAAGATAA
**
2976781 ATAAATAAATAAA-TAACTATAA
1 A-AAATAAATAAACTAAAGATAA
2976803 AGAAATAAATAAACTAAAGATAA
1 A-AAATAAATAAACTAAAGATAA
2976826 AAAATAAA
1 AAAATAAA
2976834 AAAAATACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 27 0.60
23 11 0.24
24 7 0.16
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAATAAATAAACTAAAGATAA
Found at i:2976833 original size:18 final size:17
Alignment explanation
Indices: 2976748--2976833 Score: 52
Period size: 18 Copynumber: 4.9 Consensus size: 17
2976738 AGAAAAAATA
*
2976748 TAAAGAAAATGAAA-AAAA
1 TAAAGAAAA--AAATAAAC
* *
2976766 TAAAGATAAAGATAAA-
1 TAAAGAAAAAAATAAAC
* *
2976782 TAAATAAATAAAT-AAC
1 TAAAGAAAAAAATAAAC
*
2976798 TATAAAGAAATAAATAAAC
1 --TAAAGAAAAAAATAAAC
2976817 TAAAGATAAAAAATAAA
1 TAAAGA-AAAAAATAAA
2976834 AAAAATACAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.04
16 11 0.20
17 9 0.17
18 29 0.54
19 3 0.06
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (17 bp):
TAAAGAAAAAAATAAAC
Found at i:2978830 original size:2 final size:2
Alignment explanation
Indices: 2978823--2978848 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2978813 GTCAATCAGC
2978823 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
2978849 TATTAGCAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2980921 original size:2 final size:2
Alignment explanation
Indices: 2980914--2980939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2980904 TTATTTTTAA
2980914 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
2980940 TATCTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2983331 original size:23 final size:20
Alignment explanation
Indices: 2983289--2983337 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
2983279 AAAATTACAA
*
2983289 AAATAAAATAAAATTGATTT
1 AAATAAAATAAAATTAATTT
2983309 AAATAAAATAATATAGTTAATTT
1 AAATAAAATAA-A-A-TTAATTT
2983332 AAATAA
1 AAATAA
2983338 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 1 0.04
23 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATAAAATAAAATTAATTT
Found at i:2984660 original size:11 final size:11
Alignment explanation
Indices: 2984646--2984684 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2984636 TTAAACTATT
2984646 CTTTAATATAA
1 CTTTAATATAA
*
2984657 CTTTAACTAT-T
1 CTTTAA-TATAA
2984668 CTTTAATATAA
1 CTTTAATATAA
2984679 CTTTAA
1 CTTTAA
2984685 CTAATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (11 bp):
CTTTAATATAA
Found at i:2984665 original size:30 final size:30
Alignment explanation
Indices: 2984631--2984717 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
2984621 TTCCTTAAAC
2984631 AACTATTAAACTATTCTTT-A-AT-A---T
1 AACTATTAAACTATTCTTTAATATAACTTT
2984655 AACT-TT-AACTATTCTTTAATATAACTTT
1 AACTATTAAACTATTCTTTAATATAACTTT
* *
2984683 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTATTAAACTATTCTTTAATATAACTTT
2984713 AACTA
1 AACTA
2984718 AAAAACTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 11 0.21
23 3 0.06
24 6 0.11
25 1 0.02
28 5 0.09
29 1 0.02
30 26 0.49
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.44
Consensus pattern (30 bp):
AACTATTAAACTATTCTTTAATATAACTTT
Found at i:2984667 original size:22 final size:22
Alignment explanation
Indices: 2984639--2984687 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2984629 ACAACTATTA
2984639 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
2984661 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
2984683 AACTA
1 AACTA
2984688 ATAAACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:2984704 original size:15 final size:16
Alignment explanation
Indices: 2984660--2984710 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
2984650 AATATAACTT
2984660 TAACTATTCTTTAATA
1 TAACTATTCTTTAATA
***
2984676 TAACT-TTAACTAATA
1 TAACTATTCTTTAATA
2984691 -AACTATTCTTTAATA
1 TAACTATTCTTTAATA
2984706 TAACT
1 TAACT
2984711 TAAACTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTCTTTAATA
Found at i:2984718 original size:30 final size:30
Alignment explanation
Indices: 2984661--2984725 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
2984651 ATATAACTTT
* *
2984661 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTCTTTAATATAACTTAAACTAAAA
2984691 AACTATTCTTTAATATAACTTAAACTAAAA
1 AACTATTCTTTAATATAACTTAAACTAAAA
2984721 AACTA
1 AACTA
2984726 ATTAACTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (30 bp):
AACTATTCTTTAATATAACTTAAACTAAAA
Found at i:2984732 original size:52 final size:52
Alignment explanation
Indices: 2984631--2984732 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
2984621 TTCCTTAAAC
* * *****
2984631 AACTATTAAACTATTCTTTAATATAACTTTAACTATTCTTTAATATAACTTT
1 AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAACTAATATAACTTT
2984683 AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAAACTAAT-TAACT
1 AACTAATAAACTATTCTTTAATATAACTTAAACT-AAAAACTAATATAACT
2984733 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 37 0.88
53 5 0.12
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (52 bp):
AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAACTAATATAACTTT
Found at i:2984929 original size:21 final size:21
Alignment explanation
Indices: 2984903--2984942 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2984893 TTTCTATATG
2984903 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
2984924 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
2984943 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:2984990 original size:21 final size:21
Alignment explanation
Indices: 2984966--2985008 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2984956 TTTTTTACCC
*
2984966 TAATTTATAATAATAAACTAA
1 TAATTTATAACAATAAACTAA
2984987 TAATTTATAACAATAAACTAA
1 TAATTTATAACAATAAACTAA
2985008 T
1 T
2985009 TTAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATTTATAACAATAAACTAA
Found at i:2985070 original size:35 final size:37
Alignment explanation
Indices: 2985031--2985102 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
2985021 TCTTTTATAT
2985031 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
*
2985066 AACTTAAACTACTAATAAAGTAATTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATA
2985103 TAAATTCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 5 0.16
36 2 0.06
38 17 0.53
39 8 0.25
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:2985305 original size:9 final size:9
Alignment explanation
Indices: 2985273--2985310 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2985263 CTAACAAACT
2985273 AATAATTTAA
1 AATAA-TTAA
2985283 AATAA-TAA
1 AATAATTAA
*
2985291 ACTAATTAA
1 AATAATTAA
2985300 AATAATTAA
1 AATAATTAA
2985309 AA
1 AA
2985311 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:2995317 original size:29 final size:29
Alignment explanation
Indices: 2995282--2995337 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2995272 CAGAGACTCC
*
2995282 AAGGTCGCCCGGATGCCATGGCGACCTCT
1 AAGGTCGCCCGAATGCCATGGCGACCTCT
*
2995311 AAGGTCGCCCGAATGGCATGGCGACCT
1 AAGGTCGCCCGAATGCCATGGCGACCT
2995338 ACGACAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (29 bp):
AAGGTCGCCCGAATGCCATGGCGACCTCT
Found at i:2999698 original size:15 final size:15
Alignment explanation
Indices: 2999678--2999716 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2999668 GATTATAAAC
2999678 TTGAAGCAAAAATTG
1 TTGAAGCAAAAATTG
*
2999693 TTGAAGAAAAAATTG
1 TTGAAGCAAAAATTG
*
2999708 TCGAAGCAA
1 TTGAAGCAA
2999717 TTTGCAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.23
Consensus pattern (15 bp):
TTGAAGCAAAAATTG
Found at i:3001396 original size:100 final size:100
Alignment explanation
Indices: 3001223--3001431 Score: 409
Period size: 100 Copynumber: 2.1 Consensus size: 100
3001213 TTATTATAGT
*
3001223 CATATTTATGGAAGGAGATCAAATTCTATAATATATGGACTCTTTAAAGCTTTTCAAATCTCATG
1 CATATTTATGGAAGGAGATCAAATTCTATAATATATGGACTCTTTAAAGCTTATCAAATCTCATG
3001288 ATTCTTAGACTCTTCTGACATCTAGTTCCCTGGTA
66 ATTCTTAGACTCTTCTGACATCTAGTTCCCTGGTA
3001323 CATATTTATGGAAGGAGATCAAATTCTATAATATATGGACTCTTTAAAGCTTATCAAATCTCATG
1 CATATTTATGGAAGGAGATCAAATTCTATAATATATGGACTCTTTAAAGCTTATCAAATCTCATG
3001388 ATTCTTAGACTCTTCTGACATCTAGTTCCCTGGTA
66 ATTCTTAGACTCTTCTGACATCTAGTTCCCTGGTA
3001423 CATATTTAT
1 CATATTTAT
3001432 CTTGATACAT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 108 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (100 bp):
CATATTTATGGAAGGAGATCAAATTCTATAATATATGGACTCTTTAAAGCTTATCAAATCTCATG
ATTCTTAGACTCTTCTGACATCTAGTTCCCTGGTA
Found at i:3002891 original size:16 final size:15
Alignment explanation
Indices: 3002863--3002905 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3002853 TTCGATAAAT
3002863 ATTTATAAT-ATTATA
1 ATTTA-AATGATTATA
*
3002878 ATATTATATGATTATA
1 AT-TTAAATGATTATA
3002894 ATTTAAATGATT
1 ATTTAAATGATT
3002906 TTTAGCACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATTTAAATGATTATA
Found at i:3002996 original size:305 final size:314
Alignment explanation
Indices: 3002553--3003170 Score: 1044
Period size: 311 Copynumber: 2.0 Consensus size: 314
3002543 ATTTAAATTA
3002553 TATAATATTATATTATAATTATATGATTAATTTAAATGATTTTAGCAACGAACCAAGCTACCTTA
1 TATAATATTATA-TATAATTATATGATTAATTTAAATGATTTTAGCAACGAACCAAGCTACCTTA
*
3002618 GTAAATTAAACGGATAATTGTTATCCTTGATGTCTGATTACCCAGTGACTGTAAGCTATTTGAGA
65 GTAAATTAAACGGATAATTGTTATCCTTGA----TAATTACCCAGTGACTGTAAGCTATTTGAGA
3002683 GTTCATTGTCAAATGGTTGAGAATCTTTAGAATATATA-TACCACTTGTAAT-CACTA-ATTAAT
126 GTTCATTGTCAAATGGTTGAGAATCTTTAGAATATATACTACCACTTGTAATACACTAGATTAAT
3002745 AAAAAAATAA-TATTATAATCATATACAAACTTGAAAATCTATCCACTAACTATTAAAAA-TTTG
191 AAAAAAATAAGTATTATAATCATATACAAACTTGAAAATCTATCCACTAACTATTAAAAATTTTG
3002808 AGTTATTCGAGTTGTA-TTTATAAGTTGATTTGAACTTGGAAATTCTTCGATAAATATT
256 AGTTATTCGAGTTGTATTTTATAAGTTGATTTGAACTTGGAAATTCTTCGATAAATATT
3002866 TATAATATTATA-AT-ATTATATGATTATAATTTAAATGATTTTTAGC-ACGAACCAAGCTACCT
1 TATAATATTATATATAATTATATGA-T-TAATTTAAATGA-TTTTAGCAACGAACCAAGCTACCT
3002928 TAGT-AATTAAACGGATAATTGTTATCCTT-A-AATTACCCAGTGACTGTAAGCTATTTGAGAGT
63 TAGTAAATTAAACGGATAATTGTTATCCTTGATAATTACCCAGTGACTGTAAGCTATTTGAGAGT
3002990 TCATTGTCAAATGGTTGAGAATCTTTAGAATATATACTACCACTTGTAATCACACTAGATTAATA
128 TCATTGTCAAATGGTTGAGAATCTTTAGAATATATACTACCACTTGTAAT-ACACTAGATTAATA
*
3003055 AAAAAATAATGTTTTATAATCATATACAAACTTGAAAATCTATCCACTAACTATTAAAAATTTTG
192 AAAAAATAA-GTATTATAATCATATACAAACTTGAAAATCTATCCACTAACTATTAAAAATTTTG
3003120 AGTTATTCGAGTTGTATTTTATAAGTTGATTTGAACTTGGAAATTCTTCGA
256 AGTTATTCGAGTTGTATTTTATAAGTTGATTTGAACTTGGAAATTCTTCGA
3003171 GTTGAATATA
Statistics
Matches: 292, Mismatches: 2, Indels: 22
0.92 0.01 0.07
Matches are distributed among these distances:
305 67 0.23
306 13 0.04
308 5 0.02
309 16 0.05
310 10 0.03
311 76 0.26
312 52 0.18
313 53 0.18
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (314 bp):
TATAATATTATATATAATTATATGATTAATTTAAATGATTTTAGCAACGAACCAAGCTACCTTAG
TAAATTAAACGGATAATTGTTATCCTTGATAATTACCCAGTGACTGTAAGCTATTTGAGAGTTCA
TTGTCAAATGGTTGAGAATCTTTAGAATATATACTACCACTTGTAATACACTAGATTAATAAAAA
AATAAGTATTATAATCATATACAAACTTGAAAATCTATCCACTAACTATTAAAAATTTTGAGTTA
TTCGAGTTGTATTTTATAAGTTGATTTGAACTTGGAAATTCTTCGATAAATATT
Found at i:3006749 original size:13 final size:13
Alignment explanation
Indices: 3006731--3006762 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3006721 GTATAATCAT
3006731 TCATGCTCAATAC
1 TCATGCTCAATAC
3006744 TCATGCTCAATAC
1 TCATGCTCAATAC
3006757 TCATGC
1 TCATGC
3006763 ATGCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (13 bp):
TCATGCTCAATAC
Found at i:3006862 original size:60 final size:60
Alignment explanation
Indices: 3006790--3006909 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
3006780 GGCAACCAAT
*
3006790 ATACAAAATCAATAAACATTAAGTGTAGAGGTTACTCATCCTTCTTTTGTATGACAAGAG
1 ATACAAAATCAATAAACATTAAGTGTAGAGGTTACCCATCCTTCTTTTGTATGACAAGAG
*
3006850 ATACAAAATCAATAAACATTAAGTGTAGAGGTTACCCATCCTTCTTTTGTGTGACAAGAG
1 ATACAAAATCAATAAACATTAAGTGTAGAGGTTACCCATCCTTCTTTTGTATGACAAGAG
3006910 CAATTGAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (60 bp):
ATACAAAATCAATAAACATTAAGTGTAGAGGTTACCCATCCTTCTTTTGTATGACAAGAG
Found at i:3013557 original size:2 final size:2
Alignment explanation
Indices: 3013540--3013713 Score: 84
Period size: 2 Copynumber: 92.0 Consensus size: 2
3013530 AATTATAATA
* * *
3013540 AT AT AT AA AT AT -T AT AT AT AT AT -T CT A- AA AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
3013578 AT AT AT -T TT AA AC AT AT AT -T TT A- AA 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
* *
3013617 AT AT AT AT AT AT AT -T CT A- AA ACT AT AT AT AT AT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * * * **
3013656 AA AA AT AT AT A- AT AT AT AT AT TT TT AG AA ACT AT GC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
3013698 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3013714 TCCAAAACTA
Statistics
Matches: 136, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
1 12 0.09
2 122 0.90
3 2 0.01
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3013570 original size:21 final size:22
Alignment explanation
Indices: 3013531--3013674 Score: 90
Period size: 21 Copynumber: 6.6 Consensus size: 22
3013521 GATAATAATA
*
3013531 ATTATAATA-ATA-TAT-AAAT
1 ATTATAATATATATTCTAAAAT
3013550 ATTAT-ATATATATTCTAAAAT
1 ATTATAATATATATTCTAAAAT
*
3013571 A-TATAATATATATTTTAAACATAT
1 ATTATAATATATATTCT-AA-A-AT
* * * *
3013595 ATTTTAAAATATA-TAT-ATAT
1 ATTATAATATATATTCTAAAAT
3013615 ATATATATATATATATTCTAAAACT
1 AT-TATA-ATATATATTCTAAAA-T
**
3013640 A-TATATATATATATTAAAAAAT
1 ATTATA-ATATATATTCTAAAAT
3013662 A-TATAATATATAT
1 ATTATAATATATAT
3013675 ATTTTTAGAA
Statistics
Matches: 100, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
18 3 0.03
19 8 0.08
20 9 0.09
21 26 0.26
22 15 0.15
23 21 0.21
24 7 0.07
25 11 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATAATATATATTCTAAAAT
Found at i:3013580 original size:34 final size:33
Alignment explanation
Indices: 3013536--3013655 Score: 161
Period size: 34 Copynumber: 3.6 Consensus size: 33
3013526 TAATAATTAT
*
3013536 AATA-ATATATAAATATTATATATATATTCTAA
1 AATATATATATATATATTATATATATATTCTAA
* * * *
3013568 AATATATAATATATATTTTAAACATATATTTTAA
1 AATATAT-ATATATATATTATATATATATTCTAA
3013602 AATATATATATATATATATATATATATATTCTAA
1 AATATATATATATATAT-TATATATATATTCTAA
3013636 AACTATATATATATATATTA
1 AA-TATATATATATATATTA
3013656 AAAAATATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 4 0.05
33 11 0.15
34 45 0.60
35 15 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (33 bp):
AATATATATATATATATTATATATATATTCTAA
Found at i:3014782 original size:74 final size:73
Alignment explanation
Indices: 3014558--3014900 Score: 226
Period size: 74 Copynumber: 4.6 Consensus size: 73
3014548 CCAAATGAAA
* * *** * * *
3014558 GATTCTTTGGATGGA-TCCCCTTCGCGGGTTTAAGCCAAACAAGATGACTCTCTTTCACAGTTTA
1 GATTCTTTGGAT-GACTCCCCTTCGCGGGTCTAAGTCAAGTGAGATGACTCCCTTTGA-GGTTTA
3014622 AGCCAACCTT
64 AGCCAACCTT
* * * * * * *
3014632 GATTCTTTGCATGACTCCTCTTCGCAGGTCTAAGTCAAGTGAGACGATTCCCCTTCGCGGTTTAA
1 GATTCTTTGGATGACTCCCCTTCGCGGGTCTAAGTCAAGTGAGATGACT-CCCTTTGAGGTTTAA
*** ***
3014697 ATGAGTATT
65 GCCAACCTT
*
3014706 GATTCTTTGGATGACTCCCCTTCGTGGGTCTAAGTCAAGTGAGATGACTCCCTATTGAGGTTTAA
1 GATTCTTTGGATGACTCCCCTTCGCGGGTCTAAGTCAAGTGAGATGACTCCCT-TTGAGGTTTAA
3014771 GCCAACCTT
65 GCCAACCTT
* * * ** * * *
3014780 GATTATTTGGATGGCTCCCTTTCATGGGT-TAAGTCGAA-TAAAATGACTCCCCTTCGTA-GTTT
1 GATTCTTTGGATGACTCCCCTTCGCGGGTCTAAGTC-AAGTGAGATGACT-CCCTTTG-AGGTTT
**
3014842 AAGCCAGTCTT
63 AAGCCAACCTT
* * ** * * * *
3014853 AATTTTTTTGGATGACTCCTTTTCGCGAGTTTAAGTCAAATGACATGA
1 GA-TTCTTTGGATGACTCCCCTTCGCGGGTCTAAGTCAAGTGAGATGA
3014901 TTCTTCAGGT
Statistics
Matches: 207, Mismatches: 53, Indels: 17
0.75 0.19 0.06
Matches are distributed among these distances:
73 36 0.17
74 155 0.75
75 16 0.08
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (73 bp):
GATTCTTTGGATGACTCCCCTTCGCGGGTCTAAGTCAAGTGAGATGACTCCCTTTGAGGTTTAAG
CCAACCTT
Found at i:3023201 original size:15 final size:15
Alignment explanation
Indices: 3023183--3023227 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3023173 ATCTTCAGAC
3023183 TCATCACTGAATAGA
1 TCATCACTGAATAGA
**
3023198 TCATCA-T-AGGA-A
1 TCATCACTGAATAGA
3023210 TCATCACTGAATAGA
1 TCATCACTGAATAGA
3023225 TCA
1 TCA
3023228 CAAGGAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 7 0.30
13 3 0.13
14 3 0.13
15 10 0.43
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
TCATCACTGAATAGA
Found at i:3023213 original size:27 final size:27
Alignment explanation
Indices: 3023166--3023234 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
3023156 ATTCTTATCC
* *
3023166 ATAGATCATCTTCA-GACTCATCACTGA
1 ATAGATCATCAT-AGGAATCATCACTGA
3023193 ATAGATCATCATAGGAATCATCACTGA
1 ATAGATCATCATAGGAATCATCACTGA
3023220 ATAGATCA-CA-AGGAA
1 ATAGATCATCATAGGAA
3023235 ACTAACAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 5 0.13
26 3 0.08
27 31 0.79
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (27 bp):
ATAGATCATCATAGGAATCATCACTGA
Found at i:3024520 original size:11 final size:11
Alignment explanation
Indices: 3024500--3024575 Score: 52
Period size: 11 Copynumber: 7.1 Consensus size: 11
3024490 CCCGGAAAAA
3024500 GTCAACGGTCG
1 GTCAACGGTCG
* *
3024511 TTCAATGGTCG
1 GTCAACGGTCG
* *
3024522 GTCAAAGTTCTG
1 GTCAACGGTC-G
3024534 GTCAAC-GTCG
1 GTCAACGGTCG
*
3024544 GTCAATGG--G
1 GTCAACGGTCG
*
3024553 GTCAACGCT-G
1 GTCAACGGTCG
3024563 GTCAACGGGTCG
1 GTCAAC-GGTCG
3024575 G
1 G
3024576 GTCGGGTCAG
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
9 7 0.14
10 13 0.27
11 21 0.43
12 8 0.16
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.24
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:3025168 original size:32 final size:32
Alignment explanation
Indices: 3025127--3025187 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3025117 ACGAAGAAGG
3025127 GAAATGGGGAATAATTCTGCAAAAACATACAT
1 GAAATGGGGAATAATTCTGCAAAAACATACAT
**
3025159 GAAATGGGGAATAATTCTGCGGAAACATA
1 GAAATGGGGAATAATTCTGCAAAAACATA
3025188 GGGAAATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (32 bp):
GAAATGGGGAATAATTCTGCAAAAACATACAT
Found at i:3026843 original size:15 final size:15
Alignment explanation
Indices: 3026807--3026850 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3026797 TTTTATAATA
*
3026807 AATATTTATTAATTTT
1 AATATTT-TTATTTTT
3026823 AATATTTTTATTTTT
1 AATATTTTTATTTTT
*
3026838 ACTATTTTTATTT
1 AATATTTTTATTT
3026851 AATAAATCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
AATATTTTTATTTTT
Found at i:3032816 original size:65 final size:63
Alignment explanation
Indices: 3032738--3032897 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 63
3032728 GAATAAATTG
* * *
3032738 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATTGATGCACTCAGAG-T-TTTATG
1 AACATCAAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-T-
3032801 AA
62 AA
* * *
3032803 AACATTAAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTAA
1 AACATCAAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTAA
* *
3032867 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCAAATGCATTTCATGCATCGATGCAC
3032898 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 30 0.36
65 47 0.57
66 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCAAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTAA
Found at i:3038689 original size:20 final size:21
Alignment explanation
Indices: 3038664--3038758 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
3038654 TTGTGCTTAA
3038664 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
* *
3038684 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAAAG
* *
3038706 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAAAG
* * *
3038727 TGCACCGATGCAGTCCTTGAATG
1 TGCATCGATACA--CCTTGAAAG
3038750 TGCATCGAT
1 TGCATCGAT
3038759 GCACAAGGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 19 0.32
22 13 0.22
23 17 0.28
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:3038729 original size:21 final size:22
Alignment explanation
Indices: 3038683--3038758 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
3038673 ACACCTAACA
*
3038683 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACATCCTTGAAT
* *
3038705 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCTTGAAT
* *
3038726 GTGCACCGATGCAGTCCTTGAAT
1 GTGCATCGATACA-TCCTTGAAT
3038749 GTGCATCGAT
1 GTGCATCGAT
3038759 GCACAAGGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 17 0.39
22 12 0.27
23 15 0.34
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATACATCCTTGAAT
Found at i:3038752 original size:23 final size:22
Alignment explanation
Indices: 3038683--3038761 Score: 106
Period size: 23 Copynumber: 3.6 Consensus size: 22
3038673 ACACCTAACA
3038683 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * *
3038705 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
3038726 GTGCACCGATGCAGTCCTTGAAT
1 GTGCATCGATGCA-TCCTTGAAT
3038749 GTGCATCGATGCA
1 GTGCATCGATGCA
3038762 CAAGGTTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.36
22 12 0.26
23 18 0.38
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:3038753 original size:44 final size:42
Alignment explanation
Indices: 3038664--3038758 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 42
3038654 TTGTGCTTAA
*
3038664 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCATCCTTGAATG
*
3038706 TGCATCGATACACCATGAA-GGTGCACCGATGCAGTCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-TCCTTGAATG
3038750 TGCATCGAT
1 TGCATCGAT
3038759 GCACAAGGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 14 0.29
43 13 0.27
44 21 0.44
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCATCCTTGAATG
Found at i:3038779 original size:43 final size:42
Alignment explanation
Indices: 3038682--3038783 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 42
3038672 TACACCTAAC
* *
3038682 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
* * *
3038724 AGGTGCACCGATGCAGTCCTTGAATGTGCATCGATGCACAAGGTT
1 A-GTGCATCGATGCA-TCCTTGAATGTGCATCGATACACAAGG-A
3038769 A-TGCATCGATGCATC
1 AGTGCATCGATGCATC
3038784 GATCGGGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
42 3 0.06
43 23 0.45
44 24 0.47
45 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (42 bp):
AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
Found at i:3040945 original size:2 final size:2
Alignment explanation
Indices: 3040938--3040968 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3040928 CAGCTTAAGC
*
3040938 TA TA TA TA TA TG 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
3040969 TTAATCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3041509 original size:64 final size:63
Alignment explanation
Indices: 3041433--3041619 Score: 218
Period size: 65 Copynumber: 2.9 Consensus size: 63
3041423 CACCAATCCG
** *
3041433 TGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCATGCATCGATGCACATACT
1 TGCATCGATGCACTCA--GAATATTTTGAAACATCGAATGCATTTCATGCATCGATGCACA-ACA
3041496 A
63 A
* * * *
3041497 TGCATCGATGCACTCAGAGT-TTTATGAAAACATCAAATGCATTTGATGCATCGATGCACCAGCA
1 TGCATCGATGCACTCAGAATATTT-TG-AAACATCGAATGCATTTCATGCATCGATGCA-CAACA
3041561 A
63 A
* *
3041562 TGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTTATGCATCGATGCAC
1 TGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
3041620 TCTTAGTGCA
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
62 1 0.01
63 6 0.06
64 42 0.39
65 53 0.50
66 5 0.05
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCATTTCATGCATCGATGCACAACAA
Found at i:3041529 original size:65 final size:63
Alignment explanation
Indices: 3041460--3041619 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 63
3041450 GAATAAATTG
* *
3041460 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATCGATGCACTCAGAGT-TTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACAATGCATCGATGCACTCAGACTATTT-TG-
3041524 A
63 A
* * *
3041525 AACATCAAATGCATTTGATGCATCGATGCACCAGCAATGCATCGATGCACTCAGACTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CAACAATGCATCGATGCACTCAGACTATTTTGA
*
3041589 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
3041620 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 51 0.59
66 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACAATGCATCGATGCACTCAGACTATTTTGA
Found at i:3041887 original size:14 final size:14
Alignment explanation
Indices: 3041868--3041908 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
3041858 ACAATAATCA
3041868 AGAGAGAATCAAAG
1 AGAGAGAATCAAAG
3041882 AGAGAGAATCAAAG
1 AGAGAGAATCAAAG
* *
3041896 AGAAAGCATCAAA
1 AGAGAGAATCAAA
3041909 CCTCAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.24, T:0.07
Consensus pattern (14 bp):
AGAGAGAATCAAAG
Found at i:3043136 original size:17 final size:17
Alignment explanation
Indices: 3043114--3043153 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3043104 TTTTTCGTTT
*
3043114 TTACTGCTTCATTTCTC
1 TTACTGCTTCATTGCTC
*
3043131 TTACTGCTTCGTTGCTC
1 TTACTGCTTCATTGCTC
3043148 TTACTG
1 TTACTG
3043154 TTATGAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.10, C:0.28, G:0.12, T:0.50
Consensus pattern (17 bp):
TTACTGCTTCATTGCTC
Found at i:3053129 original size:35 final size:32
Alignment explanation
Indices: 3053088--3053172 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 32
3053078 TATATTTGGT
*
3053088 TAATTTTGTTTATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTTATTACAATTTAATA-C--TTATTG
3053123 TAATTTTGTTATTATTTACAATTTAATACTTATTG
1 TAATTTTG-T-TTA-TTACAATTTAATACTTATTG
*
3053158 TAAGTTTGTTGTATT
1 TAATTTTGTT-TATT
3053173 TAAAATTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
33 3 0.07
34 3 0.07
35 21 0.48
36 1 0.02
37 4 0.09
38 12 0.27
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (32 bp):
TAATTTTGTTTATTACAATTTAATACTTATTG
Found at i:3055134 original size:16 final size:13
Alignment explanation
Indices: 3055099--3055124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3055089 ATCATATATA
3055099 ATTATAAAAAAAT
1 ATTATAAAAAAAT
3055112 ATTATAAAAAAAT
1 ATTATAAAAAAAT
3055125 TACCTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTATAAAAAAAT
Found at i:3057858 original size:21 final size:21
Alignment explanation
Indices: 3057833--3057873 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3057823 AATATTAAAA
*
3057833 AAATATTAATATTTTAAATAG
1 AAATAATAATATTTTAAATAG
3057854 AAATAATAATATTTTAAATA
1 AAATAATAATATTTTAAATA
3057874 ATTTTTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAAATAG
Found at i:3061152 original size:3 final size:3
Alignment explanation
Indices: 3061144--3061198 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
3061134 TTAGTGAGGC
3061144 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3061192 ATA ATA A
1 ATA ATA A
3061199 AGAAATATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3062131 original size:19 final size:19
Alignment explanation
Indices: 3062080--3062122 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
3062070 TTTCCTCTAG
3062080 GGGGTATCGATACACTATA
1 GGGGTATCGATACACTATA
*
3062099 -GGGTATTGATACACTATA
1 GGGGTATCGATACACTATA
3062117 GGGGTA
1 GGGGTA
3062123 ACGGTACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (19 bp):
GGGGTATCGATACACTATA
Found at i:3066107 original size:19 final size:19
Alignment explanation
Indices: 3066080--3066150 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
3066070 AAATAACTAA
*
3066080 CAAAATCGCAACACGATTT
1 CAAATTCGCAACACGATTT
* *
3066099 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACG-ATTT
*
3066119 CAATTTCGCAACAC-AGTTT
1 CAAATTCGCAACACGA-TTT
*
3066138 CCAAATTCACAAC
1 -CAAATTCGCAAC
3066151 TCGAACATGG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.02
19 15 0.37
20 25 0.61
ACGTcount: A:0.39, C:0.31, G:0.08, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACACGATTT
Found at i:3066782 original size:14 final size:14
Alignment explanation
Indices: 3066755--3066785 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3066745 TTCGATTTGC
3066755 GAAATTCGCTTTAT
1 GAAATTCGCTTTAT
3066769 GAAATTCGCTTTAT
1 GAAATTCGCTTTAT
3066783 GAA
1 GAA
3066786 TAGTTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (14 bp):
GAAATTCGCTTTAT
Found at i:3067818 original size:17 final size:18
Alignment explanation
Indices: 3067781--3067821 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3067771 ATATTATGTA
*
3067781 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
3067799 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
3067816 TTTACT
1 TTTACT
3067822 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:3069518 original size:18 final size:18
Alignment explanation
Indices: 3069495--3069530 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3069485 CACAGCAGCC
*
3069495 ACCGCAGCCATTTATGAT
1 ACCGCAGCCATATATGAT
3069513 ACCGCAGCCATATATGAT
1 ACCGCAGCCATATATGAT
3069531 GCCGTCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (18 bp):
ACCGCAGCCATATATGAT
Found at i:3070160 original size:35 final size:33
Alignment explanation
Indices: 3070121--3070205 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
3070111 ATATTTCAGT
3070121 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
3070156 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
3070191 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
3070206 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:3077588 original size:21 final size:21
Alignment explanation
Indices: 3077562--3077610 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3077552 ACTACACTAA
3077562 CAATCCTTATAATAAACAAAC
1 CAATCCTTATAATAAACAAAC
3077583 CAATCCTTATAATAAACAAAC
1 CAATCCTTATAATAAACAAAC
3077604 CAATCCT
1 CAATCCT
3077611 ATACACTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (21 bp):
CAATCCTTATAATAAACAAAC
Found at i:3083789 original size:34 final size:32
Alignment explanation
Indices: 3083727--3083796 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3083717 ACCTTACAAC
* *
3083727 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
3083759 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
3083793 TCCC
1 TCCC
3083797 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:3084183 original size:20 final size:20
Alignment explanation
Indices: 3084154--3084247 Score: 170
Period size: 20 Copynumber: 4.7 Consensus size: 20
3084144 GCAGCCTTCG
*
3084154 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
3084174 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
3084194 TGCATCGATGCACAGTAGGA
1 TGCATCGATGCACAGCAGGA
3084214 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
3084234 TGCATCGATGCACA
1 TGCATCGATGCACA
3084248 TCAAGATACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:3084265 original size:60 final size:60
Alignment explanation
Indices: 3084154--3084266 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
3084144 GCAGCCTTCG
* * * *
3084154 TGCATGGATGCACAGCAGGATGCATCGATGCACAGCAGGATGCATCGATGCACAGTAGGA
1 TGCATCGATGCACAGCAGGATGCATCGATGCACAGCAAGATACATAGATGCACAGTAGGA
* *
3084214 TGCATCGATGCACAGCAGGATGCATCGATGCACATCAAGATACATATATGCAC
1 TGCATCGATGCACAGCAGGATGCATCGATGCACAGCAAGATACATAGATGCAC
3084267 TAAGTGCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.19
Consensus pattern (60 bp):
TGCATCGATGCACAGCAGGATGCATCGATGCACAGCAAGATACATAGATGCACAGTAGGA
Found at i:3084609 original size:21 final size:21
Alignment explanation
Indices: 3084585--3084624 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3084575 ATGTTTAATG
3084585 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
3084606 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
3084625 CCAATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:3085777 original size:19 final size:20
Alignment explanation
Indices: 3085742--3085788 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3085732 CTAAATCATT
*
3085742 TTTCAAAATTTTATTTTGGC
1 TTTCAAAATTCTATTTTGGC
* *
3085762 TTTCAAAA-TCTATTTTTGT
1 TTTCAAAATTCTATTTTGGC
3085781 TTTCAAAA
1 TTTCAAAA
3085789 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTCAAAATTCTATTTTGGC
Found at i:3087071 original size:20 final size:20
Alignment explanation
Indices: 3087042--3087154 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
3087032 GCAACCTTCG
* * *
3087042 TGCATGGATGTACAAAAGGA
1 TGCATCGATGCACAACAGGA
* *
3087062 TGCATAGATGAACAACAGGA
1 TGCATCGATGCACAACAGGA
3087082 TGCATCGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
*
3087102 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAACAGGA
3087122 TGCATCGATGCACATA-AGGA
1 TGCATCGATGCACA-ACAGGA
3087142 TGCATCGATGCAC
1 TGCATCGATGCAC
3087155 TAAGTACATT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:3087222 original size:42 final size:42
Alignment explanation
Indices: 3087174--3087314 Score: 223
Period size: 42 Copynumber: 3.4 Consensus size: 42
3087164 TCGAAATGGA
3087174 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGTAG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGTAG
3087216 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGTAG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGTAG
* * *
3087258 GTGCATGGATGCACTGCAGGGGTGCATGGATGCACT-GTAG-GG
1 GTGCATGGATGCACTGCA-TGGTGCATCGATGCACTAGT-GTAG
3087300 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3087315 TTGACACCCT
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
42 78 0.83
43 16 0.17
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (42 bp):
GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGTAG
Found at i:3087283 original size:21 final size:21
Alignment explanation
Indices: 3087174--3087314 Score: 141
Period size: 21 Copynumber: 6.7 Consensus size: 21
3087164 TCGAAATGGA
*
3087174 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
3087194 GTGCATCGATGCACT--AGTGTAG
1 GTGCATGGATGCACTGCAG-G--G
*
3087216 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
3087236 GTGCATCGATGCACT--AGTGTAG
1 GTGCATGGATGCACTGCAG-G--G
3087258 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
3087279 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGCAGGG
3087300 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3087315 TTGACACCCT
Statistics
Matches: 101, Mismatches: 8, Indels: 23
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.02
20 29 0.29
21 36 0.36
22 30 0.30
23 1 0.01
24 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:3092856 original size:48 final size:47
Alignment explanation
Indices: 3092802--3093091 Score: 375
Period size: 48 Copynumber: 6.0 Consensus size: 47
3092792 AACTACTCTA
* *
3092802 TAATGAAAATTAAATGCATAATGCTGCATTTTGGCAGAAGAATGCCAC
1 TAATGAAAATTAAATGCATAACGGTGCATTTTGGCAGAA-AATGCCAC
*
3092850 TAATGAAAATTAAATGCACAACGGTGCATTTTGGCAGAAAAGTGCCAC
1 TAATGAAAATTAAATGCATAACGGTGCATTTTGGCAGAAAA-TGCCAC
* *
3092898 TAATGAAAATTAAATGCATAATGGTGCATTTTGGTAG-AAATGTACCAC
1 TAATGAAAATTAAATGCATAACGGTGCATTTTGGCAGAAAATG--CCAC
* * *
3092946 TAATAAAAATTAAATGCATAACAGTGCATTTTGGCAGAAATATGTCAC
1 TAATGAAAATTAAATGCATAACGGTGCATTTTGGCAGAAA-ATGCCAC
*
3092994 TAATGAAAATTAAATGCATAACGGTGTATTTTGGCAGAAAAATGCCAC
1 TAATGAAAATTAAATGCATAACGGTGCATTTTGGCAG-AAAATGCCAC
* * * * *
3093042 TAATGACAGTTAAATGAATAACGGTGCATTTCGGCATAAAAGATGCCAC
1 TAATGAAAATTAAATGCATAACGGTGCATTTTGGCA-GAAA-ATGCCAC
3093091 T
1 T
3093092 CATGGTTTAA
Statistics
Matches: 213, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
46 2 0.01
47 5 0.02
48 190 0.89
49 13 0.06
50 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (47 bp):
TAATGAAAATTAAATGCATAACGGTGCATTTTGGCAGAAAATGCCAC
Found at i:3093068 original size:144 final size:144
Alignment explanation
Indices: 3092802--3093072 Score: 420
Period size: 144 Copynumber: 1.9 Consensus size: 144
3092792 AACTACTCTA
* *
3092802 TAATGAAAATTAAATGCATAATGCTGCATTTTGGCAGAAGAATGCCACTAATGAAAATTAAATGC
1 TAATAAAAATTAAATGCATAAAGCTGCATTTTGGCAGAAGAATGCCACTAATGAAAATTAAATGC
* * *
3092867 ACAACGGTGCATTTTGGCAGAAAAGTGCCACTAATGAAAATTAAATGCATAATGGTGCATTTTGG
66 ACAACGGTGCATTTTGGCAGAAAAATGCCACTAATGAAAATTAAATGAATAACGGTGCATTTTGG
3092932 TAGAAATGTACCAC
131 TAGAAATGTACCAC
*
3092946 TAATAAAAATTAAATGCATAACAG-TGCATTTTGGCAGAA-ATATGTCACTAATGAAAATTAAAT
1 TAATAAAAATTAAATGCATAA-AGCTGCATTTTGGCAGAAGA-ATGCCACTAATGAAAATTAAAT
* * * *
3093009 GCATAACGGTGTATTTTGGCAGAAAAATGCCACTAATGACAGTTAAATGAATAACGGTGCATTT
64 GCACAACGGTGCATTTTGGCAGAAAAATGCCACTAATGAAAATTAAATGAATAACGGTGCATTT
3093073 CGGCATAAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
143 1 0.01
144 113 0.98
145 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (144 bp):
TAATAAAAATTAAATGCATAAAGCTGCATTTTGGCAGAAGAATGCCACTAATGAAAATTAAATGC
ACAACGGTGCATTTTGGCAGAAAAATGCCACTAATGAAAATTAAATGAATAACGGTGCATTTTGG
TAGAAATGTACCAC
Found at i:3094384 original size:14 final size:14
Alignment explanation
Indices: 3094356--3094445 Score: 96
Period size: 14 Copynumber: 7.3 Consensus size: 14
3094346 TGTTCGTGAA
3094356 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
3094370 CG-T---TTATGTT
1 CGTTCGGTTATGTT
3094380 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
3094394 CG-T---TTATGTT
1 CGTTCGGTTATGTT
3094404 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
3094418 CG-T---TTATGTT
1 CGTTCGGTTATGTT
3094428 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
3094442 CGTT
1 CGTT
3094446 TATGTTCATT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
10 27 0.42
11 3 0.05
13 3 0.05
14 31 0.48
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:3094463 original size:48 final size:48
Alignment explanation
Indices: 3094362--3094465 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
3094352 TGAACGTTCG
* *
3094362 GTTATGTTCGTTTATGTTCGTTCGGTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCGTTCGGTTATGTTCGTTTATGTTCATTCA
3094410 GTTATGTTCGTTTATGTTCGTTCGGTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCGTTCGGTTATGTTCGTTTATGTTCATTCA
*
3094458 TTTATGTT
1 GTTATGTT
3094466 TAACTCAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.56
Consensus pattern (48 bp):
GTTATGTTCGTTTATGTTCGTTCGGTTATGTTCGTTTATGTTCATTCA
Found at i:3094465 original size:24 final size:24
Alignment explanation
Indices: 3094356--3094452 Score: 194
Period size: 24 Copynumber: 4.0 Consensus size: 24
3094346 TGTTCGTGAA
3094356 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
3094380 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
3094404 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
3094428 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
3094452 C
1 C
3094453 ATTCATTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.08, C:0.13, G:0.25, T:0.54
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:3095552 original size:10 final size:10
Alignment explanation
Indices: 3095537--3095611 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
3095527 GGGTCTCTAA
3095537 CGTTTATGTT
1 CGTTTATGTT
3095547 CGTTTATGTT
1 CGTTTATGTT
3095557 CG----TGTT
1 CGTTTATGTT
*
3095563 CATTTATGTT
1 CGTTTATGTT
3095573 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
3095584 ATGTTCGTGTT
1 -CGTTTATGTT
3095595 CGTTTATGTT
1 CGTTTATGTT
3095605 CGTTTAT
1 CGTTTAT
3095612 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:3095568 original size:16 final size:16
Alignment explanation
Indices: 3095543--3095615 Score: 114
Period size: 16 Copynumber: 4.7 Consensus size: 16
3095533 CTAACGTTTA
*
3095543 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
3095559 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
3095575 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
3095591 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
3095607 T-TT-ATTTAT
1 TGTTCATTTAT
3095616 TAAATGAACG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 5 0.09
15 2 0.04
16 47 0.87
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:3101294 original size:48 final size:48
Alignment explanation
Indices: 3101242--3101510 Score: 421
Period size: 48 Copynumber: 5.6 Consensus size: 48
3101232 TACTCTATAG
* * * * *
3101242 TGAAAACTAAATGCATAATGGTGCATTTTGGAAGAAATGTGTCACTAA
1 TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAAGTGTCACTAA
* * *
3101290 TGAAAATTAAATGCATAACGGTACATTTTGGGCATAAATGTGCCACTAA
1 TGAAAATTAAATGCATAACGGTGCATTTT-GGCATAAAAGTGTCACTAA
*
3101339 TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAGGTGTCACTAA
1 TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAAGTGTCACTAA
*
3101387 TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAAGTATCACTAA
1 TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAAGTGTCACTAA
* *
3101435 TGAAAATTAAATGCATAACGGTGCATTTTGGCAGAAAAGTGCCACTAA
1 TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAAGTGTCACTAA
3101483 TGAAAATTAAATGCATAACGGTGCATTT
1 TGAAAATTAAATGCATAACGGTGCATTT
3101511 CAACATAAAA
Statistics
Matches: 206, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
48 162 0.79
49 44 0.21
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (48 bp):
TGAAAATTAAATGCATAACGGTGCATTTTGGCATAAAAGTGTCACTAA
Done.