Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 17
Found at i:2749603 original size:13 final size:13
Alignment explanation
Indices: 2749581--2749615 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2749571 GGAAAAGGGA
2749581 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
2749595 AAAATAAATAAAT
1 AAAATAAATAAAT
*
2749608 AAGATAAA
1 AAAATAAA
2749616 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:2750112 original size:18 final size:17
Alignment explanation
Indices: 2750091--2750133 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2750081 ATATATACAT
2750091 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
2750109 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
2750126 ATAA-AATA
1 ATAATAATA
2750134 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:2750130 original size:14 final size:13
Alignment explanation
Indices: 2750093--2750131 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2750083 ATATACATAT
2750093 AATAATAATAACATA
1 AATAATAA-AA-ATA
2750108 AATAATAAAAATA
1 AATAATAAAAATA
2750121 AATGAATAAAA
1 AAT-AATAAAA
2750132 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:2759847 original size:11 final size:11
Alignment explanation
Indices: 2759833--2759878 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
2759823 TTTTTTGAAA
2759833 TTTTGGCTTTT
1 TTTTGGCTTTT
*
2759844 TTTT-GTTTTT
1 TTTTGGCTTTT
*
2759854 TTTTTGC-TTT
1 TTTTGGCTTTT
2759864 TTTTGG-TTTT
1 TTTTGGCTTTT
2759874 TTTTG
1 TTTTG
2759879 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 25 0.83
11 5 0.17
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.80
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:2759852 original size:9 final size:10
Alignment explanation
Indices: 2759840--2759885 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
2759830 AAATTTTGGC
2759840 TTTTTTTTGT
1 TTTTTTTTGT
2759850 TTTTTTTT-T
1 TTTTTTTTGT
* *
2759859 GCTTTTTTTGG
1 -TTTTTTTTGT
2759870 TTTTTTTTGT
1 TTTTTTTTGT
2759880 TTTTTT
1 TTTTTT
2759886 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 1 0.03
10 29 0.97
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:2759856 original size:30 final size:30
Alignment explanation
Indices: 2759820--2759885 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2759810 TTGTTTGCAA
2759820 TTTTTTTTTG-AAATTTTGGCTTTTTTTTGT
1 TTTTTTTTTGCAAATTTTGG-TTTTTTTTGT
***
2759850 TTTTTTTTTGCTTTTTTTGGTTTTTTTTGT
1 TTTTTTTTTGCAAATTTTGGTTTTTTTTGT
2759880 TTTTTT
1 TTTTTT
2759886 AAAAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.05, C:0.03, G:0.12, T:0.80
Consensus pattern (30 bp):
TTTTTTTTTGCAAATTTTGGTTTTTTTTGT
Found at i:2759857 original size:21 final size:21
Alignment explanation
Indices: 2759833--2759877 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2759823 TTTTTTGAAA
*
2759833 TTTTGGCTTTTTTTTGTTTTT
1 TTTTGGCTTTTTTTGGTTTTT
*
2759854 TTTTTGCTTTTTTTGGTTTTT
1 TTTTGGCTTTTTTTGGTTTTT
2759875 TTT
1 TTT
2759878 GTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.82
Consensus pattern (21 bp):
TTTTGGCTTTTTTTGGTTTTT
Found at i:2761473 original size:15 final size:15
Alignment explanation
Indices: 2761453--2761482 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2761443 TTCCTTTATA
2761453 AATATTCATGGTTAG
1 AATATTCATGGTTAG
2761468 AATATTCATGGTTAG
1 AATATTCATGGTTAG
2761483 TAAATTACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
AATATTCATGGTTAG
Found at i:2763629 original size:35 final size:35
Alignment explanation
Indices: 2763590--2763661 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
2763580 CTAAAAAAAC
*
2763590 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
2763625 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
2763660 CT
1 CT
2763662 TCTTTGTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (35 bp):
CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:2764235 original size:194 final size:196
Alignment explanation
Indices: 2764004--2764394 Score: 768
Period size: 196 Copynumber: 2.0 Consensus size: 196
2763994 TCGTCGTGAA
2764004 GTTGAGTCAATCCGTTGGGGTATGATATCATTCGTTGTGAAG-T-TATATGTATATGGCCCCTTC
1 GTTGAGTCAATCCGTTGGGGTATGATATCATTCGTTGTGAAGTTGTATATGTATATGGCCCCTTC
2764067 GTTGTGAAGTTGAGCCTGAGAATTGGATATCCTTCGTCATGAAATTGAAATCCAATGTAAGTTAC
66 GTTGTGAAGTTGAGCCTGAGAATTGGATATCCTTCGTCATGAAATTGAAATCCAATGTAAGTTAC
2764132 GTTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTTGTTAGGATTTT
131 GTTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTTGTTAGGATTTT
2764197 C
196 C
2764198 GTTGAGTCAATCCGTTGGGGTATGATATCATTCGTTGTGAAGTTGTATATGTATATGGCCCCTTC
1 GTTGAGTCAATCCGTTGGGGTATGATATCATTCGTTGTGAAGTTGTATATGTATATGGCCCCTTC
2764263 GTTGTGAAGTTGAGCCTGAGAATTGGATATCCTTCGTCATGAAATTGAAATCCAATGTAAGTTAC
66 GTTGTGAAGTTGAGCCTGAGAATTGGATATCCTTCGTCATGAAATTGAAATCCAATGTAAGTTAC
2764328 GTTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTTGTTAGGATTTT
131 GTTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTTGTTAGGATTTT
2764393 C
196 C
2764394 G
1 G
2764395 GAAGCTCGAA
Statistics
Matches: 195, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
194 42 0.22
195 1 0.01
196 152 0.78
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (196 bp):
GTTGAGTCAATCCGTTGGGGTATGATATCATTCGTTGTGAAGTTGTATATGTATATGGCCCCTTC
GTTGTGAAGTTGAGCCTGAGAATTGGATATCCTTCGTCATGAAATTGAAATCCAATGTAAGTTAC
GTTGCTCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTTGTTAGGATTTT
C
Found at i:2764669 original size:34 final size:31
Alignment explanation
Indices: 2764617--2764685 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 31
2764607 CCTTACAAAC
2764617 TCCCTAGTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTCCGGGCTAAACTAGAACCTT
*
2764648 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-C-CGGGCTAAACTAGAACCTT
2764682 TCCC
1 TCCC
2764686 CTTAAAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 7 0.21
32 4 0.12
33 1 0.03
34 22 0.65
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (31 bp):
TCCCTAGTTTTCCGGGCTAAACTAGAACCTT
Found at i:2764869 original size:21 final size:21
Alignment explanation
Indices: 2764843--2764884 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2764833 CCAGAATGGG
*
2764843 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2764864 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2764885 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2765014 original size:19 final size:19
Alignment explanation
Indices: 2764990--2765056 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
2764980 GAGCCTCGGG
*
2764990 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
2765009 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* * *
2765028 GTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
2765047 TTACTATTCA
1 TTACTGTTCA
2765057 TAAAAACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:2765168 original size:30 final size:31
Alignment explanation
Indices: 2765121--2765211 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
2765111 AAATTTTGAA
2765121 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
2765150 TAAACTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2765181 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2765212 CCTTAAATTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.17
30 11 0.19
31 37 0.64
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.32
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:2765677 original size:106 final size:106
Alignment explanation
Indices: 2765484--2765700 Score: 292
Period size: 106 Copynumber: 2.0 Consensus size: 106
2765474 TGTATTGCTC
* * *
2765484 CGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTATTAACA
1 CGAGTCCAATATCATTCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTCATTAACA
* * *
2765549 GCCAATCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAATCACCCCTTCGTCGTGAAGTTGAACTTGTGCTGTCT
* * * *
2765590 TGAGTTCAATATCATTCG-CTGTGAAGTTGAAATTGGCTTTGAAACTGGGAAATTGTTCATTGAC
1 CGAGTCCAATATCATTCGTC-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTCATTAAC
* * * *
2765654 AACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAATCACCCCTTCGTCGTGAAGTTGAACTTGTGCTGTCT
2765696 CGAGT
1 CGAGT
2765701 GGCACGATAT
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 1 0.01
106 94 0.99
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCATTCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTCATTAACA
ACCAATCACCCCTTCGTCGTGAAGTTGAACTTGTGCTGTCT
Found at i:2766839 original size:74 final size:76
Alignment explanation
Indices: 2766707--2766853 Score: 194
Period size: 74 Copynumber: 2.0 Consensus size: 76
2766697 ACCCACCTTT
* *
2766707 TTTTTTTCTTTCTCTTTTTTGTTCTTTTTTCAATTTTTTCAATTTAGGGCGCCCTTTCGGGTTTT
1 TTTTTTTCTTTCTCTTTTTTGTTCTTTTTTCAATTTTTTCAACTTAGGACGCCCTTTCGGGTTTT
2766772 CACCCTAAACG
66 CACCCTAAACG
* * *
2766783 TTTTTTT-TTTCAT-TTTTTTGTTC-TTTTTCCATTTGTTT-TACTTAGGACGCCTTTTCGGGTT
1 TTTTTTTCTTTC-TCTTTTTTGTTCTTTTTTCAATTT-TTTCAACTTAGGACGCCCTTTCGGGTT
*
2766844 TTCATCCTAA
64 TTCACCCTAA
2766854 GCGAAGTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
74 38 0.60
75 17 0.27
76 8 0.13
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.58
Consensus pattern (76 bp):
TTTTTTTCTTTCTCTTTTTTGTTCTTTTTTCAATTTTTTCAACTTAGGACGCCCTTTCGGGTTTT
CACCCTAAACG
Found at i:2770259 original size:31 final size:30
Alignment explanation
Indices: 2770221--2770316 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 30
2770211 AGAGTCGAGG
2770221 GTTTACCTA-TATCTTTCGAGACATATGGACA
1 GTTTACCTAGT-TC-TTCGAGACATATGGACA
* *
2770252 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTA-GTTCTTCGAGACATATGGACA
* *
2770283 GTTTACCTAGGTTCGTCGGGAGC-TATGGACA
1 GTTTACCTA-GTTCTTCGAGA-CATATGGACA
2770314 GTT
1 GTT
2770317 GCCGAGGTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
31 55 0.93
32 3 0.05
33 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (30 bp):
GTTTACCTAGTTCTTCGAGACATATGGACA
Found at i:2774358 original size:31 final size:31
Alignment explanation
Indices: 2774320--2774391 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
2774310 GAGTCGAGGG
*
2774320 TTTACCTATG-TCTTTCGAGACATATGGACAA
1 TTTACCTAGGCTC-TTCGAGACATATGGACAA
* * *
2774351 TTTACCTAGGCTCTTCGGGACCTATGGACAG
1 TTTACCTAGGCTCTTCGAGACATATGGACAA
2774382 TTTACCTAGG
1 TTTACCTAGG
2774392 TTCGTCGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (31 bp):
TTTACCTAGGCTCTTCGAGACATATGGACAA
Found at i:2774400 original size:31 final size:31
Alignment explanation
Indices: 2774342--2774414 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
2774332 TTTCGAGACA
* *
2774342 TATGGACAATTTACCTAGGCTCTTCGGGACC
1 TATGGACAGTTTACCTAGGCTCGTCGGGACC
* *
2774373 TATGGACAGTTTACCTAGGTTCGTCGGGAGC
1 TATGGACAGTTTACCTAGGCTCGTCGGGACC
2774404 TATGGACAGTT
1 TATGGACAGTT
2774415 GCCGAGGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (31 bp):
TATGGACAGTTTACCTAGGCTCGTCGGGACC
Found at i:2780164 original size:33 final size:33
Alignment explanation
Indices: 2780116--2780178 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
2780106 CAAAATGAGA
2780116 TAAAAAAAATAAGAAAATAA-AA-GAAGTAAAAG
1 TAAAAAAAATAAGAAAA-AAGAATGAAGTAAAAG
2780148 TAAAAATAAATAAGAAAAAAGAATGAAGTAA
1 TAAAAA-AAATAAGAAAAAAGAATGAAGTAA
2780179 CGAATCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 8 0.29
33 13 0.46
34 7 0.25
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.14
Consensus pattern (33 bp):
TAAAAAAAATAAGAAAAAAGAATGAAGTAAAAG
Found at i:2780477 original size:20 final size:20
Alignment explanation
Indices: 2780425--2780477 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
2780415 TAAACAAGGT
2780425 ATAAAAAAATAATAGTAATA
1 ATAAAAAAATAATAGTAATA
2780445 ATAAGTATTAAAA-AATAGTAATA
1 ATAA--A--AAAATAATAGTAATA
2780468 ACTAAAAAAA
1 A-TAAAAAAA
2780478 GAAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
20 8 0.29
22 2 0.07
23 11 0.39
24 7 0.25
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
ATAAAAAAATAATAGTAATA
Found at i:2781087 original size:35 final size:35
Alignment explanation
Indices: 2781048--2781119 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
2781038 TAAAAAAAAC
*
2781048 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
*
2781083 CTATTCTAGATTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
2781118 CT
1 CT
2781120 TCTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:2782196 original size:19 final size:19
Alignment explanation
Indices: 2782154--2782212 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
2782144 ATAAATAAAT
*
2782154 AATAATATACAAAAGTAAATAA
1 AATAATA-ATAAAAG-AAA-AA
2782176 AATAATAATAAAAGAAAAA
1 AATAATAATAAAAGAAAAA
*
2782195 AATGAAT-ATAAAATAAAA
1 AAT-AATAATAAAAGAAAA
2782213 GGTAAAAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 15 0.44
20 6 0.18
21 6 0.18
22 7 0.21
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (19 bp):
AATAATAATAAAAGAAAAA
Found at i:2783838 original size:84 final size:84
Alignment explanation
Indices: 2783729--2784607 Score: 716
Period size: 84 Copynumber: 10.6 Consensus size: 84
2783719 GTTTGCCTCT
* * * * * * * * * *
2783729 GAGCTGAGTGTAATCAAACTAGAAGGTATTCGATTGGCAGATAGCTCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-TTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * *
2783794 CTACAGATGATGTG-CCTTG
65 CTGCAAATGATATGCCCTTG
** *
2783813 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTATCAGATAACCTTTCTCA-ACTTAAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCT-AGACTTAAGTTAT
* * * *
2783877 GTTGTAAATGATATGTCGTT-
64 GCTGCAAATGATATGCCCTTG
* * * * * *
2783897 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
2783962 TGTAAATGATATGCCCTCG
66 TGCAAATGATATGCCCTTG
* * * ** * * * * *
2783981 AAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTATCGACTTAAGCTATGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* * *
2784043 TGCAAATGATGTGTCGTT-
66 TGCAAATGATATGCCCTTG
* * *
2784061 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* *
2784126 CTACAAATGATATG-CCTGG
65 CTGCAAATGATATGCCCTTG
* * * * * * *
2784145 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
2784210 TGTAAATGATATGCCCTCG
66 TGCAAATGATATGCCCTTG
* * * * ** * * * *
2784229 AAGCTGAGTGTAATCAAACTCGGGGGTC--T-TTGGTAGATAGCCCTTTTCA-ACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT-AGACTTAAGTTATG
* *
2784290 CTGCAAATGATGTGCCATT-
65 CTGCAAATGATATGCCCTTG
* * * * * * *
2784309 GAGCCGAGCGTAGTCGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTTATAGACTTAAGTTGTA
1 GAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
2784374 CTGCAAATGATATG--CTTGG
65 CTGCAAATGATATGCCCTT-G
* * * *
2784393 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
2784458 TGTAAATGATATGCCCTCG
66 TGCAAATGATATGCCCTTG
* * * * ** * * *
2784477 AAGCTGAGTGTAATCAAACTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
*
2784539 TGCAAATGATGTG-CCTTG
66 TGCAAATGATATGCCCTTG
* * *
2784557 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCT
2784608 TGTCTTGACC
Statistics
Matches: 616, Mismatches: 154, Indels: 50
0.75 0.19 0.06
Matches are distributed among these distances:
80 67 0.11
81 110 0.18
82 8 0.01
83 127 0.21
84 298 0.48
85 6 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
TGCAAATGATATGCCCTTG
Found at i:2784072 original size:164 final size:163
Alignment explanation
Indices: 2783766--2784590 Score: 691
Period size: 164 Copynumber: 5.0 Consensus size: 163
2783756 ATTCGATTGG
* * * * * * * * * *
2783766 CAGATAGCTCTTCTCGACTTAAGCTATGCTACAGATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGA
** * * * *
2783830 ACTCGAAGGTCTTTGGTTATCAGATAACCTTTCTCA-ACTTAAGTTATGTTGTAAATGATATGTC
66 ACTCGGGGGTCTTTGG----CAGATAACCCTTAT-AGACTTAAGCTATGTTGCAAATGATATG-C
* * *
2783894 GTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGA
125 CTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
* * * *
2783933 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGA
* * * *
2783998 ACTCGGGGGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGTTGCAAATGATGTGTCGTTGA
66 ACTCGGGGGTCTTTGGCAGATAACCCTTATAGACTTAAGCTATGTTGCAAATGATATG-CCTTGA
* * *
2784063 GCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGG
130 GCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGA
* * * * * *
2784098 CAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATG-CCTGGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGA
*** * * * * * *
2784162 ACTCAAAGGTCTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCT
66 ACTCGGGGGTCTTT-G-G-CAGATAACCCTTATAGACTTAAGCTATGTTGCAAATGATATG-CCT
* * * * **
2784227 CGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGT--
127 TG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
* * * * * * * *
2784263 -AGATAGCCCTTTTCA-ACTTAAGCTATGCTGCAAATGATGTGCCATTG-AGCCGAGCGTAGTCG
1 CAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCG
*** * *
2784325 AACTCAAAGGTTTTTTGTTGGCAGACAACCCTTATAGACTTAAG-T-TGTACTGCAAATGATATG
65 AACTC---GGGGGTCT-TTGGCAGATAACCCTTATAGACTTAAGCTATGT--TGCAAATGATATG
2784388 -CTTGGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
124 CCTT--GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
* * * * *
2784429 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGA
* * * * *
2784494 ACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
66 ACTCGGGGGTCTTTGGCAGATAACCCTTATAGACTTAAGCTATGTTGCAAATGATATGCCTT-GA
*
2784559 GCTGAGCGTAATCGAACTCGAAGGTCTTTGGT
130 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
2784591 TGGCAAATAG
Statistics
Matches: 523, Mismatches: 110, Indels: 53
0.76 0.16 0.08
Matches are distributed among these distances:
163 5 0.01
164 244 0.47
165 86 0.16
166 5 0.01
167 112 0.21
168 71 0.14
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (163 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGA
ACTCGGGGGTCTTTGGCAGATAACCCTTATAGACTTAAGCTATGTTGCAAATGATATGCCTTGAG
CTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
Found at i:2784200 original size:248 final size:248
Alignment explanation
Indices: 2783762--2784595 Score: 1298
Period size: 248 Copynumber: 3.4 Consensus size: 248
2783752 AGGTATTCGA
* * *
2783762 TTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAGATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* ** * * * * *
2783827 CGAACTCGAAGGTCTTTGGTTATCAGATAACCTTTCTCA-ACTTAAGTTATGTTGTAAATGATAT
66 CGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCT-AGACTTAAGTTGTGCTGCAAATGATAT
* * *
2783891 GTC-GTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGA
130 GCCTG-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGA
*
2783955 GTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
194 GTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
* * *
2784010 TTGGCAGATAGCCCTTATCGACTTAAGCTATGTTGCAAATGATGTGTCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* *
2784074 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATAT
65 TCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
*
2784139 GCCTGGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACATATAACCCTTCTAGCCTTGAG
130 GCCTGGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
*
2784204 TTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
195 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
* * * *
2784258 TTGGTAGATAGCCCTTTTCAACTTAAGCTATGCTGCAAATGATGTGCCATT-GAGCCGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
* * * *
2784322 TCGAACTCAAAGGTTTTTTGTTGGCAGACAACCCTTATAGACTTAAGTTGTACTGCAAATGATAT
65 TCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
* *
2784387 GCTTGGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
130 GCCTGGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
2784452 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
195 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
*
2784506 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAAT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
2784571 CGAACTCGAAGGTCTTTGGTTGGCA
66 CGAACTCAAAGGTCTTTGGTTGGCA
2784596 AATAGCCCTT
Statistics
Matches: 537, Mismatches: 44, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
247 4 0.01
248 529 0.99
249 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (248 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG
CCTGGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
TATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
Found at i:2789770 original size:6 final size:6
Alignment explanation
Indices: 2789759--2789786 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2789749 CTTAGTTGCG
2789759 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
2789787 GGTATTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:2789972 original size:22 final size:21
Alignment explanation
Indices: 2789935--2790003 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
2789925 TAAAAAATAA
2789935 TAAATAAATAATAATATACAAAAG
1 TAAAT-AA-AATAATA-ACAAAAG
*
2789959 TAAATAAAATAATAATAAAAG
1 TAAATAAAATAATAACAAAAG
* *
2789980 AAAACAAAATGAATAA-AAAA-
1 TAAATAAAAT-AATAACAAAAG
2790000 TAAA
1 TAAA
2790004 AAAGGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 3 0.08
21 18 0.45
22 12 0.30
23 2 0.05
24 5 0.12
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.20
Consensus pattern (21 bp):
TAAATAAAATAATAACAAAAG
Found at i:2789978 original size:11 final size:11
Alignment explanation
Indices: 2789928--2790002 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 11
2789918 AAGTTAGTAA
2789928 AAAATAATAA-
1 AAAATAATAAT
2789938 ATAAATAATAAT
1 A-AAATAATAAT
2789950 ATACAA-AAGTAAAT
1 A-A-AATAA-T-AAT
2789964 AAAATAATAAT
1 AAAATAATAAT
* *
2789975 AAAAGAA-AAC
1 AAAATAATAAT
2789985 AAAATGAATAA-
1 AAAAT-AATAAT
2789996 AAAATAA
1 AAAATAA
2790003 AAAAGGTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.17
11 25 0.46
12 10 0.19
13 6 0.11
14 4 0.07
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2790005 original size:22 final size:21
Alignment explanation
Indices: 2789940--2790006 Score: 53
Period size: 25 Copynumber: 2.9 Consensus size: 21
2789930 AATAATAAAT
*
2789940 AAATAATAATATACAAAAGTAAATA
1 AAATAATAATA-A-AAAA--AAACA
*
2789965 AAATAATAATAAAAGAAAACA
1 AAATAATAATAAAAAAAAACA
*
2789986 AAATGAATAAAAAATAAAAAA
1 AAAT-AATAATAAA-AAAAAA
2790007 GGTAAAAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 8 0.22
22 8 0.22
23 8 0.22
24 1 0.03
25 11 0.31
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (21 bp):
AAATAATAATAAAAAAAAACA
Found at i:2791209 original size:3 final size:3
Alignment explanation
Indices: 2791196--2791237 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
2791186 TAAAATAAGA
2791196 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAAT AAT ATAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A-AT AAT AA
2791238 AACTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2791219 original size:20 final size:19
Alignment explanation
Indices: 2791182--2791249 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 19
2791172 ACGGGAAAAC
*
2791182 AAAATAA-AATAAGA-AAT
1 AAAATAATAATAATATAAT
2791199 AAAATAATAATAATAATAAT
1 AAAATAATAATAAT-ATAAT
*
2791219 AATA-AATAAT-ATATAAT
1 AAAATAATAATAATATAAT
2791236 AAAACTATATAATA
1 AAAA-TA-ATAATA
2791250 TACATTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
17 15 0.37
18 7 0.17
19 8 0.20
20 11 0.27
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (19 bp):
AAAATAATAATAATATAAT
Found at i:2791249 original size:27 final size:27
Alignment explanation
Indices: 2791184--2791237 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2791174 GGGAAAACAA
*
2791184 AATAA-AATAAGAAATAAAATAATAAT
1 AATAATAATAATAAATAAAATAATAAT
*
2791210 AATAATAATAATAAATAATAT-ATAAT
1 AATAATAATAATAAATAAAATAATAAT
2791236 AA
1 AA
2791238 AACTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (27 bp):
AATAATAATAATAAATAAAATAATAAT
Found at i:2791250 original size:20 final size:18
Alignment explanation
Indices: 2791196--2791251 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 18
2791186 TAAAATAAGA
2791196 AATAAAATAATAATA-AT
1 AATAAAATAATAATATAT
2791213 AATAATAATAAATAATATAT
1 AATAA-AAT-AATAATATAT
2791233 AATAAAACTATATAATATA
1 AATAAAA-TA-ATAATATA
2791252 CATTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 10 0.29
20 16 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAAATAATAATATAT
Found at i:2791351 original size:30 final size:31
Alignment explanation
Indices: 2791283--2791410 Score: 118
Period size: 30 Copynumber: 4.0 Consensus size: 31
2791273 TTTAAACTAT
* *
2791283 ATACTATATAAATTTTC-AAATTTTTTAAAA
1 ATACTATATAAGTTTTCAAAATGTTTTAAAA
*
2791313 AAACTATATAA-TTTTCAAAAATGTTTTAAAATTA
1 ATACTATATAAGTTTTC-AAAATGTTTT-AAA--A
* *
2791347 TATATTATATAAGTTTTCAAAAATGCTTTAAAA
1 -ATACTATATAAGTTTTC-AAAATGTTTTAAAA
* *
2791380 CTA-TATATAAGTTTTCAAAATGATTTAAAA
1 ATACTATATAAGTTTTCAAAATGTTTTAAAA
2791410 A
1 A
2791411 CCATATATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.06
30 23 0.28
31 21 0.25
32 5 0.06
33 1 0.01
34 1 0.01
35 12 0.14
36 15 0.18
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (31 bp):
ATACTATATAAGTTTTCAAAATGTTTTAAAA
Found at i:2791366 original size:36 final size:35
Alignment explanation
Indices: 2791317--2791423 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 35
2791307 TTAAAAAAAC
* *
2791317 TATATAATTTTCAAAAATGTTTTAAAATTATATAT
1 TATATAATTTTCAAAAATGCTTTAAAACTATATAT
2791352 TATATAAGTTTTCAAAAATGCTTTAAAAC--TATA-
1 TATATAA-TTTTCAAAAATGCTTTAAAACTATATAT
* * *
2791385 TATA-AGTTTTC-AAAATGATTTAAAAACCATATAT
1 TATATAATTTTCAAAAATGCTTT-AAAACTATATAT
2791419 TATAT
1 TATAT
2791424 TTTTTTTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
30 9 0.15
31 10 0.16
32 1 0.02
33 8 0.13
34 8 0.13
35 7 0.11
36 19 0.31
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
TATATAATTTTCAAAAATGCTTTAAAACTATATAT
Found at i:2791411 original size:31 final size:33
Alignment explanation
Indices: 2791284--2791411 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 33
2791274 TTAAACTATA
* *
2791284 TACTATATAAATTTTC--AAATTTTTTAAAAA-
1 TACTATATAAGTTTTCAAAAATGTTTTAAAAAC
* *
2791314 AACTATATAA-TTTTCAAAAATGTTTTAAAATTATA
1 TACTATATAAGTTTTCAAAAATGTTTTAAAA--A-C
* *
2791349 TATTATATAAGTTTTCAAAAATGCTTT-AAAAC
1 TACTATATAAGTTTTCAAAAATGTTTTAAAAAC
*
2791381 TA-TATATAAGTTTTC-AAAATGATTTAAAAAC
1 TACTATATAAGTTTTCAAAAATGTTTTAAAAAC
2791412 CATATATTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
29 5 0.06
30 18 0.22
31 30 0.36
32 2 0.02
33 2 0.02
35 11 0.13
36 15 0.18
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (33 bp):
TACTATATAAGTTTTCAAAAATGTTTTAAAAAC
Found at i:2791417 original size:31 final size:31
Alignment explanation
Indices: 2791352--2791418 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
2791342 AATTATATAT
* *
2791352 TATATAAGTTTTCAAAAATGCTTTAAAACTA
1 TATATAAGTTTTCAAAAATGATTTAAAACCA
2791383 TATATAAGTTTTC-AAAATGATTTAAAAACCA
1 TATATAAGTTTTCAAAAATGATTT-AAAACCA
2791414 TATAT
1 TATAT
2791419 TATATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (31 bp):
TATATAAGTTTTCAAAAATGATTTAAAACCA
Found at i:2801173 original size:20 final size:20
Alignment explanation
Indices: 2801145--2801201 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2801135 TTGGTTCACA
2801145 GAATATAAGATTACTAGTGG
1 GAATATAAGATTACTAGTGG
*
2801165 GAATGTAAGATTA-TCAGTGG
1 GAATATAAGATTACT-AGTGG
2801185 GAATATAAGATTACTAG
1 GAATATAAGATTACTAG
2801202 AGAATAGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (20 bp):
GAATATAAGATTACTAGTGG
Found at i:2803747 original size:127 final size:127
Alignment explanation
Indices: 2803521--2803775 Score: 510
Period size: 127 Copynumber: 2.0 Consensus size: 127
2803511 CATACATTTC
2803521 ACTGATCCACCCAGATGCGTATATATCTCCAGTTATGTTTGTTGCATAATGAGCTCTGTCAGCTC
1 ACTGATCCACCCAGATGCGTATATATCTCCAGTTATGTTTGTTGCATAATGAGCTCTGTCAGCTC
2803586 GGACCTCCTCGGTTTTAAGCAACCATAGCAGAGCAAATTCCCGGAGATCATCAATATGCATG
66 GGACCTCCTCGGTTTTAAGCAACCATAGCAGAGCAAATTCCCGGAGATCATCAATATGCATG
2803648 ACTGATCCACCCAGATGCGTATATATCTCCAGTTATGTTTGTTGCATAATGAGCTCTGTCAGCTC
1 ACTGATCCACCCAGATGCGTATATATCTCCAGTTATGTTTGTTGCATAATGAGCTCTGTCAGCTC
2803713 GGACCTCCTCGGTTTTAAGCAACCATAGCAGAGCAAATTCCCGGAGATCATCAATATGCATG
66 GGACCTCCTCGGTTTTAAGCAACCATAGCAGAGCAAATTCCCGGAGATCATCAATATGCATG
2803775 A
1 A
2803776 TTATAACACC
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (127 bp):
ACTGATCCACCCAGATGCGTATATATCTCCAGTTATGTTTGTTGCATAATGAGCTCTGTCAGCTC
GGACCTCCTCGGTTTTAAGCAACCATAGCAGAGCAAATTCCCGGAGATCATCAATATGCATG
Found at i:2806055 original size:20 final size:20
Alignment explanation
Indices: 2806030--2806069 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2806020 CAATCAGAAG
2806030 CAGTATATGCTAGAAGGAAT
1 CAGTATATGCTAGAAGGAAT
2806050 CAGTATATGCTAGAAGGAAT
1 CAGTATATGCTAGAAGGAAT
2806070 GTTAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (20 bp):
CAGTATATGCTAGAAGGAAT
Found at i:2807753 original size:31 final size:31
Alignment explanation
Indices: 2807710--2807825 Score: 94
Period size: 32 Copynumber: 3.6 Consensus size: 31
2807700 TTTTTGGTAT
*
2807710 TCGGGTCGGATTTTTTTAAAAAAAATCGGGA
1 TCGGGTCTGATTTTTTTAAAAAAAATCGGGA
2807741 TCGGGTCTGATTTTTTATTAAAAAAATAGGTTCGGG-
1 TCGGGTCTGA-TTTTT-TTAAAAAAA-A---TCGGGA
* *
2807777 TCGGGT-T-TTTTTTTTAAAAACAATTCGGGA
1 TCGGGTCTGATTTTTTTAAAAA-AAATCGGGA
* * *
2807807 TCGGATCAGGTTTTTTTAA
1 TCGGGTCTGATTTTTTTAA
2807826 GTGTGATATT
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
29 5 0.07
30 5 0.07
31 9 0.13
32 21 0.30
33 16 0.23
34 1 0.01
35 1 0.01
36 6 0.09
37 5 0.07
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (31 bp):
TCGGGTCTGATTTTTTTAAAAAAAATCGGGA
Found at i:2807764 original size:32 final size:31
Alignment explanation
Indices: 2807710--2807823 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 31
2807700 TTTTTGGTAT
*
2807710 TCGGGTCGGATTTTTTTAAAAAAAATCGGGA
1 TCGGGTCGGATTTTTTTTAAAAAAATCGGGA
* * *
2807741 TCGGGTCTGATTTTTTATTAAAAAAAT-AGGT
1 TCGGGTCGGATTTTTT-TTAAAAAAATCGGGA
*
2807772 TCGGGTCGGGTTTTTTTTTTAAAAACAATTCGGGA
1 TCGGGTC-GG-ATTTTTTTTAAAAA-AA-TCGGGA
*
2807807 TCGGATCAGG-TTTTTTT
1 TCGGGTC-GGATTTTTTT
2807824 AAGTGTGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
31 24 0.36
32 17 0.25
33 15 0.22
34 1 0.01
35 10 0.15
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (31 bp):
TCGGGTCGGATTTTTTTTAAAAAAATCGGGA
Found at i:2809366 original size:60 final size:59
Alignment explanation
Indices: 2809213--2809368 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
2809203 AATGATCCTT
* * ** * *
2809213 AAACTTTTGAATATTCCAATTTTATCATTAAGCTATGACTATCATTCTAAATTAGTCCTC
1 AAACTTTTGAACATTCCAATTTAATC-CCAAACTATGACTATCATTCTAAATTAGTCCCC
* ** * *
2809273 AGACTTTAAAACATTTCAATTTAATCCCTAAACTATGAC-ATTCATTCTAAATTGGTCCCC
1 AAACTTTTGAACATTCCAATTTAATCCC-AAACTATGACTA-TCATTCTAAATTAGTCCCC
*
2809333 AAACTTTTTGAACATTCCAATTTCATCCCAAACTAT
1 AAAC-TTTTGAACATTCCAATTTAATCCCAAACTAT
2809369 ATTTATATAC
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 1 0.01
60 56 0.73
61 20 0.26
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.38
Consensus pattern (59 bp):
AAACTTTTGAACATTCCAATTTAATCCCAAACTATGACTATCATTCTAAATTAGTCCCC
Found at i:2810648 original size:2 final size:2
Alignment explanation
Indices: 2810631--2810664 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2810621 TGTTTTCATG
*
2810631 TA TA TA AA TA TA -A 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 TA TA T
2810665 TTCTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2810764 original size:11 final size:11
Alignment explanation
Indices: 2810742--2810779 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2810732 AATCTTTGTC
2810742 TATTATTATTA
1 TATTATTATTA
2810753 TA-TATATATTA
1 TATTAT-TATTA
2810764 TATTATTATTA
1 TATTATTATTA
2810775 TATTA
1 TATTA
2810780 CCTATACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATTATTA
Found at i:2810912 original size:26 final size:29
Alignment explanation
Indices: 2810882--2810934 Score: 85
Period size: 26 Copynumber: 1.9 Consensus size: 29
2810872 ATTATATTAT
2810882 ATATATATATATT-TTTA-AAC-ATTACC
1 ATATATATATATTATTTATAACTATTACC
2810908 ATATATATATATTATTTATAACTATTA
1 ATATATATATATTATTTATAACTATTA
2810935 TTTTTGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.54
27 4 0.17
28 3 0.12
29 4 0.17
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATATATATATTATTTATAACTATTACC
Found at i:2811062 original size:53 final size:52
Alignment explanation
Indices: 2810980--2811120 Score: 135
Period size: 53 Copynumber: 2.6 Consensus size: 52
2810970 ATTTTATATA
* * *
2810980 ATTAATATATATATATATTTCTATTTATTTTCTATGTTTTTATTTAA-TTTCGT-TTT
1 ATTATTAT-TATATATA-TTATA-TTATTTT-TAT-TTTTT-TTAAACTTTCGTCTTT
*
2811036 ATTCATTATTAT-TATATTATATTATTTTTATTTTTTTTAAATCTTTTGTCTTT
1 ATT-ATTATTATATATATTATATTATTTTTATTTTTTTTAAA-CTTTCGTCTTT
* *
2811089 ATTATTATTATATATATTATTTTATTATTATT
1 ATTATTATTATATATATTATATTATTTTTATT
2811121 ATATTACCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
50 4 0.05
51 5 0.07
52 16 0.22
53 31 0.42
54 4 0.05
55 4 0.05
56 6 0.08
57 4 0.05
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (52 bp):
ATTATTATTATATATATTATATTATTTTTATTTTTTTTAAACTTTCGTCTTT
Found at i:2811095 original size:3 final size:3
Alignment explanation
Indices: 2811087--2811126 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2811077 TCTTTTGTCT
2811087 TTA TTA TTA TTA -TA TATA TTA TT- TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
2811127 CCTATACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 24 0.73
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2811372 original size:4 final size:4
Alignment explanation
Indices: 2811363--2811421 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
2811353 TTTATTCACG
* * *
2811363 TTAT TTAT TTAT CT-T TT-T TTAT TTTT TTGT TTACT TTAT TTAT TTATT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTA-T
2811411 TTATT TTAT TT
1 TTA-T TTAT TT
2811422 TCTATGTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
3 5 0.11
4 29 0.62
5 13 0.28
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:2811384 original size:18 final size:18
Alignment explanation
Indices: 2811363--2811421 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2811353 TTTATTCACG
2811363 TTATTTATTTATCTTT-TT
1 TTATTTATTTAT-TTTATT
*
2811381 TTATTT-TTT-TGTTTACT
1 TTATTTATTTAT-TTTATT
2811398 TTATTTATTTATTTTATT
1 TTATTTATTTATTTTATT
2811416 TTATTT
1 TTATTT
2811422 TCTATGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 4 0.11
17 10 0.29
18 20 0.57
19 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (18 bp):
TTATTTATTTATTTTATT
Found at i:2811402 original size:17 final size:17
Alignment explanation
Indices: 2811380--2811437 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
2811370 TTTATCTTTT
2811380 TTTATTTTTTTGTTTAC
1 TTTATTTTTTTGTTTAC
*
2811397 TTTATTTATTTAT-TTTAT
1 TTTATTT-TTT-TGTTTAC
*
2811415 TTTATTTTCTATGTTT-C
1 TTTATTTT-TTTGTTTAC
2811432 TTTATT
1 TTTATT
2811438 GAGAAAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 15 0.44
18 18 0.53
19 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTTGTTTAC
Found at i:2811404 original size:21 final size:23
Alignment explanation
Indices: 2811370--2811412 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2811360 ACGTTATTTA
*
2811370 TTTATCTTTTTTTATTT-TTTTG
1 TTTATCTTTATTTATTTATTTTG
2811392 TTTA-CTTTATTTATTTATTTT
1 TTTATCTTTATTTATTTATTTT
2811413 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTATCTTTATTTATTTATTTTG
Found at i:2811406 original size:35 final size:34
Alignment explanation
Indices: 2811321--2811437 Score: 119
Period size: 35 Copynumber: 3.3 Consensus size: 34
2811311 TTATATTTAA
* * * *
2811321 TTTACTTCATTTTTTTATTTTGTTTATTATATTTTA
1 TTTACTTTATTTATTTATTTTTTTTATT-T-TTTTG
* *
2811357 TTCACGTTATTTATTTATCTTTTTTTATTTTTTTG
1 TTTACTTTATTTATTTAT-TTTTTTTATTTTTTTG
*
2811392 TTTACTTTATTTATTTATTTTATTTTATTTTCTATG
1 TTTACTTTATTTATTTATTTT-TTTTATTTT-TTTG
2811428 TTT-CTTTATT
1 TTTACTTTATT
2811438 GAGAAAATCG
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
34 3 0.04
35 36 0.52
36 21 0.30
37 9 0.13
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (34 bp):
TTTACTTTATTTATTTATTTTTTTTATTTTTTTG
Found at i:2811566 original size:20 final size:20
Alignment explanation
Indices: 2811539--2811596 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2811529 ACGCGAAATA
2811539 AAAATCGCAACGCGATTCCC
1 AAAATCGCAACGCGATTCCC
* ** *
2811559 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTCCC
2811579 AAAATCGCAACGCGATTC
1 AAAATCGCAACGCGATTC
2811597 TTGAAAATCG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCCC
Found at i:2811605 original size:21 final size:20
Alignment explanation
Indices: 2811519--2811676 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2811509 AAATGACCAA
**
2811519 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* **
2811538 AAAAATCGCAACGCGATTCC
1 CAAAATCGCAACGCGATTTT
* ** *
2811558 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2811578 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2811599 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2811620 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2811640 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
2811661 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2811677 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 43 0.42
21 44 0.43
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2811669 original size:20 final size:20
Alignment explanation
Indices: 2811644--2811838 Score: 122
Period size: 20 Copynumber: 9.7 Consensus size: 20
2811634 GATTTTCAAT
*
2811644 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
*
2811664 AATCGCAACGCGAACAC-ATA
1 AATCGCAACGCGAATACGA-A
* * *
2811684 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
2811704 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* ** *
2811725 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAATACGAA
* * * *
2811745 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
2811765 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
** *
2811785 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAATAC-GAA
* * *
2811806 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
2811826 AATCGCAACGCGA
1 AATCGCAACGCGA
2811839 TATTTAAAGC
Statistics
Matches: 140, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 109 0.78
21 30 0.21
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:2811727 original size:61 final size:61
Alignment explanation
Indices: 2811644--2811837 Score: 248
Period size: 61 Copynumber: 3.2 Consensus size: 61
2811634 GATTTTCAAT
* ** *
2811644 AATCGCAACGCGAATATG-AAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2811704 AATCGCAACGTGTATCCGTAAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2811765 TATCGCAACGCGTATCCGT-AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2811826 AATCGCAACGCG
1 AATCGCAACGCG
2811838 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
60 28 0.25
61 84 0.75
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (61 bp):
AATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2811734 original size:81 final size:80
Alignment explanation
Indices: 2811644--2811838 Score: 239
Period size: 81 Copynumber: 2.4 Consensus size: 80
2811634 GATTTTCAAT
* * *
2811644 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATACGTAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGTAAATCG
* * *
2811709 CAACG-TGTATCCGTAA
65 CAACGAT-AATACATAA
** * * * *
2811725 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGCGTATACGTAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGTAAATCG
2811790 CAACGATAATACATAA
65 CAACGATAATACATAA
*
2811806 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATACGTAAATCGCAACGCGA
2811839 TATTTAAAGC
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 94 0.96
82 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATACGTAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGTAAATCGC
AACGATAATACATAA
Found at i:2811735 original size:41 final size:41
Alignment explanation
Indices: 2811683--2811835 Score: 211
Period size: 41 Copynumber: 3.8 Consensus size: 41
2811673 GCGAACACAT
2811683 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
** * *
2811724 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT-
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
* * * *
2811764 ATATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATA
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGTA
2811805 AAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATCCGTAAATCGCAACG
2811836 CGATATTTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 31 0.32
41 66 0.68
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
Found at i:2812261 original size:33 final size:33
Alignment explanation
Indices: 2812219--2812289 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2812209 TTCACTTAGA
2812219 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
***
2812252 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
2812285 TTTCA
1 TTTCA
2812290 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
Found at i:2812429 original size:14 final size:14
Alignment explanation
Indices: 2812410--2812464 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2812400 AGAATGACTG
2812410 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2812424 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2812443 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2812457 TCGCAACG
1 TCGCAACG
2812465 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2812447 original size:33 final size:33
Alignment explanation
Indices: 2812410--2812480 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2812400 AGAATGACTG
**
2812410 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2812443 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2812476 TCGCA
1 TCGCA
2812481 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2812498 original size:19 final size:19
Alignment explanation
Indices: 2812476--2812606 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
2812466 GAAACCAAAA
*
2812476 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2812495 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2812509 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2812528 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2812542 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2812561 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2812575 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2812594 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2812607 CTCTCGTTGC
Statistics
Matches: 89, Mismatches: 8, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
14 30 0.34
16 8 0.09
17 9 0.10
19 42 0.47
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2812517 original size:14 final size:14
Alignment explanation
Indices: 2812498--2812620 Score: 93
Period size: 14 Copynumber: 7.7 Consensus size: 14
2812488 TTTCATTTCG
2812498 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2812512 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2812531 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2812545 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2812564 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2812578 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2812595 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2812611 CGTTGCGATT
1 CGTTGCGATT
2812621 TTCATTTCAA
Statistics
Matches: 90, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
14 38 0.42
15 1 0.01
16 11 0.12
17 11 0.12
18 1 0.01
19 28 0.31
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2812523 original size:33 final size:33
Alignment explanation
Indices: 2812481--2812628 Score: 278
Period size: 33 Copynumber: 4.5 Consensus size: 33
2812471 CAAAATCGCA
2812481 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2812514 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2812547 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2812580 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2812613 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2812629 AACCAAAAGA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 111 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2814478 original size:92 final size:93
Alignment explanation
Indices: 2814321--2814788 Score: 837
Period size: 92 Copynumber: 5.1 Consensus size: 93
2814311 TAGATTGCTT
2814321 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2814386 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2814413 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2814478 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2814505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2814569 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2814596 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2814658 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2814686 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCT-AAACTGTGTATTCTTTAACACTGTGAAATAGT
2814751 ATTTGTCTTTG-TTTGTC-TTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2814778 AGTAAATTTAT
1 AGTAAATTTAT
2814789 CCATTCAAGT
Statistics
Matches: 368, Mismatches: 2, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
89 9 0.02
90 55 0.15
91 114 0.31
92 171 0.46
93 7 0.02
94 12 0.03
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2814630 original size:183 final size:182
Alignment explanation
Indices: 2814321--2814788 Score: 845
Period size: 183 Copynumber: 2.6 Consensus size: 182
2814311 TAGATTGCTT
*
2814321 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2814386 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG
2814451 TGTATTCTTTAACACTGTGAAATAGTATTTGTC-TTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTG-AA-A-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2814505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
2814569 TTTGTC-TTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
2814633 GTGTATTCTTTAACACTGTGAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2814686 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AAACTGTGTATTCTTTAACACTGTGAAATAGT
2814751 ATTTGTCTTTGTTTGTC-TTTGGTTGAAAGTAAATTTAT
65 ATTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTAT
2814789 CCATTCAAGT
Statistics
Matches: 276, Mismatches: 3, Indels: 12
0.95 0.01 0.04
Matches are distributed among these distances:
180 8 0.03
181 54 0.20
182 55 0.20
183 95 0.34
184 64 0.23
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (182 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2814870 original size:19 final size:19
Alignment explanation
Indices: 2814830--2814958 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2814820 TAGTTTACTT
* *
2814830 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2814850 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2814869 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2814888 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2814902 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2814921 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2814935 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2814954 TCGCA
1 TCGCA
2814959 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2814909 original size:33 final size:32
Alignment explanation
Indices: 2814866--2814958 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2814856 CGCGAAACCA
**
2814866 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2814898 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2814931 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2814959 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2814956 original size:52 final size:52
Alignment explanation
Indices: 2814830--2814958 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2814820 TAGTTTACTT
**
2814830 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2814882 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2814935 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2814959 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2814976 original size:19 final size:18
Alignment explanation
Indices: 2814954--2815072 Score: 101
Period size: 19 Copynumber: 6.8 Consensus size: 18
2814944 GAAACCAAAA
*
2814954 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
2814973 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
2814989 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
* *
2815006 TCGCATTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
2815022 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
2815039 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
2815058 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
2815073 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
14 15 0.19
16 10 0.12
17 10 0.12
19 46 0.57
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:2814995 original size:14 final size:14
Alignment explanation
Indices: 2814976--2815032 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2814966 TTTCATTTCG
2814976 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
2814990 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
2815007 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2815023 CGTTGCGATT
1 CGTTGCGATT
2815033 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 7 0.20
19 6 0.17
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2815001 original size:33 final size:33
Alignment explanation
Indices: 2814959--2815051 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2814949 CAAAATCGCA
*
2814959 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
** *
2814992 TTGCGATTTTGGTTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2815025 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2815052 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2815080 original size:20 final size:19
Alignment explanation
Indices: 2814954--2815088 Score: 96
Period size: 19 Copynumber: 7.6 Consensus size: 19
2814944 GAAACCAAAA
*
2814954 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
2814973 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
2814989 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
* *
2815006 TCGCATTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
2815022 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
2815039 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
2815058 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
2815078 TCGTGTTGCGA
1 TCGCGTTGCGA
2815089 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
14 18 0.19
16 6 0.06
17 6 0.06
18 1 0.01
19 49 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:2817004 original size:14 final size:14
Alignment explanation
Indices: 2816985--2817020 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2816975 ATTGTTTAAT
2816985 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2816999 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2817013 TGATTTGT
1 TGATTTGT
2817021 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2817143 original size:19 final size:17
Alignment explanation
Indices: 2817127--2817203 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 17
2817117 AAAAATGACT
2817127 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
2817146 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
2817160 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
2817179 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
2817193 ATCGCAATGCG
1 ATCGCAATGCG
2817204 TTTATAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
14 16 0.33
16 8 0.17
17 9 0.19
19 15 0.31
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:2817217 original size:33 final size:33
Alignment explanation
Indices: 2817127--2817203 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
2817117 AAAAATGACT
2817127 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2817160 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2817193 ATCGCAATGCG
1 ATCGCAATGCG
2817204 TTTATAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2817256 original size:19 final size:19
Alignment explanation
Indices: 2817232--2817605 Score: 397
Period size: 19 Copynumber: 21.4 Consensus size: 19
2817222 GATTATCTCG
2817232 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2817251 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2817270 TTGCGA--TTC--TTCG--
1 TTGCGATTTTCATTTCGCA
2817283 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2817302 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2817321 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2817340 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2817359 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2817378 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
2817392 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2817411 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2817430 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2817444 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2817464 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
2817478 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2817497 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2817511 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2817531 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
2817545 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2817565 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2817579 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2817598 TTGCGATT
1 TTGCGATT
2817606 GTATTTCCGT
Statistics
Matches: 302, Mismatches: 14, Indels: 78
0.77 0.04 0.20
Matches are distributed among these distances:
13 6 0.02
14 51 0.17
15 7 0.02
16 27 0.09
17 26 0.09
18 8 0.03
19 141 0.47
20 36 0.12
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2817266 original size:52 final size:52
Alignment explanation
Indices: 2817210--2817577 Score: 484
Period size: 52 Copynumber: 7.0 Consensus size: 52
2817200 TGCGTTTATA
*
2817210 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2817262 ATTTCGCATTGCGATTCT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2817313 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
2817370 ATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2817422 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
* * * * * *
2817475 ATGTTGGGATTTTC-ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 AT-TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2817522 ATTTCCGCATTGCGATTTTCAT-GTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2817576 AT
1 AT
2817578 GTTGGGATTT
Statistics
Matches: 281, Mismatches: 16, Indels: 36
0.84 0.05 0.11
Matches are distributed among these distances:
46 5 0.02
47 18 0.06
48 8 0.03
49 2 0.01
50 5 0.02
51 52 0.19
52 86 0.31
53 27 0.10
54 25 0.09
55 7 0.02
56 2 0.01
57 44 0.16
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2817469 original size:34 final size:33
Alignment explanation
Indices: 2817210--2817605 Score: 355
Period size: 34 Copynumber: 11.5 Consensus size: 33
2817200 TGCGTTTATA
*
2817210 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCAT-GTTGCGATTTTC
*
2817243 ATTTCGCATTGCGATTTTCAT-TT-CGCA-TTGC
1 ATTTCGCATTGCGATTTTCATGTTGCG-ATTTTC
2817274 GATTCTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 -A-T-TTCGCATTGCGATTTTCA--T-G--TTGCGATTTTC
*
2817313 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTCA--T-G--TTGCGATTTTC
*
2817351 ATTTCGCATTGCGATTTTCAT-TT-CGCA-TTGC
1 ATTTCGCATTGCGATTTTCATGTTGCG-ATTTTC
* * *
2817382 GATTCTCTCGTTGCAATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGATTTTCA--T-G--TTGCGATTTTC
*
2817422 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCAT-GTTGCGATTTTC
*
2817455 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTTTCATGTTGCGATTTTC
*
2817489 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCAT-GTTGCGATTTTC
2817522 ATTTCCGCATTGCGATTTTCATGTTGCGATTTTC
1 ATTT-CGCATTGCGATTTTCATGTTGCGATTTTC
*
2817556 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTTTCATGTTGCGATTTTC
*
2817590 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
2817606 GTATTTCCGT
Statistics
Matches: 311, Mismatches: 21, Indels: 62
0.79 0.05 0.16
Matches are distributed among these distances:
31 10 0.03
32 23 0.07
33 88 0.28
34 98 0.32
35 6 0.02
36 5 0.02
37 1 0.00
38 64 0.21
39 11 0.04
40 5 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTTTCATGTTGCGATTTTC
Found at i:2817548 original size:14 final size:14
Alignment explanation
Indices: 2817531--2817591 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 14
2817521 CATTTCCGCA
2817531 TTGCGATTTTCATG
1 TTGCGATTTTCATG
2817545 TTGCGATTTTCATTTCCG
1 TTGCGATTTTCA--T--G
2817563 CATTGCGATTTTCATG
1 --TTGCGATTTTCATG
*
2817579 TTGGGATTTTCAT
1 TTGCGATTTTCAT
2817592 TTCGCGTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 24 0.60
16 2 0.05
18 2 0.05
20 12 0.30
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTCATG
Found at i:2820112 original size:24 final size:24
Alignment explanation
Indices: 2820078--2820124 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2820068 CTGAAACATC
2820078 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2820102 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2820125 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2820827 original size:20 final size:20
Alignment explanation
Indices: 2820799--2821189 Score: 450
Period size: 20 Copynumber: 19.4 Consensus size: 20
2820789 AAATTTCAGT
* * * *
2820799 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2820819 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2820839 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2820859 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2820879 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2820899 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2820919 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2820939 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2820959 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2820979 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2820999 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
2821019 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
2821040 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2821060 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2821080 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2821100 GTTGCGATTTTACGGATACAC
1 GTTGCGA-TTTACGGATACGC
2821121 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2821141 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2821161 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2821181 GTTGCGATT
1 GTTGCGATT
2821190 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 24
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 278 0.86
21 36 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2821208 original size:81 final size:81
Alignment explanation
Indices: 2820804--2821208 Score: 398
Period size: 81 Copynumber: 5.0 Consensus size: 81
2820794 TCAGTGTTGT
* * * * * * *
2820804 GATTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATT
1 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
2820868 TACGGATTATCG--TTGC
65 TA-TGAATATCGCATTGC
*
2820884 GATTTACGGATACGCGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATT
1 GATTTACGGATACGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
2820948 TACGGATA-CGCATTGC
65 TATGAATATCGCATTGC
*
2820964 GATTTACGGATACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTT
1 GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TT
*
2821029 TATGTATTATCG--TTGC
65 TATG-AATATCGCATTGC
* * **
2821045 GATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTT
1 GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TT
* * * *
2821110 TACGGATA-CACGTTGC
65 TATGAATATCGCATTGC
* * * ** *
2821126 GATTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGA-T
1 GATTTACGGATACGCGTTGCGATTTACG-GATACGCGTTGCGATTTACGGATACGCGTTGCGATT
* *
2821189 TATTGAAAATCGCAATGC
65 TA-TGAATATCGCATTGC
2821207 GA
1 GA
2821209 ATTTGTACTA
Statistics
Matches: 278, Mismatches: 36, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.01
79 9 0.03
80 127 0.46
81 135 0.49
82 3 0.01
83 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (81 bp):
GATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTT
ATGAATATCGCATTGC
Found at i:2821436 original size:17 final size:18
Alignment explanation
Indices: 2821397--2821436 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2821387 GATTTTCTCT
2821397 TCTTTATTTACATGTTTA
1 TCTTTATTTACATGTTTA
*
2821415 T-TTTATTTACCT-TTTA
1 TCTTTATTTACATGTTTA
2821431 TCTTTA
1 TCTTTA
2821437 CTTTTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (18 bp):
TCTTTATTTACATGTTTA
Found at i:2834889 original size:39 final size:40
Alignment explanation
Indices: 2834811--2834895 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 40
2834801 TTATTTTCTA
2834811 TATTTTTATTTAATTCTTTTTATTCATTATTATATTATAT
1 TATTTTTATTTAATTCTTTTTATTCATTATTATATTATAT
* *
2834851 TATTTTT-TTTAAATT-TTTTGTCTTTATTATTATA-TATAT
1 TATTTTTATTT-AATTCTTTT-TATTCATTATTATATTATAT
2834890 TATTTT
1 TATTTT
2834896 ATTATTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
39 18 0.44
40 23 0.56
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (40 bp):
TATTTTTATTTAATTCTTTTTATTCATTATTATATTATAT
Found at i:2835011 original size:2 final size:2
Alignment explanation
Indices: 2835004--2835146 Score: 86
Period size: 2 Copynumber: 74.5 Consensus size: 2
2834994 TTAATATTAT
*
2835004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
2835046 AA CA T- TA CCA TA TA TA TA TA T- TA T- TA -A CTA T- TA TT TT TG
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * * * *
2835085 TA AA TC TT TA TG TA TA TA TA TA CA TA TT TT TA TA -A T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2835124 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2835147 TCTATTTATT
Statistics
Matches: 110, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
1 8 0.07
2 100 0.91
3 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2835254 original size:21 final size:21
Alignment explanation
Indices: 2835191--2835262 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
2835181 TTTTTATTCA
*
2835191 TTATTATTATATTATA-TA-T
1 TTATTATTATAATATATTATT
* * *
2835210 TTATTTTTA-AATCTTTTATCT
1 TTATTATTATAATATATTAT-T
2835231 TTATTATTATAATATATTATT
1 TTATTATTATAATATATTATT
2835252 TTATTATTATA
1 TTATTATTATA
2835263 TTACTTATAC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 3 0.07
19 10 0.24
21 21 0.50
22 8 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTATTATAATATATTATT
Found at i:2835477 original size:9 final size:8
Alignment explanation
Indices: 2835460--2835552 Score: 51
Period size: 9 Copynumber: 10.6 Consensus size: 8
2835450 AATTTACTTC
2835460 ATTTTTTT
1 ATTTTTTT
2835468 ATTTTGTTT
1 ATTTT-TTT
2835477 ATTATATTTT
1 ATT-T-TTTT
***
2835487 ATTCACGTT
1 ATT-TTTTT
*
2835496 ATTTATTT
1 ATTTTTTT
2835504 ATCTTTTTT
1 AT-TTTTTT
2835513 ATTTTTTT
1 ATTTTTTT
* *
2835521 GTTTACTTT
1 ATTT-TTTT
*
2835530 ATTTATTT
1 ATTTTTTT
2835538 ATTTTATTTT
1 A-TTT-TTTT
2835548 ATTTT
1 ATTTT
2835553 CTATGTTTCT
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
8 23 0.35
9 30 0.46
10 11 0.17
11 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.74
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2835503 original size:4 final size:4
Alignment explanation
Indices: 2835494--2835551 Score: 53
Period size: 4 Copynumber: 13.5 Consensus size: 4
2835484 TTTATTCACG
* * *
2835494 TTAT TTAT TTAT CTTTT TTAT TTTT TTGT TTACT TTAT TTAT TTATT TTATT
1 TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTA-T TTA-T
2835546 TTAT TT
1 TTAT TT
2835552 TCTATGTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
4 30 0.65
5 16 0.35
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:2835513 original size:13 final size:12
Alignment explanation
Indices: 2835497--2835569 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 12
2835487 ATTCACGTTA
2835497 TTTATTTATCTTT
1 TTTATTTAT-TTT
2835510 TTTATTT-TTTT
1 TTTATTTATTTT
*
2835521 GTTTACTTTATTTA
1 -TTTA-TTTATTTT
2835535 TTTATTTTATTTT
1 TTTA-TTTATTTT
*
2835548 ATTT-TCTATGTTT
1 -TTTATTTAT-TTT
2835561 CTTTATTTA
1 -TTTATTTA
2835570 CATGTTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
11 3 0.06
12 9 0.19
13 27 0.56
14 9 0.19
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:2835514 original size:17 final size:18
Alignment explanation
Indices: 2835494--2835569 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 18
2835484 TTTATTCACG
*
2835494 TTATTTATTTATCTTT-T
1 TTATTTATTTATGTTTCT
2835511 TTATTT-TTT-TGTTTACT
1 TTATTTATTTATGTTT-CT
*
2835528 TTATTTATTTAT-TTTATT
1 TTATTTATTTATGTTT-CT
*
2835546 TTATTT-TCTATGTTTCT
1 TTATTTATTTATGTTTCT
2835563 TTATTTA
1 TTATTTA
2835570 CATGTTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 4 0.08
16 3 0.06
17 24 0.49
18 17 0.35
19 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (18 bp):
TTATTTATTTATGTTTCT
Found at i:2835582 original size:17 final size:18
Alignment explanation
Indices: 2835520--2835587 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
2835510 TTTATTTTTT
* *
2835520 TGTTTACTTTATTTATTTA
1 TGTTTATTTTATTTA-CTA
*
2835539 T-TTTATTTTATTTTCTA
1 TGTTTATTTTATTTACTA
*
2835556 TGTTT-CTTTATTTAC-A
1 TGTTTATTTTATTTACTA
2835572 TGTTTATTTTATTTAC
1 TGTTTATTTTATTTAC
2835588 CTTTTATCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 6 0.15
17 20 0.49
18 14 0.34
19 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.69
Consensus pattern (18 bp):
TGTTTATTTTATTTACTA
Found at i:2838479 original size:12 final size:12
Alignment explanation
Indices: 2838462--2838500 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2838452 AAATTTATAT
2838462 AAAGCAGTGACG
1 AAAGCAGTGACG
2838474 AAAGCAGTGACG
1 AAAGCAGTGACG
** *
2838486 ATTGCATTGACG
1 AAAGCAGTGACG
2838498 AAA
1 AAA
2838501 CTTGAATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.15
Consensus pattern (12 bp):
AAAGCAGTGACG
Found at i:2844097 original size:36 final size:37
Alignment explanation
Indices: 2844034--2844106 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
2844024 TATGTGCAGG
*
2844034 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGAGGTATCGATTCCCC
2844071 GGGAACAGATT-CCCCCTGGGGAGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGAGGTATCGATTCCCC
2844107 CATAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 24 0.69
37 11 0.31
ACGTcount: A:0.18, C:0.32, G:0.32, T:0.19
Consensus pattern (37 bp):
GGGAACAGATTCCCCCCTGGGGAGGTATCGATTCCCC
Found at i:2846867 original size:36 final size:35
Alignment explanation
Indices: 2846804--2846878 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 35
2846794 TCATTGGAAA
2846804 ATATATATATATATATATTTGATTGAAAATATGGT
1 ATATATATATATATATATTTGATTGAAAATATGGT
*
2846839 ATATATATATGTATATAATTTGATTGAAAATATGGT
1 ATATATATATATATAT-ATTTGATTGAAAATATGGT
2846875 ATAT
1 ATAT
2846879 GATTGAGTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 15 0.39
36 23 0.61
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (35 bp):
ATATATATATATATATATTTGATTGAAAATATGGT
Found at i:2850229 original size:35 final size:36
Alignment explanation
Indices: 2850183--2850253 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 36
2850173 TATGTGCAGG
2850183 GGGAACAGATTCCCCCCT-GGG-GGTATCGATTCCCC
1 GGGAACAGATT-CCCCCTGGGGAGGTATCGATTCCCC
2850218 GGGAACAGATTCCCCCTGGGGAGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGAGGTATCGATTCCCC
2850254 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 6 0.18
35 14 0.41
36 14 0.41
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGAGGTATCGATTCCCC
Found at i:2852380 original size:63 final size:62
Alignment explanation
Indices: 2852293--2852413 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 62
2852283 TACATTTTTT
* * *
2852293 TCTTCTTCTAGGTAGAATTATTTAAGAAAATTTATGAATACATATTTAAAAATAGAAAAAAAA
1 TCTTCTTCTAGATAAAATTATTTAAG-AAATATATGAATACATATTTAAAAATAGAAAAAAAA
* ** *
2852356 TCTTCTTCTAGATAAAATTGTTTAAGAAATATATGGGTACATATTTAAAAATATAAAA
1 TCTTCTTCTAGATAAAATTATTTAAGAAATATATGAATACATATTTAAAAATAGAAAA
2852414 GGCAAGGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 28 0.55
63 23 0.45
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (62 bp):
TCTTCTTCTAGATAAAATTATTTAAGAAATATATGAATACATATTTAAAAATAGAAAAAAAA
Found at i:2856284 original size:18 final size:19
Alignment explanation
Indices: 2856245--2856285 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
2856235 AGTCATTCAA
2856245 GTAGTATCGATACCTAAAGG
1 GTAGTATCGATACC-AAAGG
2856265 GTAGTATCGATACC-AAGG
1 GTAGTATCGATACCAAAGG
2856283 GTA
1 GTA
2856286 CTGATAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (19 bp):
GTAGTATCGATACCAAAGG
Found at i:2857170 original size:21 final size:21
Alignment explanation
Indices: 2857042--2857199 Score: 111
Period size: 21 Copynumber: 7.4 Consensus size: 21
2857032 GGGTTCTATA
*
2857042 TGGTCCTCCGGGACATATATG
1 TGGTCCTTCGGGACATATATG
** * *
2857063 TAATCCTTTGGAACATATATG
1 TGGTCCTTCGGGACATATATG
* * * *
2857084 CGGTTCTTCGGGACACATTATT
1 TGGTCCTTCGGGACATA-TATG
* * * *
2857106 TGGTCCTTTGGAATATATAAG
1 TGGTCCTTCGGGACATATATG
* *
2857127 TGGTCATTAAGGAGA-ATTATATG
1 TGGTCCTT-CGG-GACA-TATATG
*
2857150 TGGTCCTTCGGGATATATATG
1 TGGTCCTTCGGGACATATATG
*
2857171 TGGTCCTTCAGGACATATATG
1 TGGTCCTTCGGGACATATATG
*
2857192 AGGTCCTT
1 TGGTCCTT
2857200 AGAGACAATT
Statistics
Matches: 102, Mismatches: 30, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
21 69 0.68
22 20 0.20
23 13 0.13
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TGGTCCTTCGGGACATATATG
Found at i:2857191 original size:42 final size:42
Alignment explanation
Indices: 2857042--2857199 Score: 136
Period size: 44 Copynumber: 3.7 Consensus size: 42
2857032 GGGTTCTATA
* * ** *
2857042 TGGTCCTCCGGGACATATATGTAATCCTTTGGAACATATATG
1 TGGTCCTTCAGGACATATATGTGGTCCTTTGGAATATATATG
* * * * * *
2857084 CGGTTCTTCGGGACACATTATTTGGTCCTTTGGAATATATAAG
1 TGGTCCTTCAGGACATA-TATGTGGTCCTTTGGAATATATATG
* * * * *
2857127 TGGTCATTAAGGAGAATTATATGTGGTCCTTCGGGATATATATG
1 TGGTCCTTCAGGA-CA-TATATGTGGTCCTTTGGAATATATATG
*
2857171 TGGTCCTTCAGGACATATATGAGGTCCTT
1 TGGTCCTTCAGGACATATATGTGGTCCTT
2857200 AGAGACAATT
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 26 0.29
43 29 0.33
44 33 0.37
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
TGGTCCTTCAGGACATATATGTGGTCCTTTGGAATATATATG
Found at i:2858980 original size:19 final size:19
Alignment explanation
Indices: 2858950--2858992 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2858940 CGTATAAAAG
2858950 TATTTTATATAA-TTACTT
1 TATTTTATATAATTTACTT
*
2858968 TATTTTAATATAATTTATTT
1 TATTTT-ATATAATTTACTT
2858988 TATTT
1 TATTT
2858993 AAAATTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 6 0.27
20 10 0.45
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTATATAATTTACTT
Found at i:2858993 original size:19 final size:18
Alignment explanation
Indices: 2858950--2858994 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2858940 CGTATAAAAG
*
2858950 TATTTTATATAATTACTT
1 TATTTAATATAATTACTT
*
2858968 TATTTTAATATAATTTATTT
1 TA-TTTAATATAA-TTACTT
2858988 TATTTAA
1 TATTTAA
2858995 AATTATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAATATAATTACTT
Found at i:2865243 original size:25 final size:25
Alignment explanation
Indices: 2865214--2865263 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2865204 AATTGAATCA
* *
2865214 AAATTAAAGTTTTATATATACAATT
1 AAATTAAAATTTCATATATACAATT
*
2865239 AAATTAAAATTTCATATATATAATT
1 AAATTAAAATTTCATATATACAATT
2865264 CCACCAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATTAAAATTTCATATATACAATT
Found at i:2869737 original size:23 final size:22
Alignment explanation
Indices: 2869706--2869759 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
2869696 AACAAAAAAT
* *
2869706 ATTATAAATTATATAATTTTTTA
1 ATTAAAAATTA-ATAATATTTTA
2869729 ATTAAAAA-TAATAATATTTTA
1 ATTAAAAATTAATAATATTTTA
2869750 AGTTAAAAAT
1 A-TTAAAAAT
2869760 CATTATCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTAAAAATTAATAATATTTTA
Found at i:2869742 original size:21 final size:22
Alignment explanation
Indices: 2869718--2869759 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2869708 TATAAATTAT
*
2869718 ATAATTTTTTAA-TTAAAAATA
1 ATAATATTTTAAGTTAAAAATA
2869739 ATAATATTTTAAGTTAAAAAT
1 ATAATATTTTAAGTTAAAAAT
2869760 CATTATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAATATTTTAAGTTAAAAATA
Found at i:2878754 original size:4 final size:4
Alignment explanation
Indices: 2878745--2878897 Score: 270
Period size: 4 Copynumber: 38.2 Consensus size: 4
2878735 TTACTCTGGA
2878745 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2878793 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
2878841 GTAT GTAT GTAC GTAT GTAC GTAC GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
2878889 GTAT ATAT G
1 GTAT GTAT G
2878898 AATTTGTTGC
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 143 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:2883575 original size:2 final size:2
Alignment explanation
Indices: 2883568--2883595 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2883558 CAAATGTGTC
2883568 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2883596 TGCTGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2885220 original size:187 final size:191
Alignment explanation
Indices: 2884872--2885294 Score: 662
Period size: 187 Copynumber: 2.2 Consensus size: 191
2884862 CTTATTTATA
* *
2884872 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGG--TCGAATACATATATTCGGGTCGGG
* *
2884936 TCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGAATATATATAATTTTACCTTATAT
64 TCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCTTATAT
*
2885001 ATTTAGGAATAATTATAATAATATCCCTCTATATATAA-TTTTTTCAATTAAGTCACTATTTT
129 ATTTAGGAATAATTACAATAATATCCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
***
2885063 TATTGAATAAAAATAATTTTTTTATTATTTC-GGTCGGGT-GAA-AC-TATATTTTTGTCGGGTC
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGAATACATATATTCGGGTCGGGTC
2885124 GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTACCTTATATA
66 GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCC-AAAAATATATAATTTTACCTTATATA
*
2885189 TTTAGGAATAATTACAATAATA-CCTCTCTATATATAATTTTTTTTTCAATTAAGTCATTATTTT
130 TTTAGGAATAATTACAATAATATCC-CTCTATATATAA--TTTTTTTCAATTAAGTCACTATTTT
2885253 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCG
2885295 GGTTTCTAAT
Statistics
Matches: 215, Mismatches: 9, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
186 54 0.25
187 58 0.27
188 2 0.01
189 1 0.00
190 54 0.25
191 29 0.13
192 17 0.08
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (191 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGAATACATATATTCGGGTCGGGTC
GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCTTATATAT
TTAGGAATAATTACAATAATATCCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
Found at i:2887818 original size:6 final size:6
Alignment explanation
Indices: 2887803--2887871 Score: 84
Period size: 6 Copynumber: 11.2 Consensus size: 6
2887793 TACAAAACAC
* * *
2887803 AAATAA AAATAG AAATAA AAATAA AAATAA AAATAA AATTAA AATTAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
*
2887851 AAACATA AAATAA TAAATAA A
1 AAATA-A AAATAA -AAATAA A
2887872 GTAGCAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 44 0.80
7 11 0.20
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:2887937 original size:12 final size:11
Alignment explanation
Indices: 2887922--2887957 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
2887912 CATCAAGAAT
2887922 ATAAAAAATGAA
1 ATAAAAAAT-AA
2887934 ATAAAAAATAA
1 ATAAAAAATAA
2887945 AGTAAAAAATAA
1 A-TAAAAAATAA
2887957 A
1 A
2887958 AGAGAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:2890023 original size:131 final size:134
Alignment explanation
Indices: 2889780--2890030 Score: 319
Period size: 131 Copynumber: 1.9 Consensus size: 134
2889770 ACAAAATTCA
* * * * *
2889780 TTTCAAGGGAAACAATCTCAAAGATATTTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAG
1 TTTCAAGAGAAACAATCTCAAAGA-ATTTGGTGCTTCAAGAGAAACGGTCTCAAGAGAAACAAAG
* * * * * *
2889845 TTTTATTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAAAAACTGTTTCAAAGGTTTTTTT
65 ATTTATTTAAAGGAAAACAAATTAAAAGATTTTGTTTCAAGAAAAACTGTCTCAAAGGTTTTTTT
2889910 TTGTG
130 TTGTG
* * *
2889915 TTTCAAGAGAAACAATTTCAAAG-A-TTGGTGCTTCAAGAGAAACTGTCTCAAGAGAGACAAA-A
1 TTTCAAGAGAAACAATCTCAAAGAATTTGGTGCTTCAAGAGAAACGGTCTCAAGAGAAACAAAGA
* **
2889977 TTTATTTAAAGGAAAACATATTAAAAGATTTTGTTTCAAGGGAAACTGTCTCAA
66 TTTATTTAAAGGAAAACAAATTAAAAGATTTTGTTTCAAGAAAAACTGTCTCAA
2890031 GAGAGACAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
131 46 0.46
132 31 0.31
133 1 0.01
135 21 0.21
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (134 bp):
TTTCAAGAGAAACAATCTCAAAGAATTTGGTGCTTCAAGAGAAACGGTCTCAAGAGAAACAAAGA
TTTATTTAAAGGAAAACAAATTAAAAGATTTTGTTTCAAGAAAAACTGTCTCAAAGGTTTTTTTT
TGTG
Found at i:2890029 original size:65 final size:65
Alignment explanation
Indices: 2889946--2890092 Score: 206
Period size: 65 Copynumber: 2.3 Consensus size: 65
2889936 AGATTGGTGC
* * *
2889946 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGGAAAACATATT-AAAAGATTTTG
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTATTTAAAGGAAAACAGATTCAAAA-ATTTTG
2890010 T
65 T
* * * *
2890011 TTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAATAGATTCAAAAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTATTTAAAGGAAAACAGATTCAAAAATTTTGT
*
2890076 TTCAAGGGAAACCGTCT
1 TTCAAGGGAAACTGTCT
2890093 GTAATATCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 69 0.95
66 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (65 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTATTTAAAGGAAAACAGATTCAAAAATTTTGT
Found at i:2890825 original size:21 final size:21
Alignment explanation
Indices: 2890799--2890843 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2890789 GATTTCTGGG
* *
2890799 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2890820 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2890841 CAA
1 CAA
2890844 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2892274 original size:23 final size:23
Alignment explanation
Indices: 2892248--2892315 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2892238 ATTATTATAT
2892248 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
2892271 GGCACTACAGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
2892294 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2892316 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2893130 original size:36 final size:35
Alignment explanation
Indices: 2893064--2893440 Score: 254
Period size: 36 Copynumber: 11.0 Consensus size: 35
2893054 GTGTTACACC
*
2893064 GTCTCAAGAGAGATAAAA--T-TTTTAAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTTAA-AGAAAAT
*
2893097 GTCTCAAGAGAGACAAAATTTGTTTTAGAAGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTTA-AAGAAAAT
* * * * *
2893133 GTCTCAAGTGAGACGAAATTTGTTTCAAGGAAAACA
1 GTCTCAAGAGAGACAAAATTTGTTTTAAAGAAAA-T
* * * * *
2893169 AT-TC-A-A-AG----ATTTTGTTTCAAGGGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTTAA-AGAAAAT
2893197 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTTAA-AGAAAAT
* *
2893233 GTCTCAAGAGAGACAAAA-ATGTTTTAAAAGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTT-AAAGAAAAT
* * * *
2893268 GTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACA
1 GTCTCAAGAGAGACAAAATTTGTTTTAAAGAAAA-T
* * * ***
2893304 GAT-TC-A-A-AG----ATTTTGTTTCAAGGGAAGCC
1 G-TCTCAAGAGAGACAAAATTTGTTTTAA-AGAAAAT
2893333 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTTAA-AGAAAAT
*
2893369 GTCTCAAGAGAGACAAAATTTGTTTCTAAAAGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTT-T-AAAGAAAAT
* *
2893406 GTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAA
1 GTCTCAAGAGAGACAAAA-TTTGTTTTAAAGAAAA
2893441 CAAATTCAAA
Statistics
Matches: 273, Mismatches: 41, Indels: 57
0.74 0.11 0.15
Matches are distributed among these distances:
28 13 0.05
29 21 0.08
30 6 0.02
31 2 0.01
32 6 0.02
33 19 0.07
34 1 0.00
35 44 0.16
36 125 0.46
37 27 0.10
38 9 0.03
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (35 bp):
GTCTCAAGAGAGACAAAATTTGTTTTAAAGAAAAT
Found at i:2893238 original size:136 final size:136
Alignment explanation
Indices: 2893061--2893499 Score: 715
Period size: 136 Copynumber: 3.2 Consensus size: 136
2893051 GTGGTGTTAC
*
2893061 ACCGTCTCAAGAGAGATAAAA--T-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
1 ACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
* * *
2893123 AGAAGAAACTGTCTCAAGTGAGACGAAATTTGTTTCAAGGAAAACAATTCAAAGATTTTGTTTCA
66 AAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAATTCAAAGATTTTGTTTCA
2893188 AGGGAA
131 AGGGAA
* *
2893194 ACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA-ATGTTTT
1 ACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
*
2893258 AAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTC
66 AAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACA-ATTCAAAGATTTTGTTTC
2893323 AAGGGAA
130 AAGGGAA
*
2893330 GCCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTC
1 ACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTT-
*
2893395 TAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACAAATTCAAAGTTTTTTGT
65 TAAAAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGAAAAC-AATTCAAAG-ATTTTGT
2893460 TTCAAGGGAA
127 TTCAAGGGAA
2893470 ACCGTCTCAAGAGAGACAAAACTTTGTTTT
1 ACCGTCTCAAGAGAGACAAAA-TTTGTTTT
2893500 GAGTAAATTA
Statistics
Matches: 284, Mismatches: 12, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
133 19 0.07
135 50 0.18
136 112 0.39
137 5 0.02
138 28 0.10
139 25 0.09
140 37 0.13
141 8 0.03
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (136 bp):
ACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
AAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAATTCAAAGATTTTGTTTCA
AGGGAA
Found at i:2893412 original size:37 final size:37
Alignment explanation
Indices: 2893333--2893432 Score: 166
Period size: 37 Copynumber: 2.7 Consensus size: 37
2893323 AAGGGAAGCC
*
2893333 GTCTCAAGAGAGACAAAATTTGTTT-TAAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTCTAAAAGAAAAT
*
2893369 GTCTCAAGAGAGACAAAATTTGTTTCTAAAAGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTCTAAAAGAAAAT
2893406 GTCTCAAGAGAGACAAAACTTTGTTTC
1 GTCTCAAGAGAGACAAAA-TTTGTTTC
2893433 AAGGAAAACA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 25 0.42
37 27 0.45
38 8 0.13
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (37 bp):
GTCTCAAGAGAGACAAAATTTGTTTCTAAAAGAAAAT
Found at i:2894957 original size:94 final size:94
Alignment explanation
Indices: 2894796--2894978 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
2894786 ATATGTAAAG
* ** *
2894796 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACAAATTGCCTTAGAGGG
1 ACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCAAGGCGTTTAACAAATTACCTTAGAGGG
*
2894861 ACAGCTCAAGAC-TTATTGTATATATAATC
66 ACAACTCAAG-CTTTATTGTATATATAATC
* * * *
2894890 ACCTTTATCAGGTTAGTTGAATATTATCCATAAAGCCAATGTGTTTAACCAATTA-CTCTAGAGG
1 ACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCAAGGCGTTTAACAAATTACCT-TAGAGG
*
2894954 GACAACTCTAGCTTTATTGTATATA
65 GACAACTCAAGCTTTATTGTATATA
2894979 AATATTATAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
93 3 0.04
94 74 0.96
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCAAGGCGTTTAACAAATTACCTTAGAGGG
ACAACTCAAGCTTTATTGTATATATAATC
Done.