Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 19 of 20
Found at i:2946400 original size:9 final size:9
Alignment explanation
Indices: 2946321--2946407 Score: 58
Period size: 9 Copynumber: 9.6 Consensus size: 9
2946311 AATTTAAATA
2946321 ATAATA-TT
1 ATAATATTT
2946329 ATAATTATTAT
1 ATAA-TATT-T
*
2946340 TTAATATTT
1 ATAATATTT
*
2946349 TTAATATTT
1 ATAATATTT
2946358 -T-ATA-TT
1 ATAATATTT
2946364 ATTAATA-TT
1 A-TAATATTT
2946373 ATAATTAATTTT
1 ATAA-T-A-TTT
2946385 ATAATATTT
1 ATAATATTT
*
2946394 ATTATATTT
1 ATAATATTT
2946403 ATAAT
1 ATAAT
2946408 TATAATTAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
8 9 0.14
9 34 0.52
10 7 0.11
11 5 0.08
12 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATAATATTT
Found at i:2946410 original size:36 final size:38
Alignment explanation
Indices: 2946327--2946416 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 38
2946317 AATAATAATA
* *
2946327 TTATAATTATTATTTAATATTTTTAATATTTTATATTAT
1 TTATAATTA-TAATTAATATTTATAATATTTTATATTAT
*
2946366 TAAT-ATTATAATTAAT-TTTATAATA-TTTAT-TATAT
1 TTATAATTATAATTAATATTTATAATATTTTATAT-TAT
2946401 TTATAATTATAATTAA
1 TTATAATTATAATTAA
2946417 AAAAATTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 1 0.02
35 11 0.24
36 19 0.42
37 7 0.16
38 4 0.09
39 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (38 bp):
TTATAATTATAATTAATATTTATAATATTTTATATTAT
Found at i:2948761 original size:15 final size:15
Alignment explanation
Indices: 2948741--2948770 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2948731 CCTAACACAC
2948741 TTAATACGCTCACCT
1 TTAATACGCTCACCT
2948756 TTAATACGCTCACCT
1 TTAATACGCTCACCT
2948771 AACACACCTA
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:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (15 bp):
TTAATACGCTCACCT
Found at i:2950275 original size:16 final size:17
Alignment explanation
Indices: 2950254--2950296 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2950244 AGCAATCGAA
*
2950254 AAAAAAAAGAAG-AAAT
1 AAAAAAAAGAAGCAAAG
2950270 AAAAAAAA-AAGCAAAG
1 AAAAAAAAGAAGCAAAG
*
2950286 CAAAAAAAGAA
1 AAAAAAAAGAA
2950297 AAAGAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 18 0.78
17 2 0.09
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAAGCAAAG
Found at i:2950293 original size:20 final size:19
Alignment explanation
Indices: 2950252--2950305 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
2950242 AGAGCAATCG
2950252 AAAAAAAAAAG-AAGAAAT
1 AAAAAAAAAAGAAAGAAAT
2950270 AAAAAAAAAAGCAAAGCAAA-
1 AAAAAAAAAAG-AAAG-AAAT
*
2950290 AAAAGAAAAAGAAAGA
1 AAAAAAAAAAGAAAGA
2950306 GAGAGACCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 12 0.38
19 4 0.12
20 13 0.41
21 3 0.09
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAGAAAGAAAT
Found at i:2950679 original size:22 final size:22
Alignment explanation
Indices: 2950654--2950732 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
2950644 AGCAAAATCA
2950654 AAACAGCAAGCAAGGAAA-AACG
1 AAACAGCAAGCAAGGAAAGAA-G
2950676 AAACAGCAAGCAAGGAAAGAAG
1 AAACAGCAAGCAAGGAAAGAAG
*
2950698 AAACAGCAAGCAAAGAAAGAAG
1 AAACAGCAAGCAAGGAAAGAAG
*
2950720 AAACAACAAGCAA
1 AAACAGCAAGCAA
2950733 AGCAAAACCG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
22 52 0.96
23 2 0.04
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (22 bp):
AAACAGCAAGCAAGGAAAGAAG
Found at i:2950733 original size:22 final size:22
Alignment explanation
Indices: 2950654--2950773 Score: 120
Period size: 22 Copynumber: 5.4 Consensus size: 22
2950644 AGCAAAATCA
*
2950654 AAACAGCAAGCAAGGAAA-AACG
1 AAACAGCAAGCAAAGAAAGAA-G
*
2950676 AAACAGCAAGCAAGGAAAGAAG
1 AAACAGCAAGCAAAGAAAGAAG
2950698 AAACAGCAAGCAAAGAAAGAAG
1 AAACAGCAAGCAAAGAAAGAAG
* *
2950720 AAACAACAAGCAAAGCAAA-ACCG
1 AAACAGCAAGCAAAG-AAAGA-AG
** *
2950743 AAACAGCAAATAAAG-AAGAAAA
1 AAACAGCAAGCAAAGAAAG-AAG
2950765 AAACAGCAA
1 AAACAGCAA
2950774 AGGTAGACAG
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
21 2 0.02
22 64 0.75
23 19 0.22
ACGTcount: A:0.63, C:0.17, G:0.19, T:0.01
Consensus pattern (22 bp):
AAACAGCAAGCAAAGAAAGAAG
Found at i:2950945 original size:23 final size:23
Alignment explanation
Indices: 2950915--2950958 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2950905 CTCATTTTGA
*
2950915 GTTGCATGGTCAGTAGATTAAAG
1 GTTGCATGGTCAATAGATTAAAG
*
2950938 GTTGCATGGTGAATAGATTAA
1 GTTGCATGGTCAATAGATTAA
2950959 TAAAAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (23 bp):
GTTGCATGGTCAATAGATTAAAG
Found at i:2951231 original size:39 final size:39
Alignment explanation
Indices: 2951187--2951269 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
2951177 ATGAAACGTA
*
2951187 ATTTTAAAATTTTAA-TTTTTTTATTTCCCTAAATTAAT
1 ATTTTTAAATTTTAATTTTTTTTATTTCCCTAAATTAAT
2951225 ATTTTTAAATTTTAATTTTTTTTATTTCCCTAAATTAAT
1 ATTTTTAAATTTTAATTTTTTTTATTTCCCTAAATTAAT
2951264 ATTTTT
1 ATTTTT
2951270 TTTAAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 14 0.33
39 29 0.67
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTAAATTTTAATTTTTTTTATTTCCCTAAATTAAT
Found at i:2952843 original size:17 final size:16
Alignment explanation
Indices: 2952821--2952879 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
2952811 TGATAGTAAT
2952821 AATAAAAAATAAATAAA
1 AATAAAAAATAAA-AAA
2952838 AAT-AAAAAT-AAAAA
1 AATAAAAAATAAAAAA
* *
2952852 TATATAAAATAAAAAA
1 AATAAAAAATAAAAAA
2952868 ATATAAAAAATA
1 A-ATAAAAAATA
2952880 TACACCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 11 0.31
17 12 0.34
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAAAAAATAAAAAA
Found at i:2952846 original size:16 final size:15
Alignment explanation
Indices: 2952825--2952876 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
2952815 AGTAATAATA
2952825 AAAAATAAATAAAAAT
1 AAAAATAAA-AAAAAT
*
2952841 AAAAAT-AAAAATAT
1 AAAAATAAAAAAAAT
2952855 ATAAAATAAAAAAATAT
1 A-AAAATAAAAAAA-AT
2952872 AAAAA
1 AAAAA
2952877 ATATACACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 7 0.23
16 15 0.48
17 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:2952853 original size:22 final size:21
Alignment explanation
Indices: 2952825--2952866 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2952815 AGTAATAATA
2952825 AAAAATAAATAAAAATAAAAAT
1 AAAAATAAAT-AAAATAAAAAT
*
2952847 AAAAATATATAAAATAAAAA
1 AAAAATAAATAAAATAAAAA
2952867 AATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAATAAATAAAATAAAAAT
Found at i:2952858 original size:26 final size:24
Alignment explanation
Indices: 2952821--2952881 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
2952811 TGATAGTAAT
*
2952821 AATAAAAAATA-AATAA-AAATAAA
1 AATAAAAAATATAA-AATAAAAAAA
2952844 AATAAAAATATATAAAATAAAAAAA
1 AATAAAAA-ATATAAAATAAAAAAA
*
2952869 TATAAAAAATATA
1 AATAAAAAATATA
2952882 CACCATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 8 0.24
24 10 0.30
25 15 0.45
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (24 bp):
AATAAAAAATATAAAATAAAAAAA
Found at i:2952860 original size:15 final size:14
Alignment explanation
Indices: 2952818--2952875 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
2952808 ATTTGATAGT
*
2952818 AATAATAAAAAAT-A
1 AATAA-AAAATATAA
2952832 AAT-AAAAATA-AA
1 AATAAAAAATATAA
2952844 AATAAAAATATATAA
1 AATAAAAA-ATATAA
2952859 AATAAAAAAATATAA
1 AAT-AAAAAATATAA
2952874 AA
1 AA
2952876 AATATACACC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 9 0.24
13 5 0.13
14 6 0.16
15 13 0.34
16 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAAATATAA
Found at i:2952866 original size:6 final size:6
Alignment explanation
Indices: 2952821--2952853 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2952811 TGATAGTAAT
*
2952821 AATAAA AA-ATA AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATA
2952854 TATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:2953685 original size:22 final size:23
Alignment explanation
Indices: 2953646--2953692 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2953636 ACACTCTAGT
*
2953646 AAGCAAAGCAAAATCGAAACAGC
1 AAGCAAAGCAAAAACGAAACAGC
*
2953669 AAGC-AAGGAAAAACGAAACAGC
1 AAGCAAAGCAAAAACGAAACAGC
2953691 AA
1 AA
2953693 ATAAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.60, C:0.19, G:0.19, T:0.02
Consensus pattern (23 bp):
AAGCAAAGCAAAAACGAAACAGC
Found at i:2955764 original size:21 final size:21
Alignment explanation
Indices: 2955740--2955798 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
2955730 CCTAACACAT
2955740 TTAACAAAGATATTCTAAATA
1 TTAACAAAGATATTCTAAATA
2955761 TTAACAAAGATATTCTAAATA
1 TTAACAAAGATATTCTAAATA
*
2955782 TTAACAAAGATCTTCTA
1 TTAACAAAGATATTCTA
2955799 TGTGGGTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (21 bp):
TTAACAAAGATATTCTAAATA
Found at i:2960810 original size:35 final size:36
Alignment explanation
Indices: 2960748--2960816 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
2960738 ATCAAATAAA
*
2960748 TATTTATTTTTATTAAAAAATATAATTT-ATTTATT
1 TATTTATTTTTAATAAAAAATATAATTTAATTTATT
**
2960783 TATTTATATTTTAATAAAATTTA-AATTTAATTTA
1 TATTTAT-TTTTAATAAAAAATATAATTTAATTTA
2960817 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
TATTTATTTTTAATAAAAAATATAATTTAATTTATT
Found at i:2965565 original size:75 final size:75
Alignment explanation
Indices: 2965442--2965591 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
2965432 ATCGTACCTG
2965442 ACAAATATAGCTTAATAATTGAATTTAGTTTTTGCATCAAGGTTTTTTGGTAATTATTGTTTATA
1 ACAAATATAGCTTAATAATTGAATTTAGTTTTTGCATCAAGGTTTTTTGGTAATTATTGTTTATA
2965507 AGGATAGACC
66 AGGATAGACC
2965517 ACAAATATAGCTTAATAATTGAATTTAGTTTTTGCATCAAGGTTTTTTGGTAATTATTGTTTATA
1 ACAAATATAGCTTAATAATTGAATTTAGTTTTTGCATCAAGGTTTTTTGGTAATTATTGTTTATA
2965582 AGGATAGACC
66 AGGATAGACC
2965592 TCGACGACAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (75 bp):
ACAAATATAGCTTAATAATTGAATTTAGTTTTTGCATCAAGGTTTTTTGGTAATTATTGTTTATA
AGGATAGACC
Found at i:2982199 original size:19 final size:18
Alignment explanation
Indices: 2982170--2982207 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2982160 AATTTCATTT
2982170 AAATAAATATTATTATAA
1 AAATAAATATTATTATAA
*
2982188 AAATATAATATTATTTTAA
1 AAATA-AATATTATTATAA
2982207 A
1 A
2982208 CCCATAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATAAATATTATTATAA
Found at i:2983192 original size:21 final size:21
Alignment explanation
Indices: 2983138--2983210 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
2983128 ATATAAAAAT
* * *
2983138 TATATCTTTTAATCTAATAAA
1 TATATTTTTTCATCCAATAAA
* * *
2983159 TATATTATATCATCCAATCAA
1 TATATTTTTTCATCCAATAAA
*
2983180 TATATTTTTTCAT---TTAAA
1 TATATTTTTTCATCCAATAAA
2983198 TATATTTTTTCAT
1 TATATTTTTTCAT
2983211 AAAAATATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
18 16 0.38
21 26 0.62
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTTTTTCATCCAATAAA
Found at i:2983216 original size:18 final size:18
Alignment explanation
Indices: 2983178--2983219 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2983168 TCATCCAATC
**
2983178 AATATATTTTTTCATTTA
1 AATATATTTTTTCATAAA
2983196 AATATATTTTTTCATAAA
1 AATATATTTTTTCATAAA
2983214 AATATA
1 AATATA
2983220 ATTATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATATTTTTTCATAAA
Found at i:2983251 original size:28 final size:26
Alignment explanation
Indices: 2983197--2983249 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2983187 TTTCATTTAA
2983197 ATATATTTTTTCATAAAAATATAATT
1 ATATATTTTTTCATAAAAATATAATT
* *
2983223 ATATATTTTTTTATCAAAA-ATAATT
1 ATATATTTTTTCATAAAAATATAATT
2983248 AT
1 AT
2983250 TAAATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATATTTTTTCATAAAAATATAATT
Found at i:2985426 original size:29 final size:29
Alignment explanation
Indices: 2985394--2985449 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2985384 TTTTAAGTTT
*
2985394 AAATAAATTATCAAAATATTATTATTTTA
1 AAATAAATTATCAAAATAATATTATTTTA
* * *
2985423 AAATTATTTATTAAAATAATATTATTT
1 AAATAAATTATCAAAATAATATTATTT
2985450 ATTTACGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AAATAAATTATCAAAATAATATTATTTTA
Found at i:2985555 original size:15 final size:14
Alignment explanation
Indices: 2985524--2985565 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
2985514 GAATGCAACC
2985524 TTTTAATTT-TTTT
1 TTTTAATTTATTTT
2985537 TTTTAATTTATTATT
1 TTTTAATTTATT-TT
*
2985552 TTTTAACTTATTTT
1 TTTTAATTTATTTT
2985566 ACTTGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 13 0.50
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTAATTTATTTT
Found at i:2985595 original size:16 final size:18
Alignment explanation
Indices: 2985560--2985598 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
2985550 TTTTTTAACT
2985560 TATTTTACTTGATAAAAA
1 TATTTTACTTGATAAAAA
*
2985578 TATTTTA-TT-ATTAAAA
1 TATTTTACTTGATAAAAA
2985594 TATTT
1 TATTT
2985599 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 2 0.10
18 7 0.35
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTTACTTGATAAAAA
Found at i:2985755 original size:170 final size:171
Alignment explanation
Indices: 2985570--2986000 Score: 511
Period size: 170 Copynumber: 2.5 Consensus size: 171
2985560 TATTTTACTT
* *
2985570 GATAAAAATATTTTATTATTAAAATATTTAAAATTAT-TTGATAAATATTTTAAAAA-TATTAAA
1 GATAAAAATATTTTATTATTAAAATATATAAAATTATCCT-ATAAATA-TTTAAAAATTATTAAA
* * * **
2985633 ATCTAAAATTAT-TAAAAATAAA-TTTTATGCTTAA-AAATTATCGTATTTTAATCCAAAAATGT
64 ATCTAAAATTATGT-AAAATAAATTTTTACGCTAAAGAAATTATCGTATTTTAATACAAAAACAT
2985695 CAATATACATTTTTTTAAAACTTATTATTTCATAATTTTT-AACCC
128 CAATATAC-TTTTTTT-AAACTTATTATTTCATAATTTTTAAACCC
* * *
2985740 TG-TAAAAACATTTTATTATTAAAATATATAAAACTATCCTATAAATATTTAAAAATTTTTAAAA
1 -GATAAAAATATTTTATTATTAAAATATATAAAATTATCCTATAAATATTTAAAAATTATTAAAA
*
2985804 TCTAAAATTATGTAAAATAAATTTTTTACGCTAAAGAAATTATTGTATTTTAATACAAAAACATC
65 TCTAAAATTATGTAAAATAAA-TTTTTACGCTAAAGAAATTATCGTATTTTAATACAAAAACATC
* * ** *
2985869 AATTTACTTTTTTTAGACTTATTATTTTGTAATTTTTAAATCC
129 AATATACTTTTTTTAAACTTATTATTTCATAATTTTTAAACCC
** * * * *
2985912 GATAAATGTATTTTATTATTAAAATATCTAAAATTATCCAAT-AATACTTAAAAAGTT-TCAAAA
1 GATAAAAATATTTTATTATTAAAATATATAAAATTATCCTATAAATATTTAAAAA-TTATTAAAA
* *
2985975 TATAAAATTATGTAAAACAAATTTTT
65 TCTAAAATTATGTAAAATAAATTTTT
2986001 TACACTTATG
Statistics
Matches: 225, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
169 8 0.04
170 70 0.31
171 59 0.26
172 57 0.25
173 31 0.14
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (171 bp):
GATAAAAATATTTTATTATTAAAATATATAAAATTATCCTATAAATATTTAAAAATTATTAAAAT
CTAAAATTATGTAAAATAAATTTTTACGCTAAAGAAATTATCGTATTTTAATACAAAAACATCAA
TATACTTTTTTTAAACTTATTATTTCATAATTTTTAAACCC
Found at i:2986409 original size:172 final size:167
Alignment explanation
Indices: 2986097--2986634 Score: 475
Period size: 171 Copynumber: 3.1 Consensus size: 167
2986087 TGTTATTATC
* * * **
2986097 AAATTTTAGATAGTTTAATAATAAAATGCATTTTTAGG-TT-AAAAATTAAAAAATGTTAAATCT
1 AAATTTTAAATATTTTAATAAT-AAATGCATTTTT-GGATTAAAAAATTAAGAAATAATAAATCT
* * * * * **
2986160 AAAAAAACATAAATTAAAACTTTGGTATTAAA-ATACGATAGTTTCTCAAGCCA-AAAGATTCAC
64 AAAAAAATATAAATTGAAACTTTCGTATTAAATATA--ATAGTTTCTTAAG-CATAAAAATT-GT
** **
2986223 TTTATTTAATTTTAGATTTTACAAATTTTTCAATATTTAATATA
125 TTTACATAATTTTAGATTTTA-AAATTTTAAAATATTTAATATA
* * *
2986267 AAATTTTAGATATTTTAATAATAAATGCATTTGTTGGATTAAAAAATTATGAAATAAAAAATCTA
1 AAATTTTAAATATTTTAATAATAAATGCATTT-TTGGATTAAAAAATTAAGAAATAATAAATCTA
*
2986332 AAAAAATTATAAATTGAAACTTTCGTATTAAATATAATAGTTTTTTAAGCATAAAACATATGTTT
65 AAAAAA-TATAAATTGAAACTTTCGTATTAAATATAATAGTTTCTTAAGCATAAAA-AT-TGTTT
*
2986397 TACATAATTTTAGATTTTAAAAATTTTAAAATATTTACAGCAT-
127 TACATAATTTTAGATTTT-AAAATTTTAAAATATTTA-A-TATA
** * ** * * *
2986440 -AATTTTAAATATTTTAATAATAAGATATATTTATCAAGCTAAAAAATTACGAAATAATAAGTCT
1 AAATTTTAAATATTTTAATAATAA-ATGCATTTTTGGA-TTAAAAAATTAAGAAATAATAAATCT
* ** * * *
2986504 -AAAAAATATATATTGGTATTTTCGTATTAAACTATGATAATTTCTTAAGCATAAAAATTTGTTT
64 AAAAAAATATAAATTGAAACTTTCGTATTAAA-TATAATAGTTTCTTAAGCATAAAAA-TTGTTT
*
2986568 T-CTATAATTTTAGATTTTAATATTTTAAAAATATTT-AT-TGA
127 TAC-ATAATTTTAGATTTTAAAATTTT-AAAATATTTAATAT-A
*
2986609 ATAATTTTAAATATTTCAATAATAAA
1 A-AATTTTAAATATTTTAATAATAAA
2986635 ATATATTTAT
Statistics
Matches: 308, Mismatches: 39, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
167 1 0.00
169 13 0.04
170 36 0.12
171 113 0.37
172 109 0.35
173 34 0.11
174 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (167 bp):
AAATTTTAAATATTTTAATAATAAATGCATTTTTGGATTAAAAAATTAAGAAATAATAAATCTAA
AAAAATATAAATTGAAACTTTCGTATTAAATATAATAGTTTCTTAAGCATAAAAATTGTTTTACA
TAATTTTAGATTTTAAAATTTTAAAATATTTAATATA
Found at i:2987477 original size:15 final size:15
Alignment explanation
Indices: 2987452--2987495 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
2987442 AATATTTATA
2987452 AAAATAATTAAAAAAG
1 AAAA-AATTAAAAAAG
*
2987468 AAAAAATTAAAAAAAT
1 AAAAAATT-AAAAAAG
2987484 AAAAAGATTAAA
1 AAAAA-ATTAAA
2987496 GTGGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 18 0.72
17 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAAAAATTAAAAAAG
Found at i:2987481 original size:17 final size:17
Alignment explanation
Indices: 2987449--2987495 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2987439 TTAAATATTT
2987449 ATAAAAATAATT-AAAAA
1 ATAAAAA-AATTAAAAAA
*
2987466 A-GAAAAAATTAAAAAA
1 ATAAAAAAATTAAAAAA
*
2987482 ATAAAAAGATTAAA
1 ATAAAAAAATTAAA
2987496 GTGGAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 11 0.44
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
ATAAAAAAATTAAAAAA
Found at i:2989054 original size:2 final size:2
Alignment explanation
Indices: 2989047--2989075 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2989037 AAGCATTTTA
2989047 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2989076 AACGAAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2990014 original size:25 final size:27
Alignment explanation
Indices: 2989943--2990012 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
2989933 AAACAAGCCT
* *
2989943 CCATATTTGACAAATACAAAGAAACCA
1 CCATTTTTGACAAACACAAAGAAACCA
*
2989970 CCATTTTTTACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
2989997 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2990013 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:2991933 original size:21 final size:21
Alignment explanation
Indices: 2991895--2991936 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2991885 ATCTGTTGAA
* **
2991895 ACTCCACCTGTTTTGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
2991916 ACTCCACCTGCTGCGGAGTAT
1 ACTCCACCTGCTGCGGAGTAT
2991937 TACTTGTCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
ACTCCACCTGCTGCGGAGTAT
Found at i:2995756 original size:19 final size:20
Alignment explanation
Indices: 2995728--2995774 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2995718 TTTCATCCCA
2995728 TTTTTA-TTTTTAATTTGT-
1 TTTTTATTTTTTAATTTGTG
*
2995746 TTTTTATTTTTTATTTTGTG
1 TTTTTATTTTTTAATTTGTG
2995766 TTTTTATTT
1 TTTTTATTT
2995775 AGTATATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 6 0.23
19 11 0.42
20 9 0.35
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTATTTTTTAATTTGTG
Found at i:2996100 original size:32 final size:33
Alignment explanation
Indices: 2996046--2996111 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
2996036 TGTTATTTTT
*
2996046 TATTTTATATTTATATATATTTTAAAATATTAA
1 TATTTTATATTTATATAGATTTTAAAATATTAA
* * *
2996079 TATTTTAT-TTTATGTGGATTTTAACATATTAA
1 TATTTTATATTTATATAGATTTTAAAATATTAA
2996111 T
1 T
2996112 GCATTCATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (33 bp):
TATTTTATATTTATATAGATTTTAAAATATTAA
Found at i:2998659 original size:36 final size:36
Alignment explanation
Indices: 2998605--2998674 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
2998595 TTAAAATATA
*
2998605 GAGATTACGATCTCATAATCATAATCAAAATATTTG
1 GAGATTACAATCTCATAATCATAATCAAAATATTTG
*
2998641 GAGATTACAATCTTATAATCATAATCAAAATATT
1 GAGATTACAATCTCATAATCATAATCAAAATATT
2998675 AAAAAATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (36 bp):
GAGATTACAATCTCATAATCATAATCAAAATATTTG
Found at i:3002836 original size:20 final size:20
Alignment explanation
Indices: 3002813--3002914 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 20
3002803 ATCCACGTTA
3002813 CATGCTTTGCATAATCATTT
1 CATGCTTTGCATAATCATTT
* *
3002833 CATGCTTT-CACAA-C-CTT
1 CATGCTTTGCATAATCATTT
* *
3002850 CATGATTTGCATCATCATTT
1 CATGCTTTGCATAATCATTT
*
3002870 CATGCTTT-CACAA-C-TTT
1 CATGCTTTGCATAATCATTT
** *
3002887 CATGCTTTGCATCTTTATTT
1 CATGCTTTGCATAATCATTT
3002907 CATGCTTT
1 CATGCTTT
3002915 CACAACTTTC
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
17 20 0.32
18 7 0.11
19 8 0.13
20 28 0.44
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.45
Consensus pattern (20 bp):
CATGCTTTGCATAATCATTT
Found at i:3002853 original size:17 final size:17
Alignment explanation
Indices: 3002830--3002926 Score: 88
Period size: 17 Copynumber: 5.4 Consensus size: 17
3002820 TGCATAATCA
3002830 TTTCATGCTTTCACAAC
1 TTTCATGCTTTCACAAC
* * *
3002847 CTTCATGATTTGCATCATC
1 TTTCATGCTTT-CA-CAAC
3002866 ATTTCATGCTTTCACAAC
1 -TTTCATGCTTTCACAAC
*
3002884 TTTCATGCTTTGCATCTTTA-
1 TTTCATGCTTT-CA-C--AAC
3002904 TTTCATGCTTTCACAAC
1 TTTCATGCTTTCACAAC
3002921 TTTCAT
1 TTTCAT
3002927 TCATTCATCA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.02
17 26 0.41
18 8 0.12
19 8 0.12
20 20 0.31
21 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.45
Consensus pattern (17 bp):
TTTCATGCTTTCACAAC
Found at i:3002867 original size:37 final size:37
Alignment explanation
Indices: 3002786--3002926 Score: 183
Period size: 37 Copynumber: 3.8 Consensus size: 37
3002776 TTGTTTGTTG
* * * *
3002786 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATGCTTTCA-CAAC-TTTCATGCTTTGCAT
* * *
3002825 AATCATTTCATGCTTTCACAACCTTCATGATTTGCAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
3002862 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
1 CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
* *
3002899 CTTTATTTCATGCTTTCACAACTTTCAT
1 CATCATTTCATGCTTTCACAACTTTCAT
3002927 TCATTCATCA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
37 72 0.80
38 3 0.03
39 15 0.17
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.43
Consensus pattern (37 bp):
CATCATTTCATGCTTTCACAACTTTCATGCTTTGCAT
Found at i:3003035 original size:16 final size:15
Alignment explanation
Indices: 3003011--3003052 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3003001 TTTAATTGTT
3003011 TTTTTGATTTTTTAA
1 TTTTTGATTTTTTAA
3003026 TTTCTTGA-TTTTTAA
1 TTT-TTGATTTTTTAA
*
3003041 TTTTTAATTTTT
1 TTTTTGATTTTT
3003053 ATTATTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 17 0.71
16 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTTTGATTTTTTAA
Found at i:3003036 original size:35 final size:34
Alignment explanation
Indices: 3002969--3003045 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
3002959 GATTAATTTG
3002969 AATTTTTTTTTAATTTTTGATAATTTTGGATTTTT
1 AATTTTTTTTTAATTTTT-ATAATTTTGGATTTTT
* *
3003004 AATTGTTTTTTTGATTTTT-TAATTTCTTGATTTTT
1 AATT-TTTTTTTAATTTTTATAATTT-TGGATTTTT
3003039 AATTTTT
1 AATTTTT
3003046 AATTTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 9 0.24
35 16 0.42
36 13 0.34
ACGTcount: A:0.21, C:0.01, G:0.08, T:0.70
Consensus pattern (34 bp):
AATTTTTTTTTAATTTTTATAATTTTGGATTTTT
Found at i:3003053 original size:7 final size:7
Alignment explanation
Indices: 3002975--3003053 Score: 54
Period size: 7 Copynumber: 10.9 Consensus size: 7
3002965 TTTGAATTTT
3002975 TTTTTAA
1 TTTTTAA
3002982 TTTTTGATAA
1 -TTTT--TAA
**
3002992 TTTTGGA
1 TTTTTAA
3002999 TTTTTAA
1 TTTTTAA
3003006 TTGTTT--
1 TT-TTTAA
* *
3003012 TTTTGAT
1 TTTTTAA
3003019 TTTTTAA
1 TTTTTAA
*
3003026 TTTCTTGA
1 TTT-TTAA
3003034 TTTTTAA
1 TTTTTAA
3003041 TTTTTAA
1 TTTTTAA
3003048 TTTTTA
1 TTTTTA
3003054 TTATTATGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
7 32 0.57
8 13 0.23
9 4 0.07
10 3 0.05
ACGTcount: A:0.22, C:0.01, G:0.08, T:0.70
Consensus pattern (7 bp):
TTTTTAA
Found at i:3003926 original size:29 final size:28
Alignment explanation
Indices: 3003894--3004117 Score: 132
Period size: 29 Copynumber: 7.8 Consensus size: 28
3003884 GTCTTTAACG
*
3003894 TTTTCAAAATTACATTTTGACCCTAAAC
1 TTTTTAAAATTACATTTTGACCCTAAAC
* * *
3003922 TTTTTAAAATTGCA-TTTAACCTCAAAAC
1 TTTTTAAAATTACATTTTGACC-CTAAAC
* * * *
3003950 -TTTTAACAATTACATCTTAATCTCTAAAA
1 TTTTTAA-AATTACATTTTGA-CCCTAAAC
*
3003979 TTTTTAAAATTATATTTTGATCCC-AAAGC
1 TTTTTAAAATTACATTTTGA-CCCTAAA-C
* * * ** *
3004008 TTTTTAAAATCATACTTTGACTTTTAAAA
1 TTTTTAAAATTACATTTTGAC-CCTAAAC
* * *
3004037 TTTTTGAAATTACATTTT-AACTTGAAAAC
1 TTTTTAAAATTACATTTTGACCCT--AAAC
* * * *
3004066 TTTTCAAAATTACACTTTAACCTTTAAAC
1 TTTTTAAAATTACATTTTGACC-CTAAAC
*
3004095 TTTTTGAAATTACATTTTGACCC
1 TTTTTAAAATTACATTTTGACCC
3004118 CAAAATGACC
Statistics
Matches: 149, Mismatches: 35, Indels: 24
0.72 0.17 0.12
Matches are distributed among these distances:
27 14 0.09
28 28 0.19
29 93 0.62
30 12 0.08
31 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (28 bp):
TTTTTAAAATTACATTTTGACCCTAAAC
Found at i:3004037 original size:58 final size:58
Alignment explanation
Indices: 3003894--3004122 Score: 173
Period size: 58 Copynumber: 4.0 Consensus size: 58
3003884 GTCTTTAACG
* * * * * * *
3003894 TTTTCAAAATTACATTTTGACC-CTAAACTTTTTAAAATTGCA-TTT-AACCTCAAAAC
1 TTTTCAAAATCACACTTTAACCTTTAAAATTTTTGAAATTACATTTTGAACC-CAAAAC
* * * * * * *
3003950 TTTT-AACAATTACA-TCTTAATCTCTAAAATTTTTAAAATTATATTTTGATCCCAAAGC
1 TTTTCAA-AATCACACT-TTAACCTTTAAAATTTTTGAAATTACATTTTGAACCCAAAAC
* * * * **
3004008 TTTTTAAAATCATACTTTGACTTTTAAAATTTTTGAAATTACATTTT-AACTTGAAAAC
1 TTTTCAAAATCACACTTTAACCTTTAAAATTTTTGAAATTACATTTTGAAC-CCAAAAC
* * *
3004066 TTTTCAAAATTACACTTTAACCTTTAAACTTTTTGAAATTACATTTTGACCCCAAAA
1 TTTTCAAAATCACACTTTAACCTTTAAAATTTTTGAAATTACATTTTGAACCCAAAA
3004123 TGACCTAAAA
Statistics
Matches: 136, Mismatches: 28, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
55 3 0.02
56 15 0.11
57 19 0.14
58 91 0.67
59 8 0.06
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (58 bp):
TTTTCAAAATCACACTTTAACCTTTAAAATTTTTGAAATTACATTTTGAACCCAAAAC
Found at i:3005320 original size:15 final size:15
Alignment explanation
Indices: 3005300--3005346 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
3005290 AAAAGAAATG
3005300 AAAATGAAATGAATA
1 AAAATGAAATGAATA
3005315 AAAATGAAAT-AA-A
1 AAAATGAAATGAATA
3005328 AAATATG-AATGAATA
1 AAA-ATGAAATGAATA
3005343 AAAA
1 AAAA
3005347 AAATACCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.24
14 8 0.28
15 14 0.48
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (15 bp):
AAAATGAAATGAATA
Found at i:3012029 original size:13 final size:13
Alignment explanation
Indices: 3012011--3012038 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3012001 ATACAAAGAT
3012011 CAATGTATCGATA
1 CAATGTATCGATA
3012024 CAATGTATCGATA
1 CAATGTATCGATA
3012037 CA
1 CA
3012039 TTAAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3012034 original size:33 final size:32
Alignment explanation
Indices: 3011992--3012058 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
3011982 AAATTTCCCA
3011992 AATGTATCGATACA-AAGATCAATGTATCGATAC
1 AATGTATCGATACATAAG-T-AATGTATCGATAC
3012025 AATGTATCGATACATTAAGTAATGTATCGATAC
1 AATGTATCGATACA-TAAGTAATGTATCGATAC
3012058 A
1 A
3012059 TTTTCTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 28 0.88
34 1 0.03
35 3 0.09
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (32 bp):
AATGTATCGATACATAAGTAATGTATCGATAC
Found at i:3013935 original size:13 final size:13
Alignment explanation
Indices: 3013917--3013941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3013907 TTCAACGATT
3013917 TGTATCGATACAA
1 TGTATCGATACAA
3013930 TGTATCGATACA
1 TGTATCGATACA
3013942 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3014031 original size:13 final size:13
Alignment explanation
Indices: 3014013--3014040 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3014003 ATTACTCAAA
3014013 TGTATCGATACAT
1 TGTATCGATACAT
3014026 TGTATCGATACAT
1 TGTATCGATACAT
3014039 TG
1 TG
3014041 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3014102 original size:52 final size:52
Alignment explanation
Indices: 3014046--3014174 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
3014036 CATTGATCTT
3014046 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
3014098 TGTATCGATACATACAGGCAAATTTGCCCATATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
3014150 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3014175 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:3018546 original size:12 final size:12
Alignment explanation
Indices: 3018529--3018553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3018519 TTATGTTTAG
3018529 GGCTTTTTTGAT
1 GGCTTTTTTGAT
3018541 GGCTTTTTTGAT
1 GGCTTTTTTGAT
3018553 G
1 G
3018554 ATGGACAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.28, T:0.56
Consensus pattern (12 bp):
GGCTTTTTTGAT
Found at i:3018984 original size:21 final size:21
Alignment explanation
Indices: 3018960--3018999 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3018950 TTATATTTTC
3018960 ATAAAAATATAAAT-TAATTAA
1 ATAAAAATA-AAATATAATTAA
3018981 ATAAAAATAAAATATAATT
1 ATAAAAATAAAATATAATT
3019000 TATTTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAATAAAATATAATTAA
Found at i:3019282 original size:36 final size:36
Alignment explanation
Indices: 3019237--3019308 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
3019227 AATCAAATTA
* *
3019237 TGAAAATTATAATATTGTAATTATAAGAAAAATATT
1 TGAAAATTATAATATTATAATCATAAGAAAAATATT
* * **
3019273 TGAATATTATAATTTTATAATCATAATTAAAATATT
1 TGAAAATTATAATATTATAATCATAAGAAAAATATT
3019309 AAAAAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (36 bp):
TGAAAATTATAATATTATAATCATAAGAAAAATATT
Found at i:3019679 original size:21 final size:21
Alignment explanation
Indices: 3019602--3019698 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
3019592 TTAAAATATT
*
3019602 TATATTTATATTTATATAAATA
1 TATA-TTATATTTATATAAAAA
* * * *
3019624 TGTA-TAAATTTAAATTAAAA
1 TATATTATATTTATATAAAAA
* **
3019644 TATATTTTAAATATATAAAAA
1 TATATTATATTTATATAAAAA
* *
3019665 TTTATTATATTTATAT-TAAA
1 TATATTATATTTATATAAAAA
3019685 TATATTCATATTTA
1 TATATT-ATATTTA
3019699 ATATTTATTT
Statistics
Matches: 55, Mismatches: 18, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
20 23 0.42
21 29 0.53
22 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATTATATTTATATAAAAA
Found at i:3019688 original size:15 final size:15
Alignment explanation
Indices: 3019670--3019723 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
3019660 AAAAATTTAT
3019670 TATATTTATATTAAA
1 TATATTTATATTAAA
* *
3019685 TATATTCATATT-TA
1 TATATTTATATTAAA
3019699 -ATATTTAT-TTAAA
1 TATATTTATATTAAA
*
3019712 TTTATTTATATT
1 TATATTTATATT
3019724 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 2 0.06
13 8 0.26
14 8 0.26
15 13 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTTATATTAAA
Found at i:3019709 original size:11 final size:11
Alignment explanation
Indices: 3019693--3019724 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3019683 AATATATTCA
3019693 TATTTAATATT
1 TATTTAATATT
3019704 TATTTAA-ATT
1 TATTTAATATT
3019714 TATTT-ATATT
1 TATTTAATATT
3019724 T
1 T
3019725 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 12 0.60
11 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTAATATT
Found at i:3019722 original size:27 final size:28
Alignment explanation
Indices: 3019671--3019724 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
3019661 AAAATTTATT
3019671 ATATTTATATTAAATATATTCATATTTA
1 ATATTTATATTAAATATATTCATATTTA
* *
3019699 ATATTTAT-TTAAATTTATTTATATTT
1 ATATTTATATTAAATATATTCATATTT
3019725 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTTATATTAAATATATTCATATTTA
Found at i:3023040 original size:20 final size:21
Alignment explanation
Indices: 3023009--3023047 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3022999 AATAGTAGCA
3023009 TTAATATTATTTACATTTATT
1 TTAATATTATTTACATTTATT
*
3023030 TTAAT-TTATTTATATTTA
1 TTAATATTATTTACATTTA
3023048 AAATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAATATTATTTACATTTATT
Found at i:3024524 original size:50 final size:50
Alignment explanation
Indices: 3024467--3024633 Score: 183
Period size: 50 Copynumber: 3.3 Consensus size: 50
3024457 GAAAAAAGTG
* * *
3024467 ATCATAATTGTTGATTATTTTTTATTAA-TCTTTGACAATTGAGAGAGATA
1 ATCATAATTATTGATTATTTTTTATCAACT-TTTGACAATAGAGAGAGATA
* * * * *
3024517 ATTATAATTATTGACTATTTTTTATCAACTTTTGATAATCGTGAGAGATA
1 ATCATAATTATTGATTATTTTTTATCAACTTTTGACAATAGAGAGAGATA
* * * *
3024567 ATCGTAATTATTGATTATTCTTCACCAACTTTTGACAATAGAGAGAGATA
1 ATCATAATTATTGATTATTTTTTATCAACTTTTGACAATAGAGAGAGATA
*
3024617 TGATCGTAATTATTGAT
1 --ATCATAATTATTGAT
3024634 CCTAAATAAC
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 82 0.84
51 1 0.01
52 15 0.15
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (50 bp):
ATCATAATTATTGATTATTTTTTATCAACTTTTGACAATAGAGAGAGATA
Found at i:3025071 original size:18 final size:17
Alignment explanation
Indices: 3025048--3025105 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
3025038 TTCAAAACCA
3025048 AATAAATTAAACTAAATT
1 AATAAATTAAACT-AATT
*
3025066 AATAAATTTAA-TCAATT
1 AATAAATTAAACT-AATT
*
3025083 AAATTAATTCAAACTAATT
1 -AATAAATT-AAACTAATT
3025102 AATA
1 AATA
3025106 CTCACTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 5 0.16
18 20 0.62
19 6 0.19
20 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAATTAAACTAATT
Found at i:3026591 original size:21 final size:21
Alignment explanation
Indices: 3026567--3026607 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3026557 ATTACATAAC
3026567 TAATATAAAACATATA-AAATA
1 TAATAT-AAACATATATAAATA
*
3026588 TAATATATACATATATAAAT
1 TAATATAAACATATATAAAT
3026608 TATCGAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATATAAACATATATAAATA
Found at i:3026759 original size:43 final size:43
Alignment explanation
Indices: 3026707--3026794 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
3026697 TAAAAAGGAT
3026707 AATAAAATATTATATTTATTTTCTTATTGCACCCTATAATCAG
1 AATAAAATATTATATTTATTTTCTTATTGCACCCTATAATCAG
3026750 AATAAAATATTATATTTATTTTCTTATTGCACCCTATAATCAG
1 AATAAAATATTATATTTATTTTCTTATTGCACCCTATAATCAG
3026793 AA
1 AA
3026795 GTAATTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (43 bp):
AATAAAATATTATATTTATTTTCTTATTGCACCCTATAATCAG
Found at i:3027027 original size:12 final size:12
Alignment explanation
Indices: 3027007--3027050 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
3026997 TTTAAAAATA
3027007 TATTATATTATT
1 TATTATATTATT
*
3027019 TATTTTATTA-T
1 TATTATATTATT
*
3027030 TAATATATTATT
1 TATTATATTATT
3027042 T-TTATATTA
1 TATTATATTA
3027051 ATATTTGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTATATTATT
Found at i:3027042 original size:19 final size:19
Alignment explanation
Indices: 3027021--3027073 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
3027011 ATATTATTTA
3027021 TTTTATTATTAATATATTAT
1 TTTTA-TATTAATATATTAT
*
3027041 TTTTATATTAATATTTGTAT
1 TTTTATATTAATATAT-TAT
3027061 ATTTTATAATTAA
1 -TTTTAT-ATTAA
3027074 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.34
20 8 0.28
21 6 0.21
22 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATATTAATATATTAT
Found at i:3028698 original size:18 final size:19
Alignment explanation
Indices: 3028664--3028699 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3028654 TATTCAAATC
*
3028664 TTTTAAATATTAAATAAAA
1 TTTTAAATATCAAATAAAA
3028683 TTTTAAAT-TCAAATAAA
1 TTTTAAATATCAAATAAA
3028700 TAACTTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTAAATATCAAATAAAA
Found at i:3029672 original size:2 final size:2
Alignment explanation
Indices: 3029665--3029691 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3029655 TAATACCTAA
3029665 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3029692 AATTCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3033902 original size:2 final size:2
Alignment explanation
Indices: 3033895--3033923 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3033885 GATTGCTGAT
3033895 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3033924 GTGTGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3039057 original size:26 final size:25
Alignment explanation
Indices: 3038994--3039057 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
3038984 TAGATGACTT
**
3038994 TATTTTA-AATTATATATATATTGA
1 TATTTTATAATTATATATATAACGA
*
3039018 TATATTAATAATTATATATTATAACGA
1 TAT-TTTATAATTATATA-TATAACGA
*
3039045 TATTTTATTATTA
1 TATTTTATAATTA
3039058 ATTATATGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 3 0.09
25 3 0.09
26 17 0.53
27 9 0.28
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
TATTTTATAATTATATATATAACGA
Found at i:3039235 original size:72 final size:72
Alignment explanation
Indices: 3039135--3039268 Score: 196
Period size: 72 Copynumber: 1.9 Consensus size: 72
3039125 ACTATATAAG
* * *
3039135 TATTGAAATTGTCACGTGTTAGTCATATTATATATTAAAAAATTAATTATATAATATATATAATT
1 TATTGAAATTATCACATGTTAGTCATATTATATATTAAAAAATTAATGATATAATATATATAATT
3039200 TTATATA
66 TTATATA
* * ** *
3039207 TATTGAAATTATCACATGTTGGTGATATTATATATTGTAAAATTAATGATATTATATATATA
1 TATTGAAATTATCACATGTTAGTCATATTATATATTAAAAAATTAATGATATAATATATATA
3039269 TATATATTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (72 bp):
TATTGAAATTATCACATGTTAGTCATATTATATATTAAAAAATTAATGATATAATATATATAATT
TTATATA
Found at i:3041489 original size:2 final size:2
Alignment explanation
Indices: 3041482--3041510 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3041472 CTATTTCTAT
3041482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3041511 TGTTAAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3046028 original size:11 final size:11
Alignment explanation
Indices: 3046012--3046037 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3046002 ATTTATCGAT
3046012 TAAAAAAGAAA
1 TAAAAAAGAAA
3046023 TAAAAAAGAAA
1 TAAAAAAGAAA
3046034 TAAA
1 TAAA
3046038 TGCAAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (11 bp):
TAAAAAAGAAA
Found at i:3046059 original size:14 final size:14
Alignment explanation
Indices: 3046042--3046073 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3046032 AATAAATGCA
3046042 AAGTATCACTTTTC
1 AAGTATCACTTTTC
*
3046056 AAGTATCTCTTTTC
1 AAGTATCACTTTTC
3046070 AAGT
1 AAGT
3046074 TAATCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (14 bp):
AAGTATCACTTTTC
Found at i:3049448 original size:27 final size:27
Alignment explanation
Indices: 3049376--3049497 Score: 86
Period size: 27 Copynumber: 4.5 Consensus size: 27
3049366 GAGTACCTTT
* * * *
3049376 TTTTGTAATACCCTTTTCACTACCCAAA
1 TTTT-TAATAACCTATTCATTACCTAAA
*
3049404 TTTTTAATAACCTTTTCATTACCTAAA
1 TTTTTAATAACCTATTCATTACCTAAA
* *
3049431 TTTTT-ATCACCATATTCATTATCTAAA
1 TTTTTAATAACC-TATTCATTACCTAAA
** * * * *
3049458 TTTACAACACCCTTTTCA-TATTCTAAA
1 TTTTTAATAACCTATTCATTA-CCTAAA
3049485 TTTTTAATAACCT
1 TTTTTAATAACCT
3049498 CTCTAATATT
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
26 7 0.09
27 61 0.81
28 7 0.09
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (27 bp):
TTTTTAATAACCTATTCATTACCTAAA
Found at i:3051089 original size:3 final size:3
Alignment explanation
Indices: 3051081--3051123 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3051071 TATTTAAACC
3051081 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3051124 GTTGTTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3051128 original size:3 final size:3
Alignment explanation
Indices: 3051122--3051147 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3051112 ATTATTATTA
3051122 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
3051148 ATTATTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:3052873 original size:2 final size:2
Alignment explanation
Indices: 3052866--3052892 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3052856 AAATTATTTG
3052866 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3052893 TCTGTAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3053651 original size:2 final size:2
Alignment explanation
Indices: 3053646--3053675 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3053636 GGGGGGGGGG
3053646 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3053676 ACTTATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3054879 original size:23 final size:24
Alignment explanation
Indices: 3054831--3054892 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
3054821 AATAAAATAA
* *
3054831 TTAAAATATAATATAAATATATATT
1 TTAAAAT-TTATATAAATATAAATT
3054856 TTAAAATTTATAT-AATATAAATT
1 TTAAAATTTATATAAATATAAATT
*
3054879 TT-TAATTTAT-TAAA
1 TTAAAATTTATATAAA
3054893 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 1 0.03
22 9 0.27
23 11 0.33
24 5 0.15
25 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAATTTATATAAATATAAATT
Found at i:3054881 original size:24 final size:25
Alignment explanation
Indices: 3054809--3054883 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
3054799 ATAATTACAT
* * *
3054809 AAATATGATATGAATAAA-ATAATTA
1 AAATATAATATAAATAAATAT-TTTA
*
3054834 AAATATAATATAAATATATATTTTA
1 AAATATAATATAAATAAATATTTTA
*
3054859 AAAT-TTATATAATATAAAT-TTTTA
1 AAATATAATATAA-ATAAATATTTTA
3054883 A
1 A
3054884 TTTATTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
24 13 0.31
25 27 0.64
26 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
AAATATAATATAAATAAATATTTTA
Found at i:3054942 original size:37 final size:37
Alignment explanation
Indices: 3054876--3054951 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
3054866 TATAATATAA
* * *
3054876 ATTTTTAATTTATTAAAATTTATTTAAATATA-AAAT
1 ATTTTTAATTTATTAAAATATAATAAAATATATAAAT
*
3054912 ATTTTTAATATTATTATAATATAATAAAATATATAAAT
1 ATTTTTAAT-TTATTAAAATATAATAAAATATATAAAT
3054950 AT
1 AT
3054952 AATATAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 9 0.26
37 19 0.56
38 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
ATTTTTAATTTATTAAAATATAATAAAATATATAAAT
Found at i:3055323 original size:13 final size:13
Alignment explanation
Indices: 3055305--3055350 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3055295 TTTAATATTT
3055305 TTTATTATTAATA
1 TTTATTATTAATA
*
3055318 TTTATTA-TATTAA
1 TTTATTATTAAT-A
*
3055331 TTTA-TAATAATA
1 TTTATTATTAATA
3055343 TTTATTAT
1 TTTATTAT
3055351 ATTGATAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:3055339 original size:38 final size:37
Alignment explanation
Indices: 3055272--3055350 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
3055262 TAATAATTCG
* * *
3055272 TTATTATAATTATTATTTTATAATTTAATATTTTTTA
1 TTATTATAATTATTATATTATAATTTAATAATATTTA
* *
3055309 TTATTAATATTTATTATATTA-ATTTATAATAATATTTA
1 TTATT-ATAATTATTATATTATAATT-TAATAATATTTA
3055347 TTAT
1 TTAT
3055351 ATTGATAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 8 0.23
38 27 0.77
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (37 bp):
TTATTATAATTATTATATTATAATTTAATAATATTTA
Found at i:3057283 original size:29 final size:29
Alignment explanation
Indices: 3057251--3057309 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3057241 GTATTTTATT
3057251 ATAAATACCGTTGACATAAATACATTAGC
1 ATAAATACCGTTGACATAAATACATTAGC
* ** * *
3057280 ATAATTACTTTTGATATAAATACTTTAGC
1 ATAAATACCGTTGACATAAATACATTAGC
3057309 A
1 A
3057310 CAGTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (29 bp):
ATAAATACCGTTGACATAAATACATTAGC
Found at i:3057320 original size:29 final size:29
Alignment explanation
Indices: 3057261--3057327 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
3057251 ATAAATACCG
*
3057261 TTGACATAAATACATTAGCATAATTACTT
1 TTGACATAAATACATTAGCACAATTACTT
* * * *
3057290 TTGATATAAATACTTTAGCACAGTTATTT
1 TTGACATAAATACATTAGCACAATTACTT
3057319 TTGACATAA
1 TTGACATAA
3057328 GTATTTTGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (29 bp):
TTGACATAAATACATTAGCACAATTACTT
Found at i:3057336 original size:14 final size:14
Alignment explanation
Indices: 3057317--3057348 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3057307 GCACAGTTAT
3057317 TTTTGACATAAGTA
1 TTTTGACATAAGTA
*
3057331 TTTTGACGTAAGTA
1 TTTTGACATAAGTA
3057345 TTTT
1 TTTT
3057349 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (14 bp):
TTTTGACATAAGTA
Found at i:3057397 original size:29 final size:29
Alignment explanation
Indices: 3057361--3057519 Score: 78
Period size: 29 Copynumber: 5.5 Consensus size: 29
3057351 TAAAAATATT
3057361 TTTG-CATAAATATTTTTTACAGAGGTAC
1 TTTGACATAAATATTTTTTACAGAGGTAC
* * ** *
3057389 TTTGGCATAAGTACTTTGGTA-A-AGGCAC
1 TTTGACATAAATA-TTTTTTACAGAGGTAC
* * * *
3057417 TTTTGGCGTAAGTACTTTTAGTACAGA--TAC
1 -TTTGACATAAATA-TTTT-TTACAGAGGTAC
* * *
3057447 TTTGACTATAAATA-TTTTGACACAAGTAC
1 TTTGAC-ATAAATATTTTTTACAGAGGTAC
* * * * *
3057476 TTTGACATAAGTATTTTTAATATAGGTAT
1 TTTGACATAAATATTTTTTACAGAGGTAC
3057505 TTTGACATAAATATT
1 TTTGACATAAATATT
3057520 CTGACATAAG
Statistics
Matches: 101, Mismatches: 20, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.04
28 18 0.18
29 62 0.61
30 15 0.15
31 1 0.01
32 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTGACATAAATATTTTTTACAGAGGTAC
Found at i:3057519 original size:14 final size:14
Alignment explanation
Indices: 3057447--3057531 Score: 82
Period size: 14 Copynumber: 5.9 Consensus size: 14
3057437 GTACAGATAC
*
3057447 TTTGACTATAAATAT
1 TTTGAC-ATAAGTAT
* *
3057462 TTTGACACAAGTAC
1 TTTGACATAAGTAT
3057476 TTTGACATAAGTAT
1 TTTGACATAAGTAT
*
3057490 TTTTA-ATATAGGTAT
1 TTTGACATA-A-GTAT
*
3057505 TTTGACATAAATAT
1 TTTGACATAAGTAT
*
3057519 TCTGACATAAGTA
1 TTTGACATAAGTA
3057532 CCTTTTGTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
13 3 0.05
14 36 0.63
15 15 0.26
16 3 0.05
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (14 bp):
TTTGACATAAGTAT
Found at i:3057543 original size:43 final size:43
Alignment explanation
Indices: 3057459--3057551 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 43
3057449 TGACTATAAA
* *
3057459 TATTTTGACACAAGTACTTTGACATAAGTATTTTTAATATAGG
1 TATTTTGACACAAATACTTTGACATAAGTACTTTTAATATAGG
* *
3057502 TATTTTGACATAAATA-TTCTGACATAAGTACCTTTT-GTATAGG
1 TATTTTGACACAAATACTT-TGACATAAGTA-CTTTTAATATAGG
3057545 TACTTTT
1 TA-TTTT
3057552 TGTACAGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
42 2 0.05
43 33 0.77
44 8 0.19
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (43 bp):
TATTTTGACACAAATACTTTGACATAAGTACTTTTAATATAGG
Found at i:3060196 original size:65 final size:66
Alignment explanation
Indices: 3060107--3060272 Score: 194
Period size: 66 Copynumber: 2.5 Consensus size: 66
3060097 TTGTGTTTTT
* * *
3060107 ATGCTCCACTTCTGTCACTCTCCTATATACAAGTTCTTTC-AATGGAGAAAT-GACCGTTGTAAT
1 ATGCGCCACTTC-ATCACTCTCCTATATACAAGTT-TTTCTAATGAAGAAATCGACCGTTGTAAT
*
3060170 CTC
64 CCC
* * **
3060173 ATGCGCCACTTCATCACTTTCCTATATACAAGTTTTTCTAATGAAGAAATCGATCGTTGTGGTCC
1 ATGCGCCACTTCATCACTCTCCTATATACAAGTTTTTCTAATGAAGAAATCGACCGTTGTAATCC
3060238 C
66 C
*
3060239 ATGCGCCATTTCCATCACTCTCCT-TAATACAAGT
1 ATGCGCCACTT-CATCACTCTCCTAT-ATACAAGT
3060273 ATTCTTAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 4 0.05
65 30 0.35
66 33 0.38
67 19 0.22
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (66 bp):
ATGCGCCACTTCATCACTCTCCTATATACAAGTTTTTCTAATGAAGAAATCGACCGTTGTAATCC
C
Found at i:3060370 original size:67 final size:67
Alignment explanation
Indices: 3060097--3060372 Score: 215
Period size: 67 Copynumber: 4.1 Consensus size: 67
3060087 AAGTCAACCA
* * * * * * *
3060097 TTGTGTTTTTATGCTCCACTTCTGTCACTCTCCTATATACAAGTTCTTTCAATGGAGAAAT-GAC
1 TTGTGGTTTCATGCGCCACTTCTATCACTCTCCCATATACAAGTTCTTCCAATAGAGAAATCGAC
3060161 CG
66 CG
** * * * * *
3060163 TTGTAATCTCATGCGCCACTTC-ATCACTTTCCTATATACAAGTTTTTCTAAT-GAAGAAATCGA
1 TTGTGGTTTCATGCGCCACTTCTATCACTCTCCCATATACAAGTTCTTCCAATAG-AGAAATCGA
*
3060226 TCG
65 CCG
** * * * *
3060229 TTGTGGTCCCATGCGCCATTTCCATCACTCT-CCTTAATACAAGTATTCTT--AATA-AGGAAGT
1 TTGTGGTTTCATGCGCCACTTCTATCACTCTCCCAT-ATACAAG--TTCTTCCAATAGA-GAAAT
*
3060290 CGACCA
62 CGACCG
* * * *
3060296 TTGTGGTTTTATGTGCCACTTCTGTCACTCTCCCATATACAAGTTCTTCCAATAGAGAAGTCGAC
1 TTGTGGTTTCATGCGCCACTTCTATCACTCTCCCATATACAAGTTCTTCCAATAGAGAAATCGAC
*
3060361 TG
66 CG
3060363 TTGTGGTTTC
1 TTGTGGTTTC
3060373 GTGTACTACT
Statistics
Matches: 165, Mismatches: 33, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
64 1 0.01
65 36 0.22
66 42 0.25
67 78 0.47
68 4 0.02
69 4 0.02
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (67 bp):
TTGTGGTTTCATGCGCCACTTCTATCACTCTCCCATATACAAGTTCTTCCAATAGAGAAATCGAC
CG
Found at i:3060422 original size:67 final size:67
Alignment explanation
Indices: 3060253--3060459 Score: 213
Period size: 67 Copynumber: 3.1 Consensus size: 67
3060243 GCCATTTCCA
* * * *
3060253 TCACTCTCCTTAATACAAGTATTCTTAATAAGGAAGTCGACCATTGTGGTTTTATGTGCCACTTC
1 TCACTCTCCCTAATACAAGTATTCTTAATAAAGAAGTCGACCATTGTGGTTTCATGTACCACTTC
3060318 TG
66 TG
* ** * *
3060320 TCACTCTCCC-ATATACAAG--TTCTTCCAATAGAGAAGTCGACTGTTGTGGTTTCGTGTACTAC
1 TCACTCTCCCTA-ATACAAGTATTCTT--AATAAAGAAGTCGACCATTGTGGTTTCATGTACCAC
*
3060382 TTTTG
63 TTCTG
* * * * * * *
3060387 TTACTCTCCCTAATATAAGTATTCTTAACAAAGAAGTTGACCATTGTGGTTTCATGCACTATTTC
1 TCACTCTCCCTAATACAAGTATTCTTAATAAAGAAGTCGACCATTGTGGTTTCATGTACCACTTC
3060452 TG
66 TG
3060454 TCACTC
1 TCACTC
3060460 CCACATACAA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
65 5 0.04
66 1 0.01
67 100 0.89
68 1 0.01
69 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (67 bp):
TCACTCTCCCTAATACAAGTATTCTTAATAAAGAAGTCGACCATTGTGGTTTCATGTACCACTTC
TG
Found at i:3060987 original size:15 final size:15
Alignment explanation
Indices: 3060955--3061029 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
3060945 ATACAAATCC
*
3060955 TTTGGTATAAGTATT
1 TTTGGTATAAGTACT
3060970 TTTGGTAT-AGATACT
1 TTTGGTATAAG-TACT
* *
3060985 TTTCGCATAAGTAC-
1 TTTGGTATAAGTACT
* *
3060999 TTTGGTACAAATA-T
1 TTTGGTATAAGTACT
* *
3061013 TTTGGCAAAAGTACT
1 TTTGGTATAAGTACT
3061028 TT
1 TT
3061030 GCCACAAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 21 0.46
15 23 0.50
16 2 0.04
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.44
Consensus pattern (15 bp):
TTTGGTATAAGTACT
Found at i:3061024 original size:28 final size:28
Alignment explanation
Indices: 3060970--3061062 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
3060960 TATAAGTATT
* * * *
3060970 TTTGGTATAGATACTTTTCGCATAAGTAC
1 TTTGGTACAAATA-TTTTGGCAAAAGTAC
3060999 TTTGGTACAAATATTTTGGCAAAAGTAC
1 TTTGGTACAAATATTTTGGCAAAAGTAC
** * * *
3061027 TTTGCCACAAATACTTTGACACAAAATAC
1 TTTGGTACAAATATTTTGGCA-AAAGTAC
3061056 TTTGGTA
1 TTTGGTA
3061063 GAAGTACTGT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 30 0.58
29 22 0.42
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (28 bp):
TTTGGTACAAATATTTTGGCAAAAGTAC
Found at i:3061030 original size:14 final size:15
Alignment explanation
Indices: 3060993--3061060 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 15
3060983 CTTTTCGCAT
*
3060993 AAGTACTTTGGTACA
1 AAGTACTTTGGCACA
*
3061008 AA-TATTTTGGCA-A
1 AAGTACTTTGGCACA
*
3061021 AAGTACTTTGCCACA
1 AAGTACTTTGGCACA
*
3061036 AA-TACTTTGACACA
1 AAGTACTTTGGCACA
*
3061050 AAATACTTTGG
1 AAGTACTTTGG
3061061 TAGAAGTACT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
13 3 0.07
14 29 0.66
15 12 0.27
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (15 bp):
AAGTACTTTGGCACA
Found at i:3061055 original size:15 final size:15
Alignment explanation
Indices: 3061018--3061059 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3061008 AATATTTTGG
*
3061018 CAAAAGTACTTTGCCA
1 CAAAA-TACTTTGACA
3061034 C-AAATACTTTGACA
1 CAAAATACTTTGACA
3061048 CAAAATACTTTG
1 CAAAATACTTTG
3061060 GTAGAAGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 10 0.42
15 13 0.54
16 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (15 bp):
CAAAATACTTTGACA
Found at i:3065236 original size:2 final size:2
Alignment explanation
Indices: 3065229--3065268 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3065219 ATTTATGTGT
*
3065229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3065269 AAAGGACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3065887 original size:2 final size:2
Alignment explanation
Indices: 3065872--3065906 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3065862 CTTTTTTACT
3065872 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3065907 TCGTATGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3066203 original size:23 final size:23
Alignment explanation
Indices: 3066175--3066239 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 23
3066165 TAAGATAAAC
3066175 TTAATTTAATTTTATATATTT-T
1 TTAATTTAATTTTATATATTTAT
* *
3066197 TATAATTTTTTATATTATATATTTAT
1 T-TAA--TTTAATTTTATATATTTAT
3066223 TTAATTTAATTATTATA
1 TTAATTTAATT-TTATA
3066240 CTTTATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.03
23 8 0.24
24 5 0.15
25 18 0.53
26 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAATTTAATTTTATATATTTAT
Found at i:3066538 original size:31 final size:30
Alignment explanation
Indices: 3066497--3066557 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
3066487 TGTCACTACT
3066497 AAAATCATATTTTATATTTATATAAATTTTAA
1 AAAATCATA--TTATATTTATATAAATTTTAA
3066529 AAAAT-ATATTATATTTATATAAATTTTAA
1 AAAATCATATTATATTTATATAAATTTTAA
3066558 GTTATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 21 0.72
31 3 0.10
32 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAATCATATTATATTTATATAAATTTTAA
Found at i:3069678 original size:6 final size:6
Alignment explanation
Indices: 3069667--3069695 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3069657 AAAAACCAGG
3069667 TTTAGA TTTAGA TTTAGA TTTAGA TTTAG
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAG
3069696 TCACTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TTTAGA
Found at i:3072888 original size:18 final size:16
Alignment explanation
Indices: 3072845--3072890 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3072835 AAAATATGAG
*
3072845 AATAAAAATTTATTTT
1 AATAAAATTTTATTTT
*
3072861 TATAAAATTTTATTGTT
1 AATAAAATTTTATT-TT
3072878 AATATAAATTTTA
1 AATA-AAATTTTA
3072891 CTAGGATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.48
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATAAAATTTTATTTT
Found at i:3072975 original size:13 final size:14
Alignment explanation
Indices: 3072911--3072990 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 14
3072901 TTATATTTTT
3072911 TATTATTAAATTTA
1 TATTATTAAATTTA
3072925 -A-TATT-AATTTGA
1 TATTATTAAATTT-A
3072937 TAAGTTA-TAAATTTTTAA
1 T-A-TTATTAAA--TTT-A
*
3072955 TTTTATTAAA-TTA
1 TATTATTAAATTTA
*
3072968 TATTATTAAATTTT
1 TATTATTAAATTTA
3072982 TATTATTAA
1 TATTATTAA
3072991 TAAATTAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
11 5 0.10
12 5 0.10
13 11 0.21
14 14 0.27
15 1 0.02
16 7 0.13
17 4 0.08
18 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATTAAATTTA
Found at i:3072980 original size:30 final size:31
Alignment explanation
Indices: 3072944--3073008 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
3072934 TGATAAGTTA
* *
3072944 TAAATTTTTAATT-TTATTAAATTATATTA-T
1 TAAATTTTT-ATTATTAATAAATTAAATTACT
3072974 TAAATTTTTATTATTAATAAATTAAATTACT
1 TAAATTTTTATTATTAATAAATTAAATTACT
3073005 TAAA
1 TAAA
3073009 CTGATTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 3 0.10
30 23 0.74
31 5 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TAAATTTTTATTATTAATAAATTAAATTACT
Found at i:3073136 original size:38 final size:35
Alignment explanation
Indices: 3073084--3073172 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 35
3073074 CTTATTAAAA
* * *
3073084 TATTATTTAATAAAAATATATATAAATTTTTTCATTATT
1 TATTAATTAATAAAAATA-ACATAAATTATTT-A--ATT
*
3073123 T-TTAATTAATAAAATTAACATAAATTATTTAATT
1 TATTAATTAATAAAAATAACATAAATTATTTAATT
3073157 TATTAA-TAATAAAAAT
1 TATTAATTAATAAAAAT
3073173 TTAATATCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 13 0.30
35 4 0.09
36 1 0.02
37 11 0.25
38 14 0.32
39 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (35 bp):
TATTAATTAATAAAAATAACATAAATTATTTAATT
Found at i:3073562 original size:16 final size:16
Alignment explanation
Indices: 3073541--3073582 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
3073531 AATAAAATTT
3073541 AAATTATTTATATTAA
1 AAATTATTTATATTAA
*
3073557 AAATTATACTTTTATTAA
1 AAATTAT--TTATATTAA
3073575 AAATTATT
1 AAATTATT
3073583 ATTAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 8 0.35
18 15 0.65
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTATTTATATTAA
Found at i:3074217 original size:34 final size:34
Alignment explanation
Indices: 3074171--3074240 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
3074161 TTAAATTTAT
*
3074171 TTAAATTAAATTATTAT-TTAAATAATAAAAA-AAA
1 TTAAATTAAATTATAATATT-AAT-ATAAAAATAAA
*
3074205 TTAAATTTAATTATAATATTAATATAAAAATAAA
1 TTAAATTAAATTATAATATTAATATAAAAATAAA
3074239 TT
1 TT
3074241 TTAAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 7 0.22
34 23 0.72
35 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TTAAATTAAATTATAATATTAATATAAAAATAAA
Found at i:3075909 original size:113 final size:104
Alignment explanation
Indices: 3075773--3076058 Score: 344
Period size: 113 Copynumber: 2.7 Consensus size: 104
3075763 ATATATTTTC
* * * *
3075773 TAGCTTTGTCAGTGCCTA-TTGCTCCTTATTTTTAATGAATTATAAAAATAATACATCAATTATA
1 TAGCTTTGTTAGTGCC-ACTTGCTCCTTATTTTTAATGAGTTTTAAAAATAATACATTAATTATA
* * *
3075837 CTTTTATTTTATAAATATAACCAACAACATTGTTTAAGATTTTTCAATAT
65 CTTTTA-TTT-T---TAT-----ACAACATTGTTCAACATTTGTCAATAT
*
3075887 TATC-TTGTTAGTGCCACTTGCTCCTTATTTTTAATGAGTTTTAAAAATAATACATTAATTATAC
1 TAGCTTTGTTAGTGCCACTTGCTCCTTATTTTTAATGAGTTTTAAAAATAATACATTAATTATAC
3075951 TTTTATTTTTATACAACATTGTTCAACATTTGTCAATAT
66 TTTTATTTTTATACAACATTGTTCAACATTTGTCAATAT
** * *
3075990 TAGCTTTGTTAACGCCACTTGCTCCTTAATTTTAGTGAGTTTTAAAAATAATACATTAATTATA-
1 TAGCTTTGTTAGTGCCACTTGCTCCTTATTTTTAATGAGTTTTAAAAATAATACATTAATTATAC
3076054 TTTTA
66 TTTTA
3076059 GTGCCACTTG
Statistics
Matches: 157, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
103 32 0.20
104 55 0.35
108 3 0.02
111 1 0.01
112 4 0.03
113 59 0.38
114 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (104 bp):
TAGCTTTGTTAGTGCCACTTGCTCCTTATTTTTAATGAGTTTTAAAAATAATACATTAATTATAC
TTTTATTTTTATACAACATTGTTCAACATTTGTCAATAT
Found at i:3076039 original size:104 final size:102
Alignment explanation
Indices: 3075860--3076058 Score: 308
Period size: 104 Copynumber: 1.9 Consensus size: 102
3075850 AATATAACCA
* * * * ** *
3075860 ACAACATTGTTTAAGATTTTTCAATATTATCTTGTTAGTGCCACTTGCTCCTTATTTTTAATGAG
1 ACAACATTGTTCAACATTTGTCAATATTAGCTTGTTAACGCCACTTGCTCCTTAATTTTAATGAG
3075925 TTTTAAAAATAATACATTAATTATACTTTTATTTTTAT
66 TTTTAAAAATAATACATTAATTATA-TTTTATTTTTAT
*
3075963 ACAACATTGTTCAACATTTGTCAATATTAGCTTTGTTAACGCCACTTGCTCCTTAATTTTAGTGA
1 ACAACATTGTTCAACATTTGTCAATATTAGC-TTGTTAACGCCACTTGCTCCTTAATTTTAATGA
3076028 GTTTTAAAAATAATACATTAATTATATTTTA
65 GTTTTAAAAATAATACATTAATTATATTTTA
3076059 GTGCCACTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 32 0.37
104 55 0.63
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (102 bp):
ACAACATTGTTCAACATTTGTCAATATTAGCTTGTTAACGCCACTTGCTCCTTAATTTTAATGAG
TTTTAAAAATAATACATTAATTATATTTTATTTTTAT
Found at i:3076068 original size:58 final size:59
Alignment explanation
Indices: 3076003--3076117 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 59
3075993 CTTTGTTAAC
* * *
3076003 GCCACTTGCTCCTTAATTTTAGTGAGTTTTAAAAATAATACATTAATTATA-TTTTAGT
1 GCCACTTGCTCCTTAATTTTAATGAGCTTTAAAAATAACACATTAATTATACTTTTAGT
*
3076061 GCCACTTGCTCCTTATTTTTAATGAGCTTTAAAAATAACACATTAATTATACTTTTA
1 GCCACTTGCTCCTTAATTTTAATGAGCTTTAAAAATAACACATTAATTATACTTTTA
3076118 TTTTTATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 47 0.90
59 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (59 bp):
GCCACTTGCTCCTTAATTTTAATGAGCTTTAAAAATAACACATTAATTATACTTTTAGT
Found at i:3077498 original size:19 final size:19
Alignment explanation
Indices: 3077474--3077510 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3077464 AATATAACAT
3077474 AAAAT-ATTTATATTATAAG
1 AAAATAATTTAT-TTATAAG
3077493 AAAATAATTTATTTATAA
1 AAAATAATTTATTTATAA
3077511 AAATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
AAAATAATTTATTTATAAG
Found at i:3078181 original size:2 final size:2
Alignment explanation
Indices: 3078176--3078204 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3078166 TATATATATA
3078176 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3078205 ATTCTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3078536 original size:22 final size:22
Alignment explanation
Indices: 3078506--3078551 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3078496 ATTATTATTT
* * *
3078506 ATATTTAAATGTAATTATAAAA
1 ATATATAAATATAAATATAAAA
*
3078528 ATATATAAATATAAATATATAA
1 ATATATAAATATAAATATAAAA
3078550 AT
1 AT
3078552 TATTTTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATAAATATAAATATAAAA
Found at i:3080597 original size:7 final size:7
Alignment explanation
Indices: 3080585--3080633 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
3080575 GATGTTAAAT
3080585 TAAAAAA
1 TAAAAAA
3080592 TAAAAATAA
1 T-AAAA-AA
3080601 TTAAAAAAA
1 -T-AAAAAA
*
3080610 TTAAAAA
1 TAAAAAA
3080617 TAAAAAA
1 TAAAAAA
3080624 TAAAAAA
1 TAAAAAA
3080631 TAA
1 TAA
3080634 TATAAACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 22 0.59
8 5 0.14
9 4 0.11
10 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAAAAA
Found at i:3080614 original size:19 final size:17
Alignment explanation
Indices: 3080582--3080644 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
3080572 TTTGATGTTA
3080582 AATTAAAAAATAAAAAT
1 AATTAAAAAATAAAAAT
*
3080599 AATTAAAAAA-ATTAAA-
1 AATTAAAAAATA-AAAAT
3080615 AA-TAAAAAATAAAAAAT
1 AATTAAAAAAT-AAAAAT
*
3080632 AATATAAACAATA
1 AAT-TAAAAAATA
3080645 TAGACGTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
15 7 0.19
16 6 0.16
17 16 0.43
18 1 0.03
19 7 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
AATTAAAAAATAAAAAT
Found at i:3081328 original size:10 final size:10
Alignment explanation
Indices: 3081313--3081343 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3081303 CCCCGAGAGT
3081313 TATGTATATA
1 TATGTATATA
3081323 TATGTATATA
1 TATGTATATA
*
3081333 TATATATATA
1 TATGTATATA
3081343 T
1 T
3081344 GTGGGTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (10 bp):
TATGTATATA
Found at i:3082866 original size:20 final size:20
Alignment explanation
Indices: 3082837--3082942 Score: 113
Period size: 20 Copynumber: 5.3 Consensus size: 20
3082827 TTCTACGATT
* **
3082837 TGTATTGATACATGAGTAAA
1 TGTATCGATACATGACCAAA
**
3082857 TGTATCGATACATGAGTAAA
1 TGTATCGATACATGACCAAA
**
3082877 TGTATCGATACATTTCCAAA
1 TGTATCGATACATGACCAAA
**
3082897 TGTATCGATACATTCCCAAA
1 TGTATCGATACATGACCAAA
**
3082917 TGTATCGATACATTCCCAAA
1 TGTATCGATACATGACCAAA
3082937 TGTATC
1 TGTATC
3082943 AATATAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:3082898 original size:40 final size:40
Alignment explanation
Indices: 3082854--3082942 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
3082844 ATACATGAGT
** *
3082854 AAATGTATCGATACATGAGTAAATGTATCGATACATTTCC
1 AAATGTATCGATACATGACCAAATGTATCGATACATTCCC
**
3082894 AAATGTATCGATACATTCCCAAATGTATCGATACATTCCC
1 AAATGTATCGATACATGACCAAATGTATCGATACATTCCC
3082934 AAATGTATC
1 AAATGTATC
3082943 AATATAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (40 bp):
AAATGTATCGATACATGACCAAATGTATCGATACATTCCC
Found at i:3086429 original size:20 final size:20
Alignment explanation
Indices: 3086377--3086431 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
3086367 TATGCATTTA
3086377 GATGAAAAGATGCATTAGTTG
1 GATGAAAA-ATGCATTAGTTG
3086398 GATGAAACAATGCACTT-GTT-
1 GATGAAA-AATGCA-TTAGTTG
3086418 GATGGAAAAATGCA
1 GAT-GAAAAATGCA
3086432 ACTTTTAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 9 0.29
21 19 0.61
22 3 0.10
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (20 bp):
GATGAAAAATGCATTAGTTG
Found at i:3090711 original size:17 final size:17
Alignment explanation
Indices: 3090691--3090741 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
3090681 ATATTTCCTG
3090691 AAAAGATGCATTTAGAT
1 AAAAGATGCATTTAGAT
*
3090708 AAAAAATGCATTGGTTAGAT
1 AAAAGATGCA-T--TTAGAT
3090728 AAAATGATGCATTT
1 AAAA-GATGCATTT
3090742 GTTGGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 11 0.39
21 5 0.18
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (17 bp):
AAAAGATGCATTTAGAT
Found at i:3090739 original size:21 final size:20
Alignment explanation
Indices: 3090702--3090760 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
3090692 AAAGATGCAT
3090702 TTAGATAAAAAATGCATTGG
1 TTAGATAAAAAATGCATTGG
* *
3090722 TTAGATAAAATGATGCATTTG
1 TTAGATAAAA-AATGCATTGG
*
3090743 TTGGATGAAAAAAATGCA
1 TTAGAT--AAAAAATGCA
3090761 ACTTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.31
21 13 0.41
22 5 0.16
23 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAGATAAAAAATGCATTGG
Done.