Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 39
Found at i:3969535 original size:20 final size:20
Alignment explanation
Indices: 3969493--3969548 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3969483 GAAAATGAAA
* ** *
3969493 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAATTTGACT
3969513 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
3969533 ATCGCAACGCGAATTT
1 ATCGCAACGCGAATTT
3969549 TTTCGTTGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:3969895 original size:22 final size:22
Alignment explanation
Indices: 3969868--3969947 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
3969858 GATGGAGATA
*
3969868 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
3969890 GACGGATTTCGCCGAAAATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3969912 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3969934 GACGGATGTCGCCG
1 GACGGATTTCGCCG
3969948 TAGAGAGTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3970147 original size:21 final size:20
Alignment explanation
Indices: 3970089--3970194 Score: 124
Period size: 20 Copynumber: 5.2 Consensus size: 20
3970079 AAATCGCAAC
**
3970089 GCGATAGTCAGAATATCGTT
1 GCGATAGTCAGAATCGCGTT
3970109 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
3970129 GCGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAGAATCGCGTT
* * *
3970150 TCGATAGTCCGAATCACGTT
1 GCGATAGTCAGAATCGCGTT
3970170 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
3970190 GCGAT
1 GCGAT
3970195 CACGTTTTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 53 0.75
21 14 0.20
22 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:3970176 original size:61 final size:61
Alignment explanation
Indices: 3970089--3970215 Score: 211
Period size: 61 Copynumber: 2.1 Consensus size: 61
3970079 AAATCGCAAC
3970089 GCGATAGTCAGAATATCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTT
1 GCGATAGTCAGAATATCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTT
* * *
3970150 TCGATAGTCCGAATCA-CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTTTTATCGCGTT
1 GCGATAGTCAGAAT-ATCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTT
3970211 GCGAT
1 GCGAT
3970216 TTACATATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 60 0.98
62 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (61 bp):
GCGATAGTCAGAATATCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTT
Found at i:3970236 original size:20 final size:20
Alignment explanation
Indices: 3970211--3970256 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3970201 TTATCGCGTT
3970211 GCGATTTACATATTCACATA
1 GCGATTTACATATTCACATA
* *
3970231 GCGATTTACATATTCGCATT
1 GCGATTTACATATTCACATA
3970251 GCGATT
1 GCGATT
3970257 ATCTAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
GCGATTTACATATTCACATA
Found at i:3970356 original size:20 final size:19
Alignment explanation
Indices: 3970330--3970376 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3970320 TGAAAACTGA
*
3970330 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
3970350 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
3970369 ATTGCGAT
1 ATTGCGAT
3970377 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:3970366 original size:19 final size:19
Alignment explanation
Indices: 3970342--3970378 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3970332 TGCGATAATG
*
3970342 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
3970361 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
3970379 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:3970639 original size:11 final size:11
Alignment explanation
Indices: 3970623--3970660 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3970613 GATTTATTTC
3970623 TTTTTA-TCTAT
1 TTTTTATTCT-T
3970634 TTTTTATTCTT
1 TTTTTATTCTT
3970645 TTTTTATTCTT
1 TTTTTATTCTT
3970656 TTTTT
1 TTTTT
3970661 TTGATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 23 0.88
12 3 0.12
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTCTT
Found at i:3970652 original size:18 final size:17
Alignment explanation
Indices: 3970631--3970753 Score: 56
Period size: 18 Copynumber: 6.6 Consensus size: 17
3970621 TCTTTTTATC
3970631 TATTTTTTATTCTTTTTT
1 TATTTTTTATT-TTTTTT
*
3970649 TATTCTTTT-TTTTTGATT
1 TATT-TTTTATTTTT-TTT
3970667 TATTTATTTAATTTTTTTATT
1 TATTT-TTT-A-TTTTTT-TT
*
3970688 TAATTTAATTT-TTATTGTTT
1 T-ATTT--TTTATT-TTTTTT
*
3970708 TATTTATTTATTTTCTTGT
1 TATTT-TTTATTTT-TTTT
*
3970727 TA-TTTTTA-TTTTTCT
1 TATTTTTTATTTTTTTT
3970742 TATTGTTTTATT
1 TATT-TTTTATT
3970754 CTTATGTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 30
0.70 0.05 0.25
Matches are distributed among these distances:
15 5 0.06
16 4 0.05
17 13 0.15
18 24 0.29
19 14 0.17
20 5 0.06
21 11 0.13
22 4 0.05
23 4 0.05
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTTATTTTTTTT
Found at i:3970680 original size:5 final size:4
Alignment explanation
Indices: 3970625--3970720 Score: 58
Period size: 4 Copynumber: 23.8 Consensus size: 4
3970615 TTTATTTCTT
* * *
3970625 TTTA TCTA TTT- TTTA TTCT- TTT- TTTA TTCTT TTTT TTTGA TTTA TTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TT-TA TTTA TTT-A TTTA TTTA
* *
3970673 TTTAA TTTT TTTA TTTAA TTTA ATT- TTTA TTGT- TTTA TTTA TTTA TTT
1 TTT-A TTTA TTTA TTT-A TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTT
3970721 TCTTGTTATT
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
3 10 0.14
4 48 0.65
5 16 0.22
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3970680 original size:13 final size:12
Alignment explanation
Indices: 3970625--3970720 Score: 58
Period size: 13 Copynumber: 7.9 Consensus size: 12
3970615 TTTATTTCTT
*
3970625 TTTATCTATTT-
1 TTTATTTATTTA
3970636 TTTATTCT-TTT-
1 TTTATT-TATTTA
* *
3970647 TTTATTCTTTTTT
1 TTTATT-TATTTA
3970660 TTTGATTTATTTA
1 TTT-ATTTATTTA
*
3970673 TTTAATTTTTTTA
1 TTT-ATTTATTTA
*
3970686 TTTAATTTAATT-
1 TTT-ATTTATTTA
3970698 TTTATTGT-TTTA
1 TTTATT-TATTTA
3970710 TTTATTTATTT
1 TTTATTTATTT
3970721 TCTTGTTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
11 22 0.31
12 17 0.24
13 28 0.40
14 3 0.04
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:3985127 original size:21 final size:21
Alignment explanation
Indices: 3985103--3985142 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3985093 TGAAGCAAGG
* *
3985103 GAAGCCGAGAGAGCAGCAGCA
1 GAAGCAGAGAGAGAAGCAGCA
3985124 GAAGCAGAGAGAGAAGCAG
1 GAAGCAGAGAGAGAAGCAG
3985143 TGGCAGCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.40, T:0.00
Consensus pattern (21 bp):
GAAGCAGAGAGAGAAGCAGCA
Found at i:3985559 original size:44 final size:41
Alignment explanation
Indices: 3985510--3985595 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 41
3985500 AAATGCCGTA
* *
3985510 ATATACCATACATTTAACGGCTTTTGTATCATAAAAACGCCACT
1 ATATACCA-ACATTTAACAGCGTTTGTAT--TAAAAACGCCACT
** *
3985554 ATATACCAATTTTTAGCAGCGTTTGTATTAAAAACGCCACT
1 ATATACCAACATTTAACAGCGTTTGTATTAAAAACGCCACT
3985595 A
1 A
3985596 AACCTCAACG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 14 0.38
43 15 0.41
44 8 0.22
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (41 bp):
ATATACCAACATTTAACAGCGTTTGTATTAAAAACGCCACT
Found at i:3985675 original size:86 final size:86
Alignment explanation
Indices: 3985584--3985775 Score: 201
Period size: 86 Copynumber: 2.2 Consensus size: 86
3985574 GTTTGTATTA
* ** * * * *
3985584 AAAACGCCACTAAACCTCAACGCCTATTACGGCGTTT-TAGCTA-AAAACGTCGCCAAATC-TCA
1 AAAACGCCACTAAACATCAAAACCTACTACGGCGTTTGT-G-AAGAAAACGCCACCAAA-CATCA
* * *
3985646 ACATATATTGCGGCGTTTGTGAAG
63 AAACATACTGCGGCGTTTGTGAAG
* * *
3985670 AAAACGCCGCTAAACATCAAAACCTACTGCGGCGTTTGTGAAGAAAACGCCACTAAACATCAAAA
1 AAAACGCCACTAAACATCAAAACCTACTACGGCGTTTGTGAAGAAAACGCCACCAAACATCAAAA
*
3985735 CCTACTGCGGCGTTTGTGAAG
66 CATACTGCGGCGTTTGTGAAG
*
3985756 AAAACGCCACTAAATATCAA
1 AAAACGCCACTAAACATCAA
3985776 CAACTTTGGT
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
85 2 0.02
86 84 0.97
87 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (86 bp):
AAAACGCCACTAAACATCAAAACCTACTACGGCGTTTGTGAAGAAAACGCCACCAAACATCAAAA
CATACTGCGGCGTTTGTGAAG
Found at i:3985794 original size:43 final size:43
Alignment explanation
Indices: 3985654--3985775 Score: 226
Period size: 43 Copynumber: 2.8 Consensus size: 43
3985644 CAACATATAT
*
3985654 TGCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAAAACCTAC
1 TGCGGCGTTTGTGAAGAAAACGCCACTAAACATCAAAACCTAC
3985697 TGCGGCGTTTGTGAAGAAAACGCCACTAAACATCAAAACCTAC
1 TGCGGCGTTTGTGAAGAAAACGCCACTAAACATCAAAACCTAC
*
3985740 TGCGGCGTTTGTGAAGAAAACGCCACTAAATATCAA
1 TGCGGCGTTTGTGAAGAAAACGCCACTAAACATCAA
3985776 CAACTTTGGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (43 bp):
TGCGGCGTTTGTGAAGAAAACGCCACTAAACATCAAAACCTAC
Found at i:3991780 original size:38 final size:38
Alignment explanation
Indices: 3991738--3991823 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 38
3991728 ATTCGTTTAT
* *
3991738 AAGCTATTTTATCGACT-TGTTCGTTTATGTTCATGAAC
1 AAGCTAGTTTATCGACTCT-TTCATTTATGTTCATGAAC
* *
3991776 AAGCTCGTTTATTGACTCTTTCATTTATGTTCATGAAC
1 AAGCTAGTTTATCGACTCTTTCATTTATGTTCATGAAC
*
3991814 AAGCTTGTTT
1 AAGCTAGTTT
3991824 GTAAGATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 41 0.98
39 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.45
Consensus pattern (38 bp):
AAGCTAGTTTATCGACTCTTTCATTTATGTTCATGAAC
Found at i:3992120 original size:23 final size:24
Alignment explanation
Indices: 3992076--3992127 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3992066 CGAATATTAA
*
3992076 ATGAACATATAAATAAAAATATTC
1 ATGAACATATAAACAAAAATATTC
*
3992100 ATGAACAT-TAAACAAATATATTC
1 ATGAACATATAAACAAAAATATTC
*
3992123 GTGAA
1 ATGAA
3992128 TGTTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (24 bp):
ATGAACATATAAACAAAAATATTC
Found at i:3992920 original size:15 final size:15
Alignment explanation
Indices: 3992900--3992981 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
3992890 TTTTAGAAAA
3992900 TGAATTACTGGAATT
1 TGAATTACTGGAATT
3992915 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
3992930 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
3992945 TGAATTACTGAAATT
1 TGAATTACTGGAATT
**
3992960 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
3992974 TGAATTAC
1 TGAATTAC
3992982 ATTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.19
15 47 0.81
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:3992936 original size:30 final size:30
Alignment explanation
Indices: 3992900--3992981 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
3992890 TTTTAGAAAA
** *
3992900 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
3992930 TGAATTACTGGAAAATGAATTACTGAAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
3992960 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
3992982 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:3992960 original size:45 final size:44
Alignment explanation
Indices: 3992895--3992981 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
3992885 TGGTTTTTTA
* **
3992895 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGAAATTTGAATT-CTGGAAAATGAATTACTG
3992940 GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTAC
3992982 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTACTG
Found at i:3992987 original size:20 final size:20
Alignment explanation
Indices: 3992964--3993013 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3992954 GAAATTTGAA
3992964 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3992984 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3993004 TTCTGGAAAA
1 TTCTGGAAAA
3993014 CATCTGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:3993236 original size:29 final size:27
Alignment explanation
Indices: 3993180--3993245 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
3993170 TTTACTAAAA
* *
3993180 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
3993208 TCATTATTAAATATATAAAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAAA-TTAT
3993237 TATATATTA
1 TAT-TATTA
3993246 TTAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:3993287 original size:23 final size:23
Alignment explanation
Indices: 3993239--3993350 Score: 65
Period size: 23 Copynumber: 4.7 Consensus size: 23
3993229 AAATTTATTA
*
3993239 TATATTATTAATAA-ATAATATCT
1 TATATTATT-ATAATATAATATAT
3993262 TATATTATTATAATATAAT-TGAT
1 TATATTATTATAATATAATAT-AT
*
3993285 TATTTTA-TATAATATTAAAAATATAATAT
1 TATATTATTATAATA-T----A-AT-ATAT
*
3993314 TATATTATTATAATATTAATA-AA
1 TATATTATTATAATA-TAATATAT
3993337 TATATT-TTA-AATAT
1 TATATTATTATAATAT
3993351 TTTAATAATT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 15 0.20
23 29 0.39
24 1 0.01
25 2 0.03
26 1 0.01
27 1 0.01
28 2 0.03
29 8 0.11
30 10 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
TATATTATTATAATATAATATAT
Found at i:3993309 original size:31 final size:31
Alignment explanation
Indices: 3993263--3993340 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
3993253 ATAATATCTT
* *
3993263 ATATTATTATAATATAATTGATTATTTTA-TATA
1 ATATTAATA-AATATAA-T-ATTATATTATTATA
3993296 ATATTAA-AAATATAATATTATATTATTATA
1 ATATTAATAAATATAATATTATATTATTATA
3993326 ATATTAATAAATATA
1 ATATTAATAAATATA
3993341 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 8 0.20
30 12 0.29
31 14 0.34
32 1 0.02
33 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATATTAATAAATATAATATTATATTATTATA
Found at i:3993364 original size:30 final size:31
Alignment explanation
Indices: 3993292--3993364 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
3993282 GATTATTTTA
*
3993292 TATAATATTAA-AAATATAATATTATATTAT
1 TATAATATTAATAAATATAATATTATAATAT
*
3993322 TATAATATTAATAAATAT-ATTTTA-AATAT
1 TATAATATTAATAAATATAATATTATAATAT
*
3993351 TTTAATAATTAATA
1 TATAAT-ATTAATA
3993365 TTTTGATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 9 0.24
30 23 0.61
31 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TATAATATTAATAAATATAATATTATAATAT
Found at i:3993364 original size:52 final size:52
Alignment explanation
Indices: 3993194--3993366 Score: 165
Period size: 53 Copynumber: 3.2 Consensus size: 52
3993184 ATTGAAATAT
* *
3993194 ATAAATAATATTATTCATTATTA-AATATATAAAAAAAAT-TTATTATATATTATTA
1 ATAAATAATATTA-T-ATTATTATAATAT-TAATAAATATATT-TTATATATT-TTA
** *
3993249 ATAAATAATATCTTATATTATTATAATA-TAATTGAT-TATTTTATATAATATTA
1 ATAAATAATA--TTATATTATTATAATATTAATAAATATATTTTATAT-ATTTTA
* *
3993302 AAAATATAATATTATATTATTATAATATTAATAAATATATTTTAAATATTTTA
1 ATAA-ATAATATTATATTATTATAATATTAATAAATATATTTTATATATTTTA
*
3993355 ATAATTAATATT
1 ATAAATAATATT
3993367 TTGATGAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
52 23 0.23
53 27 0.28
54 23 0.23
55 17 0.17
56 5 0.05
57 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
ATAAATAATATTATATTATTATAATATTAATAAATATATTTTATATATTTTA
Found at i:3993602 original size:42 final size:42
Alignment explanation
Indices: 3993543--3993659 Score: 216
Period size: 42 Copynumber: 2.8 Consensus size: 42
3993533 AATTACATTT
*
3993543 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
3993585 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
*
3993627 CGGAAAACGAATTACGTGAAACAAACACTGGAA
1 CGGAAAACGAATTACGTGAAACAAACACGGGAA
3993660 TTCGGGAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
Found at i:3998129 original size:54 final size:54
Alignment explanation
Indices: 3998071--3998599 Score: 731
Period size: 54 Copynumber: 9.8 Consensus size: 54
3998061 CTATACTGTC
* *
3998071 GTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCATGTACGGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* * *
3998125 GTTCATCAACTCATGATGAATTTTGTGAGTTGCACACATAGTGCTTGTACGGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* *
3998179 ATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCTTGTACGGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* * * * * *
3998233 ATTCATCAACTAATGATGAATTTTGTGGGTTGCACACGTAGTGCCTGTACTGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
*
3998287 GTTCATCAACTCATGATGAATT-TCGTGGGTTGTACACATAGTGTC-TG-ACGGTT
1 GTTCATCAACTCATGATGAATTCT-GTGGGTTGCACACATAGTG-CATGTACGGTT
* *
3998340 GTTCATCAACTCATGATGAATTATGTGGGTTGCACACATAGTGCTTGTACGGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* ** * *
3998394 GTTCATAAACTCATGATGAATTCCATGAGTTGCACACATAGTTCATGTACGGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* * * *
3998448 GTTCATAAACTTATGATGAATTATGTGGGTTGCACACATAGTGCCTGTACGGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* * *
3998502 GTTCATCAACTCATGATGAAATCCGTGGGTTGCACACATAGTGCATGTACAGTT
1 GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
* * *
3998556 GTTCATCAACACATGATGAATTCCGTGGGTTTGCACACTTAGTG
1 GTTCATCAACTCATGATGAATTCTGTGGG-TTGCACACATAGTG
3998600 TCTATTTGGT
Statistics
Matches: 428, Mismatches: 41, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
52 1 0.00
53 48 0.11
54 365 0.85
55 14 0.03
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (54 bp):
GTTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAGTGCATGTACGGTT
Found at i:3998559 original size:269 final size:270
Alignment explanation
Indices: 3998071--3998602 Score: 814
Period size: 269 Copynumber: 2.0 Consensus size: 270
3998061 CTATACTGTC
* *
3998071 GTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATCAACT
1 GTTCATCAACACATGATGAATTATGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATAAACT
*** * *
3998136 CATGATGAATTTTGTGAGTTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATT
66 CATGATGAATTCCATGAGTTGCACACATAGTGCATGTACGGTTATTCATAAACTCATGATGAATT
* * * **
3998201 CTGTGGGTTGCACACATAGTGCTTGTACGGTTATTCATCAACTAATGATGAATTTTGTGGGTTGC
131 ATGTGGGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAAATCCGTGGGTTGC
* * * * * *
3998266 ACACGTAGTGCCTGTACTGTTGTTCATCAACTCATGATGAATTTCGTGGG-TTGTACACATAGTG
196 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTTTGCACACATAGTG
3998330 TCTGACGGTT
261 TCTGACGGTT
* * *
3998340 GTTCATCAACTCATGATGAATTATGTGGGTTGCACACATAGTGCTTGTACGGTTGTTCATAAACT
1 GTTCATCAACACATGATGAATTATGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATAAACT
* * *
3998405 CATGATGAATTCCATGAGTTGCACACATAGTTCATGTACGGTTGTTCATAAACTTATGATGAATT
66 CATGATGAATTCCATGAGTTGCACACATAGTGCATGTACGGTTATTCATAAACTCATGATGAATT
* *
3998470 ATGTGGGTTGCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAAATCCGTGGGTTGC
131 ATGTGGGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAAATCCGTGGGTTGC
*
3998535 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTTTGCACACTTAGTG
196 ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTTTGCACACATAGTG
3998600 TCT
261 TCT
3998603 ATTTGGTAAT
Statistics
Matches: 235, Mismatches: 27, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
269 220 0.94
270 15 0.06
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (270 bp):
GTTCATCAACACATGATGAATTATGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATAAACT
CATGATGAATTCCATGAGTTGCACACATAGTGCATGTACGGTTATTCATAAACTCATGATGAATT
ATGTGGGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTAATGATGAAATCCGTGGGTTGC
ACACATAGTGCATGTACAGTTGTTCATCAACACATGATGAATTCCGTGGGTTTGCACACATAGTG
TCTGACGGTT
Found at i:3999349 original size:22 final size:22
Alignment explanation
Indices: 3999324--3999365 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3999314 TTATTATTTA
* *
3999324 TCAAAAATAGAAAAGAAAAATT
1 TCAAAAACAAAAAAGAAAAATT
3999346 TCAAAAACAAAAAAGAAAAA
1 TCAAAAACAAAAAAGAAAAA
3999366 AAAAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (22 bp):
TCAAAAACAAAAAAGAAAAATT
Found at i:3999369 original size:12 final size:13
Alignment explanation
Indices: 3999348--3999377 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3999338 GAAAAATTTC
3999348 AAAAACAAAAAAG
1 AAAAACAAAAAAG
3999361 AAAAA-AAAAAAG
1 AAAAACAAAAAAG
3999373 AAAAA
1 AAAAA
3999378 GTTGCCCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAG
Found at i:4000699 original size:2 final size:2
Alignment explanation
Indices: 4000687--4000730 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
4000677 AAGTGACTTA
*
4000687 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4000729 AT
1 AT
4000731 TTACTCTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4007530 original size:22 final size:20
Alignment explanation
Indices: 4007471--4007573 Score: 95
Period size: 22 Copynumber: 4.8 Consensus size: 20
4007461 GAAGAGATGA
4007471 AAAAATGAAAAGAAAAA-AG
1 AAAAATGAAAAGAAAAATAG
4007490 AGAAAATGGAAAATGGAAAATGATAG
1 A-AAAAT-GAAAA--GAAAA--ATAG
4007516 AAAAATGAAAAGAAAAAATGAG
1 AAAAATGAAAAG-AAAAAT-AG
4007538 AAAAATGAAAAG-AAAA-AG
1 AAAAATGAAAAGAAAAATAG
*
4007556 AAAAAAGAAAAAGAAAAA
1 AAAAATG-AAAAGAAAAA
4007574 GAAAGATAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 21
0.77 0.01 0.22
Matches are distributed among these distances:
18 8 0.11
19 6 0.08
20 13 0.18
21 7 0.10
22 15 0.21
23 9 0.12
24 5 0.07
25 6 0.08
26 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAAATGAAAAGAAAAATAG
Found at i:4007554 original size:6 final size:6
Alignment explanation
Indices: 4007536--4007577 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
4007526 AGAAAAAATG
4007536 AGAAAA ATG-AAA AGAAAA AGAAAAA AGAAAA AGAAAA AGAAA
1 AGAAAA A-GAAAA AGAAAA AG-AAAA AGAAAA AGAAAA AGAAA
4007578 GATAAAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 25 0.76
7 7 0.21
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:4007568 original size:13 final size:13
Alignment explanation
Indices: 4007514--4007577 Score: 62
Period size: 12 Copynumber: 4.9 Consensus size: 13
4007504 GGAAAATGAT
*
4007514 AGAAAAATG-AAA
1 AGAAAAAAGAAAA
4007526 AGAAAAAATGAGAAA
1 AGAAAAAA-GA-AAA
*
4007541 A-ATGAAAAGAAAA
1 AGA-AAAAAGAAAA
4007554 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
4007567 AG-AAAAAGAAA
1 AGAAAAAAGAAA
4007578 GATAAAGAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 16 0.36
13 16 0.36
14 4 0.09
15 8 0.18
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:4007584 original size:10 final size:10
Alignment explanation
Indices: 4007514--4007585 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 10
4007504 GGAAAATGAT
4007514 AGAAAAATGAAA
1 AGAAAAA-G-AA
*
4007526 AGAAAAA-ATG
1 AGAAAAAGA-A
4007536 AGAAAAATGAAA
1 AGAAAAA-G-AA
4007548 AGAAAAAGAA
1 AGAAAAAGAA
4007558 A-AAAGAA-AA
1 AGAAA-AAGAA
4007567 AGAAAAAGAA
1 AGAAAAAGAA
*
4007577 AGATAAAGA
1 AGAAAAAGA
4007586 GAAAATAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
9 9 0.18
10 25 0.50
11 1 0.02
12 14 0.28
13 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:4007967 original size:27 final size:27
Alignment explanation
Indices: 4007929--4007981 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
4007919 CACAATTTTG
4007929 GAGATCCTTTTGACAAAAGCTACACTC
1 GAGATCCTTTTGACAAAAGCTACACTC
*
4007956 GAGATCCTTTTGACAGAAGCTACACT
1 GAGATCCTTTTGACAAAAGCTACACT
4007982 TGAGTCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (27 bp):
GAGATCCTTTTGACAAAAGCTACACTC
Found at i:4008942 original size:37 final size:36
Alignment explanation
Indices: 4008886--4008971 Score: 136
Period size: 37 Copynumber: 2.3 Consensus size: 36
4008876 TTTGACCTTC
4008886 GAAGCAAATCAAACTTAAGCCTTCACAGAAGAGTAGT
1 GAAGCAAATC-AACTTAAGCCTTCACAGAAGAGTAGT
*
4008923 GAAGCAAATCATCTATAAGCCTTCACAGAAGAGTAGT
1 GAAGCAAATCAACT-TAAGCCTTCACAGAAGAGTAGT
*
4008960 GAAACAAATCAA
1 GAAGCAAATCAA
4008972 GATTGTTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 3 0.07
37 42 0.93
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (36 bp):
GAAGCAAATCAACTTAAGCCTTCACAGAAGAGTAGT
Found at i:4009076 original size:55 final size:55
Alignment explanation
Indices: 4008970--4009706 Score: 651
Period size: 55 Copynumber: 13.6 Consensus size: 55
4008960 GAAACAAATC
* * * * * * * **
4008970 AAGATTGTTTGAGTTCTATACTCTCTGAAGGAACAAGGAGAGGACAAGTTTT-ATG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCA-G
* * * *
4009025 AAGATTGTTCGAGTTATATACTCCCTGAACGAATAGGGAGCGGACCTGTTTTGCCG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTT-CAG
* * * *
4009081 AAGATTGTTCGAGTTTTGTACTCCCTGAATGAATAGGGAGCAGACCCAT-TTTT-ATG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGC-GAACC-TGTTTTCA-G
* *
4009137 -A-A------GA---CTATACTCCCTGAAAGAATAGGGAGTGAA-CTCATTTTCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCT-GTTTTCAG
* * ** *
4009181 AAGATTGTTCGAGTTCTATACTCCCTGAAATAATAGGGAGCGGACCCATTTTCCG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAG
* * *
4009236 AAGATTGTTCAAGTTCTATACTCCCTGAAAGAATAGGGAGTGAACCCGTTTTCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAG
* **
4009291 AAGATTGTTCGAGTTTTATACTCCCTGAAAGAATAAAGAGCGAAACC-GTTTTCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCG-AACCTGTTTTCAG
* * * *
4009346 AAGATTGTTCGAGTTCTATACTCCATGAAAGAATATGGAGC-AGACATGTTTTCAT
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGA-ACCTGTTTTCAG
* * * **
4009401 AAGATTGTTCGAGTTTTATAATCCCTGAAAAAATAGGGAGCGAACCCATTTTCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAG
* * * *
4009456 AAGATTGTTCTAGTTCTATACTCCTTGAAAGAATAGGGAGCGAACCCGTTTTCGG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAG
* * * ** *
4009511 AAAATTGTTCGA-TTTTATACTCCCTGAAAAAATAAAGAGCGAA-CTCATTTTCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCT-GTTTTCAG
* * *
4009565 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACATGTTTTCAA
1 AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAG
* * ** * *
4009620 AAGATT-TCTCGAGTTTTAT-CTCCCTGAAAGAAGAGTGGAGC-ATACCCATCTTCAA
1 AAGATTGT-TCGAGTTCTATACTCCCTGAAAGAATAG-GGAGCGA-ACCTGTTTTCAG
4009675 AAGATT-TCTCGAG-TCTTATA-TCCCTGAAAGAA
1 AAGATTGT-TCGAGTTC-TATACTCCCTGAAAGAA
4009707 GAGTAGAGCA
Statistics
Matches: 564, Mismatches: 86, Indels: 64
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 7 0.01
45 24 0.04
46 1 0.00
48 2 0.00
52 2 0.00
53 2 0.00
54 63 0.11
55 406 0.72
56 47 0.08
57 7 0.01
58 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (55 bp):
AAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAG
Found at i:4009777 original size:55 final size:55
Alignment explanation
Indices: 4009617--4009787 Score: 238
Period size: 55 Copynumber: 3.1 Consensus size: 55
4009607 GACATGTTTT
* * *
4009617 CAAAAGATTTCTCGAGTTTTATCTCCCTGAAAGAAGAGTGGAGCATACCCATCTT-
1 CAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGT-GAGCATACTCGTCTTC
*
4009672 CAAAAGATTTCTCGAGTCTTATATCCCTGAAAGAAGAGTAGAGCATACTCGT-TTC
1 CAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGT-GAGCATACTCGTCTTC
* * *
4009727 CTAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGTAGTAGACTCGTCTTC
1 CAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTG-AGCATACTCGTCTTC
4009783 CAAAA
1 CAAAA
4009788 TTGATCTGAA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
54 3 0.03
55 93 0.90
56 7 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (55 bp):
CAAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAAGAGTGAGCATACTCGTCTTC
Found at i:4011420 original size:2 final size:2
Alignment explanation
Indices: 4011413--4011455 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
4011403 TTAATAAATG
*
4011413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTC TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
4011455 T
1 T
4011456 TAATTGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4013431 original size:2 final size:2
Alignment explanation
Indices: 4013424--4013450 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4013414 GAACAAGATA
4013424 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
4013451 GTTACAAAAT
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:4014850 original size:21 final size:21
Alignment explanation
Indices: 4014816--4014994 Score: 172
Period size: 21 Copynumber: 8.6 Consensus size: 21
4014806 GATTTACATA
* *
4014816 TTCGCATTGTGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4014837 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
4014858 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
4014879 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
4014898 TTCGCGTTGCAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
4014921 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
4014940 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
4014963 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
4014982 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
4014995 TTATTCCAAA
Statistics
Matches: 126, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
19 34 0.27
21 74 0.59
23 18 0.14
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:4014877 original size:42 final size:42
Alignment explanation
Indices: 4014841--4015022 Score: 314
Period size: 42 Copynumber: 4.4 Consensus size: 42
4014831 TCCAAGTTCG
*
4014841 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
4014881 CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
4014923 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
4014965 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
4015007 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
4015023 AATCGCAACG
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
40 27 0.20
41 2 0.01
42 105 0.78
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:4015010 original size:21 final size:20
Alignment explanation
Indices: 4014862--4015011 Score: 119
Period size: 21 Copynumber: 7.2 Consensus size: 20
4014852 TCGAAGTTCG
4014862 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* *
4014881 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
*
4014900 CGCGTTGCAATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
* * *
4014923 TGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
4014942 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
* *
4014965 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAATT
4014984 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
4015007 CGTTG
1 CGTTG
4015012 TGATAGTCCA
Statistics
Matches: 102, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.01
19 33 0.32
21 41 0.40
23 27 0.26
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:4015935 original size:42 final size:42
Alignment explanation
Indices: 4015883--4016237 Score: 574
Period size: 42 Copynumber: 8.5 Consensus size: 42
4015873 TTTGGACTAT
4015883 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* *
4015925 CAACGGACTTGGAATAAATCGCAACGCAAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
4015967 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* *
4016009 CAACGAACTTAGAATAAATCGCAACGCAAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
*
4016051 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
*
4016093 CAACGAACTTAGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* *
4016135 TAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* * *
4016177 CAACGAACTTGGACT--ATCGCAACTCGAACTTGGACTATCG
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
*
4016217 CAACGAA-TTTGAA-AAATCGCA
1 CAACGAACTTGGAATAAATCGCA
4016238 TTGCGATAGT
Statistics
Matches: 290, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
39 4 0.01
40 36 0.12
42 250 0.86
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCG
Found at i:4017430 original size:17 final size:17
Alignment explanation
Indices: 4017379--4017421 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
4017369 CTCCCTGAAG
4017379 CCCGTGACCAGCTCGCA
1 CCCGTGACCAGCTCGCA
4017396 CCCGTGACCAGCTCGCA
1 CCCGTGACCAGCTCGCA
4017413 CCCGTGACC
1 CCCGTGACC
4017422 TGCAAGCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.49, G:0.23, T:0.12
Consensus pattern (17 bp):
CCCGTGACCAGCTCGCA
Found at i:4018854 original size:25 final size:24
Alignment explanation
Indices: 4018817--4018864 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
4018807 ATTACTACTT
*
4018817 TATGTATGGTATGTACATTTTTATG
1 TATGTATGGTATGCA-ATTTTTATG
*
4018842 TATGTATGTTATGCAATTTTTAT
1 TATGTATGGTATGCAATTTTTAT
4018865 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
TATGTATGGTATGCAATTTTTATG
Found at i:4020933 original size:32 final size:32
Alignment explanation
Indices: 4020897--4020962 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
4020887 GTACAATTGA
4020897 TATACGATGAGTGCATGAATCTTACATACCAT
1 TATACGATGAGTGCATGAATCTTACATACCAT
4020929 TATACGATGAGTGCATGAATCTTACATACCAT
1 TATACGATGAGTGCATGAATCTTACATACCAT
4020961 TA
1 TA
4020963 ATCGGAGTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TATACGATGAGTGCATGAATCTTACATACCAT
Found at i:4023475 original size:42 final size:42
Alignment explanation
Indices: 4023429--4023549 Score: 199
Period size: 42 Copynumber: 2.9 Consensus size: 42
4023419 CGAATCATTG
*
4023429 GGTGAATCATTGGAATTTCCAATAGGATTATTA-AATGTATTA
1 GGTGAATCATTGGAATTTCCAATAGAATTATTAGAA-GTATTA
*
4023471 GGTGAATCATTGAAATTTCCAATAGAATTATTAGAAGTATTA
1 GGTGAATCATTGGAATTTCCAATAGAATTATTAGAAGTATTA
*
4023513 GGTGAATCATTGGAATTTCCAATCGAATTATTAGAAG
1 GGTGAATCATTGGAATTTCCAATAGAATTATTAGAAG
4023550 GTTTAATCAG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
42 72 0.97
43 2 0.03
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (42 bp):
GGTGAATCATTGGAATTTCCAATAGAATTATTAGAAGTATTA
Found at i:4023988 original size:84 final size:84
Alignment explanation
Indices: 4023865--4024163 Score: 494
Period size: 84 Copynumber: 3.5 Consensus size: 84
4023855 CTTGAACGAA
4023865 AATATTTAGCCACTGTTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
1 AATATTTAGCCACTG-TTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
4023930 ATCAAACAAGCCTATAAACTC
65 ATCAAACAAGCC-ATAAACTC
* *
4023951 AATATTTAGCCATTGTTTTTT-TCATCAAACTAAGTTTGCCACTACACAATCAAAATTTAAACAA
1 AATATTTAGCCACTGTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAA
4024015 TCAAACAAGTCCATAAACTC
66 TCAAACAAG-CCATAAACTC
*
4024035 AATATTTAGCCACTG-TTTTTCCCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAA
1 AATATTTAGCCACTGTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAA
*
4024099 TCAAACAAACCCATAAACTC
66 TCAAAC-AAGCCATAAACTC
4024119 AATATTTAGCCACTGTTTTTTTTCTCATCAAACTAAGTTTGCCAC
1 AATATTTAGCCACTG--TTTTTTCTCATCAAACTAAGTTTGCCAC
4024164 AGTGTGACGG
Statistics
Matches: 200, Mismatches: 7, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
83 5 0.03
84 145 0.73
85 10 0.05
86 14 0.07
87 26 0.13
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.31
Consensus pattern (84 bp):
AATATTTAGCCACTGTTTTTTCTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACAA
TCAAACAAGCCATAAACTC
Found at i:4024293 original size:23 final size:23
Alignment explanation
Indices: 4024263--4024319 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
4024253 ATTCTCAATC
*
4024263 AGAATATGATTCAAACATTTGTT
1 AGAATATGATTCAAACAGTTGTT
4024286 AGAATATGATTCAAACAGTTGTT
1 AGAATATGATTCAAACAGTTGTT
4024309 AGAATATGATT
1 AGAATATGATT
4024320 AAAATTGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (23 bp):
AGAATATGATTCAAACAGTTGTT
Found at i:4030239 original size:4 final size:4
Alignment explanation
Indices: 4030230--4030259 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
4030220 ATATAACAAG
4030230 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
4030260 TATGTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:4030740 original size:30 final size:31
Alignment explanation
Indices: 4030698--4030767 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
4030688 CCCGAAGGAC
* * * *
4030698 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCATAGGTCACAAAGAACCTAGGTAAA
* *
4030728 CTGTCCATAGGTCCCAAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAAA
4030759 CTATCCATA
1 CTATCCATA
4030768 TGTTCCTTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (31 bp):
CTATCCATAGGTCACAAAGAACCTAGGTAAA
Found at i:4033152 original size:2 final size:2
Alignment explanation
Indices: 4033140--4033169 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4033130 CTGATCACAG
*
4033140 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4033170 TCCAAACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4036498 original size:64 final size:63
Alignment explanation
Indices: 4036424--4036580 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 63
4036414 TAATGAAGGT
* **
4036424 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATTG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
4036487 G
63 G
* * * *
4036488 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
4036551 AGTGCATCGATGCACTACTTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
4036581 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 67 0.85
65 9 0.11
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:4042828 original size:26 final size:27
Alignment explanation
Indices: 4042805--4042885 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
4042795 TTTTATTTTA
*
4042805 TATGTTCATATA-CTCATGTCATTTCT
1 TATGATCATATAGCTCATGTCATTTCT
* *
4042831 TGTGATCATGTAGCTCATGTCATTCTCT
1 TATGATCATATAGCTCATGTCATT-TCT
* *
4042859 TGTGATCATGTAGCTCA-GTCATGTTCT
1 TATGATCATATAGCTCATGTCAT-TTCT
4042886 CATATATCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 9 0.18
27 19 0.39
28 21 0.43
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (27 bp):
TATGATCATATAGCTCATGTCATTTCT
Found at i:4042866 original size:28 final size:27
Alignment explanation
Indices: 4042817--4042885 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 27
4042807 TGTTCATATA
4042817 CTCATGTCATTTCTTGTGATCATGTAG
1 CTCATGTCATTTCTTGTGATCATGTAG
4042844 CTCATGTCATTCTCTTGTGATCATGTAG
1 CTCATGTCATT-TCTTGTGATCATGTAG
4042872 CTCA-GTCATGTTCT
1 CTCATGTCAT-TTCT
4042886 CATATATCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 19 0.47
28 21 0.52
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (27 bp):
CTCATGTCATTTCTTGTGATCATGTAG
Found at i:4042894 original size:28 final size:28
Alignment explanation
Indices: 4042804--4042895 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
4042794 ATTTTATTTT
* *
4042804 ATATGTTCATATA-CTCATGTCATT-TC
1 ATATGATCATGTAGCTCATGTCATTCTC
* *
4042830 TTGTGATCATGTAGCTCATGTCATTCTC
1 ATATGATCATGTAGCTCATGTCATTCTC
* *
4042858 TTGTGATCATGTAGCTCA-GTCATGTTCTC
1 ATATGATCATGTAGCTCATGTCA--TTCTC
4042887 ATAT-ATCAT
1 ATATGATCAT
4042896 ATCATATCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.16
27 15 0.27
28 25 0.45
29 7 0.12
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (28 bp):
ATATGATCATGTAGCTCATGTCATTCTC
Found at i:4044712 original size:30 final size:30
Alignment explanation
Indices: 4044678--4044750 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
4044668 CCCGAAGGAC
4044678 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
4044708 CTATCCAGACGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
4044738 CTGTCCATAGGTC
1 CTATCCAGAGGTC
4044751 CCGAAGAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:4044776 original size:31 final size:31
Alignment explanation
Indices: 4044736--4044800 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
4044726 GATCCTCGGT
* *
4044736 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
* * **
4044767 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATAGGTCCCGAAGAACATAGGTA
4044798 AAC
1 AAC
4044801 CCTCGACTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (31 bp):
AACTATCCATAGGTCCCGAAGAACATAGGTA
Found at i:4046107 original size:14 final size:13
Alignment explanation
Indices: 4046088--4046125 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
4046078 GGAGACACGG
4046088 GAAGAAAGGAAGAA
1 GAAGAAA-GAAGAA
4046102 GAAG-AAGAA-AA
1 GAAGAAAGAAGAA
4046113 GAAGAAAGAAGAA
1 GAAGAAAGAAGAA
4046126 AGCTCTGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 8 0.36
13 4 0.18
14 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
GAAGAAAGAAGAA
Found at i:4046127 original size:14 final size:14
Alignment explanation
Indices: 4046097--4046126 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4046087 GGAAGAAAGG
4046097 AAGAAGAAGAAGAA
1 AAGAAGAAGAAGAA
4046111 AAGAAGAAAGAAGAA
1 AAGAAG-AAGAAGAA
4046126 A
1 A
4046127 GCTCTGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAGAA
Found at i:4049462 original size:60 final size:60
Alignment explanation
Indices: 4049369--4049481 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
4049359 CACGATGTCA
* ** *
4049369 ACATTTAGGTCGAACAAGCTGGTGGTTGCATGCCTTCCCCTT-GAACTTGAAGGTATCTCG
1 ACATTGAGGTCGAACAAGCTGGCAGTTGAATGCC-TCCCCTTGGAACTTGAAGGTATCTCG
* * *
4049429 ACATTGAGGTCGAAGAAGCTTGCAGTTGAATGCCTCCCCTTGGAATTTGAAGG
1 ACATTGAGGTCGAACAAGCTGGCAGTTGAATGCCTCCCCTTGGAACTTGAAGG
4049482 CATCATGTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 7 0.16
60 38 0.84
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (60 bp):
ACATTGAGGTCGAACAAGCTGGCAGTTGAATGCCTCCCCTTGGAACTTGAAGGTATCTCG
Found at i:4050401 original size:15 final size:15
Alignment explanation
Indices: 4050381--4050409 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4050371 TTATTCAATC
4050381 ATATATAATAAATAT
1 ATATATAATAAATAT
4050396 ATATATAATAAATA
1 ATATATAATAAATA
4050410 ATTTTACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATAATAAATAT
Found at i:4060116 original size:25 final size:25
Alignment explanation
Indices: 4060088--4060149 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
4060078 TTCCTCATAT
4060088 ACTGCCTGTTATTATATATATATAC
1 ACTGCCTGTTATTATATATATATAC
4060113 ACTGCCTG-TATTTATATATATATAC
1 ACTGCCTGTTA-TTATATATATATAC
*
4060138 ACTGCTTGTTAT
1 ACTGCCTGTTAT
4060150 GATTTACGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.06
25 30 0.88
26 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (25 bp):
ACTGCCTGTTATTATATATATATAC
Found at i:4063477 original size:21 final size:21
Alignment explanation
Indices: 4063448--4063499 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
4063438 ATTCTGACTA
4063448 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
4063469 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
4063490 TCGCAATGCG
1 TCGCATTGCG
4063500 GATATGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:4063532 original size:20 final size:20
Alignment explanation
Indices: 4063509--4063582 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
4063499 GGATATGTAA
* *
4063509 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
4063529 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
4063549 ATCGCAACGCGGTGCTGACT
1 ATCGCAACGCGATTCTGACT
*
4063569 ATCGCAATGCGATT
1 ATCGCAACGCGATT
4063583 TTTAAAGCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:4064201 original size:20 final size:20
Alignment explanation
Indices: 4064149--4064215 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
4064139 AGAATCGCAA
* *
4064149 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
4064168 TGCGA-TAGCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
4064187 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
4064207 TGCGATTTT
1 TGCGATTTT
4064216 AAGTTTCAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.03
19 18 0.45
20 21 0.52
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:4065918 original size:24 final size:23
Alignment explanation
Indices: 4065880--4065933 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
4065870 TGAACACACC
4065880 ATCAAATCCGAGTATTGACCAAG
1 ATCAAATCCGAGTATTGACCAAG
*
4065903 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGAGTATTGACCAAG
4065927 ATCAAAT
1 ATCAAAT
4065934 TGAATACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:4066742 original size:20 final size:20
Alignment explanation
Indices: 4066719--4066786 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
4066709 TGAAATTCGT
* *
4066719 GTTGCGACAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
4066739 GTTGCGATAATCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
4066759 GTTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
4066779 ATTGCGAT
1 GTTGCGAT
4066787 TTACATATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:4066793 original size:20 final size:20
Alignment explanation
Indices: 4066770--4066845 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
4066760 TTGCGATAGT
*
4066770 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
4066790 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
4066810 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
4066830 CATATTCGCATTGCGA
1 CATATTCGCATTGCGA
4066846 ATTCGAAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:4066804 original size:40 final size:40
Alignment explanation
Indices: 4066755--4066845 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
4066745 ATAATCAGAA
*
4066755 TCGCGTTGCGATAGT-CATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGAT-GTACATAATCGCATTGCGATTTACATAT
* *
4066795 TCGCATTGCGATTTACATATTCGCATTGCGATTTACATAT
1 TCGCATTGCGATGTACATAATCGCATTGCGATTTACATAT
4066835 TCGCATTGCGA
1 TCGCATTGCGA
4066846 ATTCGAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATGTACATAATCGCATTGCGATTTACATAT
Found at i:4075664 original size:60 final size:58
Alignment explanation
Indices: 4075536--4075711 Score: 147
Period size: 60 Copynumber: 2.9 Consensus size: 58
4075526 CATCATATGT
* * * *
4075536 CCCCAAACTATCATCTTCATTTTAAATTGATCCTTAAACTTTTAAATATTCCAATTTCA
1 CCCCAAACTAT-AGCTTCATTCTAAATTAATCCTTAAACTTTTAAATATTACAATTTCA
* * * * *
4075595 TTCCAAAACTATAGCTTGCATTCTAAATTAATCCTTAAACTTTTGAATATTATATTTTCA
1 -CCCCAAACTATAGCTT-CATTCTAAATTAATCCTTAAACTTTTAAATATTACAATTTCA
* * ** * * *
4075655 CCCCTAAACTATAAC-CCTATTTCTAAATTGGTCCTTAGACTTTTGAATATTTCAATT
1 CCCC-AAACTATAGCTTC-A-TTCTAAATTAATCCTTAAACTTTTAAATATTACAATT
4075712 CAACCGAATA
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
58 1 0.01
59 7 0.08
60 85 0.91
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (58 bp):
CCCCAAACTATAGCTTCATTCTAAATTAATCCTTAAACTTTTAAATATTACAATTTCA
Found at i:4075903 original size:61 final size:58
Alignment explanation
Indices: 4075822--4075969 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 58
4075812 TGACTAGTAT
*
4075822 ATGTGCATAGTTT-GGGATGAAATTGGAATGCTT-AAAAGGTTTAGGGATTGATTTAGAATG
1 ATGT-CATAGTTTAGGGATGAAATTGGAATG-TTCAAAA-GTTGA-GGATTGATTTAGAATG
* * *
4075882 AATGTCATAGTTTAGGGATGAAAATGAAATGTTCAAAAGTTGATGATTGATTTAGAATG
1 -ATGTCATAGTTTAGGGATGAAATTGGAATGTTCAAAAGTTGAGGATTGATTTAGAATG
** *
4075941 ATAGTCATAAATTAGGGGTGAAATTGGAA
1 AT-GTCATAGTTTAGGGATGAAATTGGAA
4075970 CATTTAAAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
58 2 0.03
59 36 0.48
60 14 0.19
61 23 0.31
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (58 bp):
ATGTCATAGTTTAGGGATGAAATTGGAATGTTCAAAAGTTGAGGATTGATTTAGAATG
Found at i:4078078 original size:29 final size:31
Alignment explanation
Indices: 4078046--4078113 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
4078036 CTTTTAAAAC
*
4078046 TTGCAATAC-AGTCCCCAACATTT-GTTTGT
1 TTGCAATACAAGTCCCCAACATTTAGTCTGT
*
4078075 TTGCAATACAATTCCCCAACATTTAGTCTGT
1 TTGCAATACAAGTCCCCAACATTTAGTCTGT
4078106 TTGCAATA
1 TTGCAATA
4078114 TGGTCCCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 9 0.26
30 13 0.37
31 13 0.37
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.37
Consensus pattern (31 bp):
TTGCAATACAAGTCCCCAACATTTAGTCTGT
Found at i:4089469 original size:26 final size:26
Alignment explanation
Indices: 4089439--4089489 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
4089429 TCTAATACAT
*
4089439 ATCCTGATGTATGTAATAATAATTAC
1 ATCCTCATGTATGTAATAATAATTAC
**
4089465 ATCCTCATGTATGTTCTAATAATTA
1 ATCCTCATGTATGTAATAATAATTA
4089490 TTAGTAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (26 bp):
ATCCTCATGTATGTAATAATAATTAC
Found at i:4091318 original size:148 final size:148
Alignment explanation
Indices: 4091050--4091345 Score: 540
Period size: 148 Copynumber: 2.0 Consensus size: 148
4091040 GATCCCTAAA
*
4091050 CTTTTAAATATTATAATTTCATTCCTAAGCTATAACTATCATTCTATGTTAGTCCTTAAACTTCT
1 CTTTTAAATATTATAATTTCATTCCTAAGCTATAACTATCATTCTACGTTAGTCCTTAAACTTCT
4091115 GAACATTTCGTTTTCATCCCCAACATTCATTCTAATTGGTCCCCAAACTTTTTGAACATTCCAAT
66 GAACATTTCGTTTTCATCCCCAACATTCATTCTAATTGGTCCCCAAACTTTTTGAACATTCCAAT
4091180 TTAACCCCAAACTATACG
131 TTAACCCCAAACTATACG
* *
4091198 CTTTTAAATATTCTAGTTTCATTCCTAAGCTATAACTATCATTCTACGTTAGTCCTTAAACTTCT
1 CTTTTAAATATTATAATTTCATTCCTAAGCTATAACTATCATTCTACGTTAGTCCTTAAACTTCT
*
4091263 GAACATTTCGTTTTCATCCCCAACATTCATTCTAAATTGGTCCCCAAAC-TTTTGAACATTCCAG
66 GAACATTTCGTTTTCATCCCCAACATTCATTCT-AATTGGTCCCCAAACTTTTTGAACATTCCAA
4091327 TTTAACCCCAAACTATACG
130 TTTAACCCCAAACTATACG
4091346 TATATACTAA
Statistics
Matches: 143, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 128 0.90
149 15 0.10
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (148 bp):
CTTTTAAATATTATAATTTCATTCCTAAGCTATAACTATCATTCTACGTTAGTCCTTAAACTTCT
GAACATTTCGTTTTCATCCCCAACATTCATTCTAATTGGTCCCCAAACTTTTTGAACATTCCAAT
TTAACCCCAAACTATACG
Found at i:4091498 original size:29 final size:29
Alignment explanation
Indices: 4091466--4091557 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
4091456 TTTGGATGGA
4091466 TTTGGGGATGAAATTGGAATATTCAAAAG
1 TTTGGGGATGAAATTGGAATATTCAAAAG
* * * *
4091495 TTTGGGGACT-AATTTAGAAAGAGTGTCATAA-
1 TTTGGGGA-TGAAATT-GGAATA-T-TCAAAAG
* *
4091526 TTTAGGGATGAAATTAGAATATTCAAAAG
1 TTTGGGGATGAAATTGGAATATTCAAAAG
4091555 TTT
1 TTT
4091558 AAAGACTAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
28 5 0.11
29 16 0.34
30 9 0.19
31 12 0.26
32 5 0.11
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (29 bp):
TTTGGGGATGAAATTGGAATATTCAAAAG
Found at i:4091536 original size:60 final size:60
Alignment explanation
Indices: 4091465--4091629 Score: 217
Period size: 60 Copynumber: 2.8 Consensus size: 60
4091455 ATTTGGATGG
* *** *
4091465 ATTTGGGGATGAAATTGGAATATTCAAAAGTTTGGGGACTAATTTAGAAAGAGTGTCATA
1 ATTTAGGGATGAAATTGGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATA
* *
4091525 ATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAACGAGAGTCATA
1 ATTTAGGGATGAAATTGGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATA
* * *
4091585 GTTAAGTGATGAAATTGGAATA-TCAAAAGTTT-AAGAACTAATTTA
1 ATTTAGGGATGAAATTGGAATATTCAAAAGTTTAAAG-ACTAATTTA
4091630 AAATGAGGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
58 3 0.03
59 19 0.20
60 71 0.76
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (60 bp):
ATTTAGGGATGAAATTGGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATA
Found at i:4092582 original size:16 final size:15
Alignment explanation
Indices: 4092557--4092590 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4092547 ATTTAATAAC
*
4092557 TTTTTATAAATATAT
1 TTTTTATAAAAATAT
4092572 TTTTATATAAAAATAT
1 TTTT-TATAAAAATAT
4092588 TTT
1 TTT
4092591 CATCTACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTATAAAAATAT
Found at i:4099213 original size:127 final size:130
Alignment explanation
Indices: 4098933--4099437 Score: 537
Period size: 127 Copynumber: 3.9 Consensus size: 130
4098923 GTCTGTTGCA
* * *
4098933 CTCTTCTTTCAGGGGAGATCAGACTTGATAT-TTCCTCTTTTTTGGGTATTCATATCAACT-TTG
1 CTCTTCTTTCAGGGGAGATCAAACTTGAT-TGTTCCTC-TTTTTGGGTAGTCAGATCAA-TGTTG
*
4098996 GAAG-A-A-TCTGCTCCACTATTC-TTCAGGGAGATAAGACTCGAGAAATCTTTGGAAGATGGTC
63 GAAGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAGACGGT-
4099057 TTTCC
127 TTT-C
* * * * *
4099062 ACTATTCTTTCAGGGGATATCAAAC-TGATTGCTCCT-ATTTTGGGTAGGCAGATCAATGTTGGA
1 -CTCTTCTTTCAGGGGAGATCAAACTTGATTGTTCCTCTTTTTGGGTAGTCAGATCAATGTTGGA
* *
4099125 AGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAAACTAGAG-AATC-TTGGAAGACGAGTTG
65 AGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAGACG-GTT-
4099188 TTC
128 TTC
* * *
4099191 CTCTT-TTTCAGGGGAGACCAAACTTGATATGTTCCTCTTTTTTGGTAGTCAGAT-TATG-TGGA
1 CTCTTCTTTCAGGGGAGATCAAACTTGAT-TGTTCCTCTTTTTGGGTAGTCAGATCAATGTTGGA
* *
4099253 AGACGAGTCTGCTCCACTATTCTTT-A-GG-GATAAGA-TCGAGAAATCTTTGGAACACTGGTTT
65 AGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAGAC-GGTTT
*
4099314 ATA
129 -TC
* * * * *
4099317 CTCTTCTTTTAGGGGAGATCAGACTTGATTTGTTCCTCTTTTTCGGGTAGTCAAATCAACGTTGA
1 CTCTTCTTTCAGGGGAGATCAAACTTGA-TTGTTCCTCTTTTT-GGGTAGTCAGATCAATGTTGG
* *
4099382 AAG-A-AGTCTGCTCC-CTCTTCTTTCAGGGAGATAAGACTTGAGAAATCTTTGGAAGA
64 AAGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAGA
4099438 GTATGCTTCA
Statistics
Matches: 315, Mismatches: 36, Indels: 47
0.79 0.09 0.12
Matches are distributed among these distances:
124 4 0.01
125 11 0.03
126 20 0.06
127 81 0.26
128 60 0.19
129 33 0.10
130 70 0.22
131 36 0.11
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (130 bp):
CTCTTCTTTCAGGGGAGATCAAACTTGATTGTTCCTCTTTTTGGGTAGTCAGATCAATGTTGGAA
GAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAGACGGTTTTC
Found at i:4099405 original size:255 final size:262
Alignment explanation
Indices: 4098912--4099465 Score: 646
Period size: 258 Copynumber: 2.1 Consensus size: 262
4098902 GTAGTCAATG
* *
4098912 TTGGAAGACGAGTCTGTTGCACTCTTCTTTCAGGGGAGATCAGACTTGATATTTCCTCTTTTTTG
1 TTGGAAGACGAGTCTGTTGCACTCTTCTTTCAGGGGAGACCAAACTTGATATTTCCTCTTTTTTG
* * *
4098977 GGTATTCATATCAACTTTGGAAGAATCTGCTCCACTATTCTTCAGGGAGATAAGACTCGAGAAAT
66 GGTAGTCAGATCAACTGTGGAAGAATCTGCTCCACTATTCTTCAGGGAGATAAGACTCGAGAAAT
* *
4099042 CTTTGGAAGATGGTCTTTCCACTATTCTTTCAGGGGATATCAAACTGATTGCTCCTATTTTGGGT
131 CTTTGGAACATGGTCTTT-CACTATTCTTTCAGGGGAGATCAAACTGATTGCTCCTATTTTGGGT
* * *
4099107 AGGCAGATCAATGTTGGAAGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAAACTAGAG-AA
195 AGGCAAATCAACGTTGAAAGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAAACTAGAGAAA
4099171 TC-
260 TCT
4099173 TTGGAAGACGAGT-TGTT-C-CTCTT-TTTCAGGGGAGACCAAACTTGATATGTTCCTCTTTTTT
1 TTGGAAGACGAGTCTGTTGCACTCTTCTTTCAGGGGAGACCAAACTTGATAT-TTCCTCTTTTTT
* *
4099234 -GGTAGTCAGAT-TA-TGTGGAAGACGAGTCTGCTCCACTATTCTTTA-GG-GATAAGA-TCGAG
65 GGGTAGTCAGATCAACTGTGGAAGA--A-TCTGCTCCACTATTCTTCAGGGAGATAAGACTCGAG
* * * * *
4099293 AAATCTTTGGAACACTGGT-TTAT-ACTCTTCTTTTAGGGGAGATCAGACTTGATTTGTTCCTCT
127 AAATCTTTGGAACA-TGGTCTT-TCACTATTCTTTCAGGGGAGATCAAAC-TGA-TTGCTCCT-A
* * *
4099356 TTTTCGGGTAGTCAAATCAACGTTGAAAG-A-AGTCTGCTCC-CTCTTCTTTCAGGGAGATAAGA
187 TTTT-GGGTAGGCAAATCAACGTTGAAAGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAAA
*
4099418 CTTGAGAAATCT
251 CTAGAGAAATCT
* *
4099430 TTGG-A-A-GAGTATGCTT-CACTATTCTTTCAGGGGAGA
1 TTGGAAGACGAGTCTG-TTGCACTCTTCTTTCAGGGGAGA
4099466 TTAACTTGAG
Statistics
Matches: 255, Mismatches: 22, Indels: 35
0.82 0.07 0.11
Matches are distributed among these distances:
254 25 0.10
255 59 0.23
256 38 0.15
257 48 0.19
258 67 0.26
259 1 0.00
260 4 0.02
261 13 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (262 bp):
TTGGAAGACGAGTCTGTTGCACTCTTCTTTCAGGGGAGACCAAACTTGATATTTCCTCTTTTTTG
GGTAGTCAGATCAACTGTGGAAGAATCTGCTCCACTATTCTTCAGGGAGATAAGACTCGAGAAAT
CTTTGGAACATGGTCTTTCACTATTCTTTCAGGGGAGATCAAACTGATTGCTCCTATTTTGGGTA
GGCAAATCAACGTTGAAAGAAGAGTCTGCTCCACTATTCTTTCAGGGAGATAAAACTAGAGAAAT
CT
Found at i:4099521 original size:55 final size:53
Alignment explanation
Indices: 4099386--4099534 Score: 196
Period size: 52 Copynumber: 2.8 Consensus size: 53
4099376 CGTTGAAAGA
*
4099386 AGTCTGCTCC-CTCTTCTTTCA-GGGAGATAAGACTTGAGAAATCTTTGGAAG
1 AGTCTGCTCCACTATTCTTTCAGGGGAGATAAGACTTGAGAAATCTTTGGAAG
* * *
4099437 AGTATGCTTCACTATTCTTTCAGGGGAGATTA-ACTTGAGAAATCTTTGGAAG
1 AGTCTGCTCCACTATTCTTTCAGGGGAGATAAGACTTGAGAAATCTTTGGAAG
* *
4099489 ATGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAGATTTGAGAAA
1 A---GTCTGCTCCACTATTCTTTCAGGGGAGATAAGACTTGAGAAA
4099535 AATTTGAGCA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
51 8 0.10
52 31 0.37
53 8 0.10
55 28 0.33
56 9 0.11
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (53 bp):
AGTCTGCTCCACTATTCTTTCAGGGGAGATAAGACTTGAGAAATCTTTGGAAG
Found at i:4100576 original size:11 final size:10
Alignment explanation
Indices: 4100559--4100589 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
4100549 TAATTATTAC
4100559 TTTTTCTTTT
1 TTTTTCTTTT
4100569 TATTTTCTTTT
1 T-TTTTCTTTT
4100580 TTTTTCTTTT
1 TTTTTCTTTT
4100590 GTTCTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:4112030 original size:3 final size:3
Alignment explanation
Indices: 4112022--4112062 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4112012 GTAATAAATT
4112022 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4112063 TCATGGGACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4119846 original size:19 final size:19
Alignment explanation
Indices: 4119821--4119864 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4119811 TTGAATTTGT
**
4119821 AAATAATAATATTTTATAA
1 AAATAATAATAAATTATAA
*
4119840 TAATAATAATAAATTATAA
1 AAATAATAATAAATTATAA
4119859 AAATAA
1 AAATAA
4119865 CAATGTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAATAAATTATAA
Found at i:4127276 original size:19 final size:19
Alignment explanation
Indices: 4127252--4127316 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
4127242 ACAACAAGAT
4127252 TATCGCAACGAACTTGGAC
1 TATCGCAACGAACTTGGAC
* * * *
4127271 TATCGCAACAAATTTGTAA
1 TATCGCAACGAACTTGGAC
4127290 TAAATCGCAACGCGAACTTGGAC
1 T--ATCGCAA--CGAACTTGGAC
4127313 TATC
1 TATC
4127317 ACAATGCGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 16 0.47
21 10 0.29
23 8 0.24
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (19 bp):
TATCGCAACGAACTTGGAC
Found at i:4127365 original size:21 final size:21
Alignment explanation
Indices: 4127341--4127387 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
4127331 TAAATCGCAA
4127341 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
4127362 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
4127383 TGCGA
1 TGCGA
4127388 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:4132215 original size:36 final size:36
Alignment explanation
Indices: 4132139--4132215 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
4132129 TGGTCATCCT
* ** * *
4132139 GCTGCTGCTAGTAACGGTACTGGGTATGTTTGGCCT
1 GCTGGTGCTAGTAACGGTACTGGGTATGTCCGACCA
*
4132175 GCTGGTGCTAGTAACGGTACTGGGTCTAG-CCGACCA
1 GCTGGTGCTAGTAACGGTACTGGGTAT-GTCCGACCA
4132211 GCTGG
1 GCTGG
4132216 CCCTAAAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (36 bp):
GCTGGTGCTAGTAACGGTACTGGGTATGTCCGACCA
Found at i:4132441 original size:27 final size:27
Alignment explanation
Indices: 4132403--4132538 Score: 238
Period size: 27 Copynumber: 5.1 Consensus size: 27
4132393 AATGATGCCC
* *
4132403 CAAAGGCCTCCAGTATCATCACAGGCA
1 CAAAGGCCTCCAGTATCATCAAAGCCA
4132430 CAAAGGCCTCCAGTATCATCAAAGCCA
1 CAAAGGCCTCCAGTATCATCAAAGCCA
4132457 CAAAGGCCTCCAGTATCATCAAAGCCA
1 CAAAGGCCTCCAGTATCATCAAAGCCA
*
4132484 CAAAGGCCTCCAGTATCATTAAAGCCA
1 CAAAGGCCTCCAGTATCATCAAAGCCA
4132511 CAAAGGCCTCCAGTATCATC-AAGCCA
1 CAAAGGCCTCCAGTATCATCAAAGCCA
4132537 CA
1 CA
4132539 GGCAAACAAG
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
26 8 0.08
27 97 0.92
ACGTcount: A:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (27 bp):
CAAAGGCCTCCAGTATCATCAAAGCCA
Found at i:4137429 original size:32 final size:32
Alignment explanation
Indices: 4137388--4137450 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4137378 TAAAGTGACA
* *
4137388 CTTGGGTAGGCTCTGAGGCCCCAAGGTACTCT
1 CTTGGGTAGGCTCTCAGGCCCCAAGATACTCT
4137420 CTTGGGTAGGCTCTCAGGCCCCAAGATACTC
1 CTTGGGTAGGCTCTCAGGCCCCAAGATACTC
4137451 CCTTAGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (32 bp):
CTTGGGTAGGCTCTCAGGCCCCAAGATACTCT
Found at i:4138707 original size:3 final size:3
Alignment explanation
Indices: 4138701--4138730 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4138691 GAGTTGTTGC
4138701 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
4138731 AGTCAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4144230 original size:2 final size:2
Alignment explanation
Indices: 4144225--4144260 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4144215 AAATTCATAC
4144225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4144261 TTATCGAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4149442 original size:13 final size:13
Alignment explanation
Indices: 4149398--4149447 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
4149388 ATTTCGACCG
4149398 AATAA-ATTATA-
1 AATAATATTATAT
* * *
4149409 AATTATAATATGT
1 AATAATATTATAT
4149422 ATATAATATTATAT
1 A-ATAATATTATAT
4149436 AATAATATTATA
1 AATAATATTATA
4149448 ATTTATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 4 0.13
12 4 0.13
13 12 0.40
14 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AATAATATTATAT
Found at i:4149455 original size:7 final size:8
Alignment explanation
Indices: 4149399--4149457 Score: 54
Period size: 7 Copynumber: 7.8 Consensus size: 8
4149389 TTTCGACCGA
4149399 ATAA-ATT
1 ATAATATT
4149406 ATAA-ATT
1 ATAATATT
4149413 ATAATATGT
1 ATAATAT-T
*
4149422 AT-ATAAT
1 ATAATATT
* *
4149429 ATTATATA
1 ATAATATT
4149437 ATAATATT
1 ATAATATT
4149445 ATAAT-TT
1 ATAATATT
4149452 ATAATA
1 ATAATA
4149458 CAAGTGGCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
7 21 0.49
8 19 0.44
9 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (8 bp):
ATAATATT
Found at i:4163593 original size:7 final size:6
Alignment explanation
Indices: 4163583--4163655 Score: 62
Period size: 7 Copynumber: 11.8 Consensus size: 6
4163573 GCTAAAAGGA
4163583 AAAACAT AAAAAT AAAGAAT AAAAAT AATAAAT AATAAAT -AAAAT AAAAA-
1 AAAA-AT AAAAAT AAA-AAT AAAAAT AA-AAAT AA-AAAT AAAAAT AAAAAT
**
4163633 GGAAA- AAAAAT AAACAAT AAAAA
1 AAAAAT AAAAAT AAA-AAT AAAAA
4163656 AGAGTAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
5 10 0.18
6 20 0.35
7 27 0.47
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:4163606 original size:13 final size:12
Alignment explanation
Indices: 4163583--4163655 Score: 62
Period size: 13 Copynumber: 5.9 Consensus size: 12
4163573 GCTAAAAGGA
4163583 AAAACATAAAAAT
1 AAAA-ATAAAAAT
4163596 AAAGAATAAAAAT
1 AAA-AATAAAAAT
4163609 AATAAATAATAAAT
1 AA-AAATAA-AAAT
4163623 -AAAATAAAAA-
1 AAAAATAAAAAT
**
4163633 GGAAA-AAAAAT
1 AAAAATAAAAAT
4163644 AAACAATAAAAA
1 AAA-AATAAAAA
4163656 AGAGTAAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
10 5 0.10
11 7 0.14
12 8 0.16
13 24 0.48
14 6 0.12
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:4163606 original size:20 final size:20
Alignment explanation
Indices: 4163583--4163626 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4163573 GCTAAAAGGA
4163583 AAAACATAA-AAATAA-AGAAT
1 AAAA-ATAATAAATAATA-AAT
4163603 AAAAATAATAAATAATAAAT
1 AAAAATAATAAATAATAAAT
4163623 AAAA
1 AAAA
4163627 TAAAAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAAATAATAAATAATAAAT
Found at i:4163614 original size:16 final size:14
Alignment explanation
Indices: 4163590--4163656 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 14
4163580 GGAAAAACAT
4163590 AAAAATAAAGAATAA
1 AAAAATAAA-AATAA
4163605 AAATAATAAATAATAA
1 AAA-AATAAA-AATAA
*
4163621 ATAAAATAAAAAGGAAA
1 A-AAAATAAAAA--TAA
4163638 AAAAATAAACAATAA
1 AAAAATAAA-AATAA
4163653 AAAA
1 AAAA
4163657 GAGTAAAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 11 0.25
16 26 0.59
17 7 0.16
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:4163857 original size:36 final size:37
Alignment explanation
Indices: 4163777--4163857 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
4163767 GATCAAATAA
* * *
4163777 AAATAAAAAAAAATATATATATATTAGTAATAGGTAT
1 AAATAATAAAAAATATATATATATTAGTAAAAAGTAT
* *
4163814 ATA-AATAAAAAATATATATGTA-TA-TAAAAAGTAAT
1 AAATAATAAAAAATATATATATATTAGTAAAAAGT-AT
4163849 AAATAATAA
1 AAATAATAA
4163858 TAATAATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
34 6 0.17
35 6 0.17
36 22 0.61
37 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (37 bp):
AAATAATAAAAAATATATATATATTAGTAAAAAGTAT
Found at i:4171983 original size:21 final size:21
Alignment explanation
Indices: 4171936--4171984 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4171926 TTTAATGTTG
4171936 GAGAGTATGGATAATAAACTA
1 GAGAGTATGGATAATAAACTA
* *
4171957 GGGAGTATGGATACTCAAAC-A
1 GAGAGTATGGATAAT-AAACTA
4171978 GAGAGTA
1 GAGAGTA
4171985 CAAGTACTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.43, C:0.08, G:0.29, T:0.20
Consensus pattern (21 bp):
GAGAGTATGGATAATAAACTA
Found at i:4173614 original size:31 final size:30
Alignment explanation
Indices: 4173581--4173682 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
4173571 ATAGAAAAAG
4173581 TTTAATAAATCTAATGATTATTTTATAATA
1 TTTAATAAATCTAATGATTATTTTATAATA
* * *
4173611 GTTTAATAAGTTTAATG-GTATTTTAT--T-
1 -TTTAATAAATCTAATGATTATTTTATAATA
*
4173638 TTTGATAAAATCTAATGATTATTTTATAACTA
1 TTTAAT-AAATCTAATGATTATTTTATAA-TA
*
4173670 TTTAA-AAAGCTAA
1 TTTAATAAATCTAA
4173683 ATGACCATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
26 5 0.09
27 8 0.14
28 9 0.16
30 15 0.27
31 15 0.27
32 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTAATAAATCTAATGATTATTTTATAATA
Found at i:4175857 original size:22 final size:21
Alignment explanation
Indices: 4175811--4175874 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
4175801 TCTATAGTAC
* *
4175811 GGTGTC-ATTTATTTTTAGAGT
1 GGTGTCAATTTA-TTTTAAAGG
4175832 GGTGTCAATATTATTTTAAAGG
1 GGTGTCAAT-TTATTTTAAAGG
4175854 GGTGTCAATTTTATTATTAAA
1 GGTGTCAA-TTTATT-TTAAA
4175875 TTTACAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 6 0.16
22 22 0.59
23 9 0.24
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
GGTGTCAATTTATTTTAAAGG
Found at i:4180817 original size:19 final size:19
Alignment explanation
Indices: 4180786--4180831 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
4180776 TCAAAGGATG
4180786 AAAA-AAAAGAATATAAAT
1 AAAATAAAAGAATATAAAT
*
4180804 AAAATAAAATAATATAAAT
1 AAAATAAAAGAATATAAAT
*
4180823 CAAATAAAA
1 AAAATAAAA
4180832 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAATAAAAGAATATAAAT
Found at i:4180941 original size:3 final size:3
Alignment explanation
Indices: 4180933--4180967 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4180923 TAAAAAAGGG
4180933 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4180968 CAAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4187299 original size:21 final size:21
Alignment explanation
Indices: 4187274--4187314 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4187264 TTGGACCTAA
4187274 AAATAAAATTAATAA-AAACAT
1 AAATAAAA-TAATAATAAACAT
4187295 AAATAAAATAATAATAAACA
1 AAATAAAATAATAATAAACA
4187315 GATAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAAAATAATAATAAACAT
Found at i:4187401 original size:12 final size:12
Alignment explanation
Indices: 4187384--4187442 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
4187374 TATATAATAT
4187384 ATATTTTTAAAA
1 ATATTTTTAAAA
4187396 ATA-TTTTAAAA
1 ATATTTTTAAAA
* *
4187407 ACTATATATT--AT
1 A-TAT-TTTTAAAA
4187419 ATATTTTTAAAA
1 ATATTTTTAAAA
*
4187431 ATATTTTCAAAA
1 ATATTTTTAAAA
4187443 TTATATATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
10 3 0.08
11 12 0.32
12 19 0.51
14 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTTTAAAA
Found at i:4187414 original size:35 final size:35
Alignment explanation
Indices: 4187336--4187817 Score: 261
Period size: 35 Copynumber: 12.8 Consensus size: 35
4187326 AAAAAAAAAA
* * *
4187336 ATATAATATATATTATATAAAAAATATTTCCAAAAAACT
1 ATATATTATATATT-T-TTAAAAATATTT--TAAAAACT
*
4187375 ATATAATATATATTTTTAAAAATATTTTAAAAACT
1 ATATATTATATATTTTTAAAAATATTTTAAAAACT
* *
4187410 ATATATTATATATTTTTAAAAATATTTTCAAAATT
1 ATATATTATATATTTTTAAAAATATTTTAAAAACT
* * *
4187445 ATATATCATATAGTTTTCAAAATATTTT-AAAACT
1 ATATATTATATATTTTTAAAAATATTTTAAAAACT
* * * *
4187479 ATATATTATATGTTTTCAAAAAAATGTTTTTAAAACT
1 ATATATTATATATTTT--TAAAAATATTTTAAAAACT
* * * *
4187516 ATATATTATATGTTTTCAAAAAAATGTTTTTTAAAACT
1 ATATATTATATATTTT--TAAAAAT-ATTTTAAAAACT
* *
4187554 ATATATTATATAAGTTTTTCAAAATGA-TTTCAAAACT
1 ATATATTATAT-A-TTTTTAAAAAT-ATTTTAAAAACT
* * *
4187591 ATATATTATATAAGTTTT-AAAATGTTTTCAAAAATT
1 ATATATTATAT-ATTTTTAAAAATATTTT-AAAAACT
* * * *
4187627 ATTTTATATATATATATATATATATATATTCAAAATGTTTTCAAAAACT
1 A---TATAT-TATATATTTTTAAAAATATT---------TT-AAAAACT
* * * *
4187676 ATATATTACATA-TATTCAAAATGTTTTCAAAAACT
1 ATATATTATATATTTTTAAAAATATTTT-AAAAACT
* * *
4187711 ATATATTATATATTTTTTCAAAATGTTTTCAAAACT
1 ATATATTATATA-TTTTTAAAAATATTTTAAAAACT
* *
4187747 ATATATTATATTATATATTTTCAAAATGTTTTCAAAAACT
1 ATATA-T-TA-TATAT-TTTTAAAAATATTTT-AAAAACT
* *
4187787 ATATAATATATACATTTTCAAAAATCATTTT
1 ATAT-AT-TATATATTTTTAAAAAT-ATTTT
4187818 CTAAAGAAAA
Statistics
Matches: 364, Mismatches: 48, Indels: 62
0.77 0.10 0.13
Matches are distributed among these distances:
34 18 0.05
35 93 0.26
36 30 0.08
37 79 0.22
38 40 0.11
39 49 0.13
40 28 0.08
41 1 0.00
44 6 0.02
45 5 0.01
46 5 0.01
49 10 0.03
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
ATATATTATATATTTTTAAAAATATTTTAAAAACT
Found at i:4187638 original size:2 final size:2
Alignment explanation
Indices: 4187631--4187655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4187621 AAAATTATTT
4187631 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 T
4187656 TCAAAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4188631 original size:173 final size:169
Alignment explanation
Indices: 4188326--4188657 Score: 459
Period size: 173 Copynumber: 1.9 Consensus size: 169
4188316 TCGTTGACAA
* * * * *
4188326 ATAACACTTCTCGTCTTGAGTTATGTTGTACTAGGCTGGGAGATTGCCCCAGATCTTTTTCTTGA
1 ATAACACTTCTCGCCTTGAGTTATGTTGTAATAGGATGAGAGATTGCCCCAGATCTTCTTCTTGA
** * * *
4188391 CTTAAAGACCTCGGCTTTAACCAGAAAGTGGTTTCTTGTTGCTACCATATGGTGGATGTGTCATC
66 CTTAAAGACCTCAACTTCAACCAGAAAGTGGTTTCTTATTGCTACCATATGGTGGATCTGTCATC
* *
4188456 GAGCTGAATGTAATCGAACTCGATAGTTTACATTGACTG
131 GAGCTGAATGGAATCGAACTCGACAGTTTACATTGACTG
* *
4188495 ATAACCCTTCTTGCCTTGAGTTATGTTGTAAT-GAGATGAGAGATTGCCCCAGATCTTCTTCTTG
1 ATAACACTTCTCGCCTTGAGTTATGTTGTAATAG-GATGAGAGATTGCCCCAGATCTTCTTC-T-
* * *
4188559 ACTGACTTGAAGACCTCAACTTCAACCAGAAAGTGGTTTTTTATTGCTACCATGTGGTGGATCTG
63 --TGACTTAAAGACCTCAACTTCAACCAGAAAGTGGTTTCTTATTGCTACCATATGGTGGATCTG
4188624 TCATCGAGCTGAATGGAATCGAACTCGACAGTTT
126 TCATCGAGCTGAATGGAATCGAACTCGACAGTTT
4188658 TTGTTGACAG
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
168 1 0.01
169 52 0.37
170 1 0.01
173 87 0.62
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (169 bp):
ATAACACTTCTCGCCTTGAGTTATGTTGTAATAGGATGAGAGATTGCCCCAGATCTTCTTCTTGA
CTTAAAGACCTCAACTTCAACCAGAAAGTGGTTTCTTATTGCTACCATATGGTGGATCTGTCATC
GAGCTGAATGGAATCGAACTCGACAGTTTACATTGACTG
Found at i:4188692 original size:173 final size:169
Alignment explanation
Indices: 4188319--4188695 Score: 432
Period size: 173 Copynumber: 2.2 Consensus size: 169
4188309 AAAGTTTTCG
* * ** * * * *
4188319 TTGACAAATAACACTTCTCGTCTTGAGTTATGTTGTACT-AGGCTGGGAGATTGCCCCAGATCTT
1 TTGACAGATAACCCTTCTCAACTTAAGTTATGTTGTAATGA-GATGAGAGATTGCCCCAGATCTT
* ** * *
4188383 TTTCTTGACTTAAAGACCTCGGCTTTAACCAGAAAGTGGTTTCTTGTTGCTACCATATGGTGGAT
65 CTTCTTGACTTAAAGACCTCAACTTCAACCAGAAAGTGGTTTCTTATTGCTACCATATGGTGGAT
* * *
4188448 GTGTCATCGAGCTGAATGTAATCGAACTCGATAGTTTACA
130 CTGTCATCGAGCTGAATGGAATCGAACTCGACAGTTTACA
* *** *
4188488 TTGACTGATAACCCTTCTTGCCTTGAGTTATGTTGTAATGAGATGAGAGATTGCCCCAGATCTTC
1 TTGACAGATAACCCTTCTCAACTTAAGTTATGTTGTAATGAGATGAGAGATTGCCCCAGATCTTC
* * *
4188553 TTCTTGACTGACTTGAAGACCTCAACTTCAACCAGAAAGTGGTTTTTTATTGCTACCATGTGGTG
66 TTC-T---TGACTTAAAGACCTCAACTTCAACCAGAAAGTGGTTTCTTATTGCTACCATATGGTG
***
4188618 GATCTGTCATCGAGCTGAATGGAATCGAACTCGACAGTTTTTG
127 GATCTGTCATCGAGCTGAATGGAATCGAACTCGACAGTTTACA
* **
4188661 TTGACAGATAGCTTTTCTCAACTTAAGTTATGTTG
1 TTGACAGATAACCCTTCTCAACTTAAGTTATGTTG
4188696 CAAATTTGAC
Statistics
Matches: 173, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
169 57 0.33
170 2 0.01
173 114 0.66
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (169 bp):
TTGACAGATAACCCTTCTCAACTTAAGTTATGTTGTAATGAGATGAGAGATTGCCCCAGATCTTC
TTCTTGACTTAAAGACCTCAACTTCAACCAGAAAGTGGTTTCTTATTGCTACCATATGGTGGATC
TGTCATCGAGCTGAATGGAATCGAACTCGACAGTTTACA
Found at i:4188776 original size:86 final size:86
Alignment explanation
Indices: 4188629--4188929 Score: 347
Period size: 86 Copynumber: 3.5 Consensus size: 86
4188619 ATCTGTCATC
* * ** ** *
4188629 GAGCTGAATGGAATCGAACTCGACA-GT-TTTTGTTGACAGATAGCTTTTCTCAACTTAAGTTAT
1 GAGCTGAGTGTAATCGAACTCGA-AGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTAT
* * *
4188692 GTTGCAAATTTGACATGCCCTT
65 GCTGTAAATTTGATATGCCCTT
* * * *
4188714 GAGCTGAGTGTATTCGAACTCGAAGGTCTTTTGATGACATATATCCCTTCTCGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
* * *
4188779 CTATAAATTTGATGTG-CCTCG
66 CTGTAAATTTGATATGCCCT-T
* *
4188800 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGTTGACAGATAGCCCTTCTCGCCTTGTGCTAT
1 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTAT
* **
4188865 GCTGTAAATTGGATATGCGTTT
65 GCTGTAAATTTGATATGCCCTT
*
4188887 GAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGACAGATA
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATA
4188930 ACTTTGATGT
Statistics
Matches: 181, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.01
85 25 0.14
86 82 0.45
87 72 0.40
88 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (86 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG
CTGTAAATTTGATATGCCCTT
Found at i:4188958 original size:87 final size:87
Alignment explanation
Indices: 4188712--4188929 Score: 269
Period size: 87 Copynumber: 2.5 Consensus size: 87
4188702 TGACATGCCC
* * * ** * *
4188712 TTGAGCTGAGTGTATTCGAACTCGAAGGTC-TTTTGATGACATATATCCCTTCTCGCCTTGAGTT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCATTTTGTTGACAGATAGACCTTATCGCCTTGAGCT
* * * *
4188776 ATGCTATAAATTTGATGTGCCT
66 ATGCTGTAAATTGGATATGCGT
** * * * *
4188798 CGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTTGTTGACAGATAGCCCTTCTCGCCTTGTGCT
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCATTTTGTTGACAGATAGACCTTATCGCCTTGAGCT
4188863 ATGCTGTAAATTGGATATGCGT
66 ATGCTGTAAATTGGATATGCGT
4188885 TTGAGCTGAGTGTAATCGAACTCGAAGGT-ATTTTGTTGACAGATA
1 TTGAGCTGAGTGTAATCGAACTCGAAGGTCATTTTGTTGACAGATA
4188930 ACTTTGATGT
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 42 0.36
87 74 0.64
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (87 bp):
TTGAGCTGAGTGTAATCGAACTCGAAGGTCATTTTGTTGACAGATAGACCTTATCGCCTTGAGCT
ATGCTGTAAATTGGATATGCGT
Found at i:4189199 original size:84 final size:84
Alignment explanation
Indices: 4188934--4189399 Score: 634
Period size: 84 Copynumber: 5.6 Consensus size: 84
4188924 CAGATAACTT
* *
4188934 TGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* * *
4188999 CCTTGAGCTACGCTGCAAA
66 CCTTGAGTTATGCTGTAAA
* * * * *
4189018 TGATGTGCCTTTGAGCTGAGTGTAGTCGAACTCGAATGTC-TTGGTTGACATATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
4189082 CCTTGAGTTATGCTGTAAA
66 CCTTGAGTTATGCTGTAAA
*
4189101 TGATGTGCCTTTGAGCTGAGTGTGATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
*
4189166 CCTTGAGTTATGCTGCAAA
66 CCTTGAGTTATGCTGTAAA
** * * *
4189185 TGATGCACATTTGAGCAT-AGTATAATCGAACTCGAAGGTC--TTGATTGACAGATAACCCTTCT
1 TGATGTGCCTTTGAGC-TGAGTGTAATCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCT
*
4189247 TGCCTTGAGTTATGCTGTAAA
64 CGCCTTGAGTTATGCTGTAAA
* * * * * * *
4189268 TGATATGCTTTTGAGTTGAGTGTAATCAAACTCGAAGGACTTTTGTTGGCAGATAGCCCCTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
*
4189333 CCTTGAGCTATGCTGTAAA
66 CCTTGAGTTATGCTGTAAA
* *
4189352 TGATGCGCCTTTGAGCTGAGTGGAATCGAACTCGAAGGTCTTTTGTTG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
4189400 AAGGTGTTTT
Statistics
Matches: 331, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
82 4 0.01
83 139 0.42
84 184 0.56
85 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
CCTTGAGTTATGCTGTAAA
Found at i:4189216 original size:167 final size:167
Alignment explanation
Indices: 4188934--4189393 Score: 697
Period size: 167 Copynumber: 2.8 Consensus size: 167
4188924 CAGATAACTT
* *
4188934 TGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* * * * *
4188999 CCTTGAGCTACGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAGTCGAACTCGAATGTCTTGGTT
66 CCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGATT
*
4189064 GACATATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
131 GACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
*
4189101 TGATGTGCCTTTGAGCTGAGTGTGATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* * * *
4189166 CCTTGAGTTATGCTGCAAATGATGCACATTTGAGCAT-AGTATAATCGAACTCGAAGGTCTTGAT
66 CCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGC-TGAGTGTAATCGAACTCGAAGGTCTTGAT
*
4189230 TGACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAA
130 TGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* * * * * * *
4189268 TGATATGCTTTTGAGTTGAGTGTAATCAAACTCGAAGGACTTTTGTTGGCAGATAGCCCCTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* *
4189333 CCTTGAGCTATGCTGTAAATGATGCGCCTTTGAGCTGAGTGGAATCGAACTCGAAGGTCTT
66 CCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
4189394 TTGTTGAAGG
Statistics
Matches: 263, Mismatches: 28, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
166 1 0.00
167 261 0.99
168 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (167 bp):
TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
CCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGATT
GACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
Found at i:4190238 original size:65 final size:64
Alignment explanation
Indices: 4190149--4190295 Score: 170
Period size: 65 Copynumber: 2.3 Consensus size: 64
4190139 TTTTGAATAC
* * * * * ***
4190149 AATTTATGCACTGATACACAGTCATGCATCGATGCACTCTGGAT-TTTATTAAAACATCGAATTG
1 AATTTGTGCACCGATGCACAGTCATGCATCGATGCACCCCGGATATTT-TTAAAACATCGAAGAA
* * *
4190213 ATTTTGTGCACCGATGCACAAGTCATGCATCGATGCACCCCGGCTATTTTTGAAACATCGAAGAA
1 AATTTGTGCACCGATGCAC-AGTCATGCATCGATGCACCCCGGATATTTTTAAAACATCGAAGAA
4190278 AATTTGTGCACCGATGCA
1 AATTTGTGCACCGATGCA
4190296 TACCCTAGTG
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 15 0.22
65 51 0.74
66 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
AATTTGTGCACCGATGCACAGTCATGCATCGATGCACCCCGGATATTTTTAAAACATCGAAGAA
Found at i:4192213 original size:21 final size:21
Alignment explanation
Indices: 4192189--4192228 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4192179 AAGACTTTAT
4192189 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
4192210 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
4192229 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:4194238 original size:23 final size:22
Alignment explanation
Indices: 4194210--4194289 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
4194200 ACACTATCTA
4194210 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * *
4194233 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
* * *
4194254 GTGCACCAAAGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
*
4194277 GTACATCGATGCA
1 GTGCATCGATGCA
4194290 CTCTGCTGTG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 15 0.36
23 27 0.64
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:4196239 original size:25 final size:26
Alignment explanation
Indices: 4196211--4196290 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 26
4196201 AAATATTTTG
*
4196211 TTGTTTTTAT-TTTGGATGTTTGAAT
1 TTGTTTATATATTTGGATGTTTGAAT
* *
4196236 TTGTTGGAT-GA-TTGGATGTTTGAAT
1 TTGTT-TATATATTTGGATGTTTGAAT
* *
4196261 TTATTATATATATTTGGTATGTTTAAAT
1 TTGTT-TATATATTTGG-ATGTTTGAAT
4196289 TT
1 TT
4196291 TCTCTTCGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
25 25 0.60
26 2 0.05
27 4 0.10
28 11 0.26
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (26 bp):
TTGTTTATATATTTGGATGTTTGAAT
Done.