Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 137 of 240
Found at i:42655744 original size:10 final size:10
Alignment explanation
Indices: 42655729--42655766 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
42655719 GCTCGTTTCC
*
42655729 AGCTCACTCG
1 AGCTCAATCG
42655739 AGCTCAAGTC-
1 AGCTCAA-TCG
42655749 AGCTCAATCG
1 AGCTCAATCG
42655759 AGCTCAAT
1 AGCTCAAT
42655767 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:42655753 original size:20 final size:20
Alignment explanation
Indices: 42655728--42655765 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42655718 AGCTCGTTTC
*
42655728 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
42655748 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
42655766 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:42655772 original size:20 final size:20
Alignment explanation
Indices: 42655729--42655789 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
42655719 GCTCGTTTCC
* * *
42655729 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
42655749 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
42655769 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
42655789 A
1 A
42655790 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:42655783 original size:11 final size:10
Alignment explanation
Indices: 42655739--42655785 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
42655729 AGCTCACTCG
*
42655739 AGCTCAAGTC
1 AGCTCAATTC
42655749 AGCTCAA-TC
1 AGCTCAATTC
*
42655758 GAGCTCAATTT
1 -AGCTCAATTC
42655769 AGCTACAATTC
1 AGCT-CAATTC
42655780 AGCTCA
1 AGCTCA
42655786 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:42657191 original size:16 final size:14
Alignment explanation
Indices: 42657160--42657220 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
42657150 AAAAAAAATC
42657160 AAAAAAAATTTCGA
1 AAAAAAAATTTCGA
*
42657174 AAAAAAAATTGATTG-
1 AAAAAAAATT--TCGA
42657189 AAAAAAAA-TTC--
1 AAAAAAAATTTCGA
42657200 AAAAAAAA-TT-GA
1 AAAAAAAATTTCGA
42657212 AAAAAAAAT
1 AAAAAAAAT
42657221 CGAGCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 10 0.25
12 9 0.22
14 11 0.28
15 8 0.20
16 2 0.05
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAAAAATTTCGA
Found at i:42657205 original size:10 final size:11
Alignment explanation
Indices: 42657149--42657218 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 11
42657139 ATTGGAGTAA
42657149 CAAAAAAAA-T
1 CAAAAAAAATT
42657159 CAAAAAAAATTT
1 CAAAAAAAA-TT
42657171 CGAAAAAAAAATTGATT
1 C---AAAAAAA---ATT
*
42657188 GAAAAAAAATT
1 CAAAAAAAATT
42657199 CAAAAAAAATT
1 CAAAAAAAATT
*
42657210 GAAAAAAAA
1 CAAAAAAAA
42657219 ATCGAGCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
10 9 0.18
11 21 0.43
12 2 0.04
14 7 0.14
15 7 0.14
17 2 0.04
18 1 0.02
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:42657231 original size:38 final size:39
Alignment explanation
Indices: 42657150--42657234 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
42657140 TTGGAGTAAC
*
42657150 AAAAAAAATCAAAAAAAATTTCGAAAAAAAAATTGATTG-A
1 AAAAAAAATCAAAAAAAATTTCGAAAAAAAAATCGA--GCA
*
42657190 AAAAAAATTCAAAAAAAA-TT-GAAAAAAAAATCGAGCA
1 AAAAAAAATCAAAAAAAATTTCGAAAAAAAAATCGAGCA
42657227 AAAAAAAA
1 AAAAAAAA
42657235 GAAAAGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 1 0.02
37 8 0.20
38 13 0.32
39 2 0.05
40 17 0.41
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.15
Consensus pattern (39 bp):
AAAAAAAATCAAAAAAAATTTCGAAAAAAAAATCGAGCA
Found at i:42660332 original size:20 final size:20
Alignment explanation
Indices: 42660307--42660344 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42660297 AGCTCGTTTC
* *
42660307 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCAAGCTCAAGT
42660327 CAGCTCAATCAAGCTCAA
1 CAGCTCAATCAAGCTCAA
42660345 TTTAGCTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCAAGCTCAAGT
Found at i:42660351 original size:20 final size:19
Alignment explanation
Indices: 42660308--42660368 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
42660298 GCTCGTTTCC
* * *
42660308 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATC-AGCTCAATTT
42660328 AGCTCAATCAAGCTCAATTT
1 AGCTCAATC-AGCTCAATTT
42660348 AGCTACAATTCAGCTC-ATTT
1 AGCT-CAA-TCAGCTCAATTT
42660368 A
1 A
42660369 TTTTATTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 25 0.71
21 8 0.23
22 2 0.06
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (19 bp):
AGCTCAATCAGCTCAATTT
Found at i:42660362 original size:11 final size:10
Alignment explanation
Indices: 42660318--42660364 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
42660308 AGCTCACTCG
*
42660318 AGCTCAAGTC
1 AGCTCAATTC
42660328 AGCTCAA-TC
1 AGCTCAATTC
*
42660337 AAGCTCAATTT
1 -AGCTCAATTC
42660348 AGCTACAATTC
1 AGCT-CAATTC
42660359 AGCTCA
1 AGCTCA
42660365 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:42667203 original size:23 final size:22
Alignment explanation
Indices: 42667152--42667203 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
42667142 CCTCGTCTTT
*
42667152 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
42667174 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
42667197 TTCTTTT
1 TTCTTTT
42667204 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:42671830 original size:56 final size:55
Alignment explanation
Indices: 42671714--42671831 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
42671704 TGCATGCTTT
* * * *
42671714 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
42671768 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
42671824 CATTAAAT
1 CATTAAAT
42671832 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:42672480 original size:20 final size:20
Alignment explanation
Indices: 42672455--42672509 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
42672445 ACGAGTTAAA
* *
42672455 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
42672475 TTGAGCTCGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
42672495 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
42672510 TTGAACCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:42673865 original size:21 final size:23
Alignment explanation
Indices: 42673821--42673866 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
42673811 CACCTGCAAG
* *
42673821 AAACACATTAAAATGAGTTTATT
1 AAACACATTAAAATCAGCTTATT
42673844 AAACACATTAAAA-CA-CTTATT
1 AAACACATTAAAATCAGCTTATT
42673865 AA
1 AA
42673867 TCATAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (23 bp):
AAACACATTAAAATCAGCTTATT
Found at i:42679216 original size:15 final size:15
Alignment explanation
Indices: 42679196--42679250 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
42679186 TAGCTTCTTC
42679196 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
42679211 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
42679226 -TTTTTTTTCACG-A
1 TTTTTTTTTCACGAA
42679239 TTTTTGTTTTCA
1 TTTTT-TTTTCA
42679251 ACTTGATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.03
14 16 0.42
15 21 0.55
ACGTcount: A:0.16, C:0.13, G:0.07, T:0.64
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:42679305 original size:12 final size:12
Alignment explanation
Indices: 42679288--42679344 Score: 98
Period size: 12 Copynumber: 4.8 Consensus size: 12
42679278 ATGGAAACCA
42679288 AATTTTTTTTTG
1 AATTTTTTTTTG
42679300 AA-TTTTTTTTG
1 AATTTTTTTTTG
42679311 AATTTTTTTTTG
1 AATTTTTTTTTG
*
42679323 AAATTTTTTTTG
1 AATTTTTTTTTG
42679335 AATTTTTTTT
1 AATTTTTTTT
42679345 GAAGAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.26
12 31 0.74
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:42679307 original size:11 final size:11
Alignment explanation
Indices: 42679291--42679347 Score: 96
Period size: 11 Copynumber: 5.0 Consensus size: 11
42679281 GAAACCAAAT
42679291 TTTTTTTTGAA
1 TTTTTTTTGAA
42679302 TTTTTTTTGAA
1 TTTTTTTTGAA
42679313 TTTTTTTTTGAAA
1 -TTTTTTTTG-AA
42679326 TTTTTTTTGAA
1 TTTTTTTTGAA
42679337 TTTTTTTTGAA
1 TTTTTTTTGAA
42679348 GAAACTACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
11 24 0.55
12 18 0.41
13 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:42680382 original size:21 final size:23
Alignment explanation
Indices: 42680338--42680383 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
42680328 CACCTGCAAG
* *
42680338 AAACACATTAAAATGAGTTTATT
1 AAACACATTAAAATCAGCTTATT
42680361 AAACACATTAAAA-CA-CTTATT
1 AAACACATTAAAATCAGCTTATT
42680382 AA
1 AA
42680384 TCATAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (23 bp):
AAACACATTAAAATCAGCTTATT
Found at i:42683534 original size:11 final size:11
Alignment explanation
Indices: 42683518--42683561 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
42683508 GAGAAGAAAT
42683518 TTGAAAAAAAA
1 TTGAAAAAAAA
42683529 TTGAAAAAAAA
1 TTGAAAAAAAA
*
42683540 TCGAAAAAAAA
1 TTGAAAAAAAA
*
42683551 TTTAAAAAAAA
1 TTGAAAAAAAA
42683562 AATCGAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (11 bp):
TTGAAAAAAAA
Found at i:42683548 original size:24 final size:24
Alignment explanation
Indices: 42683521--42683568 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
42683511 AAGAAATTTG
*
42683521 AAAAAAAATT-GAAAAAAAATCGA
1 AAAAAAAATTAAAAAAAAAATCGA
*
42683544 AAAAAAATTTAAAAAAAAAATCGA
1 AAAAAAAATTAAAAAAAAAATCGA
42683568 A
1 A
42683569 GTATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAAAAAATTAAAAAAAAAATCGA
Found at i:42698530 original size:27 final size:27
Alignment explanation
Indices: 42698499--42698676 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42698489 TAAATTGTAC
42698499 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42698526 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42698552 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42698580 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42698608 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42698635 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42698662 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42698677 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42698613 original size:82 final size:81
Alignment explanation
Indices: 42698500--42698655 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42698490 AAATTGTACA
* *
42698500 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42698564 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42698581 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42698646 TGCGAGTTGA
65 TGCGAATTGA
42698656 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42698667 original size:82 final size:81
Alignment explanation
Indices: 42698496--42698676 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42698486 GATTAAATTG
* *
42698496 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42698561 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42698577 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42698641 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42698659 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42698677 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42705771 original size:11 final size:11
Alignment explanation
Indices: 42705711--42705754 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
42705701 AGATTCGTGA
*
42705711 AAAAAAAAATTG
1 AAAAAAAAA-TC
42705723 AAAAAAAAATC
1 AAAAAAAAATC
42705734 AAAAAAAAATC
1 AAAAAAAAATC
*
42705745 AAAGAAAAAT
1 AAAAAAAAAT
42705755 TAATTGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.11
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:42707999 original size:18 final size:19
Alignment explanation
Indices: 42707976--42708014 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42707966 GAACAAAAAG
* *
42707976 AAAAGATGG-GAAAAGAAA
1 AAAAGAGGGAGAAAACAAA
42707994 AAAAGAGGGAGAAAACAAA
1 AAAAGAGGGAGAAAACAAA
42708013 AA
1 AA
42708015 GAAAAAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (19 bp):
AAAAGAGGGAGAAAACAAA
Found at i:42708003 original size:17 final size:18
Alignment explanation
Indices: 42707970--42708016 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
42707960 GCAAAGGAAC
*
42707970 AAAAAGAAAAGATGGGA-
1 AAAAAAAAAAGATGGGAG
42707987 AAAGAAAAAAAGA-GGGAG
1 AAA-AAAAAAAGATGGGAG
*
42708005 AAAACAAAAAGA
1 AAAAAAAAAAGA
42708017 AAAAGTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAGATGGGAG
Found at i:42710390 original size:20 final size:19
Alignment explanation
Indices: 42710367--42710431 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
42710357 AAGCTCAAAC
42710367 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
42710387 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
42710407 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
42710427 GAGCT
1 GAGCT
42710432 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:42712245 original size:33 final size:33
Alignment explanation
Indices: 42712207--42712269 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
42712197 GATTACTCAC
42712207 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
42712240 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
42712270 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:42712296 original size:21 final size:21
Alignment explanation
Indices: 42712267--42712322 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
42712257 CAAGCTCTCT
*
42712267 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
42712288 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
42712309 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
42712323 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:42712309 original size:18 final size:18
Alignment explanation
Indices: 42712284--42712371 Score: 77
Period size: 18 Copynumber: 4.7 Consensus size: 18
42712274 TCTTTTTTCG
42712284 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
42712303 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCAATTT
* ** *
42712323 CTCTCACTTTTTCGATTT
1 CTTTTTCTTTTTCAATTT
*
42712341 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
42712359 CTTTTTCTTTTTC
1 CTTTTTCTTTTTC
42712372 TCGCTCAATG
Statistics
Matches: 52, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
18 34 0.65
19 3 0.06
20 7 0.13
21 8 0.15
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:42712315 original size:14 final size:14
Alignment explanation
Indices: 42712266--42712322 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
42712256 TCAAGCTCTC
42712266 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
42712279 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
42712293 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
42712307 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
42712321 TT
1 TT
42712323 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:42712369 original size:5 final size:6
Alignment explanation
Indices: 42712284--42712372 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
42712274 TCTTTTTTCG
* * * **
42712284 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * **
42712335 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CT
42712373 CGCTCAATGG
Statistics
Matches: 60, Mismatches: 21, Indels: 4
0.71 0.25 0.05
Matches are distributed among these distances:
6 48 0.80
7 9 0.15
8 3 0.05
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:42713432 original size:12 final size:12
Alignment explanation
Indices: 42713416--42713486 Score: 63
Period size: 12 Copynumber: 5.7 Consensus size: 12
42713406 TTTTTGCTCG
42713416 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
42713428 CTTTTTTTTTGA
1 ATTTTTTTTTCA
42713440 ATTTTTTTTTCA
1 ATTTTTTTTTCA
42713452 ATCAAATTTTTTTTCA
1 AT----TTTTTTTTCA
* *
42713468 AATTTTTTTT-G
1 ATTTTTTTTTCA
42713479 ATTTTTTT
1 ATTTTTTT
42713487 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
11 7 0.15
12 30 0.62
16 11 0.23
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:42713432 original size:24 final size:24
Alignment explanation
Indices: 42713405--42713451 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42713395 TCTTTTCTTT
42713405 TTTTTTGCTCG-ATTTTTTTTTCAC
1 TTTTTT-CTCGAATTTTTTTTTCAC
* *
42713429 TTTTTTTTTGAATTTTTTTTTCA
1 TTTTTTCTCGAATTTTTTTTTCA
42713452 ATCAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTTTTCTCGAATTTTTTTTTCAC
Found at i:42713436 original size:30 final size:30
Alignment explanation
Indices: 42713373--42713437 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
42713363 TTAAACTTGA
*
42713373 TTTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCACCTTTTTTTTCCTTTCT
*
42713403 TTTTTTTTGCTCGA-TTTTTTTTTCACTTT-T
1 TTTTTTTTGCTC-ACCTTTTTTTTC-CTTTCT
42713433 TTTTT
1 TTTTT
42713438 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (30 bp):
TTTTTTTTGCTCACCTTTTTTTTCCTTTCT
Found at i:42715113 original size:20 final size:19
Alignment explanation
Indices: 42715090--42715154 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
42715080 AAGCTCAAAC
42715090 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
42715110 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
42715130 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
42715150 GAGCT
1 GAGCT
42715155 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:42718296 original size:15 final size:15
Alignment explanation
Indices: 42718264--42718297 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42718254 GTTCAACGAA
*
42718264 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
42718279 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
42718294 GAGG
1 GAGG
42718298 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:42724570 original size:8 final size:9
Alignment explanation
Indices: 42724548--42724581 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42724538 CAAAAAAATC
42724548 AGTCAAAAA
1 AGTCAAAAA
42724557 AGTCAAAAA
1 AGTCAAAAA
42724566 A-TCAAAAA
1 AGTCAAAAA
*
42724574 AGACAAAA
1 AGTCAAAA
42724582 TTCAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.71, C:0.12, G:0.09, T:0.09
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:42730070 original size:19 final size:18
Alignment explanation
Indices: 42730034--42730073 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42730024 TTTCCACTCG
*
42730034 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
42730052 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
42730071 TTT
1 TTT
42730074 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:42731151 original size:14 final size:14
Alignment explanation
Indices: 42731134--42731186 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
42731124 GAACTAGCTC
42731134 TTTTTTT-ACAATT
1 TTTTTTTCACAATT
*
42731147 CTTTTTTCACAATT
1 TTTTTTTCACAATT
*
42731161 TTTTTTTCAAAATT
1 TTTTTTTCACAATT
42731175 TTTTTTTCACAA
1 TTTTTTTCACAA
42731187 CTTGATATCC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
13 6 0.17
14 29 0.83
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:42731245 original size:15 final size:14
Alignment explanation
Indices: 42731221--42731256 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
42731211 GAATGGAAAC
* *
42731221 TTTTTATTTTCGAA
1 TTTTTTTTTTTGAA
42731235 TTTTTTTTTTTGAA
1 TTTTTTTTTTTGAA
42731249 TTTTTTTT
1 TTTTTTTT
42731257 CAAGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTTTGAA
Found at i:42741280 original size:20 final size:20
Alignment explanation
Indices: 42741233--42741280 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
42741223 AGTAAGCTCG
42741233 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
42741253 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
42741273 GTTGAGCT
1 GTTGAGCT
42741281 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:42742685 original size:17 final size:18
Alignment explanation
Indices: 42742663--42742696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42742653 ACAACACTCC
*
42742663 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
42742680 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
42742697 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:42742803 original size:15 final size:16
Alignment explanation
Indices: 42742778--42742809 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
42742768 TATCTCACAC
42742778 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
42742794 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
42742809 T
1 T
42742810 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:42743794 original size:14 final size:14
Alignment explanation
Indices: 42743777--42743826 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
42743767 TTTTTTTCAC
42743777 TTTTTTTT-GAATT
1 TTTTTTTTCGAATT
*
42743790 TTTTTTTCAATCAAATT
1 TTTTTTT---TCGAATT
42743807 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
42743821 TTTTTT
1 TTTTTT
42743827 GATTTTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
16 1 0.03
17 11 0.35
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:42747296 original size:20 final size:20
Alignment explanation
Indices: 42747267--42747315 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42747257 TTTTCTCTCG
*
42747267 CTTTCCTTTTCGTCTTTTCA
1 CTTTCATTTTCGTCTTTTCA
* *
42747287 TTTTCATTTTCTTCTTTTCA
1 CTTTCATTTTCGTCTTTTCA
42747307 CTTT-ATTTT
1 CTTTCATTTT
42747316 TCTCTTCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.67
Consensus pattern (20 bp):
CTTTCATTTTCGTCTTTTCA
Found at i:42747316 original size:20 final size:20
Alignment explanation
Indices: 42747273--42747345 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
42747263 CTCGCTTTCC
* *
42747273 TTTTCGTCTTTTCATTTTCA-
1 TTTTCTTCTTTTCACTTT-AT
42747293 TTTTCTTCTTTTCACTTTAT
1 TTTTCTTCTTTTCACTTTAT
*
42747313 TTTTC-TCTTCTC-CTTT-T
1 TTTTCTTCTTTTCACTTTAT
42747330 TCTTT-TTC-TTTCACTT
1 T-TTTCTTCTTTTCACTT
42747346 GTTTTAACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.11
18 12 0.27
19 7 0.16
20 21 0.47
ACGTcount: A:0.07, C:0.23, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTTCTTCTTTTCACTTTAT
Found at i:42755187 original size:1 final size:1
Alignment explanation
Indices: 42755177--42755221 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
42755167 TTACAGGTAT
* * *
42755177 AAAAAGAAAAAAAGAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42755222 GCATAGTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:42755199 original size:11 final size:11
Alignment explanation
Indices: 42755183--42755222 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
42755173 GTATAAAAAG
42755183 AAAAAAAGAAA
1 AAAAAAAGAAA
42755194 AAAAAAAGAAA
1 AAAAAAAGAAA
42755205 AAAAAAA-AAA
1 AAAAAAAGAAA
42755215 AAAAAAAG
1 AAAAAAAG
42755223 CATAGTGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:42755209 original size:21 final size:21
Alignment explanation
Indices: 42755183--42755222 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42755173 GTATAAAAAG
*
42755183 AAAAAAAGAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAGAA
42755204 AAAAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAG
42755223 CATAGTGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAAAGAA
Found at i:42755219 original size:19 final size:19
Alignment explanation
Indices: 42755177--42755219 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
42755167 TTACAGGTAT
*
42755177 AAAAAGAAAAAAAGAAAAA
1 AAAAAGAAAAAAAAAAAAA
42755196 AAAAAGAAAAAAAAAAAAA
1 AAAAAGAAAAAAAAAAAAA
42755215 AAAAA
1 AAAAA
42755220 AAGCATAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAAAAA
Found at i:42772574 original size:26 final size:27
Alignment explanation
Indices: 42772519--42772692 Score: 176
Period size: 27 Copynumber: 6.6 Consensus size: 27
42772509 ATATTGAGCC
* * * *
42772519 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42772546 CGCACACTTAGTGC-ACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
42772572 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
42772599 CGCAC-CTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42772625 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42772652 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42772679 CGCAC-CTTAGTGCT
1 CGCACACTTAGTGCT
42772693 GTACAATTTA
Statistics
Matches: 124, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
26 53 0.43
27 70 0.56
28 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42772599 original size:53 final size:53
Alignment explanation
Indices: 42772519--42772692 Score: 194
Period size: 53 Copynumber: 3.3 Consensus size: 53
42772509 ATATTGAGCC
* * *
42772519 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCACGTAGTCAAAT
* * *
42772572 CGCACACTTAGTGCTACATAGTCAACTCGCAC-CTTAGTGC-CGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCACG--TAGTCAAAT
* ** *
42772625 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGC-ACGTAGTCAAAT
42772679 CGCAC-CTTAGTGCT
1 CGCACACTTAGTGCT
42772693 GTACAATTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
51 2 0.02
52 9 0.09
53 70 0.69
54 20 0.20
56 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCACGTAGTCAAAT
Found at i:42780516 original size:27 final size:27
Alignment explanation
Indices: 42780486--42780663 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
42780476 ATATTGAGCC
* *
42780486 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
42780513 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42780540 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** ** *
42780568 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
42780595 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
42780622 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42780649 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
42780664 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42780625 original size:82 final size:81
Alignment explanation
Indices: 42780507--42780662 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
42780497 TGCTATATAA
* * *
42780507 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
*
42780572 CTCTTAGTGCCGCATGG
65 CCCTTAGTGCCGCATGG
* * **
42780589 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42780653 CCCTTAGTGC
65 CCCTTAGTGC
42780663 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
CCTTAGTGCCGCATGG
Found at i:42790128 original size:29 final size:29
Alignment explanation
Indices: 42790086--42790164 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
42790076 CGACAGTCGT
* * * *
42790086 AACCGTCCCATTTCATATTCGATGGTTGA
1 AACCATCCCTTTTCATAATCCATGGTTGA
*
42790115 AACCATCCCTTTTCATTAATCCATGGTTGT
1 AACCATCCCTTTTCA-TAATCCATGGTTGA
* *
42790145 CACCATCCCTATTCATAATC
1 AACCATCCCTTTTCATAATC
42790165 AATAGCCGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.43
30 24 0.57
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.35
Consensus pattern (29 bp):
AACCATCCCTTTTCATAATCCATGGTTGA
Found at i:42796277 original size:79 final size:81
Alignment explanation
Indices: 42796176--42796360 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
42796166 GCTACTCGTT
* * *
42796176 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
42796239 GAATTTAGTAAC-TCGCA
64 GAATATAGTAACTTAGCA
* ** *
42796256 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGA
* *
42796320 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
42796336 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42796361 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGA
ATATAGTAACTTAGCA
Found at i:42796360 original size:40 final size:40
Alignment explanation
Indices: 42796157--42796360 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
42796147 CGGAATTTAA
** *
42796157 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42796197 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42796237 CCGAATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42796276 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42796316 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42796356 CCGGA
1 CCGGA
42796361 CATCATTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 91 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42803524 original size:79 final size:81
Alignment explanation
Indices: 42803423--42803607 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
42803413 GCTACTCGTT
* * *
42803423 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
42803486 GAATTTAGTAAC-TCGCA
64 GAATATAGTAACTTAGCA
* * ** *
42803503 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGA
* *
42803567 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
42803583 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42803608 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 52 0.58
80 34 0.38
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGA
ATATAGTAACTTAGCA
Found at i:42803607 original size:40 final size:40
Alignment explanation
Indices: 42803404--42803607 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
42803394 CGGAATTTAA
** *
42803404 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42803444 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42803484 CCGAATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42803523 CCGGA-ATTAGTATCTCGTACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42803563 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42803603 CCGGA
1 CCGGA
42803608 CATCATTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 31 0.23
40 91 0.67
41 11 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42806951 original size:25 final size:25
Alignment explanation
Indices: 42806917--42807053 Score: 132
Period size: 25 Copynumber: 5.5 Consensus size: 25
42806907 TACCGATTTA
* *
42806917 AGCTCTTATGAGCTTACCGTTACTC
1 AGCTCGTATGAGCTTACCGTTATTC
42806942 AGCTCGTATGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* ** * *
42806967 AACTCAAAAGAGCTTACTGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* *
42806992 AGCTCGTAGGAGCTTAGCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * * * *
42807017 AACTTGAAGGAGCTTACCGTT-TAC
1 AGCTCGTATGAGCTTACCGTTATTC
*
42807041 AGCTCATATGAGC
1 AGCTCGTATGAGC
42807054 ATACATGTAT
Statistics
Matches: 89, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
24 10 0.11
25 79 0.89
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:42806994 original size:50 final size:50
Alignment explanation
Indices: 42806926--42807053 Score: 168
Period size: 50 Copynumber: 2.6 Consensus size: 50
42806916 AAGCTCTTAT
*
42806926 GAGCTTACCGTTACTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
1 GAGCTTACCGTTATTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
* * * ** *
42806976 GAGCTTACTGTTATTCAGCTCGTAGGAGCTTAGCGTTATTCAACTTGAAG
1 GAGCTTACCGTTATTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
* *
42807026 GAGCTTACCGTT-TACAGCTCATATGAGC
1 GAGCTTACCGTTATTCAGCTCGTATGAGC
42807054 ATACATGTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 13 0.19
50 54 0.81
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
GAGCTTACCGTTATTCAGCTCGTATGAGCTTACCGTTATTCAACTCAAAA
Found at i:42817586 original size:40 final size:40
Alignment explanation
Indices: 42817530--42817617 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
42817520 ATTGGTACTC
42817530 TCTGTCTGGTGCGTTTC-AGTTGGATTAG-TTCTTATGAGCT
1 TCTGTCTGGTGCGTTTCGA-TTGGATTAGCTT-TTATGAGCT
* *
42817570 TCTGTCTGGTGTGTTTCGATTGGATTAGCTTTTATGTGCT
1 TCTGTCTGGTGCGTTTCGATTGGATTAGCTTTTATGAGCT
42817610 TCTGTCTG
1 TCTGTCTG
42817618 TCGTCTTCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (40 bp):
TCTGTCTGGTGCGTTTCGATTGGATTAGCTTTTATGAGCT
Found at i:42828184 original size:21 final size:21
Alignment explanation
Indices: 42828158--42828205 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
42828148 CCAGTCAGTG
42828158 TACACGGGCATGTGAAGTAGC
1 TACACGGGCATGTGAAGTAGC
*
42828179 TACACGGGCGTGTGAAGTAGC
1 TACACGGGCATGTGAAGTAGC
*
42828200 CACACG
1 TACACG
42828206 ACCATATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (21 bp):
TACACGGGCATGTGAAGTAGC
Found at i:42829215 original size:23 final size:22
Alignment explanation
Indices: 42829189--42829231 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42829179 GAGAAATAAA
*
42829189 AATTAAGTGAAAATTTAAGAGGG
1 AATTAAGAG-AAATTTAAGAGGG
*
42829212 AATTGAGAGAAATTTAAGAG
1 AATTAAGAGAAATTTAAGAG
42829232 AGATTTGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (22 bp):
AATTAAGAGAAATTTAAGAGGG
Found at i:42829227 original size:22 final size:22
Alignment explanation
Indices: 42829199--42829241 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42829189 AATTAAGTGA
*
42829199 AAATTTAAGAGGGAATTGAGAG
1 AAATTTAAGAGAGAATTGAGAG
*
42829221 AAATTTAAGAGAGATTTGAGA
1 AAATTTAAGAGAGAATTGAGA
42829242 ATGTGAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (22 bp):
AAATTTAAGAGAGAATTGAGAG
Found at i:42833721 original size:56 final size:56
Alignment explanation
Indices: 42833632--42833756 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
42833622 TATGTAAAAC
* ** *
42833632 TATGTAAAATTATTAAGCCCAATAACTTTTGTTAATGGTTAGTAA-ATTTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGA-TTATCAAAT
42833688 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
*
42833744 TAGGTAAAATTAT
1 TATGTAAAATTAT
42833757 GTTATGGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 62 0.98
57 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
Found at i:42833776 original size:23 final size:23
Alignment explanation
Indices: 42833750--42833858 Score: 164
Period size: 23 Copynumber: 4.7 Consensus size: 23
42833740 AAATTAGGTA
* *
42833750 AAATTATGTTATGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAAAT
42833773 AAATTAGGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAAAT
*
42833796 AAATTAAGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAAAT
*
42833819 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAAAT
* *
42833842 AAATTAGGGTAGAGTTT
1 AAATTAGGTTAGGGTTT
42833859 AGGGTTATGG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAAAT
Found at i:42833925 original size:29 final size:29
Alignment explanation
Indices: 42833857--42834718 Score: 1296
Period size: 29 Copynumber: 30.2 Consensus size: 29
42833847 AGGGTAGAGT
*
42833857 TTAGGGTTATGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
**
42833886 TTAATTGTTAGGGTTTTTAATTAAATTAGG
1 TT-AGGGTTAGGGTTTTTAATTAAATTAGG
*
42833916 TTAAGGTTAGGG-TTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42833944 GTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42833973 TTAGGGTTAGGATTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834002 TTAAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834031 TTTAGGGTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834061 TTAGGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834090 TTAAGGTTAGGG-TTTTAATTAAATTAAGG
1 TTAGGGTTAGGGTTTTTAATTAAATT-AGG
42834119 -TAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834147 TTTAGGTTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTAGGGTTTTTAATTAAATTAGG
* *
42834177 TTAAGGTTAGGG-TTTTAATTATATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834205 GTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834234 TTA--G-T---GTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834257 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
* *
42834286 GTACGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834315 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834344 TTAAGGTTAGGG-TTTTAATT--A-TA--
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834367 TTAGGG-TAGGG-TTTTAATTATATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834394 GTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834423 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834452 TTAGGGTTAGAGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834481 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834510 TTAAGGTTAGGG-TTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
* *
42834538 GTAGGGTTAGGGTTTTTAATCAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834567 TTTAGTGTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834597 TTAAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834626 TTAAGGTTAGGG-TTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834654 GTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
42834683 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
42834712 CTAGGGT
1 TTAGGGT
42834719 ATGAAATAAA
Statistics
Matches: 761, Mismatches: 48, Indels: 48
0.89 0.06 0.06
Matches are distributed among these distances:
22 13 0.02
23 26 0.03
24 1 0.00
25 5 0.01
26 3 0.00
27 6 0.01
28 142 0.19
29 458 0.60
30 107 0.14
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (29 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGG
Found at i:42834109 original size:23 final size:22
Alignment explanation
Indices: 42834083--42834125 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
42834073 TTTTTAATTA
*
42834083 AATTAAGTTAAGGTTAGGGTTTT
1 AATTAAATTAAGG-TAGGGTTTT
42834106 AATTAAATTAAGGTAGGGTT
1 AATTAAATTAAGGTAGGGTT
42834126 AGGGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (22 bp):
AATTAAATTAAGGTAGGGTTTT
Found at i:42834377 original size:22 final size:22
Alignment explanation
Indices: 42834351--42834401 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
42834341 AGGTTAAGGT
42834351 TAGGGTTTTAATTATATTAGGG
1 TAGGGTTTTAATTATATTAGGG
42834373 TAGGGTTTTAATTATATTAGGG
1 TAGGGTTTTAATTATATTAGGG
42834395 TAGGGTT
1 TAGGGTT
42834402 AGGGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.45
Consensus pattern (22 bp):
TAGGGTTTTAATTATATTAGGG
Found at i:42834752 original size:26 final size:25
Alignment explanation
Indices: 42834722--42834779 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
42834712 CTAGGGTATG
42834722 AAATAAA-TTACGATTTTTATTACATC
1 AAATAAACTT-CGA-TTTTATTACATC
* *
42834748 AAATAGAACTTCTATTTTATTATATC
1 AAATA-AACTTCGATTTTATTACATC
42834774 AAATAA
1 AAATAA
42834780 TATCAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 21 0.75
27 4 0.14
28 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (25 bp):
AAATAAACTTCGATTTTATTACATC
Found at i:42837058 original size:10 final size:10
Alignment explanation
Indices: 42837039--42837104 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
42837029 GCCATTGATG
*
42837039 AAAATATAAA
1 AAAATTTAAA
42837049 AAAATTTAAA
1 AAAATTTAAA
* *
42837059 ATTATTTTAAA
1 A-AAATTTAAA
*
42837070 AAAATATAAA
1 AAAATTTAAA
*
42837080 AAAATTTGAA
1 AAAATTTAAA
**
42837090 ATTATTTAAA
1 AAAATTTAAA
42837100 AAAAT
1 AAAAT
42837105 GAAATTGAGG
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
10 34 0.81
11 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:42837074 original size:31 final size:30
Alignment explanation
Indices: 42837039--42837104 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
42837029 GCCATTGATG
42837039 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTA-TTTAAA
*
42837070 AAAATATAAAAAAATTTGAAATTATTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTAAA
42837100 AAAAT
1 AAAAT
42837105 GAAATTGAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.32
31 23 0.68
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTAAA
Found at i:42837086 original size:21 final size:21
Alignment explanation
Indices: 42837045--42837086 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42837035 GATGAAAATA
* **
42837045 TAAAAAAATTTAAAATTATTT
1 TAAAAAAATATAAAAAAATTT
42837066 TAAAAAAATATAAAAAAATTT
1 TAAAAAAATATAAAAAAATTT
42837087 GAAATTATTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAAAATATAAAAAAATTT
Found at i:42837163 original size:22 final size:21
Alignment explanation
Indices: 42837138--42837188 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
42837128 TAATATGGAT
*
42837138 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
42837160 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
42837182 TTGAGAG
1 TTGAGAG
42837189 TTTAAGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:42837221 original size:22 final size:22
Alignment explanation
Indices: 42837193--42837235 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
42837183 TGAGAGTTTA
42837193 AGAGGATTTTGGAATGAAATTG
1 AGAGGATTTTGGAATGAAATTG
42837215 AGAGGATTTTGGAATGAAATT
1 AGAGGATTTTGGAATGAAATT
42837236 AAGATAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (22 bp):
AGAGGATTTTGGAATGAAATTG
Found at i:42843528 original size:29 final size:30
Alignment explanation
Indices: 42843484--42843544 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
42843474 AGTCACTTAC
42843484 AAATTGGAAGAATACTTGAAAACATTAAAG
1 AAATTGGAAGAATACTTGAAAACATTAAAG
* *
42843514 AAATT-GAAGAGTACTTTAAAACATTAAAG
1 AAATTGGAAGAATACTTGAAAACATTAAAG
42843543 AA
1 AA
42843545 TCTTAGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.25
Consensus pattern (30 bp):
AAATTGGAAGAATACTTGAAAACATTAAAG
Found at i:42850042 original size:35 final size:35
Alignment explanation
Indices: 42849995--42850064 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
42849985 ATCCCCCCAA
*
42849995 TCCCCAATCCCCTTTCTCTTTTTCTATCGTGACGC
1 TCCCCAACCCCCTTTCTCTTTTTCTATCGTGACGC
42850030 TCCCCAACCCCCTTTCTCTTTTTCTATCGTGACGC
1 TCCCCAACCCCCTTTCTCTTTTTCTATCGTGACGC
42850065 AGAGAGCCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.11, C:0.41, G:0.09, T:0.39
Consensus pattern (35 bp):
TCCCCAACCCCCTTTCTCTTTTTCTATCGTGACGC
Found at i:42851185 original size:20 final size:20
Alignment explanation
Indices: 42851160--42851197 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42851150 GGTGGGTTAC
42851160 AGATTTCCATTTACCATTTT
1 AGATTTCCATTTACCATTTT
*
42851180 AGATTTCCATTTATCATT
1 AGATTTCCATTTACCATT
42851198 AACGAGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (20 bp):
AGATTTCCATTTACCATTTT
Found at i:42861931 original size:34 final size:34
Alignment explanation
Indices: 42861888--42861956 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
42861878 ACATGTTATG
* *
42861888 ACATCAATCCTTTAGCCTAGATTCTTTCTTGTAA
1 ACATCAATCCTGTAGCCTAGATTCTCTCTTGTAA
42861922 ACATCAATCCTGTAGCCTAGATTCTCTCTTGTAA
1 ACATCAATCCTGTAGCCTAGATTCTCTCTTGTAA
42861956 A
1 A
42861957 TTTAGTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (34 bp):
ACATCAATCCTGTAGCCTAGATTCTCTCTTGTAA
Found at i:42863595 original size:23 final size:23
Alignment explanation
Indices: 42863568--42863620 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
42863558 AGTGTTATTG
42863568 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* *
42863591 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
42863614 ATCAGTG
1 ATCAGTG
42863621 TGGCACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:42879261 original size:13 final size:13
Alignment explanation
Indices: 42879243--42879290 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
42879233 ATCTCCATAA
* *
42879243 AACCATTTAGTTT
1 AACCATTTCGTAT
*
42879256 AACCATTTCGTAC
1 AACCATTTCGTAT
42879269 AACCATTTCGTAT
1 AACCATTTCGTAT
42879282 AACCATTTC
1 AACCATTTC
42879291 ATTTTACACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (13 bp):
AACCATTTCGTAT
Found at i:42880913 original size:45 final size:43
Alignment explanation
Indices: 42880836--42880964 Score: 125
Period size: 45 Copynumber: 2.9 Consensus size: 43
42880826 TGTGTACCAG
* * * * *
42880836 GTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCTATCGG
1 GTATCATTGATTAT-AAGGT-GTTGCTATGTGCTGATTCCACCGA
*
42880881 GT-TCTATTGATTATGAAGGTGATTGCTATGTGCTGTTTCCACCGA
1 GTATC-ATTGATTAT-AAGGTG-TTGCTATGTGCTGATTCCACCGA
* *
42880926 GTATCATTGACTATAAGGGTGGTGCTATGTGCTGATTCC
1 GTATCATTGATTATAA-GGTGTTGCTATGTGCTGATTCC
42880965 GAAGTGTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
44 21 0.30
45 47 0.67
46 2 0.03
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (43 bp):
GTATCATTGATTATAAGGTGTTGCTATGTGCTGATTCCACCGA
Found at i:42887440 original size:14 final size:15
Alignment explanation
Indices: 42887414--42887444 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
42887404 TGGAAGGATA
42887414 AAATTATAAATAATG
1 AAATTATAAATAATG
42887429 AAATTA-AAATAATG
1 AAATTATAAATAATG
42887443 AA
1 AA
42887445 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AAATTATAAATAATG
Found at i:42888287 original size:40 final size:40
Alignment explanation
Indices: 42888207--42888423 Score: 211
Period size: 40 Copynumber: 5.5 Consensus size: 40
42888197 TATATGAATT
* **
42888207 TACTTCAGTA-CCCTGAATGCACATACGTGCCCCTACTTG
1 TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
* * * * *
42888246 TACTTCGGTACCCTTTAATGCACATGCATGCCTCTGTTTG
1 TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
* * * *
42888286 TACTTCGATACCCCTGAATGCACATACGTTCCACTATTTG
1 TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
** * *
42888326 TACTTTAGTACCCCTGAATGCAAATACGTACCCCTGTTTG
1 TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
* * * * **
42888366 TACTTTGATACCCCTAAATGCACATATGTGCCATTGTTTG
1 TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
* *
42888406 TACTTTGGTACCTCTGAA
1 TACTTCGGTACCCCTGAA
42888424 AACATTATAA
Statistics
Matches: 143, Mismatches: 34, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
39 9 0.06
40 134 0.94
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (40 bp):
TACTTCGGTACCCCTGAATGCACATACGTGCCCCTGTTTG
Found at i:42893714 original size:6 final size:6
Alignment explanation
Indices: 42893699--42893738 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
42893689 TTAAAATATT
* *
42893699 TATGTA TATGTG TATGTA TATGTA AATGTA TATGTA TATG
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATG
42893739 CATGTCTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (6 bp):
TATGTA
Found at i:42895132 original size:3 final size:3
Alignment explanation
Indices: 42895124--42895184 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
42895114 TAAGAAACAT
* *
42895124 AGA AGA AGA AGA AGA AGA AAA AGA TAGA AGA AGA AGA AGA AGA AAA
1 AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
* *
42895170 AGA AAA AAA AGA AGA
1 AGA AGA AGA AGA AGA
42895185 GGATGAGGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:42895156 original size:25 final size:25
Alignment explanation
Indices: 42895122--42895172 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42895112 AATAAGAAAC
42895122 ATAGAAGAAGAAGAAGAAGAAAAAG
1 ATAGAAGAAGAAGAAGAAGAAAAAG
42895147 ATAGAAGAAGAAGAAGAAGAAAAAG
1 ATAGAAGAAGAAGAAGAAGAAAAAG
42895172 A
1 A
42895173 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (25 bp):
ATAGAAGAAGAAGAAGAAGAAAAAG
Found at i:42897411 original size:19 final size:19
Alignment explanation
Indices: 42897381--42897417 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
42897371 CAAATTAATA
42897381 AAAAAATGAAAGAACTAAAT
1 AAAAAATGAAAGAA-TAAAT
42897401 AAAAAAT-AAAGAATAAA
1 AAAAAATGAAAGAATAAA
42897418 AGGTACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAAATGAAAGAATAAAT
Found at i:42897577 original size:3 final size:3
Alignment explanation
Indices: 42897569--42897596 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
42897559 ACTTATATAT
42897569 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42897597 AAGTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42899602 original size:217 final size:217
Alignment explanation
Indices: 42899222--42900207 Score: 1623
Period size: 217 Copynumber: 4.5 Consensus size: 217
42899212 TTCGATCCAT
* * * *
42899222 TCCACTGCAACATCAGGGAGATAAGACTAGATGCAATTTGCTCTCTGCAACTTCAGATAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
*** * * * * * *
42899287 ATCTGTGGTTTTAATCAGCTCCACTGCAACTTCAAGGAGATAGGATCATCAGCTTTAATCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTC
* * * *
42899352 CACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGAT
131 CACTACAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGAT
42899417 AAGACCTGCTTACTTAGTCTGC
196 AAGACCTGCTTACTTAGTCTGC
*
42899439 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
42899504 ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTC
* * *
42899569 CACTATAACTTCAAGGAGATAAGGTTTGCCATCTTCAGTCTGCTTCACTGCAACTTCAGGAGGAT
131 CACTACAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGAT
*
42899634 AAGGCCTGCTTACTTAGTCTGC
196 AAGACCTGCTTACTTAGTCTGC
*
42899656 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAGCTTCAGAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
* *
42899721 ATCCAAGATTTTAATCCGCTCCATTGCAACTTCAGAGAGATAGGATTATCGGCTTTAACCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTC
* * *
42899786 CAC-AGTAACTTCAGGGAGATAAGGTTTTCCATCTTCAGTCTGCCTCACTGCAACTTCAGCAGGA
131 CACTA-CAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGA
42899850 TAAGACCTGCTTACTTAGTCTGC
195 TAAGACCTGCTTACTTAGTCTGC
42899873 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
* * *
42899938 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTT
66 ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTC
* *
42900003 CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
131 CACTACAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGAT
*
42900068 AAGACCTGTTTACTTAGTCTGC
196 AAGACCTGCTTACTTAGTCTGC
42900090 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
* * *
42900155 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAAGGAGATAGGATTATCGGC
66 ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGC
42900208 CACCGATCCG
Statistics
Matches: 723, Mismatches: 44, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
216 1 0.00
217 722 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (217 bp):
TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
ATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTC
CACTACAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGAT
AAGACCTGCTTACTTAGTCTGC
Found at i:42900102 original size:44 final size:44
Alignment explanation
Indices: 42899345--42900116 Score: 264
Period size: 44 Copynumber: 17.8 Consensus size: 44
42899335 TCAGCTTTAA
* **
42899345 TCTGCTCCACTGCAACTTCAGG-GAGATAAGA-TTCGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCT-GTTA-CTT-AG
*
42899390 TCTAC-CTCACTGCAACTTCAGGAG-GATAAGACCTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGAGAGATAAGACCTG-TTACTTAG
* * *
42899434 TCTGCTCCACTGCAACTTCAGG-GAGATAAGA-CTAGATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCT-GTTACTTAG
* * * *
42899475 TCTGCT-CTCTACAACTTCA-GAGAGATAAGATCCAAGATT--TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CC-TG-TTACTTAG
* * * * ** *
42899518 TCCGCTCCACTGCAACTTCAGG-GAGATAGGA-TTATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGT-TAC-TTAG
* ** * *** **
42899562 CCTGCTCCACTATAACTTCAAG-GAGATAAGGTTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGTTA-CTT-AG
* *
42899607 TCTGCTTCACTGCAACTTCAGGAG-GATAAGGCCTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTG-TTACTTAG
* * *
42899651 TCTGCTCCACTGCAACTTCAGG-GAGATAAGA-CTAGATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCT-GTTACTTAG
* * * *
42899692 TCTGCT-CTCTGCAGCTTCA-GAGAGATAAGATCCAAGATT--TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CC-TG-TTACTTAG
* * * * * ** *
42899735 TCCGCTCCATTGCAACTTCA-GAGAGATAGGA-TTATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGT-TAC-TTAG
* * * * *
42899779 CCTGCTCCACAGTAACTTCAGG-GAGATAAG--GTTTTCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGTT--A-CTT-AG
*
42899824 TCTGC-CTCACTGCAACTTCAGCAG-GATAAGACCTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGAGAGATAAGACCTG-TTACTTAG
* * *
42899868 TCTGCTCCACTGCAACTTCAGG-GAGATAAGA-CTAGATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCT-GTTACTTAG
* * *
42899909 TCTGCT-CTCTGCAACTTCA-GAGAGATAAGATCCAAGATT--TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CC-TG-TTACTTAG
* * * * * * ** *
42899952 TCCGCTCCACTACAACTTTAGG-GAGATAGGA-TTATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGT-TAC-TTAG
* * *** **
42899996 CCTGCTTCACTGCAACTTCAGG-GAGATAAGGTTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGTTA-CTT-AG
*
42900041 TCTGCCCCACTGCAACTTCAGGAG-GATAAGACCTGTTTACTTAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTG-TTACTTAG
42900085 TCTGCTCCACTGCAACTTCAGG-GAGATAAGAC
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGAC
42900117 TAGATGCGAT
Statistics
Matches: 540, Mismatches: 116, Indels: 143
0.68 0.15 0.18
Matches are distributed among these distances:
39 3 0.01
40 64 0.12
41 18 0.03
42 12 0.02
43 36 0.07
44 266 0.49
45 129 0.24
46 9 0.02
47 1 0.00
48 2 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGAGAGATAAGACCTGTTACTTAG
Found at i:42912290 original size:24 final size:23
Alignment explanation
Indices: 42912247--42912296 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
42912237 TATATATATG
42912247 CATATATAAATAAAAAATAATTA
1 CATATATAAATAAAAAATAATTA
*
42912270 CATATATATATAAAAAAATAATTA
1 CATATATAAAT-AAAAAATAATTA
42912294 CAT
1 CAT
42912297 TATCAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
CATATATAAATAAAAAATAATTA
Found at i:42924057 original size:27 final size:28
Alignment explanation
Indices: 42924007--42924060 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
42923997 CAATTATATC
42924007 GCATTATTTGTTATTCGGCAGTTTTACT
1 GCATTATTTGTTATTCGGCAGTTTTACT
**
42924035 GCATTA-TTGTTATTCGGTGGTTTTAC
1 GCATTATTTGTTATTCGGCAGTTTTAC
42924061 CACTTCGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (28 bp):
GCATTATTTGTTATTCGGCAGTTTTACT
Found at i:42931518 original size:14 final size:15
Alignment explanation
Indices: 42931493--42931521 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42931483 TATCTTTAAA
42931493 TGTGATTGTATGTAT
1 TGTGATTGTATGTAT
42931508 TGTGA-TGTATGTAT
1 TGTGATTGTATGTAT
42931522 GAAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TGTGATTGTATGTAT
Found at i:42935984 original size:76 final size:76
Alignment explanation
Indices: 42935852--42935993 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
42935842 TTCGGCAGCC
* * *
42935852 ACAATTAACTTCAGCTGGACACCATTTAAGACATCATTAAATTCGATAGTAGCAAGACAAATTAA
1 ACAATTAAATTCAGCTGGACACCATTTAAGACATCATTAAATTCGACAGCAGCAAGACAAATTAA
42935917 ATGATGTAATG
66 ATGATGTAATG
* * *
42935928 ACAATTAAATTCAGCTGGACACCATTTAAGACATCATTAAATTTGGCAGCCA-CAAGACACATTA
1 ACAATTAAATTCAGCTGGACACCATTTAAGACATCATTAAATTCGACAG-CAGCAAGACAAATTA
42935992 AA
65 AA
42935994 GTGGCTCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 58 0.98
77 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (76 bp):
ACAATTAAATTCAGCTGGACACCATTTAAGACATCATTAAATTCGACAGCAGCAAGACAAATTAA
ATGATGTAATG
Found at i:42938144 original size:24 final size:24
Alignment explanation
Indices: 42938100--42938154 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
42938090 GCCTGTGTCT
* * *
42938100 GCATTTGTATCTGAATCTGAATAC
1 GCATCTGTATCTGAATATGAACAC
*
42938124 GCATCTGTATCTGATTATGAACAC
1 GCATCTGTATCTGAATATGAACAC
*
42938148 ACATCTG
1 GCATCTG
42938155 ACTCTGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (24 bp):
GCATCTGTATCTGAATATGAACAC
Found at i:42938221 original size:15 final size:16
Alignment explanation
Indices: 42938192--42938221 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42938182 CTTGATGATA
42938192 ATTTATGAGTATAATT
1 ATTTATGAGTATAATT
42938208 ATTTATGA-TATAAT
1 ATTTATGAGTATAAT
42938222 GTTGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
ATTTATGAGTATAATT
Found at i:42950781 original size:28 final size:28
Alignment explanation
Indices: 42950718--42950843 Score: 191
Period size: 28 Copynumber: 4.5 Consensus size: 28
42950708 ATATTAAGTC
*
42950718 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
42950745 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
42950773 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
42950801 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
42950830 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42950844 CGAGATCACC
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.24
28 51 0.55
29 19 0.21
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42959431 original size:9 final size:10
Alignment explanation
Indices: 42959404--42959428 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42959394 CGCCTTTTTC
42959404 TTCTTTCTTT
1 TTCTTTCTTT
42959414 TTCTTTCTTT
1 TTCTTTCTTT
42959424 TTCTT
1 TTCTT
42959429 CTTCAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:42960630 original size:56 final size:56
Alignment explanation
Indices: 42960570--42960741 Score: 192
Period size: 56 Copynumber: 3.1 Consensus size: 56
42960560 TTCAATAGTA
42960570 TTTTTAATAAATAAATTTAATTGAATAGAATATTTTTATATTTTTAATTCAAATGG
1 TTTTTAATAAATAAATTTAATTGAATAGAATATTTTTATATTTTTAATTCAAATGG
* * ** * * * *
42960626 TTTTTATTTAATTGAATATTTTTTTGAAT--AA-ATTATTA-ATTGTTTTATTCAAAAGTA
1 TTTTTA-ATAAAT-AA-ATTTAATTGAATAGAATATTTTTATATT-TTTAATTCAAATG-G
42960683 TTTTTAATAAATAAATTTAATTGAATAGAATA-TTTTATATTTTTAATTCAAATGG
1 TTTTTAATAAATAAATTTAATTGAATAGAATATTTTTATATTTTTAATTCAAATGG
42960738 TTTT
1 TTTT
42960742 CATTTAATTG
Statistics
Matches: 91, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
54 10 0.11
55 9 0.10
56 44 0.48
57 16 0.18
58 2 0.02
59 10 0.11
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (56 bp):
TTTTTAATAAATAAATTTAATTGAATAGAATATTTTTATATTTTTAATTCAAATGG
Found at i:42960761 original size:113 final size:113
Alignment explanation
Indices: 42960542--42960771 Score: 435
Period size: 113 Copynumber: 2.0 Consensus size: 113
42960532 ATCTAACAAA
*
42960542 AAATTATTAATTGTTTTATTCAATAGTATTTTTAATAAATAAATTTAATTGAATAGAATATTTTT
1 AAATTATTAATTGTTTTATTCAAAAGTATTTTTAATAAATAAATTTAATTGAATAGAATATTTTT
*
42960607 ATATTTTTAATTCAAATGGTTTTTATTTAATTGAATATTTTTTTGAAT
66 ATATTTTTAATTCAAATGGTTTTCATTTAATTGAATATTTTTTTGAAT
42960655 AAATTATTAATTGTTTTATTCAAAAGTATTTTTAATAAATAAATTTAATTGAATAGAATA-TTTT
1 AAATTATTAATTGTTTTATTCAAAAGTATTTTTAATAAATAAATTTAATTGAATAGAATATTTTT
42960719 ATATTTTTAATTCAAATGGTTTTCATTTAATTGAATATTTTTTTGAAT
66 ATATTTTTAATTCAAATGGTTTTCATTTAATTGAATATTTTTTTGAAT
42960767 AAATT
1 AAATT
42960772 GAACAAAATT
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
112 56 0.49
113 59 0.51
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (113 bp):
AAATTATTAATTGTTTTATTCAAAAGTATTTTTAATAAATAAATTTAATTGAATAGAATATTTTT
ATATTTTTAATTCAAATGGTTTTCATTTAATTGAATATTTTTTTGAAT
Found at i:42962337 original size:26 final size:26
Alignment explanation
Indices: 42962240--42962588 Score: 208
Period size: 26 Copynumber: 13.8 Consensus size: 26
42962230 TATTGTTTAT
* *
42962240 TTATTTATTTTAAAATCTTTTCATATA
1 TTATTTATTTTAAACTATTTT-ATATA
*
42962267 TTACTTAATTTT-AACTATTTTAT-TA
1 TTA-TTTATTTTAAACTATTTTATATA
* * *
42962292 TTACTTATTTT-AAGTTTTTTCATATA
1 TTATTTATTTTAAACTATTTT-ATATA
42962318 TTA-TTATTTTAAACTATTTTATACT-
1 TTATTTATTTTAAACTATTTTATA-TA
* * * *
42962343 TTATTAATTTTAAATTGTTTTATATG
1 TTATTTATTTTAAACTATTTTATATA
* * * *
42962369 GTATTCATTTCAAACTGTTTTAT-T-
1 TTATTTATTTTAAACTATTTTATATA
* *
42962393 GTATATTATTTTAAACTATTATATATA
1 TTAT-TTATTTTAAACTATTTTATATA
* **
42962420 TTATTTATTTTAAATTGCTTTATATA
1 TTATTTATTTTAAACTATTTTATATA
** *
42962446 -TA--TA-TTCCAACTATTTTATATT
1 TTATTTATTTTAAACTATTTTATATA
** *
42962468 TTATTTATGATAAGA-T-TTTT-CATA
1 TTATTTATTTTAA-ACTATTTTATATA
** * * *
42962492 TGGTTTATTTTGAACCATTTTGTATA
1 TTATTTATTTTAAACTATTTTATATA
** * *
42962518 TTATTTATTTTAAAAAAATTCATATA
1 TTATTTATTTTAAACTATTTTATATA
42962544 TTATTTATTTTAAAC-ATTTT-TATA
1 TTATTTATTTTAAACTATTTTATATA
* *
42962568 TTATTTACTTTAAATTATTTT
1 TTATTTATTTTAAACTATTTT
42962589 TTACATATTA
Statistics
Matches: 246, Mismatches: 57, Indels: 40
0.72 0.17 0.12
Matches are distributed among these distances:
22 12 0.05
23 5 0.02
24 44 0.18
25 57 0.23
26 107 0.43
27 14 0.06
28 7 0.03
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
TTATTTATTTTAAACTATTTTATATA
Found at i:42962353 original size:51 final size:49
Alignment explanation
Indices: 42962235--42962433 Score: 165
Period size: 51 Copynumber: 3.9 Consensus size: 49
42962225 AAATTTATTG
*
42962235 TTTA-TTTATTTATTTTAAAATCTTTTCATATATTACTTAATTTT-AACTAT
1 TTTATTTTA-TTATTTT-AAATTTTTTCATATATTA-TTAATTTTAAACTAT
*
42962285 TTTATTATTACTTATTTTAAGTTTTTTCATATATTATT-ATTTTAAACTAT
1 TTTATT-TTA-TTATTTTAAATTTTTTCATATATTATTAATTTTAAACTAT
** * * *
42962335 TTTATACTTTATTAATTTTAAATTGTTTT-ATATGGTATTCATTTCAAACTGT
1 TTTAT--TTTATT-ATTTTAAATT-TTTTCATATATTATTAATTTTAAACTAT
* * *
42962387 TTTATTGTATATTATTTTAAACTATTAT-ATATATTATTTATTTTAAA
1 TTTATT-T-TATTATTTTAAA-TTTTTTCATATATTATTAATTTTAAA
42962434 TTGCTTTATA
Statistics
Matches: 124, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
49 5 0.04
50 20 0.16
51 64 0.52
52 35 0.28
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (49 bp):
TTTATTTTATTATTTTAAATTTTTTCATATATTATTAATTTTAAACTAT
Found at i:42962588 original size:24 final size:24
Alignment explanation
Indices: 42962507--42962581 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
42962497 TATTTTGAAC
*
42962507 CATTTTGTATATTATTTATTTTAAAAA
1 CATTTT-TATATTATTTACTTT--AAA
* ** *
42962534 AATTCATATATTATTTATTTTAAA
1 CATTTTTATATTATTTACTTTAAA
42962558 CATTTTTATATTATTTACTTTAAA
1 CATTTTTATATTATTTACTTTAAA
42962582 TTATTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 23 0.56
26 15 0.37
27 3 0.07
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (24 bp):
CATTTTTATATTATTTACTTTAAA
Found at i:42963977 original size:27 final size:27
Alignment explanation
Indices: 42963947--42964036 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
42963937 GTTTATTTAT
42963947 TTATTTTAAAATCTTTTCATATATTAC
1 TTATTTTAAAATCTTTTCATATATTAC
* *
42963974 TTATTTTAAACTGTTTT-AT-TATTAC
1 TTATTTTAAAATCTTTTCATATATTAC
**
42963999 TTATTTTAAGTTTCTTTTTCATATATTA-
1 TTATTTTAA-AATC-TTTTCATATATTAC
42964027 TTATTTTAAA
1 TTATTTTAAA
42964037 CTATTTTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 15 0.28
26 3 0.06
27 19 0.36
28 11 0.21
29 5 0.09
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (27 bp):
TTATTTTAAAATCTTTTCATATATTAC
Found at i:42964058 original size:26 final size:25
Alignment explanation
Indices: 42963947--42964178 Score: 145
Period size: 26 Copynumber: 9.1 Consensus size: 25
42963937 GTTTATTTAT
* *
42963947 TTATTTTAAAATCTTTTCATATATTA
1 TTATTTTAAACTATTTT-ATATATTA
*
42963973 CTTATTTTAAACTGTTTTAT-TATTA
1 -TTATTTTAAACTATTTTATATATTA
*
42963998 CTTATTTTAAGTTTCT-TTTTCATATATTA
1 -TTATTTTAA---ACTATTTT-ATATATTA
42964027 TTATTTTAAACTATTTTATACT-TTA
1 TTATTTTAAACTATTTTATA-TATTA
* * **
42964052 TTAATTTTAAATTGTTTTATATGGTA
1 TT-ATTTTAAACTATTTTATATATTA
* * *
42964078 TTCATTTCAAACTGTTTTAT-TGTATA
1 TT-ATTTTAAACTATTTTATATAT-TA
*
42964104 TTATTTTAAACTATTATATATATTA
1 TTATTTTAAACTATTTTATATATTA
* **
42964129 TTTATTTTAAATTGCTTTATATA-TA
1 -TTATTTTAAACTATTTTATATATTA
** *
42964154 -T-TTTCGAACTATTTTATATTTTA
1 TTATTTTAAACTATTTTATATATTA
42964177 TT
1 TT
42964179 TATGATAAGT
Statistics
Matches: 166, Mismatches: 25, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
22 13 0.08
23 3 0.02
24 1 0.01
25 46 0.28
26 66 0.40
27 19 0.11
28 13 0.08
29 5 0.03
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (25 bp):
TTATTTTAAACTATTTTATATATTA
Found at i:42966689 original size:25 final size:25
Alignment explanation
Indices: 42966653--42966706 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
42966643 AATAAATTAG
42966653 CATGCATGCTTCCTTGAATGCCGTT
1 CATGCATGCTTCCTTGAATGCCGTT
* * * *
42966678 CATGCATTCTTCTTTTAATGCTGTT
1 CATGCATGCTTCCTTGAATGCCGTT
42966703 CATG
1 CATG
42966707 TACCTGCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (25 bp):
CATGCATGCTTCCTTGAATGCCGTT
Found at i:42967823 original size:12 final size:11
Alignment explanation
Indices: 42967806--42967835 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
42967796 TATCTTGACC
42967806 TTTTCTTTTCAT
1 TTTTCTTTTC-T
42967818 TTTTCTTTTCT
1 TTTTCTTTTCT
42967829 TTTTCTT
1 TTTTCTT
42967836 GGTGCCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:42969088 original size:24 final size:24
Alignment explanation
Indices: 42969049--42969098 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
42969039 TGTCTTCATT
* * *
42969049 TGTATCTGAATCTGAATACGCATC
1 TGTATCTGAATATGAACACACATC
*
42969073 TGTATCTGATTATGAACACACATC
1 TGTATCTGAATATGAACACACATC
42969097 TG
1 TG
42969099 ACTCTGTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (24 bp):
TGTATCTGAATATGAACACACATC
Found at i:42970126 original size:23 final size:24
Alignment explanation
Indices: 42970077--42970126 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
42970067 TAAGAAACTC
* *
42970077 TTTACTTTAGTTACTTTAGTTATA
1 TTTACTTTAGTTACTTTAGTAAAA
42970101 TTTACTTTAG-TACTTTAGTAAAA
1 TTTACTTTAGTTACTTTAGTAAAA
42970124 TTT
1 TTT
42970127 TTGAGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTACTTTAGTTACTTTAGTAAAA
Found at i:42973184 original size:22 final size:22
Alignment explanation
Indices: 42973103--42973185 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
42973093 TATGACATTT
*
42973103 TGATATG-ATATATGATAAGCTC
1 TGATATGTA-ATATGATATGCTC
** * * *
42973125 AAATATGTTACATGATATGCTT
1 TGATATGTAATATGATATGCTC
* * *
42973147 TGATTTGTTATGTGATATGCTC
1 TGATATGTAATATGATATGCTC
42973169 TGATATGTAATATGATA
1 TGATATGTAATATGATA
42973186 CGAAATTTTG
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (22 bp):
TGATATGTAATATGATATGCTC
Found at i:42977139 original size:31 final size:31
Alignment explanation
Indices: 42977101--42977208 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
42977091 TTAATATAAC
*
42977101 ATTTGGTACCTAAACTTTACACTTTTTCTTA
1 ATTTGGTACCTAAACTTTACACTTTTTCCTA
42977132 ATTTGGTACCTAAAC--T---CTTTTTGGCCTA
1 ATTTGGTACCTAAACTTTACACTTTTT--CCTA
* * *
42977160 ATTTGGTACATGAACTTGACA-TTTTATCCTA
1 ATTTGGTACCTAAACTTTACACTTTT-TCCTA
42977191 ATTTGGTACCTAAACTTT
1 ATTTGGTACCTAAACTTT
42977209 TTTTTAGCCC
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
26 6 0.10
28 16 0.26
29 1 0.02
31 34 0.55
32 4 0.06
33 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTTACACTTTTTCCTA
Found at i:42977193 original size:59 final size:60
Alignment explanation
Indices: 42977101--42977265 Score: 192
Period size: 59 Copynumber: 2.8 Consensus size: 60
42977091 TTAATATAAC
* * * * *
42977101 ATTTGGTACCTAAACTTTACACTTTTTCTTAATTTGGTACCTAAAC-TCTTTTTGGCCTA
1 ATTTGGTACATGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTCTTTTTAGCCCA
* *
42977160 ATTTGGTACATGAACTTGACA-TTTTATCCTAATTTGGTACCTAAACTTTTTTTTAGCCCA
1 ATTTGGTACATGAACTTGACACTTTT-TCTTAATTTGGTACCTAAACTTCTTTTTAGCCCA
* * *
42977220 ATTTGGTA-ACTGAACTAGACATTTTTTTATTAATTTGGTACCTAAA
1 ATTTGGTACA-TGAACTTGACA-CTTTTTCTTAATTTGGTACCTAAA
42977266 TTTATTAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
58 4 0.04
59 38 0.42
60 28 0.31
61 17 0.19
62 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (60 bp):
ATTTGGTACATGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTCTTTTTAGCCCA
Found at i:42977241 original size:60 final size:60
Alignment explanation
Indices: 42977130--42977265 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 60
42977120 CACTTTTTCT
* * * *
42977130 TAATTTGGTACCTAAACTCTTTTTGGCCTAATTTGGTACATGAACTTGACA-TTTTATCC
1 TAATTTGGTACCTAAACTCTTTTTAGCCCAATTTGGTACATGAACTAGACATTTTTATAC
* * *
42977189 TAATTTGGTACCTAAACTTTTTTTTAGCCCAATTTGGTA-ACTGAACTAGACATTTTTTTAT
1 TAATTTGGTACCTAAAC-TCTTTTTAGCCCAATTTGGTACA-TGAACTAGACATTTTTATAC
42977250 TAATTTGGTACCTAAA
1 TAATTTGGTACCTAAA
42977266 TTTATTAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 18 0.27
60 28 0.42
61 21 0.31
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (60 bp):
TAATTTGGTACCTAAACTCTTTTTAGCCCAATTTGGTACATGAACTAGACATTTTTATAC
Found at i:42979234 original size:19 final size:18
Alignment explanation
Indices: 42979199--42979235 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42979189 AATGAAGACT
42979199 TTGCATAAAAAGAAAAAA
1 TTGCATAAAAAGAAAAAA
*
42979217 TTGCATAAAAAGACAAAA
1 TTGCATAAAAAGAAAAAA
42979235 T
1 T
42979236 ACCAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (18 bp):
TTGCATAAAAAGAAAAAA
Found at i:42984606 original size:56 final size:55
Alignment explanation
Indices: 42984546--42984653 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 55
42984536 TTTAATCATG
* * * *
42984546 CCTATCTGATAGGCGCGAATCAATATTTTATGTA-AATTTTTTTTCATTTAATTGCA
1 CCTATCTAACAGGCACGAATCAAT-TTTT-TGTATAAATTTTTTTCATTTAATTGCA
*
42984602 CCTATCTAACAGGCACGAATCAATTTTTTGTATTAAATTTTTTTCGTTTAAT
1 CCTATCTAACAGGCACGAATCAATTTTTTGTA-TAAATTTTTTTCATTTAAT
42984654 AAAATATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 4 0.09
55 4 0.09
56 37 0.82
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (55 bp):
CCTATCTAACAGGCACGAATCAATTTTTTGTATAAATTTTTTTCATTTAATTGCA
Found at i:42984768 original size:27 final size:27
Alignment explanation
Indices: 42984738--42984852 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 27
42984728 GATAGGCGTT
* * *
42984738 ACTAGTTGAGCCTATCTCAGAGGTGCG
1 ACTAGTTCAGCCTATCTCACAGGCGCG
*
42984765 ACTAGTTGAGCCTATCTCACAGGCGCG
1 ACTAGTTCAGCCTATCTCACAGGCGCG
*
42984792 GCTAGTTCAGCCTATCTCACAGGCGCG
1 ACTAGTTCAGCCTATCTCACAGGCGCG
* * *
42984819 GCTAGTTCAGCCTATCTGACAGGCGTG
1 ACTAGTTCAGCCTATCTCACAGGCGCG
*
42984846 AGTAGTT
1 ACTAGTT
42984853 GTGCCTAACT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (27 bp):
ACTAGTTCAGCCTATCTCACAGGCGCG
Found at i:42984858 original size:27 final size:27
Alignment explanation
Indices: 42984740--42984869 Score: 138
Period size: 27 Copynumber: 4.8 Consensus size: 27
42984730 TAGGCGTTAC
* * *
42984740 TAGTTGAGCCTATCTCAGAGGTGCGAC
1 TAGTTGAGCCTATCTCACAGGCGCGAG
42984767 TAGTTGAGCCTATCTCACAGGCGCG-G
1 TAGTTGAGCCTATCTCACAGGCGCGAG
*
42984793 CTAGTTCAGCCTATCTCACAGGCGCG-G
1 -TAGTTGAGCCTATCTCACAGGCGCGAG
* * *
42984820 CTAGTTCAGCCTATCTGACAGGCGTGAG
1 -TAGTTGAGCCTATCTCACAGGCGCGAG
* * *
42984848 TAGTTGTGCCTAACTCAAAGGC
1 TAGTTGAGCCTATCTCACAGGC
42984870 ACGAATGGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
27 89 0.99
28 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (27 bp):
TAGTTGAGCCTATCTCACAGGCGCGAG
Done.