Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold448
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: 460345
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 41382 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:205 original size:27 final size:27
Alignment explanation
Indices: 171--462 Score: 284
Period size: 27 Copynumber: 10.8 Consensus size: 27
161 ACGCCAGTTA
171 TTATGTAAGTTATGTAAGTTATTTAAG
1 TTATGTAAGTTATGTAAGTTATTTAAG
*
198 TTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGTTATTTAAG
* *
225 TTATGTAATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATTTAAG
** * * *
252 ACATTTAATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATTTAAG
* * * *
279 TTATTTAATTTACT-TAATTTATGTAAG
1 TTATGTAAGTTA-TGTAAGTTATTTAAG
* * * * *
306 TTATGTAAGATATTTAATTTACTTAAT
1 TTATGTAAGTTATGTAAGTTATTTAAG
*
333 TTATGTAAGTTAT-TCAAGATATTTAAG
1 TTATGTAAGTTATGT-AAGTTATTTAAG
* * *
360 TTATGTAAGTTATGTAAATTACTTAAT
1 TTATGTAAGTTATGTAAGTTATTTAAG
* *
387 TTATGTAAGTTATGTAAGATATTTAAT
1 TTATGTAAGTTATGTAAGTTATTTAAG
* *
414 TTACT-TAATTTATGTAAGTTATTCAAG
1 TTA-TGTAAGTTATGTAAGTTATTTAAG
* * *
441 ATATTTAATTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAGTTAT
463 GTGAAACCGT
Statistics
Matches: 226, Mismatches: 33, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
26 3 0.01
27 220 0.97
28 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.49
Consensus pattern (27 bp):
TTATGTAAGTTATGTAAGTTATTTAAG
Found at i:214 original size:36 final size:36
Alignment explanation
Indices: 172--464 Score: 268
Period size: 36 Copynumber: 8.1 Consensus size: 36
162 CGCCAGTTAT
* *
172 TATGTAAGTTATGTAAGTTATTTAAGTTATGTAAGT
1 TATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGT
* *
208 TATGTAAGTTATTTAATTTATGTAATTTATGTAAGT
1 TATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGT
** *
244 TATGTAAGACATTTAATTTATGTAAGTTATGTAAGT
1 TATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGT
* * * * *
280 TATTTAATTTACTTAATTTATGTAAGTTATGTAAGA
1 TATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGT
* * * * *
316 TATTTAATTTACTTAATTTATGTAAGTTAT-TCAAGA
1 TATGTAAGTTATTTAAGTTATGTAAGTTATGT-AAGT
* * * *
352 TATTTAAGTTATGTAAGTTATGTAAATTACT-TAATT
1 TATGTAAGTTATTTAAGTTATGTAAGTTA-TGTAAGT
* * * * *
388 TATGTAAGTTATGTAAGATATTTAATTTACT-TAATT
1 TATGTAAGTTATTTAAGTTATGTAAGTTA-TGTAAGT
* * * *
424 TATGTAAGTTATTCAAGATATTTAATTTATGTAAGT
1 TATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGT
460 TATGT
1 TATGT
465 GAAACCGTCC
Statistics
Matches: 227, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
35 2 0.01
36 223 0.98
37 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.49
Consensus pattern (36 bp):
TATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGT
Found at i:247 original size:63 final size:63
Alignment explanation
Indices: 171--464 Score: 425
Period size: 63 Copynumber: 4.7 Consensus size: 63
161 ACGCCAGTTA
* *
171 TTATGTAAGTTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA-TGTAAT
1 TTATGTAAGTTATGTAAGATATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTACT-TAAT
*
234 TTATGTAAGTTATGTAAGACATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTACTTAAT
1 TTATGTAAGTTATGTAAGATATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTACTTAAT
* * ** * *
297 TTATGTAAGTTATGTAAGATATTTAATTTACT-TAATTTATGTAAGTTATTCAAGATATTTAAG
1 TTATGTAAGTTATGTAAGATATTTAATTTA-TGTAAGTTATGTAAGTTATTTAATTTACTTAAT
* *
360 TTATGTAAGTTATGTAA-ATTACTTAATTTATGTAAGTTATGTAAGATATTTAATTTACTTAAT
1 TTATGTAAGTTATGTAAGA-TATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTACTTAAT
423 TTATGTAAGTTAT-TCAAGATATTTAATTTATGTAAGTTATGT
1 TTATGTAAGTTATGT-AAGATATTTAATTTATGTAAGTTATGT
465 GAAACCGTCC
Statistics
Matches: 206, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
62 3 0.01
63 200 0.97
64 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.49
Consensus pattern (63 bp):
TTATGTAAGTTATGTAAGATATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTACTTAAT
Found at i:635 original size:20 final size:20
Alignment explanation
Indices: 610--659 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
600 CCTTAAACCT
*
610 GAACTCGAATATTAAACCCC
1 GAACTCGAACATTAAACCCC
* * *
630 GAACTCTAACCTTAGACCCC
1 GAACTCGAACATTAAACCCC
*
650 AAACTCGAAC
1 GAACTCGAAC
660 TCTAAATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (20 bp):
GAACTCGAACATTAAACCCC
Found at i:728 original size:20 final size:20
Alignment explanation
Indices: 678--734 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
668 TCGAATCCAA
*
678 GTTTAGGGTTCAAGGTTCGGG
1 GTTTAGGGTTCAAGGTT-TGG
* *
699 GTTCA-AGTTCAAGGTTTGG
1 GTTTAGGGTTCAAGGTTTGG
718 GTTTAGGGTTC-AGGTTT
1 GTTTAGGGTTCAAGGTTT
735 AAGATTTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.16, C:0.09, G:0.37, T:0.39
Consensus pattern (20 bp):
GTTTAGGGTTCAAGGTTTGG
Found at i:1446 original size:11 final size:12
Alignment explanation
Indices: 1430--1463 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1420 TGTTATAAAA
1430 AATTAC-GAGTT
1 AATTACAGAGTT
*
1441 AATTACAGAGCT
1 AATTACAGAGTT
1453 AATTACAGAGT
1 AATTACAGAGT
1464 GCTGGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (12 bp):
AATTACAGAGTT
Found at i:3027 original size:336 final size:332
Alignment explanation
Indices: 2311--3242 Score: 945
Period size: 336 Copynumber: 2.8 Consensus size: 332
2301 TCAATTATGC
* * * * *
2311 TTTAATGCACAGTTCTGGCGTTTTCTGTAAAAATGCCAGTAAAAATTAATTTGCTTAAGCTATAT
1 TTTAATGCACATTTCTGGCGTTTTCTGT-TAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAAC
** * * * *
2376 GGGGTCGTTTAGACAATATTTTAAGTCA-TTTTGCGGCGTTTTGTGCAAAAACGCCATTATAAAT
65 GAAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCG-TTTGTTCAAAAACGCCA-CAAAAAT
* * *
2440 TAAGAGAAACGGCGCCGTTGGATTAATTTAGAGAAAATGCTAAGTTAAAAACTAGTACAGAAACG
128 TAACAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGTTAAAAACT-GTACAGAAACG
* * ** *
2505 ACGTCGTTTAG-ACAAAATTTTAAGACAATTTTGCAGCGCATCCTGAACAAACGCCGCTATTGCT
192 GCGTCGTTTAGCA-AAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCT
* * * * *
2569 TGTACGTTTACGGCGTTTTCTAAAAAGCGCCACTAAAATTTAAAGTTCTAATCCAAAACGACGCC
256 TGTACATTTACAGCGTTTTCTAAAAAGAGCCACTAAAAATGAAAGTTCTAATCCAAAACGACGCC
*
2634 ATTTTATTAAGC
321 ATTTTATTAAGA
* * * *
2646 TGTAAAGCACATTTTTGGCGTTTTCTGATTAAACGCTAGTAAAAATTAATTTGCTTAAGCTAAAC
1 TTTAATGCACATTTCTGGCGTTTTCTG-TTAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAAC
* * * * * *
2711 GAAGCCGTTTAGGCAATATTTTATGTCACTTTTGTGGCGTTTGGTTTAAAAACGCTACAAAAATT
65 GAAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCGTTT-GTTCAAAAACGCCACAAAAATT
* * * *
2776 AACAGAAACGGTGTCGTTGAATTAATATAGAGAAAATGCTAAGTATAAAAGCATGTACAGAGACG
129 AACAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGT-TAAAAAC-TGTACAGAAACG
* * * * * * *
2841 GCGCCGTTTAGCAAAAATTTTAAGACACTTTCGCTGCTTTTATTGAACAAACGCCACTATAGCTT
192 GCGTCGTTTAGCAAAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCTT
** * ** * * **
2906 GTGTATTTGCAGCG-TTTCTAGACCAGAGCCAC-AAAGAATGAAGGTTCTAATCCGAAACGGTGC
257 GTACATTTACAGCGTTTTCTA-AAAAGAGCCACTAAA-AATGAAAGTTCTAATCCAAAACGACGC
* *
2969 CGTTTTGTTAAGA
320 CATTTTATTAAGA
* * * * *
2982 TTTAATGCACATTTCTGGCGTTTTCCGTTAAAGCACCACTAAAAATTAATTTGCTTAAGTTAGAC
1 TTTAATGCACATTTCTGGCGTTTTCTGTTAAA-CGCCAGTAAAAATTAATTTGCTTAAGCTAAAC
** * * ** *
3047 GTCGACGTTTAGCCAATATTTCAAGTCACTTTTGCGGCGTTTCCTGAACAAACGCCACGAAAAAT
65 GAAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCGTTTGTTCAA-AAACGCCAC-AAAAAT
* * * *** *
3112 TATCATAAATGGCGCCGTTTTGTTAATATAGAGAAAATGCTAAGTTAAAAATCGTGGACAGAAAC
128 TAACAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGTTAAAAA-C-TGTACAGAAAC
* * * * * * *
3177 AGCGTCGTTCAACCAAAATTTTAAGTCACTTTTGCGGCGTTTCTTGCACAAACGCCGCTATTGCT
191 GGCGTCGTTTAGCAAAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCT
3242 T
256 T
3243 AAGCATTAGC
Statistics
Matches: 484, Mismatches: 101, Indels: 22
0.80 0.17 0.04
Matches are distributed among these distances:
335 142 0.29
336 234 0.48
337 108 0.22
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (332 bp):
TTTAATGCACATTTCTGGCGTTTTCTGTTAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAACG
AAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCGTTTGTTCAAAAACGCCACAAAAATTAA
CAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGTTAAAAACTGTACAGAAACGGCGT
CGTTTAGCAAAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCTTGTAC
ATTTACAGCGTTTTCTAAAAAGAGCCACTAAAAATGAAAGTTCTAATCCAAAACGACGCCATTTT
ATTAAGA
Found at i:4422 original size:14 final size:14
Alignment explanation
Indices: 4403--4431 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4393 TTAAAAAACA
4403 ATCAGTAATCATGT
1 ATCAGTAATCATGT
4417 ATCAGTAATCATGT
1 ATCAGTAATCATGT
4431 A
1 A
4432 CCTAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
ATCAGTAATCATGT
Found at i:4844 original size:114 final size:114
Alignment explanation
Indices: 4664--4978 Score: 431
Period size: 114 Copynumber: 2.8 Consensus size: 114
4654 ACTTACCCAT
4664 AAACGCCACTAAATCCCCCGAAAGCT-CAGAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGC
1 AAACGCCACTAAAT-CCCCGAAAGCTCCA-AAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGC
*
4728 GCTTTCTCAAAAACGCCGCTAAAGCCCTGGGCATTAG-AGGTGCTTA-ATTAA
64 GCTTTCTCAAAAACGCCACTAAAGCCCTGGGCATTAGCA-GTGCTTACA-TAA
* * *
4779 AAATGCCACTAAATCCCCGAAAGCTCCAAAAATGGTGTCGTTGGGCTTAGGTATTTTTGCGGCGC
1 AAACGCCACTAAATCCCCGAAAGCTCCAAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGC
* *
4844 TTTCTCAAAAACGCCACTAAAGCCCTTGGCATTTGCAGTGCTTACATAA
66 TTTCTCAAAAACGCCACTAAAGCCCTGGGCATTAGCAGTGCTTACATAA
* * * * * * *
4893 AAACACCACTAAATCGCCAAAAGCTCAAAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGCGC
1 AAACGCCACTAAATCCCCGAAAGCTCCAAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGC
*
4958 TTAACT-AAAAACGCCACTAAA
66 TT-TCTCAAAAACGCCACTAAA
4979 TCCGCGAAAA
Statistics
Matches: 179, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
114 160 0.89
115 19 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (114 bp):
AAACGCCACTAAATCCCCGAAAGCTCCAAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGC
TTTCTCAAAAACGCCACTAAAGCCCTGGGCATTAGCAGTGCTTACATAA
Found at i:5013 original size:188 final size:186
Alignment explanation
Indices: 4769--5126 Score: 452
Period size: 188 Copynumber: 1.9 Consensus size: 186
4759 CATTAGAGGT
* * **
4769 GCTTAATTAAAAATGCCACTAAATCCCCGAAAGCTCCAAAAATGGTGTCGTTGGGCTTAGGTATT
1 GCTTAACTAAAAACGCCACTAAATCCCCGAAAGCTCCAAAAACAGTGTCGTTGGGCTTAGGT-TT
* *
4834 -TTTGCGGCGCTTT-CTCAAAAACGCCACTAAAGCCCTTGGCATTTGCAGTGCTTACATAAAAAC
65 CTTTGCGGCGCTTTAC-CAAAAACGCCACTAAAGCCCTTAGCATTAGCAGTGCTTACATAAAAAC
4897 ACCACTAAATCGCCAAAAGCTCAAAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGC
129 ACCACTAAATCGCCAAAAGCTC-AAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGC
* * *
4956 GCTTAACTAAAAACGCCACTAAATCCGCGAAAAGCT-TAGAAAACAGTGTCGTTGGGCTTATGTT
1 GCTTAACTAAAAACGCCACTAAATCCCCG-AAAGCTCCA-AAAACAGTGTCGTTGGGCTTAGGTT
** * * * * *
5020 TCTTTGCGGCGCTTTACCGTAAATGCCGCTAAAGCCCTTAGCGTTAGCGGTGCTTACCTAAAAAC
64 TCTTTGCGGCGCTTTACCAAAAACGCCACTAAAGCCCTTAGCATTAGCAGTGCTTACATAAAAAC
* * * ** *
5085 GCCGCTAAATCTCTGAAAGCTCAGAAACGGCGTCGTTAGGCT
129 ACCACTAAATCGCCAAAAGCTCAAAAACGGCGTCGTTAGGCT
5127 TACGTTTTTT
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
187 48 0.33
188 96 0.66
189 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (186 bp):
GCTTAACTAAAAACGCCACTAAATCCCCGAAAGCTCCAAAAACAGTGTCGTTGGGCTTAGGTTTC
TTTGCGGCGCTTTACCAAAAACGCCACTAAAGCCCTTAGCATTAGCAGTGCTTACATAAAAACAC
CACTAAATCGCCAAAAGCTCAAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGC
Found at i:5508 original size:15 final size:16
Alignment explanation
Indices: 5474--5508 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5464 GAAATTAGGG
*
5474 ATTTCAGGGGGGAAAG
1 ATTTCAGGGGGGAAAA
5490 ATTTCA-GGGGGAAAA
1 ATTTCAGGGGGGAAAA
5505 ATTT
1 ATTT
5509 ATAAATGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.26
Consensus pattern (16 bp):
ATTTCAGGGGGGAAAA
Found at i:6460 original size:14 final size:14
Alignment explanation
Indices: 6433--6471 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
6423 ACATAATCCT
*
6433 TAACCCCTAGACCCC
1 TAACCCTTA-ACCCC
6448 TAACCCTTAACCCC
1 TAACCCTTAACCCC
*
6462 CAACCCTTAA
1 TAACCCTTAA
6472 ACCATAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.31, C:0.49, G:0.03, T:0.18
Consensus pattern (14 bp):
TAACCCTTAACCCC
Found at i:6481 original size:15 final size:14
Alignment explanation
Indices: 6463--6522 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
6453 CTTAACCCCC
6463 AACCCTTAAACCATA
1 AACCC-TAAACCATA
* *
6478 AACCATAATCCATA
1 AACCCTAAACCATA
*
6492 ATCCCTAAACACATA
1 AACCCTAAAC-CATA
* *
6507 ATCCCTAAACCTTA
1 AACCCTAAACCATA
6521 AA
1 AA
6523 ATTTGGATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
14 19 0.51
15 18 0.49
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:6522 original size:22 final size:21
Alignment explanation
Indices: 6469--6522 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
6459 CCCCAACCCT
6469 TAAACCATAAACCATAATCCA
1 TAAACCATAAACCATAATCCA
* * *
6490 TAATCCCTAAACACATAATCCC
1 TAAACCATAAAC-CATAATCCA
*
6512 TAAACCTTAAA
1 TAAACCATAAA
6523 ATTTGGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCATAAACCATAATCCA
Found at i:7223 original size:41 final size:41
Alignment explanation
Indices: 7165--7409 Score: 312
Period size: 41 Copynumber: 6.0 Consensus size: 41
7155 TTTAAATCCT
** *
7165 TGAGCATTAGCGGCGCTTTATCAAAAACGCCACTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * * *
7206 CGAGCATTAGCGGCGCTTTTCCAAAAACTCCGCTAAAGCCA
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* *
7247 GGAGCATTAGCGGCGCTTTCCCAAAAACGCCGTTAAAAG-CC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCT-AAAGCCC
* *
7288 TGAGCATTAGCGGCACTTTCCCAAAAACGCCGCTAAAGCCT
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * * *
7329 TGAGCATTAGCGGCGCTTTCACAGAAACGTCGCTAAATCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * *
7370 TGGGCATTAGTGGCGCTTTCCCAAAAATGCCGCTAAAGCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCC
7410 TCGAAAGCTC
Statistics
Matches: 174, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 4 0.02
41 166 0.95
42 4 0.02
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
Found at i:8621 original size:19 final size:19
Alignment explanation
Indices: 8597--8642 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
8587 TTAAAGAAAA
8597 AATTAATTAATATTTAT-AT
1 AATTAATTAATA-TTATGAT
**
8616 AATTAAAAAATATTATGAT
1 AATTAATTAATATTATGAT
8635 -ATTAATTA
1 AATTAATTA
8643 TTTTGTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATTAATTAATATTATGAT
Found at i:11195 original size:19 final size:20
Alignment explanation
Indices: 11171--11211 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11161 TCTGTTTTGA
*
11171 TTTTA-TTTATTCTACTCTG
1 TTTTATTTTATTCTACTATG
*
11190 TTTTATTTTGTTCTACTATG
1 TTTTATTTTATTCTACTATG
11210 TT
1 TT
11212 GTAGTACCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTATTTTATTCTACTATG
Found at i:20002 original size:14 final size:16
Alignment explanation
Indices: 19972--20003 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
19962 TAAAAAGTTA
19972 TGTACTAGGGAATTTT
1 TGTACTAGGGAATTTT
19988 TGTA-TAGGG-ATTTT
1 TGTACTAGGGAATTTT
20002 TG
1 TG
20004 GCTCTAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (16 bp):
TGTACTAGGGAATTTT
Found at i:54663 original size:27 final size:27
Alignment explanation
Indices: 54633--54886 Score: 312
Period size: 27 Copynumber: 9.4 Consensus size: 27
54623 GGGTATAATA
54633 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
54660 GTCATTTTACCCTATATGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * * * **
54687 CTCATTCTAACCTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
54714 GTCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * *
54741 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
54768 GTAATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
54795 GTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTTG
** *
54822 GTCATTTTACTTTATTGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
54849 GTCATTTTACCCTAT-GAGGGTATTTTG
1 GTCATTTTACCCTATAG-GGGTATTTTG
54876 GTCATTTTACC
1 GTCATTTTACC
54887 TATTTTAGGG
Statistics
Matches: 196, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 1 0.01
27 195 0.99
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Found at i:56484 original size:24 final size:23
Alignment explanation
Indices: 56439--56487 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
56429 AATTTATCGT
*
56439 ATTTTTACTGGCAGCTTGTTTGC
1 ATTTTTACTGGCAGATTGTTTGC
* *
56462 ATTTTTACTGGTAGAATTTTTTGC
1 ATTTTTACTGGCAG-ATTGTTTGC
56486 AT
1 AT
56488 ATTGGTATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (23 bp):
ATTTTTACTGGCAGATTGTTTGC
Found at i:62864 original size:19 final size:19
Alignment explanation
Indices: 62837--62891 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
62827 AAATCCCAAA
62837 TTTTGATACCCATATCTTT
1 TTTTGATACCCATATCTTT
* *
62856 TTTTTATACTCATATC--T
1 TTTTGATACCCATATCTTT
*
62873 TTCTGATACCCATATCTTT
1 TTTTGATACCCATATCTTT
62892 GACTTTTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
19 15 0.52
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTGATACCCATATCTTT
Found at i:62886 original size:17 final size:17
Alignment explanation
Indices: 62840--62891 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
62830 TCCCAAATTT
*
62840 TGATACCCATATCTTTTTT
1 TGATACCCATATC--TTTC
* *
62859 TTATACTCATATCTTTC
1 TGATACCCATATCTTTC
62876 TGATACCCATATCTTT
1 TGATACCCATATCTTT
62892 GACTTTTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 17 0.61
19 11 0.39
ACGTcount: A:0.23, C:0.23, G:0.04, T:0.50
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:84967 original size:23 final size:23
Alignment explanation
Indices: 84937--84984 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
84927 TTAAAACATA
* *
84937 TAAATATTTCATAT-ATTAATAT
1 TAAATATTTAATATAATTAAGAT
84959 TAAAGTATTTAATATAATTAAGAT
1 TAAA-TATTTAATATAATTAAGAT
84983 TA
1 TA
84985 TATAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TAAATATTTAATATAATTAAGAT
Found at i:86410 original size:31 final size:31
Alignment explanation
Indices: 86375--86440 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
86365 CATAGATGAA
*
86375 AATACTATACTTAGAGCACCAGATCCATCAC
1 AATACTACACTTAGAGCACCAGATCCATCAC
* *
86406 AATACTACACTTAGGGCACCAGATCCATCAG
1 AATACTACACTTAGAGCACCAGATCCATCAC
86437 AATA
1 AATA
86441 TGATGCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.21
Consensus pattern (31 bp):
AATACTACACTTAGAGCACCAGATCCATCAC
Found at i:102823 original size:63 final size:62
Alignment explanation
Indices: 102693--102823 Score: 149
Period size: 62 Copynumber: 2.1 Consensus size: 62
102683 GAGACACAGA
* * ** * *
102693 CGTGTGTCCAAGTCGTGTGACACATTATTGTTATTAGAGACCACACGAGTCAGAGACATGGG
1 CGTGTGTCCAAGCCGTGTGACACACTATTGCGATTAGAGACCACACGAGGCAGAAACATGGG
* *
102755 TGTGTGTCCAAGCCGTGTGACTCACTATTTGCGATCTA-AGACCACAC-AGGCAGACAACATGGG
1 CGTGTGTCCAAGCCGTGTGACACACTA-TTGCGAT-TAGAGACCACACGAGGCAGA-AACATGGG
102818 CGTGTG
1 CGTGTG
102824 ACAGGCCGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
62 29 0.51
63 26 0.46
64 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (62 bp):
CGTGTGTCCAAGCCGTGTGACACACTATTGCGATTAGAGACCACACGAGGCAGAAACATGGG
Found at i:104311 original size:18 final size:19
Alignment explanation
Indices: 104284--104319 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
104274 CAAAAAAACT
104284 AAAATAATTTTTAAAATTC
1 AAAATAATTTTTAAAATTC
104303 AAAAT-ATTTTTAAAATT
1 AAAATAATTTTTAAAATT
104320 TTCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTC
Found at i:110811 original size:25 final size:26
Alignment explanation
Indices: 110783--110839 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
110773 TTTACATCTC
*
110783 AAAAAATTATAAAA-A-AATTATATAT
1 AAAAAATTA-AAAACATAAATATATAT
110808 AAAAAATTAAAAACTATAAATATATAT
1 AAAAAATTAAAAAC-ATAAATATATAT
110835 AAAAA
1 AAAAA
110840 TAAATCTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 9 0.32
26 1 0.04
27 14 0.50
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAAATTAAAAACATAAATATATAT
Found at i:114590 original size:60 final size:59
Alignment explanation
Indices: 114474--114590 Score: 128
Period size: 60 Copynumber: 2.0 Consensus size: 59
114464 AGTATTTAAG
** * * ** *
114474 ATTTTTTTTTGTCCAATTAGGTACCTAAAGTTAGTTTTAAGGTTCAATTTGGTACCTCA
1 ATTTTTTTTTGTCCAATTAAATACATAAACTTAGTTTTAAGGTTCAAAATGATACCTCA
* *
114533 ATTTTTTTTTGGTCCACTTAAATACATAAACTTAGCTTTT-TGGTTCAAAATGATACCT
1 ATTTTTTTTT-GTCCAATTAAATACATAAACTTAG-TTTTAAGGTTCAAAATGATACCT
114591 GAACTTGGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 10 0.21
60 33 0.70
61 4 0.09
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (59 bp):
ATTTTTTTTTGTCCAATTAAATACATAAACTTAGTTTTAAGGTTCAAAATGATACCTCA
Found at i:120554 original size:29 final size:29
Alignment explanation
Indices: 120506--120893 Score: 488
Period size: 29 Copynumber: 13.2 Consensus size: 29
120496 NNNNNNNNNN
*
120506 TTAGGGTTTTTAATTGAATTGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
*
120535 TTGGGGTTTTTAATTAAATTGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
* * * * *
120564 CTAGGGTGTTTAATTAAGTTAGGTTAAGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
* ** *
120593 TTAGGGTTTTTAATTAAGTTATGTTAGGA
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
*
120622 TTAGGGTTTTTAATTGAATTGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
* *
120651 TTAGGGTTTTTAATTAAGTTTGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
*
120680 TTAGGGTTTTTAATTTAATTGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
* *
120709 TTAGGGTTTTTAATTAAGTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
*
120738 TTAGGGTTTTTAATTGAATTGGGTTAGGGTTAGGG
1 TTAGGGTTTTTAATT-AA----ATT-GGGTTAGGG
*
120773 TTAGGGTTTTTAATTGAATTGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
* *
120802 TTAGGGTTTTTAATTAAGTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
* * * * *
120831 TTGGGGGTTTTAACTGAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
120860 TTAGGGTTTTTAATTAAATTGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTGGGTTAGGG
120889 TTAGG
1 TTAGG
120894 AATAAATTTC
Statistics
Matches: 310, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
29 279 0.90
30 4 0.01
34 4 0.01
35 23 0.07
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.44
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTGGGTTAGGG
Found at i:120866 original size:35 final size:35
Alignment explanation
Indices: 120701--120809 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 35
120691 AATTTAATTG
120701 GGTTAGGGTTA-GGG-TTT--TT-AATTAAGTTA-
1 GGTTAGGGTTAGGGGTTTTAATTGAATTAAGTTAG
* **
120730 GGTTAGGGTTAGGGTTTTTAATTGAATTGGGTTAG
1 GGTTAGGGTTAGGGGTTTTAATTGAATTAAGTTAG
* **
120765 GGTTAGGGTTAGGGTTTTTAATTGAATTGGGTTAG
1 GGTTAGGGTTAGGGGTTTTAATTGAATTAAGTTAG
120800 GGTTAGGGTT
1 GGTTAGGGTT
120810 TTTAATTAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
29 11 0.15
30 2 0.03
31 3 0.04
33 2 0.03
34 8 0.11
35 45 0.63
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (35 bp):
GGTTAGGGTTAGGGGTTTTAATTGAATTAAGTTAG
Found at i:121119 original size:21 final size:21
Alignment explanation
Indices: 121093--121142 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
121083 CTTTCTCTAG
* *
121093 CTTCCGGTGGCGG-TTGTTGTT
1 CTTCCGGTGG-GGATTCTGGTT
121114 CTTCCGGTGGGGATTCTGGTT
1 CTTCCGGTGGGGATTCTGGTT
121135 CTTCCGGT
1 CTTCCGGT
121143 ACGACATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.02, C:0.22, G:0.36, T:0.40
Consensus pattern (21 bp):
CTTCCGGTGGGGATTCTGGTT
Found at i:121413 original size:18 final size:18
Alignment explanation
Indices: 121387--121427 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
121377 GGACTCGAAA
121387 AAGGATACATATAAGGGT
1 AAGGATACATATAAGGGT
*
121405 AAGGGTACATATAAGGGT
1 AAGGATACATATAAGGGT
*
121423 TAGGA
1 AAGGA
121428 AACGCACCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (18 bp):
AAGGATACATATAAGGGT
Found at i:122081 original size:7 final size:7
Alignment explanation
Indices: 122069--122093 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
122059 TATACATAAT
122069 AATACTA
1 AATACTA
122076 AATACTA
1 AATACTA
122083 AATACTA
1 AATACTA
122090 AATA
1 AATA
122094 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:128745 original size:24 final size:24
Alignment explanation
Indices: 128713--128762 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
128703 TGGTGGAGGT
*
128713 GACACGTGTGTTGCAACCAAATCA
1 GACACGTGTGGTGCAACCAAATCA
*
128737 GACACGTGTGGTGCAACCGAATCA
1 GACACGTGTGGTGCAACCAAATCA
128761 GA
1 GA
128763 TCACATGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (24 bp):
GACACGTGTGGTGCAACCAAATCA
Found at i:133506 original size:16 final size:17
Alignment explanation
Indices: 133487--133519 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
133477 AAATTTATAC
*
133487 ATATATA-ATATGAAAA
1 ATATATAGAAATGAAAA
133503 ATATATAGAAATGAAAA
1 ATATATAGAAATGAAAA
133520 TTATTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
ATATATAGAAATGAAAA
Found at i:134284 original size:20 final size:20
Alignment explanation
Indices: 134261--134299 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
134251 GTGTCGTGAC
*
134261 TCTGGTCCTGATGTCGCGAT
1 TCTGGTCCTGATGTAGCGAT
134281 TCTGGTCCTGATGTAGCGA
1 TCTGGTCCTGATGTAGCGA
134300 CTTTAGCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.31, T:0.33
Consensus pattern (20 bp):
TCTGGTCCTGATGTAGCGAT
Found at i:138591 original size:31 final size:31
Alignment explanation
Indices: 138553--138613 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
138543 TACATAGACG
138553 AAAATACTACACTTAGGACACCAGATCCATT
1 AAAATACTACACTTAGGACACCAGATCCATT
*
138584 AAAATACTACACTTAGGGCACCAGATCCAT
1 AAAATACTACACTTAGGACACCAGATCCAT
138614 CGGAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.21
Consensus pattern (31 bp):
AAAATACTACACTTAGGACACCAGATCCATT
Found at i:143557 original size:3 final size:3
Alignment explanation
Indices: 143551--143583 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
143541 GTTGCTGTTG
*
143551 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
143584 CTCTTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:143811 original size:22 final size:21
Alignment explanation
Indices: 143755--143811 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
143745 AAGATGTAGT
143755 ATGCTATTATTTTTAAATTATC
1 ATGC-ATTATTTTTAAATTATC
* **
143777 AT-TAACATGTTTTAAATTTATC
1 ATGCATTAT-TTTTAAA-TTATC
143799 ATGCATTATTTTT
1 ATGCATTATTTTT
143812 TAGTAATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 13 0.50
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (21 bp):
ATGCATTATTTTTAAATTATC
Found at i:145498 original size:33 final size:33
Alignment explanation
Indices: 145461--145543 Score: 166
Period size: 33 Copynumber: 2.5 Consensus size: 33
145451 ATTATTATTA
145461 TTATTATTATTATTATTATTAAGCTAATCAATT
1 TTATTATTATTATTATTATTAAGCTAATCAATT
145494 TTATTATTATTATTATTATTAAGCTAATCAATT
1 TTATTATTATTATTATTATTAAGCTAATCAATT
145527 TTATTATTATTATTATT
1 TTATTATTATTATTATT
145544 TACCCATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (33 bp):
TTATTATTATTATTATTATTAAGCTAATCAATT
Found at i:145533 original size:3 final size:3
Alignment explanation
Indices: 145440--145514 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
145430 CGACTTCGTT
*** *
145440 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA AGC TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
145488 TCAA TT- TTA TTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA
145515 AGCTAATCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:145607 original size:16 final size:16
Alignment explanation
Indices: 145573--145612 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
145563 TTAGATTTTG
*
145573 TTATATATATACATAC
1 TTATATATATACACAC
*
145589 TTATATATATACACGC
1 TTATATATATACACAC
*
145605 TTACATAT
1 TTATATAT
145613 TTCCAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATATATATACACAC
Found at i:146506 original size:19 final size:19
Alignment explanation
Indices: 146469--146507 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
146459 CTTTGTATTT
*
146469 ATTTCAATTTGGCTCTCAA
1 ATTTCAATTTGGATCTCAA
* *
146488 ATTTCAATTTTGATTTCAA
1 ATTTCAATTTGGATCTCAA
146507 A
1 A
146508 ATTAGTCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTTCAATTTGGATCTCAA
Found at i:146550 original size:3 final size:3
Alignment explanation
Indices: 146544--146576 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
146534 GTTGTTGTTG
*
146544 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
146577 CTCTTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:146804 original size:22 final size:21
Alignment explanation
Indices: 146748--146804 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
146738 AAGATGTAGT
146748 ATGCTATTATTTTTAAATTATC
1 ATGC-ATTATTTTTAAATTATC
* **
146770 AT-TAACATGTTTTAAATTTATC
1 ATGCATTAT-TTTTAAA-TTATC
146792 ATGCATTATTTTT
1 ATGCATTATTTTT
146805 TAGTCTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 13 0.50
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (21 bp):
ATGCATTATTTTTAAATTATC
Found at i:148000 original size:95 final size:96
Alignment explanation
Indices: 147889--148076 Score: 283
Period size: 98 Copynumber: 1.9 Consensus size: 96
147879 AAATTTTTGG
147889 TGGTGGCCTGCAAATGGCCGGCACCACCTTTTTTGGGGG-ATTT-TTTTGTT-ACTTTTTTCGTG
1 TGGTGGCCTGCAAATGGCCGGCACCACC-TTTTTGGGGGAATTTGTTTT-TTCACTTTTTTCGTG
* *
147951 TCAATAGTAGGTATTAGTATACAAAAAAAATTT
64 TCAATAGCAGGTATCAGTATACAAAAAAAATTT
* *
147984 TGGTGGCCTGCCAATGGCCGGCAGCACCTTTTTGGGGGAAAATTTGTTTTTTCACTTTTTTCGTG
1 TGGTGGCCTGCAAATGGCCGGCACCACCTTTTTGGGGG--AATTTGTTTTTTCACTTTTTTCGTG
148049 TCAATAGCAGGTATCAGTATACAAAAAA
64 TCAATAGCAGGTATCAGTATACAAAAAA
148077 GTAAAAAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
94 10 0.12
95 26 0.31
97 6 0.07
98 42 0.50
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (96 bp):
TGGTGGCCTGCAAATGGCCGGCACCACCTTTTTGGGGGAATTTGTTTTTTCACTTTTTTCGTGTC
AATAGCAGGTATCAGTATACAAAAAAAATTT
Found at i:148149 original size:143 final size:142
Alignment explanation
Indices: 147984--148251 Score: 398
Period size: 143 Copynumber: 1.9 Consensus size: 142
147974 AAAAAAATTT
* *
147984 TGGTGGCCTGCCAATGGCCGGCAGCACC-TTTTTGGGGGAAAATTTGTTTTTTCACTTTTTTCGT
1 TGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGGGGG--AATTT-TTTTTT-ACTTTTTTCGT
* * **
148048 GTCAATAGCAGGTATCAGTATAC-AAAAAAG-TAAAAAAAAATTGGTGGTGGTTTGCCAATGGTA
62 GTCAATAACAGGTATAAGTATACGAAAAAAGATAAAAAAAAATTGGTGGTGGCCTGCCAATGGTA
148111 AAAAATATATTTTTGG
127 AAAAATATATTTTTGG
*
148127 TGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGTGGGAATTTTTTTTTACTTTTTTCGTGTCA
1 TGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGGGGGAATTTTTTTTTACTTTTTTCGTGTCA
*
148192 ATAACAGGTATAAGTATACGAAAAAAGTATAAAAAAAAATTTGTGGTGGCCTGCCAATGG
66 ATAACAGGTATAAGTATACGAAAAAAG-ATAAAAAAAAATTGGTGGTGGCCTGCCAATGG
148252 CCAGCACCAC
Statistics
Matches: 113, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
140 32 0.28
141 13 0.12
142 5 0.04
143 54 0.48
144 9 0.08
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (142 bp):
TGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGGGGGAATTTTTTTTTACTTTTTTCGTGTCA
ATAACAGGTATAAGTATACGAAAAAAGATAAAAAAAAATTGGTGGTGGCCTGCCAATGGTAAAAA
ATATATTTTTGG
Found at i:148181 original size:238 final size:236
Alignment explanation
Indices: 147872--148333 Score: 626
Period size: 238 Copynumber: 1.9 Consensus size: 236
147862 AAAAACTAAA
* *
147872 AAAAAAAAAATTTTTGGTGGTGGCCTGCAAATGGCCGGCACCACCTTTTTTGGGGGATTTTTTTG
1 AAAAAAAAAATTTTTGGTGGTGGCCTACAAATGGCCGGCACCACCTTTTTTGGGGAATTTTTTTG
** *
147937 TTACTTTTTTCGTGTCAATAGTAGGTATTAGTATAC-AAAAAAAATTT-TGGTGGCCTGCCAATG
66 TTACTTTTTTCGTGTCAATAACAGGTATAAGTATACAAAAAAAAATTTGTGGTGGCCTGCCAATG
* * * *
148000 GCCGGCAGCACCTTTTTGGGGGAAAATTTGTTTTTTCACTTTTTTCGTGTCAATAGCAGGTATCA
131 GCCAGCACCACCTTTTTGGGGG-AAA-TT-TTTTTT-A-ATTTTTCGTGTCAATAACAGGTATCA
148065 GTATAC-AAAAAAGTAAAAAAAAATTGGTGGTGGTTTGCCAATGGT
191 GTATACAAAAAAAGTAAAAAAAAATTGGTGGTGGTTTGCCAATGGT
* * *
148110 AAAAAATATATTTTTGGTGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGTGGGAATTTTTTT
1 AAAAAAAAAATTTTTGGTGGTGGCCTACAAATGGCCGGCACCACCTTTTTTG-GGGAATTTTTTT
148175 -TTACTTTTTTCGTGTCAATAACAGGTATAAGTATACGAAAAAAGTATAAAAAAAAATTTGTGGT
65 GTTACTTTTTTCGTGTCAATAACAGGTATAAGTATAC-----------AAAAAAAAATTTGTGGT
*
148239 GGCCTGCCAATGGCCAGCACCACCTTTTTTGGGGAAATTTTTTTTAATTTTTCGTGTCAATAACA
119 GGCCTGCCAATGGCCAGCACCACCTTTTTGGGGGAAATTTTTTTTAATTTTTCGTGTCAATAACA
148304 GGTATCAGTATACAAAAAAAGTAAAAAAAA
184 GGTATCAGTATACAAAAAAAGTAAAAAAAA
148334 TTCCCCAAAC
Statistics
Matches: 196, Mismatches: 13, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
238 81 0.41
239 11 0.06
246 30 0.15
247 17 0.09
248 6 0.03
249 2 0.01
250 14 0.07
251 35 0.18
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (236 bp):
AAAAAAAAAATTTTTGGTGGTGGCCTACAAATGGCCGGCACCACCTTTTTTGGGGAATTTTTTTG
TTACTTTTTTCGTGTCAATAACAGGTATAAGTATACAAAAAAAAATTTGTGGTGGCCTGCCAATG
GCCAGCACCACCTTTTTGGGGGAAATTTTTTTTAATTTTTCGTGTCAATAACAGGTATCAGTATA
CAAAAAAAGTAAAAAAAAATTGGTGGTGGTTTGCCAATGGT
Found at i:148324 original size:106 final size:107
Alignment explanation
Indices: 148126--148333 Score: 339
Period size: 106 Copynumber: 2.0 Consensus size: 107
148116 TATATTTTTG
* * *
148126 GTGGTGGCCTACCAATGGCCGGCACCACCTTTTTTGTGGGAATTTTTTTTTACTTTTTTCGTGTC
1 GTGGTGGCCTACCAATGGCCAGCACCACCTTTTTTGTGGGAAATTTTTTTTACATTTTTCGTGTC
*
148191 AATAACAGGTATAAGTATACGAAAAAAGTATAAAAAAAAATTT
66 AATAACAGGTATAAGTATACAAAAAAAGTA-AAAAAAAAATTT
*
148234 GTGGTGGCCTGCCAATGGCCAGCACCACCTTTTTTG-GGGAAATTTTTTTTA-ATTTTTCGTGTC
1 GTGGTGGCCTACCAATGGCCAGCACCACCTTTTTTGTGGGAAATTTTTTTTACATTTTTCGTGTC
*
148297 AATAACAGGTATCAGTATACAAAAAAAGTAAAAAAAA
66 AATAACAGGTATAAGTATACAAAAAAAGTAAAAAAAA
148334 TTCCCCAAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
105 7 0.07
106 39 0.41
107 14 0.15
108 34 0.36
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (107 bp):
GTGGTGGCCTACCAATGGCCAGCACCACCTTTTTTGTGGGAAATTTTTTTTACATTTTTCGTGTC
AATAACAGGTATAAGTATACAAAAAAAGTAAAAAAAAAATTT
Found at i:150121 original size:42 final size:42
Alignment explanation
Indices: 150062--150145 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
150052 GCAGTTTTCG
*
150062 TTACCTCTGCAACATCATGTAGTTGTCCGGTAGTGAAATTGA
1 TTACCTCTGCAACATCATATAGTTGTCCGGTAGTGAAATTGA
* *
150104 TTACCTCTGCAACATCATATAGTTGTTCTGTAGTGAAATTGA
1 TTACCTCTGCAACATCATATAGTTGTCCGGTAGTGAAATTGA
150146 ACACTGCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (42 bp):
TTACCTCTGCAACATCATATAGTTGTCCGGTAGTGAAATTGA
Found at i:152080 original size:55 final size:55
Alignment explanation
Indices: 151980--152158 Score: 292
Period size: 55 Copynumber: 3.3 Consensus size: 55
151970 ACTTTTTTTT
* *
151980 TCATTCATTTCAATTTT-TTTTTCTACATCTAACA--CTTTTTTTTCATTTAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
152032 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
* *
152087 TCATTTATTTCAATTTAATTTTTCTACATCTAACACCCTGTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
*
152142 TCATTTATTTTAATTTT
1 TCATTTATTTCAATTTT
152159 TTGAATTTTA
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
52 16 0.14
53 17 0.14
55 85 0.72
ACGTcount: A:0.24, C:0.20, G:0.01, T:0.56
Consensus pattern (55 bp):
TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
Found at i:152313 original size:108 final size:108
Alignment explanation
Indices: 152169--152383 Score: 387
Period size: 108 Copynumber: 2.0 Consensus size: 108
152159 TTGAATTTTA
*
152169 TTTTTTTACATAAAGGTGGTGTCGGCCATTGCCAGGCCACCACCAAAAATTATTT-TTTTTGAAT
1 TTTTTTTACATAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAATT-TTTATTTTTGAAT
152233 TTTTTCGTATACTGGTGCCAGACAATGACAACCAAAATGTAAAT
65 TTTTTCGTATACTGGTGCCAGACAATGACAACCAAAATGTAAAT
152277 TTTTTTTACATAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAATTTTTATTTTTGAATT
1 TTTTTTTACATAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAATTTTTATTTTTGAATT
* *
152342 TTTTCGTATACTGGTGCCGGCCAATGACAACCAAAATGTAAA
66 TTTTCGTATACTGGTGCCAGACAATGACAACCAAAATGTAAA
152384 AAAAAAAAAA
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
107 3 0.03
108 100 0.97
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (108 bp):
TTTTTTTACATAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAATTTTTATTTTTGAATT
TTTTCGTATACTGGTGCCAGACAATGACAACCAAAATGTAAAT
Found at i:153641 original size:56 final size:55
Alignment explanation
Indices: 153554--153716 Score: 215
Period size: 55 Copynumber: 3.0 Consensus size: 55
153544 CACTTTTTTT
* *
153554 TCATTCATTTCAA--TT-TTTTTCTACGTCTAACACCCTTTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCC-TTTTTTTTCATTCAATC
*
153607 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCTTTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
* * ** *
153662 TAATTTATTTCAATTTTATTTTTTTACATCTAATTTCCCTTTATTTTCATTCAAT
1 TCATTTATTTCAATTTTATTTTTCTACATCTAA-CACCCTTTTTTTTCATTCAAT
153717 TTTATTTTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
53 12 0.12
55 49 0.51
56 36 0.37
ACGTcount: A:0.23, C:0.20, G:0.01, T:0.56
Consensus pattern (55 bp):
TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
Found at i:154971 original size:30 final size:30
Alignment explanation
Indices: 154925--155022 Score: 117
Period size: 34 Copynumber: 3.1 Consensus size: 30
154915 ATTTCTTATG
*
154925 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
154956 CCAATATTTGATACCCATATCATATCTTTGA-TTT
1 CCAATATTTGATA-CC----CATATCTTTGACTTT
*
154990 CCATTATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
155020 CCA
1 CCA
155023 TAAATATGGA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 9 0.15
33 2 0.03
34 15 0.25
35 11 0.19
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:154998 original size:34 final size:35
Alignment explanation
Indices: 154941--155010 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
154931 TCTCGATACC
154941 CATATCTTTGACTTTCCAATATTTGATACCCATAT
1 CATATCTTTGACTTTCCAATATTTGATACCCATAT
*
154976 CATATCTTTGA-TTTCCATTATTTGATACCCATAT
1 CATATCTTTGACTTTCCAATATTTGATACCCATAT
155010 C
1 C
155011 TTTGACTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 23 0.68
35 11 0.32
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (35 bp):
CATATCTTTGACTTTCCAATATTTGATACCCATAT
Found at i:159425 original size:2 final size:2
Alignment explanation
Indices: 159418--159444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
159408 TAATTTACAA
159418 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
159445 ATAATGTCTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:159636 original size:30 final size:30
Alignment explanation
Indices: 159600--159682 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
159590 CAATATCTCA
159600 ATACCCATATCTTTGACTTTCCAATATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
* *
159630 ATACCCATATCTTTGACTTTCTATTATTTG
1 ATACCCATATCTTTGACTTTCCAATATTTG
159660 ATACCCATATCTTTGACTTTCCA
1 ATACCCATATCTTTGACTTTCCA
159683 TAAATATGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.25, C:0.24, G:0.06, T:0.45
Consensus pattern (30 bp):
ATACCCATATCTTTGACTTTCCAATATTTG
Found at i:159644 original size:15 final size:15
Alignment explanation
Indices: 159600--159675 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
159590 CAATATCTCA
159600 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** *
159615 ACTTTCCA-ATATTTG
1 A-TACCCATATCTTTG
159630 ATACCCATATCTTTG
1 ATACCCATATCTTTG
** * *
159645 ACTTTCTAT-TATTTG
1 A-TACCCATATCTTTG
159660 ATACCCATATCTTTG
1 ATACCCATATCTTTG
159675 A
1 A
159676 CTTTCCATAA
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
14 8 0.19
15 27 0.63
16 8 0.19
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (15 bp):
ATACCCATATCTTTG
Found at i:160761 original size:43 final size:43
Alignment explanation
Indices: 160709--160803 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
160699 TTTTAAAGGT
* *
160709 TTCTTTAGCGGCGTTTCTGAAAAAAGTGCCGCTTAAGGTCATG
1 TTCTTTAGCGGCGTTTCTGAAAAAAGCGCCGCTAAAGGTCATG
* ** *
160752 TTCTTTAGCGGCGTTTGTGATGAATGCGCCGCTAAAGGTCATG
1 TTCTTTAGCGGCGTTTCTGAAAAAAGCGCCGCTAAAGGTCATG
160795 TTCTTTAGC
1 TTCTTTAGC
160804 AGTGTTTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
TTCTTTAGCGGCGTTTCTGAAAAAAGCGCCGCTAAAGGTCATG
Found at i:161916 original size:11 final size:11
Alignment explanation
Indices: 161902--161977 Score: 86
Period size: 11 Copynumber: 6.9 Consensus size: 11
161892 TTTAAATAGA
161902 AATTTGAGAGG
1 AATTTGAGAGG
161913 AATTTGAGAGG
1 AATTTGAGAGG
161924 AAATTT-AGAGG
1 -AATTTGAGAGG
*
161935 AATTTGAAAGG
1 AATTTGAGAGG
161946 AATTTGAGA-G
1 AATTTGAGAGG
161956 AATATT-AGAGAG
1 AAT-TTGAGAG-G
*
161968 AAATTGAGAG
1 AATTTGAGAG
161978 AAAGGATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
10 12 0.21
11 32 0.57
12 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:161939 original size:33 final size:33
Alignment explanation
Indices: 161902--161977 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
161892 TTTAAATAGA
161902 AATTTGAGAGGAATTTGAGAGGAA-ATTTAGAG-G
1 AATTTGAGAGGAATTTGAGA-GAATA-TTAGAGAG
*
161935 AATTTGAAAGGAATTTGAGAGAATATTAGAGAG
1 AATTTGAGAGGAATTTGAGAGAATATTAGAGAG
*
161968 AAATTGAGAG
1 AATTTGAGAG
161978 AAAGGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 9 0.24
33 29 0.76
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (33 bp):
AATTTGAGAGGAATTTGAGAGAATATTAGAGAG
Found at i:165810 original size:124 final size:124
Alignment explanation
Indices: 165590--165939 Score: 571
Period size: 124 Copynumber: 2.8 Consensus size: 124
165580 TTATTTCGAG
* *
165590 TTGACGTTTCTG-GTCAAATAGTATAAAATCAG-CTCTACCAGGATGCTATTTGAGAATAAAATG
1 TTGACGTTTCTGAG-CAAATAGTATAAAATC-GCCTCTACCAGGATGCTATTTGAGAAGAAATTG
165653 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
*
165714 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACTAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* **
165779 AAATCGCACCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
*
165838 TTGACGTTTCTGAGGAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTG-GTAAGAAATTGT
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAG-AAGAAATTGT
* *
165902 GAAATCGTGCCCTCGTGGACACGATTTTGCTACAGTAG
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
165940 TAAGTTTGGG
Statistics
Matches: 212, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
123 2 0.01
124 209 0.99
125 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
Found at i:173161 original size:51 final size:51
Alignment explanation
Indices: 173085--173267 Score: 366
Period size: 51 Copynumber: 3.6 Consensus size: 51
173075 NNNNNNNNNN
173085 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
173136 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
173187 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
173238 TTTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAG
173268 AATTTAGGAA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 132 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (51 bp):
TTTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTGAAATTAAATATGGG
Found at i:173264 original size:22 final size:22
Alignment explanation
Indices: 173239--173303 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
173229 AAATATGGGT
*
173239 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTAGGAAGGAAA
173261 TTGAGAGAATTTAGGAAGGAAA
1 TTGAGAGAATTTAGGAAGGAAA
* *
173283 TTGAGAGGA-TTAGAAAGGAAA
1 TTGAGAGAATTTAGGAAGGAAA
173304 AATTAGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 11 0.28
22 29 0.73
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (22 bp):
TTGAGAGAATTTAGGAAGGAAA
Found at i:174423 original size:149 final size:144
Alignment explanation
Indices: 174237--174666 Score: 405
Period size: 158 Copynumber: 2.9 Consensus size: 144
174227 TAATTTGGTT
* *
174237 ATATATTTTAAATATTGTTTTATTAATAATTTTATTTAATATATCGTTATTTAAATAAAAAAATT
1 ATATATTTTAAATATTATTTTATCAATAATTTTATTTAATATATCGTTATTTAAATAAAAAAATT
* * * ** * * * *
174302 ATAAAAACATATATATGAGTAACCTGTGCATCACACGGGATAAAAAATTAGTATATTATATTTCA
66 AT-AAAAC--ACACA--AGCAACCCATGAATCACACGAGATAAAAAACTAATATATTATATTTCA
*
174367 AAAACTTAAGTATTTTTTA
126 AAAACTTAAGTATATTTTA
* * **
174386 ATATCTTTTAAATATTATTTTATCAATAATTTTATTTAATATATCGTTATTTAAATAATAATTTT
1 ATATATTTTAAATATTATTTTATCAATAATTTTATTTAATATATCGTTATTTAAATAAAAAAATT
*
174451 ATAAAACACACAAGCAACCCATGAATCACACGAGATAGAAAACTAATATATTATATTTCAAAAAC
66 ATAAAACACACAAGCAACCCATGAATCACACGAGATAAAAAACTAATATATTATATTTCAAAAAC
*
174516 TTGAGTATATTTTAAATTTTGA
131 TTAAG--TA---T--ATTTT-A
* * * * *
174538 TTATATCTTAATTTTAAATATTGTTTAATCAAAAATTTTATTTAATATATCATTATTTAAATAAT
1 --ATA---T-ATTTTAAATATTATTTTATCAATAATTTTATTTAATATATCGTTATTTAAATAAA
** * * *
174603 AATTTTATAAAACAAACTAA-CAACCCATGCATCACACGAGATAAAAAATTAAT-TATTTATATT
60 AAAATTATAAAACACAC-AAGCAACCCATGAATCACACGAGATAAAAAACTAATATA-TTATATT
174666 T
123 T
174667 GAAGCTTTGA
Statistics
Matches: 238, Mismatches: 27, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
144 49 0.21
146 5 0.02
148 5 0.02
149 62 0.26
151 4 0.02
152 1 0.00
154 3 0.01
157 3 0.01
158 104 0.44
159 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (144 bp):
ATATATTTTAAATATTATTTTATCAATAATTTTATTTAATATATCGTTATTTAAATAAAAAAATT
ATAAAACACACAAGCAACCCATGAATCACACGAGATAAAAAACTAATATATTATATTTCAAAAAC
TTAAGTATATTTTA
Found at i:175245 original size:24 final size:24
Alignment explanation
Indices: 175213--175263 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
175203 GATTTAGTAT
* *
175213 TTAGTATAATATATTTAACATTTA
1 TTAGCATAATATATTTAACATTGA
*
175237 TTAGCATAATATATTTGACATTGA
1 TTAGCATAATATATTTAACATTGA
175261 TTA
1 TTA
175264 AAATTAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (24 bp):
TTAGCATAATATATTTAACATTGA
Found at i:177823 original size:25 final size:25
Alignment explanation
Indices: 177777--177839 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
177767 TATAAATATC
*
177777 AATAAA-TTAAATATAATAATTAAT
1 AATAAATTTAAATAGAATAATTAAT
*
177801 AATAAATTTAAATAGAATCATTAAT
1 AATAAATTTAAATAGAATAATTAAT
177826 AATAAATTTAAATA
1 AATAAATTTAAATA
177840 TGTGTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAAATTTAAATAGAATAATTAAT
Found at i:181627 original size:46 final size:46
Alignment explanation
Indices: 181558--181732 Score: 237
Period size: 46 Copynumber: 3.8 Consensus size: 46
181548 AGTGTGGAAC
* * *
181558 GTAGGTATGG--TTTCAGTAAAGAAAACCATACTAACTTTTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
181602 GTAGGTATGATATTTCGGTAAAGAAAACCATGCTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
181648 GTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
181694 GTAGGTATGGTATTTCCGTGAAGAAAACCATATTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
181733 ATAGCATTGT
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 9 0.08
46 106 0.92
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:192452 original size:15 final size:15
Alignment explanation
Indices: 192432--192461 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
192422 GAGTATGGTA
192432 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
192447 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
192462 TACTAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:194101 original size:27 final size:31
Alignment explanation
Indices: 194037--194102 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 31
194027 TCTCTTTCAA
*
194037 CAAATATTACAAAATAATTCAAAATAACATT
1 CAAAAATTACAAAATAATTCAAAATAACATT
*
194068 CAAAAATTA-AAAAT-ATTCATAA-AA-ATT
1 CAAAAATTACAAAATAATTCAAAATAACATT
*
194095 CTAAAATT
1 CAAAAATT
194103 TATCTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 10 0.31
28 2 0.06
29 7 0.22
30 5 0.16
31 8 0.25
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (31 bp):
CAAAAATTACAAAATAATTCAAAATAACATT
Found at i:194739 original size:17 final size:18
Alignment explanation
Indices: 194707--194741 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
194697 GAAAATCTAA
*
194707 TTTACATGCTTTAATTAG
1 TTTACATGCATTAATTAG
194725 TTTACATG-ATTAATTAG
1 TTTACATGCATTAATTAG
194742 AGCATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTACATGCATTAATTAG
Found at i:195443 original size:23 final size:23
Alignment explanation
Indices: 195417--195470 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
195407 CAAACTAATC
195417 CTCTCAAATTTCC-TCTC-AATTT
1 CTCTCAAATTTCCTTC-CAAATTT
195439 GCTCTCAAA-TTCCTTCCAAATTT
1 -CTCTCAAATTTCCTTCCAAATTT
195462 CTCTCAAAT
1 CTCTCAAAT
195471 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.41
Consensus pattern (23 bp):
CTCTCAAATTTCCTTCCAAATTT
Found at i:195469 original size:11 final size:12
Alignment explanation
Indices: 195415--195470 Score: 66
Period size: 11 Copynumber: 4.9 Consensus size: 12
195405 CACAAACTAA
195415 TCCTCTCAAATT
1 TCCTCTCAAATT
195427 TCCTCTC-AATT
1 TCCTCTCAAATT
*
195438 TGCTCTCAAA-T
1 TCCTCTCAAATT
195449 TCCT-TCCAAATT
1 TCCTCT-CAAATT
195461 T-CTCTCAAAT
1 TCCTCTCAAAT
195471 CCATATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 1 0.03
11 25 0.66
12 12 0.32
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (12 bp):
TCCTCTCAAATT
Found at i:195493 original size:51 final size:51
Alignment explanation
Indices: 195430--195529 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
195420 TCAAATTTCC
195430 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * *
195481 TCTCAATTTGCTCTCAAATTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTT
195530 TTAAATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:197366 original size:18 final size:18
Alignment explanation
Indices: 197339--197378 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
197329 TAGGTGCGTT
* *
197339 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
197357 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
197375 TCCT
1 TCCT
197379 TTTCTGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:197962 original size:21 final size:21
Alignment explanation
Indices: 197959--198194 Score: 316
Period size: 21 Copynumber: 11.0 Consensus size: 21
197949 TAAAAACCCT
*
197959 AACCCTAACCCTTAATCTAAA
1 AACCCTAACCCTTAACCTAAA
*
197980 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACCTAAA
*
198001 AACCCTAAACCCTTAACATAAA
1 AACCCT-AACCCTTAACCTAAA
198023 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACCTAAA
*
198044 AACCCTAACCCTT-ATCTAAAA
1 AACCCTAACCCTTAACCT-AAA
*
198065 CCCTAACACTAACCCTTAACCTAAA
1 ----AACCCTAACCCTTAACCTAAA
*
198090 AACCCTAACCATTAACCTAAA
1 AACCCTAACCCTTAACCTAAA
*
198111 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACCTAAA
*
198132 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACCTAAA
198154 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACCTAAA
198175 AACCCTAACCC-TAACC-AAA
1 AACCCTAACCCTTAACCTAAA
198194 A
1 A
198195 TGCATATTTA
Statistics
Matches: 195, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.02
20 8 0.04
21 124 0.64
22 41 0.21
25 15 0.08
26 3 0.02
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTAACCCTTAACCTAAA
Found at i:197970 original size:43 final size:41
Alignment explanation
Indices: 197959--198194 Score: 285
Period size: 43 Copynumber: 5.5 Consensus size: 41
197949 TAAAAACCCT
* *
197959 AACCCTAACCCTTAATCTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACCC-TAACCTAAAAACCCTAACCCTTAACCTAAA
*
198001 AACCCTAAACCCTTAACATAAAAACCCTAACCCTTAACCTAAA
1 AACCCT-AACCC-TAACCTAAAAACCCTAACCCTTAACCTAAA
* * *
198044 AACCCTAACCCTTATCTAAAACCCTAACACTAACCCTTAACCTAAA
1 AACCCTAACCCTAACCT-AAA----AACCCTAACCCTTAACCTAAA
* *
198090 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACC-CTAACCTAAAAACCCTAACCCTTAACCTAAA
*
198132 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAA
1 AACCCT-AACCC-TAACCTAAAAACCCTAACCCTTAACCTAAA
198175 AACCCTAACCCTAACC-AAAA
1 AACCCTAACCCTAACCTAAAA
198195 TGCATATTTA
Statistics
Matches: 169, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.02
41 7 0.04
42 44 0.26
43 77 0.46
46 33 0.20
47 4 0.02
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (41 bp):
AACCCTAACCCTAACCTAAAAACCCTAACCCTTAACCTAAA
Found at i:197978 original size:27 final size:27
Alignment explanation
Indices: 197938--198122 Score: 99
Period size: 21 Copynumber: 8.0 Consensus size: 27
197928 TAAATCCTTA
197938 AACCCTTAACCTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
*
197965 AACCCTTAATCT--AAA----AACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
* *
197986 AACCCTTAACTTAAAAACCCTAA--A-
1 AACCCTTAACCTAAAAACCCTAACCCT
*
198010 --CCCTTAACATAAAAACCCT------
1 AACCCTTAACCTAAAAACCCTAACCCT
198029 AACCCTTAACCTAAAAACCCT------
1 AACCCTTAACCTAAAAACCCTAACCCT
* *
198050 AACCCTT-ATCT-AAAACCCTAACACT
1 AACCCTTAACCTAAAAACCCTAACCCT
198075 AACCCTTAACCTAAAAACCCTAA-CC-
1 AACCCTTAACCTAAAAACCCTAACCCT
198100 -A---TTAACCTAAAAACCCTAACCCT
1 AACCCTTAACCTAAAAACCCTAACCCT
198123 TAACTTAAAA
Statistics
Matches: 131, Mismatches: 9, Indels: 40
0.73 0.05 0.22
Matches are distributed among these distances:
19 8 0.06
20 3 0.02
21 59 0.45
22 20 0.15
23 3 0.02
24 1 0.01
25 10 0.08
26 4 0.03
27 23 0.18
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCCTAACCCT
Found at i:197994 original size:64 final size:64
Alignment explanation
Indices: 197922--198186 Score: 247
Period size: 64 Copynumber: 4.1 Consensus size: 64
197912 TTAATTGACA
* *** *
197922 AACCCTTAAATCCTT-AAACCCTTAA-CCTAAAAACCCTAACCCTAACCCTTAATCTAAAAACCC
1 AACCCTTAAA--CTTAAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCC
197985 T
64 T
* * *
197986 AACCCTT-AACTTAAAAACCCTAAACCCTTAACATAAAAACCCTAACCCTTAACCTAAAAACCCT
1 AACCCTTAAACTT-AAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCCT
* * * *
198050 AACCCTT-ATC-TAAAACCCTAACACTAACCCT-TAACCTAAAAACCCTAACCATTAACCTAAAA
1 AACCCTTAAACTTAAAACCCT---A--AACCCTAAAAAC-AAAAACCCTAACCCTTAACCTAAAA
198112 ACCCT
60 ACCCT
* ***
198117 AACCCTT-AACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCT
1 AACCCTTAAACTT-AAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCCT
198181 AACCCT
1 AACCCT
198187 AACCAAAATG
Statistics
Matches: 169, Mismatches: 20, Indels: 24
0.79 0.09 0.11
Matches are distributed among these distances:
61 3 0.02
62 8 0.05
63 12 0.07
64 89 0.53
65 2 0.01
66 2 0.01
67 44 0.26
68 1 0.01
69 8 0.05
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (64 bp):
AACCCTTAAACTTAAAACCCTAAACCCTAAAAACAAAAACCCTAACCCTTAACCTAAAAACCCT
Found at i:198077 original size:110 final size:112
Alignment explanation
Indices: 197938--198190 Score: 413
Period size: 110 Copynumber: 2.3 Consensus size: 112
197928 TAAATCCTTA
* * *
197938 AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAATCTAAAAACCCTAACCCTTAACTTAAAAA
1 AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
198003 CCCTAAACCCTTAACATAAAAACCCT-AACCCTTAACCTAAAAACCCT
66 CCCT-AACCCTTAACATAAAAACCCTAAACCCTTAACCTAAAAACCCT
* *
198050 AACCCTT-ATCT-AAAACCCTAACACTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
1 AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
* *
198113 CCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT
66 CCCTAACCCTTAACATAAAAACCCTAAACCCTTAACCTAAAAACCCT
198160 AACCCTTAACCTAAAAACCCTAACCCTAACC
1 AACCCTTAACCTAAAAACCCTAACCCTAACC
198191 AAAATGCATA
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
109 20 0.16
110 79 0.61
111 6 0.05
112 24 0.19
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (112 bp):
AACCCTTAACCTAAAAACCCTAACCCTAACCCTTAACCTAAAAACCCTAACCATTAACCTAAAAA
CCCTAACCCTTAACATAAAAACCCTAAACCCTTAACCTAAAAACCCT
Found at i:198214 original size:131 final size:131
Alignment explanation
Indices: 197959--198194 Score: 411
Period size: 131 Copynumber: 1.8 Consensus size: 131
197949 TAAAAACCCT
* *
197959 AACCCTAACCCTTAATCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
1 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
* * *
198024 ACCCTAACCCTTAACCTAAAAACCCTAACCCTTATCTAAAACCCTAACACTAACCCTTAACCTAA
66 ACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACCAAAACCATAACACTAACCCTTAACCTAA
198089 A
131 A
*
198090 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAA
1 AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
198155 ACCCTAACCCTTAACCTAAAAACCCTAACCC-TAACCAAAA
66 ACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACCAAAA
198195 TGCATATTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
130 7 0.07
131 93 0.93
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (131 bp):
AACCCTAACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACATAAAA
ACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACCAAAACCATAACACTAACCCTTAACCTAA
A
Found at i:208952 original size:77 final size:76
Alignment explanation
Indices: 208783--209330 Score: 726
Period size: 74 Copynumber: 7.2 Consensus size: 76
208773 TTGCAAAAAT
* *
208783 TATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGAGATGTGAGTTGGGCCTCGGG
1 TATTTTTCAATTTCTGTTTT-TGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* *
208848 TCACACACTGAGG
65 -CACACGCCGAGG
*
208861 TATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTT-TGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
208926 CACACGCCAAGG
65 CACACGCCGAGG
* * * *
208938 TATTTTTTAATTTCTATTTTTGTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTG-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
209003 TCACACGTCGAGG
65 -CACACGCCGAGG
*
209016 TATTTTTCAATTTCTGTTTTTTGAAAAAATAAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTG-TTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
209081 CACACGCCGATG
65 CACACGCCGAGG
* * *
209093 TATTTTTTAATTTCTATTTTT--AAAAATCAGCTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
1 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
***
209156 ACATTTCGAGG
66 ACACGCCGAGG
* *
209167 TACTTTTCAATTTCTGTTTTT--AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGC
1 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
* *
209230 ACATGCCAAGG
66 ACACGCCGAGG
** * ** *
209241 TACATTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGG
1 TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC-TCGGG
*
209306 CACATGCCGAGG
65 CACACGCCGAGG
*
209318 TATCTTTCAATTT
1 TATTTTTCAATTT
209331 ATATTTAAAA
Statistics
Matches: 422, Mismatches: 42, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
74 132 0.31
76 42 0.10
77 116 0.27
78 126 0.30
79 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (76 bp):
TATTTTTCAATTTCTGTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
ACACGCCGAGG
Found at i:209066 original size:155 final size:153
Alignment explanation
Indices: 208783--209330 Score: 766
Period size: 155 Copynumber: 3.6 Consensus size: 153
208773 TTGCAAAAAT
* ** * *
208783 TATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGAGATGTGAGTTGGGCCTCGGG
1 TATTTTTCAATTTCTATTTT-TTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* * *
208848 TCACAC-ACTGAGGTATTTTTCAATTTCTGTTTTCTGAAAAAATCAACTCATAATGCGATAGGTG
65 -CACACGTC-GAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTG
208912 AGTTGAGCCTCGGGCACACGCCAAGG
128 AGTTGAGCCTCGGGCACACGCCAAGG
* *
208938 TATTTTTTAATTTCTATTTTTGTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTT-TCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
209003 TCACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATAAACTCATAATGCGAGAGGTGA
65 -CACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGA
* *
209068 GTTGAGCCTCGGGCACACGCCGATG
129 GTTGAGCCTCGGGCACACGCCAAGG
* *
209093 TATTTTTTAATTTCTA-TTTTT-AAAAATCAGCTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
1 TATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
** * *
209156 ACATTTCGAGGTACTTTTCAATTTCTG-TTTTT--AAAAATCAACTCATAATGCGAGAAGTGAGT
66 ACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGT
*
209218 TGAGCCTCGGGCACATGCCAAGG
131 TGAGCCTCGGGCACACGCCAAGG
** *
209241 TACATTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGG
1 TATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC-TCGGG
* * *
209306 CACATGCCGAGGTATCTTTCAATTT
65 CACACGTCGAGGTATTTTTCAATTT
209331 ATATTTAAAA
Statistics
Matches: 356, Mismatches: 32, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
148 61 0.17
149 5 0.01
150 40 0.11
151 50 0.14
152 39 0.11
153 1 0.00
154 5 0.01
155 154 0.43
156 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (153 bp):
TATTTTTCAATTTCTATTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
ACACGTCGAGGTATTTTTCAATTTCTGTTTTTTGAAAAAATCAACTCATAATGCGAGAGGTGAGT
TGAGCCTCGGGCACACGCCAAGG
Found at i:209511 original size:30 final size:30
Alignment explanation
Indices: 209480--209633 Score: 143
Period size: 30 Copynumber: 5.2 Consensus size: 30
209470 TTCGTTTTTT
*
209480 TCAAAATTATATTTTAACCCCCTAAACTTT-
1 TCAAAATTACATTTTAA-CCCCTAAACTTTC
* * ** *
209510 TCAAAATTACAATTTGACCATTAAAATTTC
1 TCAAAATTACATTTTAACCCCTAAACTTTC
*
209540 TTAAAATTACATTTTAACCCCTAAACTTTC
1 TCAAAATTACATTTTAACCCCTAAACTTTC
**
209570 TTTAAATTACATTTTAA-CCCTAAACTTTC
1 TCAAAATTACATTTTAACCCCTAAACTTTC
** * * * *
209599 TTGAAATTACTTTTTAGCACCTAAAATTT-
1 TCAAAATTACATTTTAACCCCTAAACTTTC
209628 TCAAAA
1 TCAAAA
209634 ATTGCATATT
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
29 39 0.38
30 63 0.62
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (30 bp):
TCAAAATTACATTTTAACCCCTAAACTTTC
Found at i:209606 original size:59 final size:59
Alignment explanation
Indices: 209482--209633 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 59
209472 CGTTTTTTTC
* * *
209482 AAAATTATATTTTAACCCCCTAAACTTTTCAAAATTACAATTTGACCATTAAAATTTCTT
1 AAAATTACATTTTAA-CCCCTAAACTTTTCAAAATTACAATTTAACCACTAAAATTTCTT
** * *
209542 AAAATTACATTTTAACCCCTAAACTTTCTTTAAATTACATTTTAACC-CTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTT-TCAAAATTACAATTTAACCACTAAAATTTCTT
* * * * *
209601 GAAATTACTTTTTAGCACCTAAAATTTTCAAAA
1 AAAATTACATTTTAACCCCTAAACTTTTCAAAA
209634 ATTGCATATT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 4 0.05
59 44 0.57
60 29 0.38
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTTAACCCCTAAACTTTTCAAAATTACAATTTAACCACTAAAATTTCTT
Found at i:210209 original size:25 final size:24
Alignment explanation
Indices: 210179--210250 Score: 92
Period size: 25 Copynumber: 3.0 Consensus size: 24
210169 GGGCCGAACG
210179 AAGAAGAAATGAGAGAAAAAAAATA
1 AAGAAGAAA-GAGAGAAAAAAAATA
* *
210204 AAGAAGAAAGAAAGAAAAAAAAGGA
1 AAGAAGAAAGAGAGAAAAAAAA-TA
*
210229 AAGAAGAAAAAGA-AAAAAAAAT
1 AAGAAGAAAGAGAGAAAAAAAAT
210251 TAAAAACAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (24 bp):
AAGAAGAAAGAGAGAAAAAAAATA
Found at i:210232 original size:14 final size:13
Alignment explanation
Indices: 210192--210249 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 13
210182 AAGAAATGAG
*
210192 AGAAAAAAAATAA
1 AGAAAAAAAAGAA
*
210205 AG--AAGAAAGAA
1 AGAAAAAAAAGAA
210216 AGAAAAAAAAGGAA
1 AGAAAAAAAA-GAA
*
210230 AGAAGAAAAAGAA
1 AGAAAAAAAAGAA
210243 A-AAAAAA
1 AGAAAAAA
210250 TTAAAAACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 9 0.24
12 5 0.14
13 11 0.30
14 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:210538 original size:15 final size:17
Alignment explanation
Indices: 210518--210555 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
210508 CAGCAGGCCA
210518 AAAAAAGGAAAAA-G-G
1 AAAAAAGGAAAAATGAG
210533 AAAAAA-GAAAAATGAG
1 AAAAAAGGAAAAATGAG
210549 AAAAAAG
1 AAAAAAG
210556 AAGAAGGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 7 0.35
16 7 0.35
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAAGGAAAAATGAG
Found at i:210556 original size:16 final size:14
Alignment explanation
Indices: 210518--210562 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
210508 CAGCAGGCCA
210518 AAAAAAGGAAAAAGG
1 AAAAAA-GAAAAAGG
210533 AAAAAAGAAAAATGAG
1 AAAAAAGAAAAA-G-G
*
210549 AAAAAAGAAGAAGG
1 AAAAAAGAAAAAGG
210563 CTCGTTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 12 0.44
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAGG
Found at i:210685 original size:6 final size:6
Alignment explanation
Indices: 210676--210722 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
210666 TATTTTTAGC
* * *
210676 ATTTTT ATTTTT ATTTAT ATGTTT AATTTT A-TTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
210722 A
1 A
210723 ATTTAGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:210727 original size:5 final size:5
Alignment explanation
Indices: 210678--210720 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
210668 TTTTTAGCAT
210678 TTTTA TTTTTA TTTATA TGTTTAA TTTTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTT-TA T-TTT-A TTTTA TTTTA TTTTA TTTT
210721 TAATTTAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 18 0.53
6 12 0.35
7 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:211765 original size:36 final size:34
Alignment explanation
Indices: 211684--211752 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
211674 TGATTATTAC
211684 AATTATAATTTAATTTAGAATTATTAGTTAAAAAT
1 AATTATAATTTAATTTAGAATTATTAG-TAAAAAT
*
211719 AATTATAATTTAATTTTGAAATTATTA-TAAAAAT
1 AATTATAATTTAATTTAG-AATTATTAGTAAAAAT
211753 GATTTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 7 0.22
35 17 0.53
36 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (34 bp):
AATTATAATTTAATTTAGAATTATTAGTAAAAAT
Found at i:212459 original size:22 final size:22
Alignment explanation
Indices: 212431--212485 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
212421 CAATGAGTAC
212431 AAATATATA-TT-AGAAATTATAA
1 AAATATATATTTAAG-AATTA-AA
212453 AAATATATTATTTAATGAATTAAA
1 AAATATA-TATTTAA-GAATTAAA
212477 AAATATATA
1 AAATATATA
212486 AAATCACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.24
23 4 0.14
24 11 0.38
25 6 0.21
26 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATATATATTTAAGAATTAAA
Found at i:219549 original size:177 final size:178
Alignment explanation
Indices: 219252--219606 Score: 595
Period size: 177 Copynumber: 2.0 Consensus size: 178
219242 CGACATAATA
* * *
219252 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTTTTTTACGGGATTACAGACTTATTTA
1 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTCTTTTACGGGACTACAGACTCATTTA
*
219317 GATTATCTATTGAAGTAAGTTGTCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
66 GATTATCTATTGAAGTAAGTTGCCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
* * * *
219382 AGTTTGAACTTTGATAATCAATGAGCTAATATTTGCTTGTCACAATTT
131 AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
219430 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGA-TTCTTTTACGGGACTACAGACTCATTTA
1 ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTCTTTTACGGGACTACAGACTCATTTA
* * * *
219494 GATTATCTATTGAAGTAAGTTGCCTTTCTCGCAATGTAAACTTTCTTACAATGTCACTTGTCTTT
66 GATTATCTATTGAAGTAAGTTGCCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
219559 AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
131 AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
219607 CGCTATGTAT
Statistics
Matches: 165, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
177 129 0.78
178 36 0.22
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (178 bp):
ATCATTCTCAGTATTTGAATCAAATGCTCACTTTGATTTCTTTTACGGGACTACAGACTCATTTA
GATTATCTATTGAAGTAAGTTGCCTTTCTAGCAATGCAAACGTTCTTACAATGTCACTTATCTTT
AGTTTGAACTTAGACAATCAATGAACTAATATTTGCTTATCACAATTT
Found at i:222661 original size:21 final size:21
Alignment explanation
Indices: 222631--222672 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
222621 CTATCACTTA
222631 GGGACAATCAATGGAAACTGT
1 GGGACAATCAATGGAAACTGT
* *
222652 GGGACCATCAATGGAAGCTGT
1 GGGACAATCAATGGAAACTGT
222673 AGGTCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (21 bp):
GGGACAATCAATGGAAACTGT
Found at i:235594 original size:18 final size:19
Alignment explanation
Indices: 235571--235606 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
235561 GGTAAAGCGG
235571 TCGG-TTAACCGAATTTTT
1 TCGGTTTAACCGAATTTTT
235589 TCGGTTTAACCGAATTTT
1 TCGGTTTAACCGAATTTT
235607 GCAGGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGGTTTAACCGAATTTTT
Found at i:236625 original size:9 final size:9
Alignment explanation
Indices: 236611--236677 Score: 98
Period size: 9 Copynumber: 7.2 Consensus size: 9
236601 CCAATTTATT
236611 TTCGGGTAA
1 TTCGGGTAA
236620 TTCGGGTAA
1 TTCGGGTAA
*
236629 TTTTCTGGTAA
1 --TTCGGGTAA
236640 TTCGGGTAA
1 TTCGGGTAA
236649 TTCGGGTAA
1 TTCGGGTAA
*
236658 TTCGGATAA
1 TTCGGGTAA
236667 TTCGGGTAA
1 TTCGGGTAA
236676 TT
1 TT
236678 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
9 44 0.85
11 8 0.15
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.39
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:236653 original size:29 final size:27
Alignment explanation
Indices: 236611--236677 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 27
236601 CCAATTTATT
236611 TTCGGGTAATTCGGGTAATTTTCTGG-TAA
1 TTCGGGTAATTCGGGTAA--TTC-GGATAA
236640 TTCGGGTAATTCGGGTAATTCGGATAA
1 TTCGGGTAATTCGGGTAATTCGGATAA
236667 TTCGGGTAATT
1 TTCGGGTAATT
236678 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 2 0.05
27 17 0.46
29 18 0.49
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.39
Consensus pattern (27 bp):
TTCGGGTAATTCGGGTAATTCGGATAA
Found at i:237776 original size:6 final size:6
Alignment explanation
Indices: 237729--237764 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
237719 GATTTTTTCC
237729 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
237765 GGAGAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:238272 original size:20 final size:20
Alignment explanation
Indices: 238249--238294 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
238239 AATAAACACC
238249 AAAAATTTATTTTAAAAATA
1 AAAAATTTATTTTAAAAATA
* *
238269 AAAAAATTATTTTAAAATTA
1 AAAAATTTATTTTAAAAATA
238289 AAAAAT
1 AAAAAT
238295 AAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTTATTTTAAAAATA
Found at i:239749 original size:38 final size:39
Alignment explanation
Indices: 239673--239749 Score: 88
Period size: 38 Copynumber: 2.0 Consensus size: 39
239663 CAGATAATCA
* * *
239673 CAGTTTGGGCTTAAGCCCCTTTTCAGTATCAAATCAGTC
1 CAGTTTGGGCTTAAGCCCCATCTCAGTATCAAAACAGTC
239712 CAGTTTGGGCCTT-AG-CCCATCTCAGTA-CAAAAACAGTC
1 CAGTTTGGG-CTTAAGCCCCATCTCAGTATC-AAAACAGTC
239750 ATGCAGTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
37 1 0.03
38 18 0.55
39 11 0.33
40 3 0.09
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (39 bp):
CAGTTTGGGCTTAAGCCCCATCTCAGTATCAAAACAGTC
Found at i:243140 original size:29 final size:29
Alignment explanation
Indices: 243108--243192 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
243098 TTTAATGTGT
243108 AATTGTATACATGAACTTTAATTTGGTGC
1 AATTGTATACATGAACTTTAATTTGGTGC
* * * *
243137 AATTATATGCATGAAACTCTAATTGTGGTTC
1 AATTGTATACATG-AACTTTAATT-TGGTGC
* * *
243168 AAATGTATACTTAAAACTTTAATTT
1 AATTGTATACAT-GAACTTTAATTT
243193 TGATTTAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 11 0.26
30 10 0.23
31 22 0.51
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (29 bp):
AATTGTATACATGAACTTTAATTTGGTGC
Found at i:244351 original size:3 final size:3
Alignment explanation
Indices: 244343--244386 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
244333 TCATCAAACA
244343 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
244387 TCTAAGTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:245748 original size:27 final size:27
Alignment explanation
Indices: 245718--245788 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
245708 AGGCCAATGG
*
245718 CATTGGCGGCACCAATGGTGCCAAAGC
1 CATTGGCGGCACCAATGGTGCCAAAAC
245745 CATTGGCGGCACCAATGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
245772 CATTGGCAGCACCAATG
1 CATTGGCGGCACCAATG
245789 CCATAATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:245844 original size:27 final size:27
Alignment explanation
Indices: 245814--245871 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
245804 TGGTGGTGGG
*
245814 GGAAGGAGAGGGAAAGAAAGAAAGA-AA
1 GGAAGGAGA-GGAAAGAAAGAAAAAGAA
245841 GGAAGGAGAGGAAAGAAAGAAAAAGAA
1 GGAAGGAGAGGAAAGAAAGAAAAAGAA
245868 GGAA
1 GGAA
245872 AGAAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (27 bp):
GGAAGGAGAGGAAAGAAAGAAAAAGAA
Found at i:245870 original size:18 final size:18
Alignment explanation
Indices: 245829--245931 Score: 69
Period size: 16 Copynumber: 5.8 Consensus size: 18
245819 GAGAGGGAAA
245829 GAAAGAAAGAAAGGAAGGAGAG
1 GAAAGAAAGAAA--AA-GA-AG
245851 GAAAGAAAGAAAAAGAAG
1 GAAAGAAAGAAAAAGAAG
*
245869 GAAAG-AA-AAAGA-AAG
1 GAAAGAAAGAAAAAGAAG
245884 G--AGAAGAGAAAAA-AAG
1 GAAAGAA-AGAAAAAGAAG
*
245900 GAAAG-AAGAATAAG-AG
1 GAAAGAAAGAAAAAGAAG
245916 GAAATGAGAAGAAAAA
1 GAAA-GA-AAGAAAAA
245932 ATAAAGAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
13 2 0.03
14 1 0.01
15 5 0.07
16 24 0.35
17 4 0.06
18 9 0.13
19 9 0.13
20 2 0.03
22 12 0.18
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (18 bp):
GAAAGAAAGAAAAAGAAG
Found at i:245928 original size:47 final size:48
Alignment explanation
Indices: 245826--246013 Score: 124
Period size: 47 Copynumber: 3.9 Consensus size: 48
245816 AAGGAGAGGG
* *
245826 AAAGAAAGAAAGAAAG-GAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAA
1 AAAGAAA-AAAGAAAGAAAAAGA-AGGAAAG-AAGAAAAAGAAGGAAAGAA
** *
245876 AAAGAAAGGAGAAGAGAAAAA-AAGGAAAGAAGAATAAG-AGGAAATG-A
1 AAAGAAAAAAGAA-AGAAAAAGAAGGAAAGAAGAAAAAGAAGGAAA-GAA
* * **
245923 GAAGAAAAAATAAAGAAAAAGAAGGAAAGAA-AAGGA-AAGGAGAAGAGA
1 AAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAGAAAAAGAAGGA-AAGA-A
** * *
245971 AAA-AAAAAAGAAGAGGGAATGAAGGAAGGAA-AAAAA-AAGGAAA
1 AAAGAAAAAAGAA-AGAAAAAGAAGGAAAGAAGAAAAAGAAGGAAA
246014 AAAGGTAATT
Statistics
Matches: 110, Mismatches: 19, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
46 15 0.14
47 38 0.35
48 34 0.31
49 11 0.10
50 10 0.09
51 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (48 bp):
AAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAGAAAAAGAAGGAAAGAA
Found at i:245977 original size:46 final size:46
Alignment explanation
Indices: 245890--245978 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 46
245880 AAAGGAGAAG
* *
245890 AGAAAAAAAGGAAAGAAGAATAAGAGGAAATGAGAAGAAAAAATAA
1 AGAAAAAAAGGAAAGAAGAAGAAGAGGAAATGAGAAAAAAAAATAA
245936 AGAAAAAGAAGGAAAGAA-AAGGAA-AGGAGAA-GAGAAAAAAAAA
1 AGAAAAA-AAGGAAAGAAGAA-GAAGAGGA-AATGAGAAAAAAAAA
245979 AGAAGAGGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
46 24 0.63
47 14 0.37
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (46 bp):
AGAAAAAAAGGAAAGAAGAAGAAGAGGAAATGAGAAAAAAAAATAA
Found at i:248631 original size:11 final size:11
Alignment explanation
Indices: 248611--248650 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
248601 TTAAAAATAC
248611 CTTCTTTTTCT
1 CTTCTTTTTCT
*
248622 CTTCTCTTTCT
1 CTTCTTTTTCT
248633 C-TCTTTTTCT
1 CTTCTTTTTCT
248643 CTTCTTTT
1 CTTCTTTT
248651 CCACAACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:248638 original size:21 final size:20
Alignment explanation
Indices: 248613--248651 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
248603 AAAAATACCT
248613 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
248634 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
248652 CACAACACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:248864 original size:110 final size:110
Alignment explanation
Indices: 248671--248890 Score: 440
Period size: 110 Copynumber: 2.0 Consensus size: 110
248661 TCTTTTTCTT
248671 CTTTTTTTTCTTCTGGTTTTTCTCCCTTCAGCTGGGCAGAGGTCGTGTTTATAACACGAGTAGTG
1 CTTTTTTTTCTTCTGGTTTTTCTCCCTTCAGCTGGGCAGAGGTCGTGTTTATAACACGAGTAGTG
248736 CCGCCAATGCCTTTGGCACCATTGGTGCCGCCAATGCCATTGGCC
66 CCGCCAATGCCTTTGGCACCATTGGTGCCGCCAATGCCATTGGCC
248781 CTTTTTTTTCTTCTGGTTTTTCTCCCTTCAGCTGGGCAGAGGTCGTGTTTATAACACGAGTAGTG
1 CTTTTTTTTCTTCTGGTTTTTCTCCCTTCAGCTGGGCAGAGGTCGTGTTTATAACACGAGTAGTG
248846 CCGCCAATGCCTTTGGCACCATTGGTGCCGCCAATGCCATTGGCC
66 CCGCCAATGCCTTTGGCACCATTGGTGCCGCCAATGCCATTGGCC
248891 TAATCAGGCT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.35
Consensus pattern (110 bp):
CTTTTTTTTCTTCTGGTTTTTCTCCCTTCAGCTGGGCAGAGGTCGTGTTTATAACACGAGTAGTG
CCGCCAATGCCTTTGGCACCATTGGTGCCGCCAATGCCATTGGCC
Found at i:248967 original size:27 final size:27
Alignment explanation
Indices: 248937--249004 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 27
248927 GTTTTTTTTA
248937 TATATTTTGGTAAATAATAAAAA-TAAT
1 TATATTTTGGTAAATAA-AAAAATTAAT
*
248964 TATAATAATTTGGTAAATAAAAAAATTTAT
1 TAT-AT--TTTGGTAAATAAAAAAATTAAT
*
248994 AATATTTTGGT
1 TATATTTTGGT
249005 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 9 0.26
28 2 0.06
29 7 0.20
30 17 0.49
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (27 bp):
TATATTTTGGTAAATAAAAAAATTAAT
Found at i:248976 original size:30 final size:27
Alignment explanation
Indices: 248933--249004 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 27
248923 TTTTGTTTTT
248933 TTTAT-ATATTTTGGTAAATAATAAAAA
1 TTTATAATATTTTGGTAAATAA-AAAAA
*
248960 TAATTATAATAATTTGGTAAATAAAAAAA
1 T--TTATAATATTTTGGTAAATAAAAAAA
248989 TTTATAATATTTTGGT
1 TTTATAATATTTTGGT
249005 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 15 0.38
29 10 0.25
30 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (27 bp):
TTTATAATATTTTGGTAAATAAAAAAA
Found at i:250147 original size:32 final size:30
Alignment explanation
Indices: 250111--250171 Score: 104
Period size: 32 Copynumber: 2.0 Consensus size: 30
250101 AATTTTTTTA
250111 ATTTTAAAAATTCAAAAAAAATTATAAAAAAT
1 ATTTTAAAAATTC-AAAAAAATTA-AAAAAAT
250143 ATTTTAAAAATTCAAAAAAATTAAAAAAA
1 ATTTTAAAAATTCAAAAAAATTAAAAAAA
250172 GTGTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.21
31 10 0.34
32 13 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (30 bp):
ATTTTAAAAATTCAAAAAAATTAAAAAAAT
Found at i:268061 original size:3 final size:3
Alignment explanation
Indices: 268005--268049 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
267995 ATTATAATAC
* ** *
268005 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TCC TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
268050 AGGTGTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:271489 original size:17 final size:18
Alignment explanation
Indices: 271459--271492 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
271449 AATTTAGCCA
*
271459 TTTTTTATATATTTTTAT
1 TTTTTTATAAATTTTTAT
271477 TTTTTTA-AAATTTTTA
1 TTTTTTATAAATTTTTA
271493 CATTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATAAATTTTTAT
Found at i:271697 original size:18 final size:18
Alignment explanation
Indices: 271674--271710 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
271664 TACTGAGGAG
271674 ATGGACGATAATCAGAAT
1 ATGGACGATAATCAGAAT
271692 ATGGACGATAATCAGAAT
1 ATGGACGATAATCAGAAT
271710 A
1 A
271711 CTAAGTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
ATGGACGATAATCAGAAT
Found at i:273761 original size:12 final size:12
Alignment explanation
Indices: 273740--273821 Score: 51
Period size: 12 Copynumber: 6.8 Consensus size: 12
273730 AAAAACGAAA
*
273740 TGATTAAAAACT
1 TGATGAAAAACT
* *
273752 TGATGGAAAATT
1 TGATGAAAAACT
*
273764 TTATGAAAAGACT
1 TGATGAAAA-ACT
*
273777 CGATGAAAAACT
1 TGATGAAAAACT
* *
273789 TTA-AAAAGAACT
1 TGATGAAA-AACT
* *
273801 TGCTGCAAAACT
1 TGATGAAAAACT
273813 TGAT-AAAAA
1 TGATGAAAAA
273822 AAACTTGGTA
Statistics
Matches: 50, Mismatches: 17, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
11 7 0.14
12 32 0.64
13 11 0.22
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:273791 original size:25 final size:24
Alignment explanation
Indices: 273745--273791 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
273735 CGAAATGATT
* * *
273745 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTCGATGAAAAACTTTATG
273769 AAAAGACTCGATGAAAAACTTTA
1 AAAA-ACTCGATGAAAAACTTTA
273792 AAAAGAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAAACTCGATGAAAAACTTTATG
Found at i:273840 original size:15 final size:14
Alignment explanation
Indices: 273807--273871 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
273797 AACTTGCTGC
273807 AAAACTTGATAAAA
1 AAAACTTGATAAAA
* *
273821 AAAACTTGGTAATTA
1 AAAACTTGATAA-AA
273836 AAAACTTGATAAAA
1 AAAACTTGATAAAA
* * *
273850 GAAA-TAGATGAAA
1 AAAACTTGATAAAA
*
273863 AATACTTGA
1 AAAACTTGA
273872 AGAAAGAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
13 9 0.23
14 18 0.46
15 12 0.31
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (14 bp):
AAAACTTGATAAAA
Done.