Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 18 of 145
Found at i:5721344 original size:52 final size:52
Alignment explanation
Indices: 5721287--5721389 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
5721277 ACAAATCCTA
*
5721287 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
* *
5721339 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCGAAAAATCTGTCAAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
5721390 TCCATATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
Found at i:5721363 original size:22 final size:22
Alignment explanation
Indices: 5721338--5721379 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5721328 TTCTCTCAAA
5721338 CTCTCAATTTCCTTCCAAAATC
1 CTCTCAATTTCCTTCCAAAATC
*
5721360 CTCTCAATTTCCTTCGAAAA
1 CTCTCAATTTCCTTCCAAAA
5721380 ATCTGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATC
Found at i:5721466 original size:31 final size:31
Alignment explanation
Indices: 5721422--5721488 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
5721412 CCTCAATTTC
*
5721422 ATTTTTTTTAATAATTTCAAA-TTTTTTTAT
1 ATTTTTTTAAATAATTTCAAATTTTTTTTAT
*
5721452 ATTTTTTTAAAATAATTTTAAATTTTTTTTAT
1 ATTTTTTT-AAATAATTTCAAATTTTTTTTAT
5721484 ATTTT
1 ATTTT
5721489 CATCAATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 8 0.24
31 11 0.33
32 14 0.42
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTTTAAATAATTTCAAATTTTTTTTAT
Found at i:5721608 original size:14 final size:15
Alignment explanation
Indices: 5721579--5721612 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5721569 AAATTTTAAA
5721579 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
5721594 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
5721608 TTTTA
1 TTTTA
5721613 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:5724250 original size:109 final size:109
Alignment explanation
Indices: 5724117--5724532 Score: 294
Period size: 109 Copynumber: 3.7 Consensus size: 109
5724107 TAAAATCCCT
* * *
5724117 AACCCTGACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTA-ATTAAAAACCCTTACCCTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTACA-TAAAAACCCTAACCATA
*** * **
5724181 TTTTAATTTAATTAAAAGCCCTTACCCT-ATTTTAATTTAATTAAA
65 ACCTAATTTAATTAAAAGCCCTAACCCTGA-CCTAATTTAATTAAA
** * ** * *
5724226 AATTCTAACCTAATTTAGTTAAAAA-CCTAACCCTAACCTATTTTACATGAAAACCCTAACCATA
1 AACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTTACATAAAAACCCTAACCATA
* *
5724290 ACCTATTTTAATTAAAATCCCTAACCCTGACCTAATTTAATTAAA
65 ACCTAATTTAATTAAAAGCCCTAACCCTGACCTAATTTAATTAAA
*
5724335 AACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAATTT-A-GT---TAAAAACCCTAAC
1 AACCCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTACATAAAAACCCTAAC
* * * *
5724395 CCTAACCTATTTTACATGAAAA-CCCTAACCCTAACCT-ATCTTAATTAAAA
61 CATAACCTAATTTA-ATTAAAAGCCCTAACCCTGACCTAAT-TTAATT-AAA
* * * * ** * *
5724445 TCTCTAACCCTAACCTAATTTAATTGAAAACTCTTACCATGATTTATCATTTTATTTGAAATCCC
1 -----AACCCTAACCTAATTTAATTAAAAACCCTAACC-TAATTTA--A-TTTACATAAAAACCC
*
5724510 TAACCCTAACCTAATTTAATTAA
57 TAACCATAACCTAATTTAATTAA
5724533 TGTAAAAACC
Statistics
Matches: 243, Mismatches: 38, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
108 7 0.03
109 134 0.55
110 31 0.13
111 5 0.02
112 1 0.00
114 21 0.09
115 15 0.06
116 1 0.00
118 4 0.02
119 24 0.10
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.34
Consensus pattern (109 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTTACATAAAAACCCTAACCATAA
CCTAATTTAATTAAAAGCCCTAACCCTGACCTAATTTAATTAAA
Found at i:5724261 original size:23 final size:23
Alignment explanation
Indices: 5724213--5724257 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5724203 TACCCTATTT
*
5724213 TAATTTAATTAAAAATTCTAACC
1 TAATTTAATTAAAAATCCTAACC
*
5724236 TAATTTAGTTAAAAA-CCTAACC
1 TAATTTAATTAAAAATCCTAACC
5724258 CTAACCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATTTAATTAAAAATCCTAACC
Found at i:5724317 original size:138 final size:135
Alignment explanation
Indices: 5724088--5724482 Score: 488
Period size: 138 Copynumber: 2.9 Consensus size: 135
5724078 TGAAAACCCT
* * * * * * *
5724088 AACCATAACCTATTTTAATTAAAATCCCTAACCCTGACCTAATTTA-ATTAAAAACCCTAACCTA
1 AACCCTAACCTAATTTAGTTAAAA-ACCTAACCCTAACCTATTTTACA-TGAAAACCCTAACCTA
** * * * ** *
5724152 ATTTAATTTAATTAAAAACCCTTACCCTATTTTAATTTAATTAAAAGCCCTTACCCTATTTTAAT
64 ACCTATTTTAATTAAAATCCCTAACCCTA-CCTAATTTAATTAAAA-CCCTTACCCTAATTTAAT
5724217 TTAATTAAA
127 TTAATTAAA
**
5724226 AATTCTAACCTAATTTAGTTAAAAACCTAACCCTAACCTATTTTACATGAAAACCCTAACCATAA
1 AACCCTAACCTAATTTAGTTAAAAACCTAACCCTAACCTATTTTACATGAAAACCCTAACC-TAA
*
5724291 CCTATTTTAATTAAAATCCCTAACCCTGACCTAATTTAATTAAAAACCC-TAACCTAATTTAATT
65 CCTATTTTAATTAAAATCCCTAACCCT-ACCTAATTTAATT-AAAACCCTTACCCTAATTTAATT
5724355 TAATTAAA
128 TAATTAAA
5724363 AACCCTAACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTA
1 AACCCTAACCTAATTTAGTTAAAAA-CCTAACCCTAACCTATTTTACATGAAAACCCTAA-CCTA
* * *
5724428 ACCTATCTTAATTAAAATCTCTAACCCTAACCTAATTTAATTGAAAACTCTTACC
64 ACCTATTTTAATTAAAATCCCTAACCCT-ACCTAATTTAATT-AAAACCCTTACC
5724483 ATGATTTATC
Statistics
Matches: 224, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
137 75 0.33
138 139 0.62
139 10 0.04
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (135 bp):
AACCCTAACCTAATTTAGTTAAAAACCTAACCCTAACCTATTTTACATGAAAACCCTAACCTAAC
CTATTTTAATTAAAATCCCTAACCCTACCTAATTTAATTAAAACCCTTACCCTAATTTAATTTAA
TTAAA
Found at i:5724339 original size:23 final size:23
Alignment explanation
Indices: 5724312--5724395 Score: 105
Period size: 23 Copynumber: 3.4 Consensus size: 23
5724302 TAAAATCCCT
*
5724312 AACCCTGACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
5724335 AACCCTAACCTAATTTAATTTAATTAAA
1 AACCCTAACC-----TAATTTAATTAAA
*
5724363 AACCCTAACCTAATTTAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
5724386 AACCCTAACC
1 AACCCTAACC
5724396 CTAACCTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
23 31 0.57
28 23 0.43
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:5724469 original size:29 final size:28
Alignment explanation
Indices: 5724056--5724532 Score: 368
Period size: 29 Copynumber: 16.9 Consensus size: 28
5724046 NNNNNNNNNN
* *
5724056 CCTAACCCTAACCTATTTTACATGAAAAC
1 CCTAACCCTAACCTAATTTA-ATTAAAAC
* *
5724085 CCTAACCATAACCTATTTTAATTAAAATC
1 CCTAACCCTAACCTAATTTAATTAAAA-C
*
5724114 CCTAACCCTGACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATT-AAAAC
**
5724143 CCTAA-CCTAATTTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATT-AAAAC
* ***
5724171 CCTTACCCTATTTTAATTTAATTAAAAGC
1 CCTAACCCTAACCTAATTTAATTAAAA-C
* ***
5724200 CCTTACCCTATTTTAATTTAATT-AAA-
1 CCTAACCCTAACCTAATTTAATTAAAAC
** * *
5724226 ---AATTCTAACCTAATTTAGTTAAAAA
1 CCTAACCCTAACCTAATTTAATTAAAAC
* *
5724251 CCTAACCCTAACCTATTTTACATGAAAAC
1 CCTAACCCTAACCTAATTTA-ATTAAAAC
* *
5724280 CCTAACCATAACCTATTTTAATTAAAATC
1 CCTAACCCTAACCTAATTTAATTAAAA-C
*
5724309 CCTAACCCTGACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATT-AAAAC
**
5724338 CCTAA-CCTAATTTAATTTAATT-AAA-
1 CCTAACCCTAACCTAATTTAATTAAAAC
*
5724363 ---AACCCTAACCTAATTTAGTTAAAAAC
1 CCTAACCCTAACCTAATTTAATT-AAAAC
* *
5724389 CCTAACCCTAACCTATTTTACATGAAAAC
1 CCTAACCCTAACCTAATTTA-ATTAAAAC
5724418 CCTAACCCTAACCT-ATCTTAATTAAAATC
1 CCTAACCCTAACCTAAT-TTAATTAAAA-C
*
5724447 TCTAACCCTAACCTAATTTAATTGAAAAC
1 CCTAACCCTAACCTAATTTAATT-AAAAC
* * * * ** * *
5724476 TCTTACCATGATTTATCATTTTATTTGAAATC
1 CCTAACCCTAACCTA--A-TTTAATT-AAAAC
5724508 CCTAACCCTAACCTAATTTAATTAA
1 CCTAACCCTAACCTAATTTAATTAA
5724533 TGTAAAAACC
Statistics
Matches: 367, Mismatches: 54, Indels: 55
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.01
23 27 0.07
24 3 0.01
25 3 0.01
26 3 0.01
28 80 0.22
29 212 0.58
30 16 0.04
31 1 0.00
32 20 0.05
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (28 bp):
CCTAACCCTAACCTAATTTAATTAAAAC
Found at i:5729419 original size:23 final size:22
Alignment explanation
Indices: 5729348--5729438 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 22
5729338 ATCAACTATT
5729348 AATATTTTAA-TAT-TAAATAT-
1 AATA-TTTAAGTATATAAATATG
*
5729368 -ATATTATAAGTTATATTAAATAATA
1 AATATT-TAAG-TATA-TAAAT-ATG
5729393 AATACTTTATAGTATA-AAATATG
1 AATA-TTTA-AGTATATAAATATG
*
5729416 AATATTTAATTATATAAATATG
1 AATATTTAAGTATATAAATATG
5729438 A
1 A
5729439 TAATTTGTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
18 2 0.03
19 6 0.10
21 8 0.14
22 12 0.21
23 11 0.19
24 6 0.10
26 9 0.16
27 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (22 bp):
AATATTTAAGTATATAAATATG
Found at i:5730296 original size:2 final size:2
Alignment explanation
Indices: 5730291--5730329 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5730281 TTATAAAAAG
*
5730291 TA TA TA -A TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5730330 AAACGCTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5735505 original size:447 final size:448
Alignment explanation
Indices: 5734671--5735565 Score: 1783
Period size: 447 Copynumber: 2.0 Consensus size: 448
5734661 TTTCAGATGG
5734671 CCTTCGAGTCTGGACTAGTGACTCAACCTATTATCAAATCTAGCTTTGAGTAACCATCCTTATTA
1 CCTTCGAGTCTGGACTAGTGACTCAACCTATTATCAAATCTAGCTTTGAGTAACCATCCTTATTA
5734736 TTATTATCCCGCAGAATTCAAAGAATAGAGGTAGAACCTAAATGAAAAGCAATTATTAAACACAA
66 TTATTATCCCGCAGAATTCAAAGAATAGAGGTAGAACCTAAATGAAAAGCAATTATTAAACACAA
5734801 GAAATAAAATAATTTATAGACAATTGGAGATTGCCATATCTTTCTTTCTTTGGAAAAAGAATCTT
131 GAAATAAAATAATTTATAGACAATTGGAGATTGCCATATCTTTCTTTCTTTGGAAAAAGAATCTT
5734866 ATATTTTTCTTGGTTGCGCTAAACCAAGACCAAATCTTCCAACCCACACCTTATAAGCTACAATT
196 ATATTTTTCTTGGTTGCGCTAAACCAAGACCAAATCTTCCAACCCACACCTTATAAGCTACAATT
5734931 ATTTATTTCAAATGGTTTACTCTCATTCTTTACGATTTAGGTACGGAACATATAATTTATATAAA
261 ATTTATTTCAAATGGTTTACTCTCATTCTTTACGATTTAGGTACGGAACATATAATTTATATAAA
5734996 TTACAATACCAACAATATTTAACAATATTTGATGCATTATCGGTGCATAAATTTTATATATCATT
326 TTACAATACCAACAATATTTAACAATATTTGATGCATTATCGGTGCATAAATTTTATATATCATT
5735061 AATAAATAATAATATTATAATCAATATTAAATTAAATAAAAAAT-AAAAATAAAAAAT
391 AATAAATAATAATATTATAATCAATATTAAATTAAATAAAAAATAAAAAATAAAAAAT
5735118 CCTTCGAGTCTGGACTAGTGACTCAACCTATTATCAAATCTAGCTTTGAGTAACCATCCTTATTA
1 CCTTCGAGTCTGGACTAGTGACTCAACCTATTATCAAATCTAGCTTTGAGTAACCATCCTTATTA
5735183 TTATTATCCCGCAGAATTCAAAGAATAGAGGTAGAACCTAAATGAAAAGCAATTATTAAACACAA
66 TTATTATCCCGCAGAATTCAAAGAATAGAGGTAGAACCTAAATGAAAAGCAATTATTAAACACAA
5735248 GAAATAAAATAATTTATAGACAATTGGAGATTGCCATATCTTTCTTTCTTTGGAAAAAGAATCTT
131 GAAATAAAATAATTTATAGACAATTGGAGATTGCCATATCTTTCTTTCTTTGGAAAAAGAATCTT
5735313 ATATTTTTCTTGGTTGCGCTAAACCAAGACCAAATCTTCCAACCCACACCTTATAAGCTACAATT
196 ATATTTTTCTTGGTTGCGCTAAACCAAGACCAAATCTTCCAACCCACACCTTATAAGCTACAATT
5735378 ATTTATTTCAAATGGTTTACTCTCATTCTTTACGATTTAGGTACGGAACATATAATTTATATAAA
261 ATTTATTTCAAATGGTTTACTCTCATTCTTTACGATTTAGGTACGGAACATATAATTTATATAAA
5735443 TTACAATACCAACAATATTTAACAATATTTGATGCATTATCGGTGCATAAATTTTATATATCATT
326 TTACAATACCAACAATATTTAACAATATTTGATGCATTATCGGTGCATAAATTTTATATATCATT
5735508 AATAAATAATAATATTATAATCAATATTAAATTAAATAAAAAATAAAAAATAAAAAAT
391 AATAAATAATAATATTATAATCAATATTAAATTAAATAAAAAATAAAAAATAAAAAAT
5735566 TTATTAATAA
Statistics
Matches: 447, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
447 434 0.97
448 13 0.03
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (448 bp):
CCTTCGAGTCTGGACTAGTGACTCAACCTATTATCAAATCTAGCTTTGAGTAACCATCCTTATTA
TTATTATCCCGCAGAATTCAAAGAATAGAGGTAGAACCTAAATGAAAAGCAATTATTAAACACAA
GAAATAAAATAATTTATAGACAATTGGAGATTGCCATATCTTTCTTTCTTTGGAAAAAGAATCTT
ATATTTTTCTTGGTTGCGCTAAACCAAGACCAAATCTTCCAACCCACACCTTATAAGCTACAATT
ATTTATTTCAAATGGTTTACTCTCATTCTTTACGATTTAGGTACGGAACATATAATTTATATAAA
TTACAATACCAACAATATTTAACAATATTTGATGCATTATCGGTGCATAAATTTTATATATCATT
AATAAATAATAATATTATAATCAATATTAAATTAAATAAAAAATAAAAAATAAAAAAT
Found at i:5735562 original size:6 final size:7
Alignment explanation
Indices: 5735541--5735565 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5735531 ATATTAAATT
5735541 AAATAAA
1 AAATAAA
5735548 AAATAAA
1 AAATAAA
5735555 AAATAAA
1 AAATAAA
5735562 AAAT
1 AAAT
5735566 TTATTAATAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:5735574 original size:22 final size:22
Alignment explanation
Indices: 5735549--5735592 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5735539 TTAAATAAAA
5735549 AATAAAAAATAAAAAATTTATT
1 AATAAAAAATAAAAAATTTATT
* * *
5735571 AATAAATACTAATAAATTTATT
1 AATAAAAAATAAAAAATTTATT
5735593 TAAACATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAAAATAAAAAATTTATT
Found at i:5736268 original size:17 final size:16
Alignment explanation
Indices: 5736246--5736277 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5736236 ATTAATTGAT
5736246 TTTCTTCCTTTTATTTC
1 TTTCTTCC-TTTATTTC
5736263 TTTCTTCCTTTATTT
1 TTTCTTCCTTTATTT
5736278 ATTTACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCTTCCTTTATTTC
Found at i:5736400 original size:17 final size:17
Alignment explanation
Indices: 5736374--5736413 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5736364 ATTCTTCTCA
*
5736374 AAAATTAATATATAA-TT
1 AAAATAAATATA-AATTT
5736391 AAAATAAATATAAATTT
1 AAAATAAATATAAATTT
5736408 AAAATA
1 AAAATA
5736414 TTTAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAAATATAAATTT
Found at i:5743258 original size:89 final size:89
Alignment explanation
Indices: 5743094--5743261 Score: 198
Period size: 89 Copynumber: 1.9 Consensus size: 89
5743084 AGTTAGGCCC
* * * *
5743094 TGACTTGGCAACTTTTCCCACATTGGGCCTGAACATTTTGTTGTCCGAATTAGGTCCTAAACGTG
1 TGACTTCGCAACTTTTCCAACATTGGGCCTGAACATTTTGTTGTCCGAATTAAGCCCTAAACGTG
* **
5743159 GCAATTGTTCTCACGTTGGGACTT
66 ACAACAGTTCTCACGTTGGGACTT
* *
5743183 TGACTTCGCAAC-TTTCTCAACATTAGGGCCTGAAC-TTTTTTTGTCC-AAGTTAAGCCCTGAAC
1 TGACTTCGCAACTTTTC-CAACATT-GGGCCTGAACATTTTGTTGTCCGAA-TTAAGCCCTAAAC
*
5743245 TTGACAACAGTTCTCAC
63 GTGACAACAGTTCTCAC
5743262 ATTGAACCCT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
88 6 0.09
89 50 0.76
90 10 0.15
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (89 bp):
TGACTTCGCAACTTTTCCAACATTGGGCCTGAACATTTTGTTGTCCGAATTAAGCCCTAAACGTG
ACAACAGTTCTCACGTTGGGACTT
Found at i:5743273 original size:148 final size:148
Alignment explanation
Indices: 5742998--5743274 Score: 319
Period size: 148 Copynumber: 1.9 Consensus size: 148
5742988 TTTTAAGTTT
** * *
5742998 GGTCCTAAATTTGCCAATTGTTCTCACATTGGGACTTGGACTTGAAAATTTTTCCCACATTGGGA
1 GGTCCTAAACGTGCCAATTGTTCTCACATTGGGACTTGGACTTGAAAATTTCTCCAACATTGGGA
* * * * ** **
5743063 TATGAACTTCTTTTTAGTTCAAGTTAGGCCCTGACTTGGCAACTTTTCCCACATTGGGCCTGAAC
66 CATGAACTTCTTTTTAGTCCAAGTTAAGCCCTGACTTGACAACAGTTCCCACATTGACCCTGAAC
5743128 ATTTTGTTGTCCGAATTA
131 ATTTTGTTGTCCGAATTA
* * * * *
5743146 GGTCCTAAACGTGGCAATTGTTCTCACGTTGGGACTTTGACTTCGCAACTTTCT-CAACATTAGG
1 GGTCCTAAACGTGCCAATTGTTCTCACATTGGGACTTGGACTT-GAAAATTTCTCCAACATT-GG
* *
5743210 G-CCTGAACTT-TTTTT-GTCCAAGTTAAGCCCTGAACTTGACAACAGTTCTCACATTGAACCCT
64 GACATGAACTTCTTTTTAGTCCAAGTTAAGCCCTG-ACTTGACAACAGTTCCCACATTG-ACCCT
5743272 GAA
127 GAA
5743275 TTTAATAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
146 15 0.14
147 24 0.23
148 57 0.54
149 10 0.09
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (148 bp):
GGTCCTAAACGTGCCAATTGTTCTCACATTGGGACTTGGACTTGAAAATTTCTCCAACATTGGGA
CATGAACTTCTTTTTAGTCCAAGTTAAGCCCTGACTTGACAACAGTTCCCACATTGACCCTGAAC
ATTTTGTTGTCCGAATTA
Found at i:5745829 original size:17 final size:17
Alignment explanation
Indices: 5745792--5745830 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5745782 TTATTTATTT
*
5745792 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
5745809 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
5745826 TATTG
1 TATTG
5745831 AATTGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:5747762 original size:40 final size:39
Alignment explanation
Indices: 5747702--5747842 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 39
5747692 AACACATTAG
* *
5747702 TTTGGCACCCAGTGCCTCATCGAAAAATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGAAAAATCCAAAGT-ATAA
* **
5747742 TTTGACACCCAGTGTCTCATCGGTTAAA-CCAAAGTA-AA
1 TTTGACACCCAGTGCCTCATC-GAAAAATCCAAAGTATAA
* * *
5747780 -TTGGCACCTAGTGCCTCATCGAATAAATCCGAAGTGATAA
1 TTTGACACCCAGTGCCTCATCGAA-AAATCCAAAGT-ATAA
* *
5747820 ATTGACACCCAGTGTCTCATCGA
1 TTTGACACCCAGTGCCTCATCGA
5747843 CTCAAAGTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
36 1 0.01
37 20 0.25
38 8 0.10
39 2 0.02
40 27 0.33
41 23 0.28
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGAAAAATCCAAAGTATAA
Found at i:5750349 original size:3 final size:3
Alignment explanation
Indices: 5750341--5750368 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5750331 GGATCTATCC
5750341 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5750369 TTCGAAGTCA
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:5750750 original size:9 final size:9
Alignment explanation
Indices: 5750736--5750765 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5750726 ATACGTACAT
5750736 ATATATATA
1 ATATATATA
5750745 ATATATATA
1 ATATATATA
5750754 ATATATAATA
1 ATATAT-ATA
5750764 AT
1 AT
5750766 GTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.75
10 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATATA
Found at i:5750954 original size:2 final size:2
Alignment explanation
Indices: 5750947--5750972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5750937 CCTAAGTCAC
5750947 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
5750973 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5753528 original size:3 final size:3
Alignment explanation
Indices: 5753520--5753563 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5753510 ATAATTTCTC
5753520 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5753564 ATCAGTTCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5760057 original size:24 final size:25
Alignment explanation
Indices: 5760021--5760085 Score: 62
Period size: 29 Copynumber: 2.5 Consensus size: 25
5760011 AATTAAAATT
5760021 ATTTAATTA-TTTTAT-AAAAATAAA
1 ATTTAA-TACTTTTATAAAAAATAAA
5760045 ATTTAATACTTTTTTTATACAAAAATAAA
1 ATTTAATAC---TTTTATA-AAAAATAAA
*
5760074 ATTCAATACTTT
1 ATTTAATACTTT
5760086 GTTTTTGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 2 0.06
24 6 0.18
26 3 0.09
27 6 0.18
29 17 0.50
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAATACTTTTATAAAAAATAAA
Found at i:5762106 original size:4 final size:4
Alignment explanation
Indices: 5762097--5762135 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
5762087 TACTCCTCAG
5762097 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
5762136 CAATAATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:5767216 original size:43 final size:43
Alignment explanation
Indices: 5767162--5767250 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
5767152 AAATGTTTTC
5767162 CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
1 CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
*
5767205 CATTTTTTAATCCAAGATTGTGACTTTATCCGGCATTGATAAA
1 CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
5767248 CAT
1 CAT
5767251 ATTCTTCTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (43 bp):
CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
Found at i:5767483 original size:17 final size:18
Alignment explanation
Indices: 5767446--5767483 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5767436 GAAAATTTTT
* *
5767446 AATTAAACCGATTACATC
1 AATTAAACAGATGACATC
5767464 AATTAAACAGATGA-ATC
1 AATTAAACAGATGACATC
5767481 AAT
1 AAT
5767484 AACTTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTAAACAGATGACATC
Found at i:5767666 original size:55 final size:51
Alignment explanation
Indices: 5767563--5767671 Score: 164
Period size: 55 Copynumber: 2.1 Consensus size: 51
5767553 ATAAGAATCA
* *
5767563 GATTTTATATAATATTAAAAATAATACATTTTTTAATATGTGATGTGATGT
1 GATTTTATATAATACTAAAAATAATACATTTTTTAACATGTGATGTGATGT
5767614 GATTTTATATAATACTAAAAATAAAAATAACATTTTTTAACATGTGATGTGATGT
1 GATTTTATATAATACTAAAAAT---AAT-ACATTTTTTAACATGTGATGTGATGT
5767669 GAT
1 GAT
5767672 GTGATTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
51 21 0.40
54 3 0.06
55 28 0.54
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (51 bp):
GATTTTATATAATACTAAAAATAATACATTTTTTAACATGTGATGTGATGT
Found at i:5775543 original size:21 final size:21
Alignment explanation
Indices: 5775519--5775559 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5775509 TCACCCATGT
*
5775519 TATTTTTAAATTTTTTTTAAA
1 TATTTATAAATTTTTTTTAAA
*
5775540 TATTTATATATTTTTTTTAA
1 TATTTATAAATTTTTTTTAA
5775560 TTCAATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATAAATTTTTTTTAAA
Found at i:5781504 original size:1 final size:1
Alignment explanation
Indices: 5781498--5781615 Score: 182
Period size: 1 Copynumber: 118.0 Consensus size: 1
5781488 GATACTTTCA
* * *
5781498 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
5781563 TTTTTTGTTTTGTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5781616 GCAGACTGTG
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 105 1.00
ACGTcount: A:0.00, C:0.02, G:0.03, T:0.95
Consensus pattern (1 bp):
T
Found at i:5781628 original size:51 final size:51
Alignment explanation
Indices: 5781524--5781628 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 51
5781514 TTTTTTTTTT
** * *
5781524 TTTCTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTG
1 TTTCTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTGTTTTTTTCAGCTGTG
5781575 TTTCTTTTTTTTTTTTTTTTTTTTTT-TTTTTTTT-TTTTTTTGCAGACTGTG
1 TTTCTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTGTTTTTTT-CAG-CTGTG
5781626 TTT
1 TTT
5781629 GATGCACCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 7 0.15
50 9 0.19
51 32 0.67
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (51 bp):
TTTCTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTGTTTTTTTCAGCTGTG
Found at i:5783334 original size:20 final size:20
Alignment explanation
Indices: 5783288--5783338 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5783278 ATATTTTCAA
* * **
5783288 TTATTTTTACTTTATTTTTT
1 TTATTTTTATTTTAATTGAT
*
5783308 TTCTTTTTATTTTAATTGAT
1 TTATTTTTATTTTAATTGAT
5783328 TTATTTTTATT
1 TTATTTTTATT
5783339 AAAACTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
TTATTTTTATTTTAATTGAT
Found at i:5785802 original size:31 final size:31
Alignment explanation
Indices: 5785767--5785825 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
5785757 AGTGATTTAA
5785767 TATAA-ATATAAAT-ATATATATAATTATTATT
1 TATAATATATAAATAATATA-AT-ATTATTATT
*
5785798 TATAATATATAACTAATATAATATTATT
1 TATAATATATAAATAATATAATATTATT
5785826 TTATAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 11 0.44
32 9 0.36
33 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TATAATATATAAATAATATAATATTATTATT
Found at i:5785824 original size:24 final size:25
Alignment explanation
Indices: 5785764--5785824 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
5785754 ATTAGTGATT
5785764 TAATATAA-A-TATAAATATATATA
1 TAATATAATATTATAAATATATATA
*
5785787 TAAT-TATTATT-TATAATATATA-A
1 TAATATAATATTATA-AATATATATA
5785810 CTAATATAATATTAT
1 -TAATATAATATTAT
5785825 TTTATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 2 0.07
23 8 0.27
24 13 0.43
25 6 0.20
26 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATATAATATTATAAATATATATA
Found at i:5787360 original size:18 final size:19
Alignment explanation
Indices: 5787323--5787361 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5787313 ATTACAAAAT
* *
5787323 AATTTAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
5787342 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
5787360 AA
1 AA
5787362 ATTTTAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:5789387 original size:23 final size:23
Alignment explanation
Indices: 5789352--5789396 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
5789342 TTAATCTCGA
5789352 TTTTTTTATTTTTAAGAATTTAGT
1 TTTTTTTATTTTTAA-AATTTAGT
5789376 TTTTTTTATTTTTAAAATTTA
1 TTTTTTTATTTTTAAAATTTA
5789397 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTTTATTTTTAAAATTTAGT
Found at i:5796300 original size:31 final size:30
Alignment explanation
Indices: 5796257--5796317 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
5796247 ATTCATTATA
*
5796257 GGAAAATTAAATAA-AGAAA-ATGACTAAATT
1 GGAAAATGAAATAATA-AAAGATGA-TAAATT
5796287 GGAAAGATGAAATAATAAAAGATGATAAATT
1 GGAAA-ATGAAATAATAAAAGATGATAAATT
5796318 AATTAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.19
31 17 0.63
32 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (30 bp):
GGAAAATGAAATAATAAAAGATGATAAATT
Found at i:5796793 original size:24 final size:25
Alignment explanation
Indices: 5796741--5796787 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5796731 TAGCTCTCAT
* *
5796741 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
5796766 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
5796788 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:5797002 original size:24 final size:25
Alignment explanation
Indices: 5796970--5797058 Score: 121
Period size: 24 Copynumber: 3.6 Consensus size: 25
5796960 TATTGGCTCG
5796970 TATGAGCTTCCCATTAATGGCTCTC
1 TATGAGCTTCCCATTAATGGCTCTC
5796995 TATG-GCTTCCCATTAATGGCTCTC
1 TATGAGCTTCCCATTAATGGCTCTC
* * *
5797019 T-GGAGCTTCCCGTTACATGGCTCAC
1 TATGAGCTTCCCATTA-ATGGCTCTC
5797044 -ATGAGCTTCCCATTA
1 TATGAGCTTCCCATTA
5797059 TGTGCTCGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.02
24 31 0.55
25 24 0.43
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (25 bp):
TATGAGCTTCCCATTAATGGCTCTC
Found at i:5797049 original size:25 final size:24
Alignment explanation
Indices: 5796871--5797058 Score: 118
Period size: 24 Copynumber: 7.5 Consensus size: 24
5796861 TGGCTCTTCG
*
5796871 GAGCTTCCCGATTAAAGGCTCTGTCAT
1 GAGCTTCCC-ATTAATGGCTC--TCAT
* **
5796898 GAGCTTCTCGATTAATTGGCTCTCCG
1 GAGCTTC-CCATTAA-TGGCTCTCAT
* *
5796924 GAGCTTCCCGA-TATTGGCT-TCCTT
1 GAGCTTCCC-ATTAATGGCTCT-CAT
* * *
5796948 GAACTTTCTCGA-TATTGGCTCGT-AT
1 GAGC-TTC-CCATTAATGGCTC-TCAT
5796973 GAGCTTCCCATTAATGGCTCTCTAT
1 GAGCTTCCCATTAATGGCTCTC-AT
5796998 G-GCTTCCCATTAATGGCTCTC-T
1 GAGCTTCCCATTAATGGCTCTCAT
* *
5797020 GGAGCTTCCCGTTACATGGCTCACAT
1 -GAGCTTCCCATTA-ATGGCTCTCAT
5797046 GAGCTTCCCATTA
1 GAGCTTCCCATTA
5797059 TGTGCTCGTA
Statistics
Matches: 129, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
22 1 0.01
23 5 0.04
24 50 0.39
25 42 0.33
26 12 0.09
27 13 0.10
28 6 0.05
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCATTAATGGCTCTCAT
Found at i:5797071 original size:24 final size:24
Alignment explanation
Indices: 5796963--5797073 Score: 120
Period size: 24 Copynumber: 4.6 Consensus size: 24
5796953 TTCTCGATAT
5796963 TGGCTCGTATGAGCTTCCCATTAA
1 TGGCTCGTATGAGCTTCCCATTAA
*
5796987 TGGCTCTCTATG-GCTTCCCATTAA
1 TGGCTC-GTATGAGCTTCCCATTAA
* *
5797011 TGGCTC-TCTGGAGCTTCCCGTTACA
1 TGGCTCGTAT-GAGCTTCCCATTA-A
**
5797036 TGGCTCACATGAGCTTCCCATT-A
1 TGGCTCGTATGAGCTTCCCATTAA
5797059 TGTGCTCGTATGAGC
1 TG-GCTCGTATGAGC
5797074 ATTCTCGAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.03
23 4 0.05
24 44 0.60
25 22 0.30
26 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (24 bp):
TGGCTCGTATGAGCTTCCCATTAA
Found at i:5798532 original size:27 final size:27
Alignment explanation
Indices: 5798502--5798575 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
5798492 GCTTCAAAGA
** *
5798502 GCCACAATCACTATGTTGCACTGAAGT
1 GCCACAATCACTATGTTGCACCAAAAT
* * *
5798529 GCCACGATCATTAAGTTGCACCAAAAT
1 GCCACAATCACTATGTTGCACCAAAAT
*
5798556 GCCACTATCACTGAT-TTGCA
1 GCCACAATCACT-ATGTTGCA
5798576 TCGAACTGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (27 bp):
GCCACAATCACTATGTTGCACCAAAAT
Found at i:5807021 original size:31 final size:35
Alignment explanation
Indices: 5806953--5807026 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
5806943 ATTCTATAAT
*
5806953 AATTTACAATAAATTCTTATTTATTGGCAAATAAAA
1 AATTTACAATAAATTCTTATTTATT-GCAAAGAAAA
5806989 AATTT-CAATAAATTCTTA-TT-TT-CAAAGGAAAA
1 AATTTACAATAAATTCTTATTTATTGCAAA-GAAAA
5807021 AATTTA
1 AATTTA
5807027 TAAATCCTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 4 0.11
32 9 0.26
33 2 0.06
34 2 0.06
35 13 0.37
36 5 0.14
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (35 bp):
AATTTACAATAAATTCTTATTTATTGCAAAGAAAA
Found at i:5812283 original size:11 final size:11
Alignment explanation
Indices: 5812245--5812298 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
5812235 TAAATCCTTT
*
5812245 CTCTC-AATTT
1 CTCTCAAATTC
5812255 CTCTCTAATATT-
1 CTCTC-AA-ATTC
5812267 CTCTCAAATTC
1 CTCTCAAATTC
5812278 CTCTCAAATTC
1 CTCTCAAATTC
5812289 CTCTCAAATT
1 CTCTCAAATT
5812299 TCTATTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.20
11 23 0.57
12 6 0.15
13 3 0.08
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:5812364 original size:13 final size:12
Alignment explanation
Indices: 5812342--5812372 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
5812332 TTTAAAAAAG
5812342 TTTTAATTTTTT
1 TTTTAATTTTTT
5812354 TTTTGAATTTTTT
1 TTTT-AATTTTTT
5812367 TTTTAA
1 TTTTAA
5812373 ATCGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:5817574 original size:14 final size:15
Alignment explanation
Indices: 5817547--5817577 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5817537 TGTCTTGGTG
5817547 TCGAAAATTAAAAAA
1 TCGAAAATTAAAAAA
*
5817562 TCGAAAATAAAAAAA
1 TCGAAAATTAAAAAA
5817577 T
1 T
5817578 ACGATACCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
TCGAAAATTAAAAAA
Found at i:5820550 original size:30 final size:30
Alignment explanation
Indices: 5820516--5820573 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5820506 GTAGTCAAAG
*
5820516 CCGTGTGTCTCACACGACCAAGAGACACGT
1 CCGTGTATCTCACACGACCAAGAGACACGT
*
5820546 CCGTGTATCTCACACGGCCAAGAGACAC
1 CCGTGTATCTCACACGACCAAGAGACAC
5820574 CCTCATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (30 bp):
CCGTGTATCTCACACGACCAAGAGACACGT
Found at i:5820587 original size:30 final size:30
Alignment explanation
Indices: 5820521--5820589 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
5820511 CAAAGCCGTG
* * *
5820521 TGTCTCACACGACCAAGAGACACGTCCGTG
1 TGTCTCACACGACCAAGAGACACCTCCATA
* *
5820551 TATCTCACACGGCCAAGAGACACC-CTCATA
1 TGTCTCACACGACCAAGAGACACCTC-CATA
5820581 TGTCTCACA
1 TGTCTCACA
5820590 TAGCCGTGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (30 bp):
TGTCTCACACGACCAAGAGACACCTCCATA
Found at i:5830875 original size:25 final size:24
Alignment explanation
Indices: 5830832--5830884 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
5830822 AAGTTGAAGC
5830832 GAGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
5830856 GAGCCTATATCGGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
5830881 GAGC
1 GAGC
5830885 TGCAGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:5831539 original size:44 final size:45
Alignment explanation
Indices: 5831388--5831567 Score: 353
Period size: 45 Copynumber: 4.0 Consensus size: 45
5831378 AATTCATATT
5831388 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
5831433 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
5831478 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTG-CC
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
5831522 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
5831567 C
1 C
5831568 TATACTTTTA
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
44 44 0.33
45 90 0.67
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (45 bp):
CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
Found at i:5831564 original size:89 final size:90
Alignment explanation
Indices: 5831388--5831567 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 90
5831378 AATTCATATT
5831388 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCCCAATTAAATCAAATTCACAT
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCCCAATTAAATCAAATTCACAT
5831453 TTTAGGCAAAAGTATCATTTTGCCC
66 TTTAGGCAAAAGTATCATTTTGCCC
5831478 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTG-CCCAATTAAATCAAATTCACAT
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCCCAATTAAATCAAATTCACAT
5831542 TTTAGGCAAAAGTATCATTTTGCCC
66 TTTAGGCAAAAGTATCATTTTGCCC
5831567 C
1 C
5831568 TATACTTTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 48 0.53
90 42 0.47
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (90 bp):
CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCCCAATTAAATCAAATTCACAT
TTTAGGCAAAAGTATCATTTTGCCC
Found at i:5832790 original size:11 final size:11
Alignment explanation
Indices: 5832765--5832798 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5832755 ATAATTTAAT
5832765 AAATAAAAATAA
1 AAATAAAAAT-A
5832777 AAATAAAAATA
1 AAATAAAAATA
*
5832788 AAATATAAATA
1 AAATAAAAATA
5832799 GACACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5832798 original size:6 final size:6
Alignment explanation
Indices: 5832765--5832796 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
5832755 ATAATTTAAT
5832765 AAATAA AAATAA AAATAA AAATAA AATATAA A
1 AAATAA AAATAA AAATAA AAATAA AA-ATAA A
5832797 TAGACACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:5832938 original size:56 final size:56
Alignment explanation
Indices: 5832852--5832963 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
5832842 TTGGAGAGAA
5832852 GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
1 GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
*
5832908 GAAATGGATACAAATGGAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
1 GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
5832964 CAAGACTTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (56 bp):
GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
Found at i:5833006 original size:37 final size:37
Alignment explanation
Indices: 5832965--5833039 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
5832955 TGTTAATTTC
*
5832965 AAGACTTATGTTATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
5833002 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
5833039 A
1 A
5833040 TTTGGATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:5833029 original size:17 final size:17
Alignment explanation
Indices: 5832970--5833030 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5832960 ATTTCAAGAC
*
5832970 TTATGTTATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
5832987 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
5833006 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
5833024 TTATGTA
1 TTATGTA
5833031 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 4 0.12
20 9 0.28
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:5833058 original size:9 final size:9
Alignment explanation
Indices: 5833046--5833078 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5833036 TCAATTTGGA
5833046 TAATTCGGT
1 TAATTCGGT
5833055 TAATTCAGG-
1 TAATTC-GGT
5833064 TAATTCGGT
1 TAATTCGGT
5833073 TAATTC
1 TAATTC
5833079 TTAACCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:5834202 original size:20 final size:20
Alignment explanation
Indices: 5834163--5834203 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5834153 AATAAGAACA
* **
5834163 ATATTTTAATTTTAGGATAT
1 ATATATTAATTTTAAAATAT
5834183 ATATATTAATTTTAAAATAT
1 ATATATTAATTTTAAAATAT
5834203 A
1 A
5834204 ATTATATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATATTAATTTTAAAATAT
Found at i:5837503 original size:3 final size:3
Alignment explanation
Indices: 5837497--5837585 Score: 106
Period size: 3 Copynumber: 29.7 Consensus size: 3
5837487 TCAGCAACAA
* * * * *
5837497 CAG CAG CAG CAA CAA CAG CAG CAG CAA CAA CAG CAG CAG CAG CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
5837545 CAG CAG CAG CAG CAG CAA CAA CAG CAA CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
5837586 ACAACAACAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.43, C:0.34, G:0.24, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:5837508 original size:15 final size:15
Alignment explanation
Indices: 5837488--5837623 Score: 164
Period size: 15 Copynumber: 9.1 Consensus size: 15
5837478 GAGGCATGCT
5837488 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
5837503 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
5837518 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
*
5837533 CAGCAGCAACAGCAG
1 CAGCAACAACAGCAG
* * *
5837548 CAGCAGCAGCAGCAA
1 CAGCAACAACAGCAG
* *
5837563 CAACAGCAACAGCAG
1 CAGCAACAACAGCAG
* * *
5837578 CAGCAGCAACAACAA
1 CAGCAACAACAGCAG
* * *
5837593 CAACAACAACAACAA
1 CAGCAACAACAGCAG
5837608 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
5837623 C
1 C
5837624 CGCAGCAGCA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 107 1.00
ACGTcount: A:0.48, C:0.34, G:0.18, T:0.00
Consensus pattern (15 bp):
CAGCAACAACAGCAG
Found at i:5837515 original size:9 final size:9
Alignment explanation
Indices: 5837488--5837621 Score: 106
Period size: 9 Copynumber: 14.6 Consensus size: 9
5837478 GAGGCATGCT
5837488 CAGCAACAA
1 CAGCAACAA
5837497 CAGCAGCAGCAA
1 CAGCA--A-CAA
* * *
5837509 CAACAGCAG
1 CAGCAACAA
5837518 CAGCAACAA
1 CAGCAACAA
* *
5837527 CAGCAGCAG
1 CAGCAACAA
*
5837536 CAGCAACAG
1 CAGCAACAA
* *
5837545 CAGCAGCAG
1 CAGCAACAA
*
5837554 CAGCAGCAA
1 CAGCAACAA
* *
5837563 CAACAGCAA
1 CAGCAACAA
* *
5837572 CAGCAGCAG
1 CAGCAACAA
5837581 CAGCAACAA
1 CAGCAACAA
*
5837590 CAACAACAA
1 CAGCAACAA
*
5837599 CAACAACAA
1 CAGCAACAA
5837608 CAGCAACAA
1 CAGCAACAA
5837617 CAGCA
1 CAGCA
5837622 GCCGCAGCAG
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
9 96 0.92
11 1 0.01
12 7 0.07
ACGTcount: A:0.49, C:0.34, G:0.18, T:0.00
Consensus pattern (9 bp):
CAGCAACAA
Found at i:5837590 original size:3 final size:3
Alignment explanation
Indices: 5837560--5837618 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
5837550 GCAGCAGCAG
* * * * *
5837560 CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
*
5837608 CAG CAA CAA CA
1 CAA CAA CAA CA
5837619 GCAGCCGCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.56, C:0.34, G:0.10, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:5837656 original size:12 final size:12
Alignment explanation
Indices: 5837614--5837656 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5837604 ACAACAGCAA
5837614 CAACAGCAGCCG
1 CAACAGCAGCCG
* *
5837626 CAGCAGCAGTCG
1 CAACAGCAGCCG
**
5837638 CCCCAGCAGCCG
1 CAACAGCAGCCG
5837650 CAACAGC
1 CAACAGC
5837657 CCCAACAACG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.28, C:0.44, G:0.26, T:0.02
Consensus pattern (12 bp):
CAACAGCAGCCG
Found at i:5838426 original size:13 final size:14
Alignment explanation
Indices: 5838393--5838439 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
5838383 GGTAGGTTTG
5838393 TTTGATCTCTTTCA
1 TTTGATCTCTTTCA
5838407 TTTGATCTC-TT-A
1 TTTGATCTCTTTCA
5838419 TATTGATCTCTTTCA
1 T-TTGATCTCTTTCA
5838434 TTTGAT
1 TTTGAT
5838440 GCTTCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.07
13 10 0.33
14 16 0.53
15 2 0.07
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (14 bp):
TTTGATCTCTTTCA
Found at i:5839404 original size:6 final size:6
Alignment explanation
Indices: 5839393--5839422 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5839383 TGGCTCAGTT
5839393 GCAACA GCAACA GCAACA GCAACA G-AACA G
1 GCAACA GCAACA GCAACA GCAACA GCAACA G
5839423 TAGCTCACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.50, C:0.30, G:0.20, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:5848545 original size:40 final size:40
Alignment explanation
Indices: 5848482--5848562 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
5848472 TTTTATGCTT
5848482 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
1 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
* *
5848522 GTTTTGCTATATGCAGCTTTGTAATTATCAAAGAACAAAG
1 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
5848562 G
1 G
5848563 GTTGTCTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (40 bp):
GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
Found at i:5855284 original size:363 final size:363
Alignment explanation
Indices: 5854619--5855317 Score: 1157
Period size: 363 Copynumber: 1.9 Consensus size: 363
5854609 CACATATATG
*
5854619 CATATTTTACCAAATATGTTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
1 CATATTTTACCAAATATGCTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
*
5854684 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAATATACCAAACATAGCCCTTTAAAT
66 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
* *
5854749 GGCTATTTACAACCAAAATATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
131 AGCTATTTACAACCAAAACATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
* ** * *
5854814 ACCAAAATTAGTTTCATGCCTGTACCGAAAATGGGTCGGTGGGTAGTGTGAGTGATCTCTACCAA
196 ACCAAAATTAGTTTCATACCTGTACAAAAAATGGGCCGGTGGATAGTGTGAGTGATCTCTACCAA
*
5854879 GCTTCCAACCCGATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTT-A
261 GCTTCCAACCCAATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTTGA
5854943 GTGCTTAGTAAGTTCATATAAAACAGAGGATCAAGATAA
326 -TGCTTAGTAAGTTCATATAAAACAGAGGATCAAGATAA
*
5854982 CATATTTTACCAAATATGCTATCTTGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
1 CATATTTTACCAAATATGCTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
5855047 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
66 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
* * * *
5855112 AGCTATTTACAACCAAAACATGTATGTGTCATCAATGGCTAAGTTAACCTATACATGTCATTATA
131 AGCTATTTACAACCAAAACATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
** * * * *
5855177 ACCAAAATTAGTTTCATATTTGTATAAAAAATGGGCCGGTGGATCGTGTGAGTGATCTTTGCCAA
196 ACCAAAATTAGTTTCATACCTGTACAAAAAATGGGCCGGTGGATAGTGTGAGTGATCTCTACCAA
** * *
5855242 GCTTCCAACCCAATGAGCCTCCGAGATTTATAAAATAGAGGAAATACAACTGAATAAGCACTTGA
261 GCTTCCAACCCAATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTTGA
5855307 TGCTTAGTAAG
326 TGCTTAGTAAG
5855318 CCCGTATAAT
Statistics
Matches: 310, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
363 309 1.00
364 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (363 bp):
CATATTTTACCAAATATGCTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
AGCTATTTACAACCAAAACATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
ACCAAAATTAGTTTCATACCTGTACAAAAAATGGGCCGGTGGATAGTGTGAGTGATCTCTACCAA
GCTTCCAACCCAATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTTGA
TGCTTAGTAAGTTCATATAAAACAGAGGATCAAGATAA
Found at i:5855802 original size:24 final size:24
Alignment explanation
Indices: 5855775--5855864 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 24
5855765 TATTTAGAAT
*
5855775 GCTCATGCGAGCA-TATAACGGGTA
1 GCTCATGAGAGCACT-TAACGGGTA
*
5855799 GCTC-TGAAGAGCACTTAACGAGTA
1 GCTCATG-AGAGCACTTAACGGGTA
5855823 GCTCA-GAGTAGCACTTAACGGGTA
1 GCTCATGAG-AGCACTTAACGGGTA
*
5855847 GCTC-CGAAGAGCACTTAA
1 GCTCATG-AGAGCACTTAA
5855865 TTAGGAAGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 4 0.07
24 50 0.88
25 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (24 bp):
GCTCATGAGAGCACTTAACGGGTA
Found at i:5867963 original size:32 final size:31
Alignment explanation
Indices: 5867915--5867992 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 31
5867905 AGTTATTCAT
5867915 AAAATTAAT-T-AT-ATAAAAAATATTTTAA
1 AAAATTAATATAATGATAAAAAATATTTTAA
* * **
5867943 AAACTTAAATATGATGATAAATTATATTTTAA
1 AAAATT-AATATAATGATAAAAAATATTTTAA
5867975 AAAATTAATATAATGATA
1 AAAATTAATATAATGATA
5867993 CATGATATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 1 0.02
31 13 0.32
32 19 0.46
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (31 bp):
AAAATTAATATAATGATAAAAAATATTTTAA
Found at i:5867991 original size:31 final size:31
Alignment explanation
Indices: 5867934--5868015 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
5867924 TATATAAAAA
* * *
5867934 ATATTTTAAAAACTTAAATATGATGATAAATT
1 ATATTTTAAAAAATT-AATATAATGATAAATG
*
5867966 ATATTTTAAAAAATTAATATAATGATACATG
1 ATATTTTAAAAAATTAATATAATGATAAATG
*
5867997 ATA-TTTAAATAATCTAATA
1 ATATTTTAAAAAAT-TAATA
5868016 AATTAGTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 9 0.20
31 21 0.48
32 14 0.32
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (31 bp):
ATATTTTAAAAAATTAATATAATGATAAATG
Found at i:5868026 original size:31 final size:31
Alignment explanation
Indices: 5867970--5868046 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
5867960 TAAATTATAT
* *
5867970 TTTAAAAAAT-TAATATAATGATACATGATA
1 TTTAAATAATCTAATATAATGATACATGAAA
* *
5868000 TTTAAATAATCTAATA-AATTAGTACATTAAA
1 TTTAAATAATCTAATATAATGA-TACATGAAA
*
5868031 TATAAATTAATCTAAT
1 TTTAAA-TAATCTAAT
5868047 TTTTTATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 13 0.33
31 17 0.44
32 9 0.23
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (31 bp):
TTTAAATAATCTAATATAATGATACATGAAA
Found at i:5870566 original size:31 final size:31
Alignment explanation
Indices: 5870531--5870609 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
5870521 TTAATATACT
* *
5870531 ATTTGGTATCTTACTTTGG-TTTCAAAGTTCA
1 ATTTGGTATCTAAATTTGGATTT-AAAGTTCA
*
5870562 ATTTGGTATCTAAATTTGGATTTAAGGTTCA
1 ATTTGGTATCTAAATTTGGATTTAAAGTTCA
* *
5870593 CTTTGGTACCTAAATTT
1 ATTTGGTATCTAAATTT
5870610 TTTTAATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 39 0.93
32 3 0.07
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.47
Consensus pattern (31 bp):
ATTTGGTATCTAAATTTGGATTTAAAGTTCA
Found at i:5876206 original size:6 final size:6
Alignment explanation
Indices: 5876197--5876231 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5876187 TTTTTTCTTT
*
5876197 TAAAAA TAAAAA TAAGAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
5876232 TCTTGGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:5883726 original size:5 final size:5
Alignment explanation
Indices: 5883718--5883777 Score: 79
Period size: 5 Copynumber: 12.2 Consensus size: 5
5883708 TTTTTTACTT
* *
5883718 ATATA ATATA ATACA ATATA ATATA ATATA ATATA ATAT- ATAATA AAATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
5883768 ATAT- ATATA A
1 ATATA ATATA A
5883778 AACATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 6 0.12
5 41 0.85
6 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:5884520 original size:25 final size:25
Alignment explanation
Indices: 5884475--5884618 Score: 93
Period size: 25 Copynumber: 5.8 Consensus size: 25
5884465 TGGTTTTTAC
* *
5884475 GAGCTTCCCGA-TAACTAGCTCTTAT
1 GAGCTTCCTGATTAA-TGGCTCTTAT
* ***
5884500 GAGTTTCCTGATTAATGGCTCTCCG
1 GAGCTTCCTGATTAATGGCTCTTAT
* * *
5884525 GAGCTTCCCGA-TATTGGCTCGTAT
1 GAGCTTCCTGATTAATGGCTCTTAT
*
5884549 GAGCTTCCTG-TTAATGGCTCTCCA-
1 GAGCTTCCTGATTAATGGCTCT-TAT
** *
5884573 GAGCTTCCTG-TTACATGGCTCACAA
1 GAGCTTCCTGATTA-ATGGCTCTTAT
5884598 GAGCTTCCTG-TTATATGGCTC
1 GAGCTTCCTGATTA-ATGGCTC
5884619 GAAAGAACTT
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
24 40 0.42
25 52 0.55
26 3 0.03
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTTAT
Found at i:5884566 original size:24 final size:23
Alignment explanation
Indices: 5884492--5884618 Score: 94
Period size: 25 Copynumber: 5.2 Consensus size: 23
5884482 CCGATAACTA
*
5884492 GCTCTTATGAGTTTCCTGATTAATG
1 GCTC-TATGAGCTTCCTG-TTAATG
** * * *
5884517 GCTCTCCGGAGCTTCCCGATATTG
1 GCTCT-ATGAGCTTCCTGTTAATG
5884541 GCTCGTATGAGCTTCCTGTTAATG
1 GCTC-TATGAGCTTCCTGTTAATG
5884565 GCTCTCCA-GAGCTTCCTGTTACATG
1 GCTCT--ATGAGCTTCCTGTTA-ATG
* *
5884590 GCTCACAAGAGCTTCCTGTTATATG
1 GCTC-TATGAGCTTCCTGTTA-ATG
5884615 GCTC
1 GCTC
5884619 GAAAGAACTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
23 1 0.01
24 40 0.49
25 41 0.50
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (23 bp):
GCTCTATGAGCTTCCTGTTAATG
Found at i:5884592 original size:49 final size:48
Alignment explanation
Indices: 5884475--5884618 Score: 162
Period size: 49 Copynumber: 2.9 Consensus size: 48
5884465 TGGTTTTTAC
* * * *
5884475 GAGCTTCCCGATAACTAGCTCTTATGAGTTTCCTGATTAATGGCTCTCCG
1 GAGCTTCCCGATAA-TGGCTCATATGAGCTTCCTG-TTAATGGCTCTCCA
* *
5884525 GAGCTTCCCGATATTGGCTCGTATGAGCTTCCTGTTAATGGCTCTCCA
1 GAGCTTCCCGATAATGGCTCATATGAGCTTCCTGTTAATGGCTCTCCA
* * * *
5884573 GAGCTTCCTGTTACATGGCTCACAAGAGCTTCCTGTTATATGGCTC
1 GAGCTTCCCGATA-ATGGCTCATATGAGCTTCCTGTTA-ATGGCTC
5884619 GAAAGAACTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
48 24 0.30
49 37 0.46
50 20 0.25
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (48 bp):
GAGCTTCCCGATAATGGCTCATATGAGCTTCCTGTTAATGGCTCTCCA
Found at i:5884624 original size:25 final size:25
Alignment explanation
Indices: 5884525--5884624 Score: 98
Period size: 25 Copynumber: 4.1 Consensus size: 25
5884515 TGGCTCTCCG
* * * *
5884525 GAGCTTCCCGATAT-TGGCTCGTAT
1 GAGCTTCCTGTTATATGGCTCGAAA
***
5884549 GAGCTTCCTGTTA-ATGGCTCTCCA
1 GAGCTTCCTGTTATATGGCTCGAAA
*
5884573 GAGCTTCCTGTTACATGGCTC-ACAA
1 GAGCTTCCTGTTATATGGCTCGA-AA
5884598 GAGCTTCCTGTTATATGGCTCGAAA
1 GAGCTTCCTGTTATATGGCTCGAAA
5884623 GA
1 GA
5884625 ACTTTCCATT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 30 0.48
25 32 0.51
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCGAAA
Found at i:5891836 original size:13 final size:13
Alignment explanation
Indices: 5891815--5892047 Score: 185
Period size: 13 Copynumber: 18.1 Consensus size: 13
5891805 CTAATTTTAT
5891815 AACAGTATATTAA
1 AACAGTATATTAA
* *
5891828 AATAGTATATTAC
1 AACAGTATATTAA
*
5891841 AA-A-T-T-TTAT
1 AACAGTATATTAA
5891850 AACAGTATATTAA
1 AACAGTATATTAA
*
5891863 ACCAGTATATT--
1 AACAGTATATTAA
5891874 -ACAGTAATAATT-A
1 AACAGT-AT-ATTAA
*** *
5891887 AGGTGTAGTATTTAT
1 AACAGTA-TA-TTAA
*
5891902 AACAGTATACTAA
1 AACAGTATATTAA
*
5891915 AACATTATATTAA
1 AACAGTATATTAA
5891928 AACAGTATATTAA
1 AACAGTATATTAA
*
5891941 AACAGTATATTTAT
1 AACAGTATA-TTAA
*
5891955 AACAATATATTAA
1 AACAGTATATTAA
*
5891968 AACATTATATTAA
1 AACAGTATATTAA
* *
5891981 AACAATATATTTAT
1 AACAGTATA-TTAA
*
5891995 AACAGTATACTAA
1 AACAGTATATTAA
*
5892008 AACAATATATTAA
1 AACAGTATATTAA
*
5892021 AACAATATATTAA
1 AACAGTATATTAA
*
5892034 AACAGTATAATAA
1 AACAGTATATTAA
5892047 A
1 A
5892048 CTAGTTATTT
Statistics
Matches: 176, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
9 5 0.03
10 6 0.03
11 4 0.02
12 5 0.03
13 123 0.70
14 29 0.16
15 4 0.02
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (13 bp):
AACAGTATATTAA
Found at i:5891853 original size:35 final size:35
Alignment explanation
Indices: 5891807--5891876 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
5891797 AACATTGACT
*
5891807 AATTTTATAACAGTATATTAAAATAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAGTATATTACA
*
5891842 AATTTTATAACAGTATATTAAACCAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAGTATATTACA
5891877 GTAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (35 bp):
AATTTTATAACAGTATATTAAAACAGTATATTACA
Found at i:5891964 original size:40 final size:40
Alignment explanation
Indices: 5891915--5892031 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
5891905 AGTATACTAA
* *
5891915 AACATTATATTAAAACAGTATATTAAAACAGTATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
*
5891955 AACAATATATTAAAACATTATATTAAAACAATATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
* * *
5891995 AACAGTATACTAAAACAATATATTAAAACAATATATT
1 AACAATATATTAAAACAGTATATTAAAACAATATATT
5892032 AAAACAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (40 bp):
AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
Found at i:5891969 original size:53 final size:53
Alignment explanation
Indices: 5891895--5892047 Score: 218
Period size: 53 Copynumber: 2.9 Consensus size: 53
5891885 TAAGGTGTAG
* *
5891895 TATTTATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
* *
5891948 TATTTATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATA-TTAAAACAGTA
* * * *
5892002 TA-CTAAAACAATATATTAAAACAATATATTAAAACAGTATAATAAA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAA
5892048 CTAGTTATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.03
53 74 0.83
54 12 0.13
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (53 bp):
TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
Found at i:5892066 original size:53 final size:52
Alignment explanation
Indices: 5891895--5892067 Score: 201
Period size: 53 Copynumber: 3.3 Consensus size: 52
5891885 TAAGGTGTAG
* *
5891895 TATTT-ATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGT
1 TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATT-AAACAGT
*
5891947 ATATTT-ATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAG-
1 -TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATA-TTA-AACAGT
* * *
5892000 TATACTAA-AACAATATATTAAAACAATATATTAAAACAGTATAATAAACTAGT
1 TAT-TTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAC-AGT
*
5892053 TATTTAATTACAATA
1 TATTTAATAACAATA
5892068 GATCAAACTT
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.03
52 10 0.10
53 83 0.80
54 8 0.08
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (52 bp):
TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAACAGT
Found at i:5892938 original size:35 final size:35
Alignment explanation
Indices: 5892873--5892942 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
5892863 AACATTGACT
* *
5892873 AATTTTATAATAGTATATTAAAATAATATATTACA
1 AATTTTATAACAGTATATTAAAACAATATATTACA
* *
5892908 AATTTTATAACAGTATATTAAACCAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAATATATTACA
5892943 TTAATAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (35 bp):
AATTTTATAACAGTATATTAAAACAATATATTACA
Found at i:5897158 original size:13 final size:13
Alignment explanation
Indices: 5897137--5897369 Score: 181
Period size: 13 Copynumber: 18.1 Consensus size: 13
5897127 CTAATTTTAT
5897137 AACAGTATATTAA
1 AACAGTATATTAA
* *
5897150 AATAGTATATTAC
1 AACAGTATATTAA
*
5897163 AA-A-T-T-TTAT
1 AACAGTATATTAA
5897172 AACAGTATATTAA
1 AACAGTATATTAA
* *
5897185 ACCAGTATATTAC
1 AACAGTATATTAA
** *
5897198 ATTAATA-ATT-A
1 AACAGTATATTAA
*** *
5897209 AGGTGTAGTATTTAT
1 AACAGTA-TA-TTAA
*
5897224 AACAGTATACTAA
1 AACAGTATATTAA
*
5897237 AACATTATATTAA
1 AACAGTATATTAA
5897250 AACAGTATATTAA
1 AACAGTATATTAA
*
5897263 AACAGTATATTTAT
1 AACAGTATA-TTAA
*
5897277 AACAATATATTAA
1 AACAGTATATTAA
*
5897290 AACATTATATTAA
1 AACAGTATATTAA
* *
5897303 AACAATATATTTAT
1 AACAGTATA-TTAA
*
5897317 AACAGTATACTAA
1 AACAGTATATTAA
*
5897330 AACAATATATTAA
1 AACAGTATATTAA
*
5897343 AACAATATATTAA
1 AACAGTATATTAA
*
5897356 AACAGTATAATAA
1 AACAGTATATTAA
5897369 A
1 A
5897370 CTAGTTATTT
Statistics
Matches: 174, Mismatches: 36, Indels: 20
0.76 0.16 0.09
Matches are distributed among these distances:
9 5 0.03
10 2 0.01
11 5 0.03
12 5 0.03
13 127 0.73
14 26 0.15
15 4 0.02
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (13 bp):
AACAGTATATTAA
Found at i:5897175 original size:35 final size:35
Alignment explanation
Indices: 5897129--5897198 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
5897119 AACATTGACT
*
5897129 AATTTTATAACAGTATATTAAAATAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAGTATATTACA
*
5897164 AATTTTATAACAGTATATTAAACCAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAGTATATTACA
5897199 TTAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (35 bp):
AATTTTATAACAGTATATTAAAACAGTATATTACA
Found at i:5897286 original size:40 final size:40
Alignment explanation
Indices: 5897237--5897353 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
5897227 AGTATACTAA
* *
5897237 AACATTATATTAAAACAGTATATTAAAACAGTATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
*
5897277 AACAATATATTAAAACATTATATTAAAACAATATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
* * *
5897317 AACAGTATACTAAAACAATATATTAAAACAATATATT
1 AACAATATATTAAAACAGTATATTAAAACAATATATT
5897354 AAAACAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (40 bp):
AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
Found at i:5897291 original size:53 final size:53
Alignment explanation
Indices: 5897217--5897369 Score: 218
Period size: 53 Copynumber: 2.9 Consensus size: 53
5897207 TAAGGTGTAG
* *
5897217 TATTTATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
* *
5897270 TATTTATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATA-TTAAAACAGTA
* * * *
5897324 TA-CTAAAACAATATATTAAAACAATATATTAAAACAGTATAATAAA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAA
5897370 CTAGTTATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.03
53 74 0.83
54 12 0.13
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (53 bp):
TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
Found at i:5897388 original size:53 final size:52
Alignment explanation
Indices: 5897217--5897389 Score: 201
Period size: 53 Copynumber: 3.3 Consensus size: 52
5897207 TAAGGTGTAG
* *
5897217 TATTT-ATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGT
1 TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATT-AAACAGT
*
5897269 ATATTT-ATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAG-
1 -TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATA-TTA-AACAGT
* * *
5897322 TATACTAA-AACAATATATTAAAACAATATATTAAAACAGTATAATAAACTAGT
1 TAT-TTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAC-AGT
*
5897375 TATTTAATTACAATA
1 TATTTAATAACAATA
5897390 GATCAAACTT
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.03
52 10 0.10
53 83 0.80
54 8 0.08
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (52 bp):
TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAACAGT
Found at i:5904306 original size:37 final size:38
Alignment explanation
Indices: 5904244--5904318 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
5904234 CTTGAAGCTA
5904244 AAATATGGAAGACCAGCTCTAAACCCTCTTCCATGGCT
1 AAATATGGAAGACCAGCTCTAAACCCTCTTCCATGGCT
5904282 AAATATGGAAGA-CAGCTCTAAACCCTCTTCCATGGCT
1 AAATATGGAAGACCAGCTCTAAACCCTCTTCCATGGCT
5904319 GTTTTCCACC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 25 0.68
38 12 0.32
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (38 bp):
AAATATGGAAGACCAGCTCTAAACCCTCTTCCATGGCT
Found at i:5911471 original size:17 final size:16
Alignment explanation
Indices: 5911444--5911478 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5911434 TAACATAAAG
*
5911444 ACCAATTTTTTATTTA
1 ACCAATTTTTTATCTA
5911460 ACCAATTTTTTTATCTA
1 ACCAA-TTTTTTATCTA
5911477 AC
1 AC
5911479 ATGTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (16 bp):
ACCAATTTTTTATCTA
Found at i:5911900 original size:79 final size:79
Alignment explanation
Indices: 5911769--5911927 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
5911759 CTACACTAAT
*
5911769 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAGTTTTTATACACTAAAAA
1 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
*
5911834 TATAATTTATCCTG
66 AATAATTTATCCTG
5911848 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
1 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
5911913 AATAATTTATCCTG
66 AATAATTTATCCTG
5911927 A
1 A
5911928 CTTGACTCGT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (79 bp):
ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
AATAATTTATCCTG
Found at i:5919369 original size:80 final size:79
Alignment explanation
Indices: 5919235--5919391 Score: 287
Period size: 80 Copynumber: 2.0 Consensus size: 79
5919225 GTGGTAATGT
*
5919235 GGCTAAACATGGACATGACACGTGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
1 GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
5919300 TAAAAAAATTTTACC
66 T-AAAAAATTTTACC
*
5919315 GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCTTAGCTTCAATTATTC
1 GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
5919380 TAAAAAATTTTA
66 TAAAAAATTTTA
5919392 AAAAGTTGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 11 0.15
80 64 0.85
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (79 bp):
GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
TAAAAAATTTTACC
Found at i:5919458 original size:12 final size:12
Alignment explanation
Indices: 5919421--5919468 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
5919411 ACATTTATAT
*
5919421 AAATTTAAAAAA
1 AAATTTATAAAA
* *
5919433 ATAATTTTTTAAA
1 A-AATTTATAAAA
5919446 AAATTTATAAAA
1 AAATTTATAAAA
5919458 AAATTTA-AAAA
1 AAATTTATAAAA
5919469 TAAGAAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 4 0.13
12 17 0.57
13 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTTATAAAA
Found at i:5919510 original size:26 final size:27
Alignment explanation
Indices: 5919455--5919523 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
5919445 AAAATTTATA
* *
5919455 AAAAAATTTAAAAATA-AGAAACTTAT
1 AAAAAATTAAAAAATATAGAAACTTAC
*
5919481 AAAAAATTGAAAAATATAGACAA-TT-C
1 AAAAAATTAAAAAATATAGA-AACTTAC
5919507 AAAAAA-TAAAAAATATA
1 AAAAAATTAAAAAATATA
5919524 TAATTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 10 0.26
26 21 0.55
27 5 0.13
28 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAAATTAAAAAATATAGAAACTTAC
Found at i:5922504 original size:3 final size:3
Alignment explanation
Indices: 5922496--5922527 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5922486 GAGATTTTGA
5922496 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5922528 ATTCACTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5923607 original size:47 final size:47
Alignment explanation
Indices: 5923538--5923631 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
5923528 AGATCTAAGA
5923538 TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
1 TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
*
5923585 TTTTAGGAACCAGTTACCAAAATATTTTATGCGCATAACTTATCTGC
1 TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
5923632 CAATATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (47 bp):
TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
Found at i:5927864 original size:82 final size:82
Alignment explanation
Indices: 5927764--5928100 Score: 656
Period size: 82 Copynumber: 4.1 Consensus size: 82
5927754 TACTGAAATT
5927764 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
1 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
5927829 GAAAAAAAGAAAAAGGC
66 GAAAAAAAGAAAAAGGC
5927846 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
1 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
5927911 GAAAAAAAGAAAAAGGC
66 GAAAAAAAGAAAAAGGC
5927928 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
1 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
5927993 GAAAAAAAGAAAAAGGC
66 GAAAAAAAGAAAAAGGC
5928010 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
1 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
5928075 GAAAAAAAGAAAAAGGC
66 GAAAAAAAGAAAAAGGC
* *
5928092 ATCAGAATT
1 TTCAAAATT
5928101 GAAAACATCG
Statistics
Matches: 253, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 253 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (82 bp):
TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
GAAAAAAAGAAAAAGGC
Found at i:5942926 original size:1 final size:1
Alignment explanation
Indices: 5942869--5942912 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
5942859 ACTGATTCCC
*
5942869 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5942913 CAAAGTCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:5947173 original size:29 final size:30
Alignment explanation
Indices: 5947109--5947173 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
5947099 AGTCTTGAAA
**
5947109 TTATATATAAATTTTGATTTTGTGTAATT-
1 TTATATATAAATTTTGATTTAATGTAATTC
*
5947138 TTATATATAAAATTTTGATTTAATTTAATTC
1 TTATATAT-AAATTTTGATTTAATGTAATTC
5947169 TTATA
1 TTATA
5947174 AATTAACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.26
30 18 0.58
31 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (30 bp):
TTATATATAAATTTTGATTTAATGTAATTC
Found at i:5948187 original size:3 final size:3
Alignment explanation
Indices: 5948179--5948210 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5948169 CGGATTGTAA
5948179 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5948211 AGAAATATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5948410 original size:20 final size:19
Alignment explanation
Indices: 5948385--5948427 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5948375 ATTAGTTACT
* *
5948385 TATTTACTATTTTGATTTTC
1 TATTTAATATATTG-TTTTC
5948405 TATTTAATATATTGTTTTC
1 TATTTAATATATTGTTTTC
5948424 TATT
1 TATT
5948428 GTTTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (19 bp):
TATTTAATATATTGTTTTC
Found at i:5956327 original size:25 final size:25
Alignment explanation
Indices: 5956257--5956337 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 25
5956247 GACACACCAC
* *
5956257 AGCTCGCATGAGCTT-TCTGATACTT
1 AGCTCGCATGAGCTTCTC-GTTATTT
*
5956282 AGCTCGCATGAGCTTCCCGTTATTT
1 AGCTCGCATGAGCTTCTCGTTATTT
*
5956307 AGCTCGCATGAGCTTCTCGTTATTC
1 AGCTCGCATGAGCTTCTCGTTATTT
5956332 AGCTCG
1 AGCTCG
5956338 AAAGAACTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCTCGTTATTT
Found at i:5957217 original size:38 final size:39
Alignment explanation
Indices: 5957159--5957235 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
5957149 ATCCAACCAA
*
5957159 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
5957198 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
5957236 TACTCTTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:5957390 original size:17 final size:17
Alignment explanation
Indices: 5957370--5957435 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
5957360 TAATTTCAAG
5957370 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
5957387 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
5957405 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
5957424 AATTATGTAATG
1 AATTATGTAATG
5957436 ATTCAATTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 20 0.56
18 4 0.11
19 4 0.11
20 8 0.22
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:5957394 original size:37 final size:37
Alignment explanation
Indices: 5957367--5957441 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
5957357 TGCTAATTTC
* *
5957367 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* * *
5957404 AAGACTTATGTAATATTTTTAATTATGTAATGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
5957441 A
1 A
5957442 TTTGGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:5957460 original size:9 final size:9
Alignment explanation
Indices: 5957448--5957488 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
5957438 TCAATTTGGG
5957448 TAATTCGGT
1 TAATTCGGT
5957457 TAATTCGGT
1 TAATTCGGT
*
5957466 TAATTAGGT
1 TAATTCGGT
*
5957475 TAATTCAGT
1 TAATTCGGT
5957484 TAATT
1 TAATT
5957489 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:5959845 original size:24 final size:24
Alignment explanation
Indices: 5959787--5959866 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
5959777 GCTTATCCGG
* *
5959787 GCAATATAACAGGAAGCTCACAAAGA
1 GCAAT-TAATAGGTAGCTC-CAAAGA
* * *
5959813 GC-CTATAATGGGTAGCTCTAAAGA
1 GCAAT-TAATAGGTAGCTCCAAAGA
*
5959837 GCAATTAATAGGTAGCTCCGAAGA
1 GCAATTAATAGGTAGCTCCAAAGA
5959861 GCAATT
1 GCAATT
5959867 TAACGGGAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 29 0.66
25 13 0.30
26 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (24 bp):
GCAATTAATAGGTAGCTCCAAAGA
Found at i:5974517 original size:31 final size:31
Alignment explanation
Indices: 5974476--5974544 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
5974466 AAGGTAACTT
*
5974476 AATAACTTAGTAACTTAAATAAAAACTCTCG
1 AATAATTTAGTAACTTAAATAAAAACTCTCG
* * * *
5974507 AATAATTTAGTTACTTAAATGAAAACTTTTG
1 AATAATTTAGTAACTTAAATAAAAACTCTCG
5974538 AATAATT
1 AATAATT
5974545 CAGTGATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (31 bp):
AATAATTTAGTAACTTAAATAAAAACTCTCG
Found at i:5975142 original size:15 final size:13
Alignment explanation
Indices: 5975118--5975154 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5975108 ATATATATTT
5975118 AAAAATT-ATAT-
1 AAAAATTAATATA
5975129 AAAAATATAATATA
1 AAAAAT-TAATATA
5975143 AAAAATTAATAT
1 AAAAATTAATAT
5975155 GGTCGGGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.26
12 1 0.04
13 10 0.43
14 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAATATA
Found at i:5975263 original size:13 final size:13
Alignment explanation
Indices: 5975245--5975279 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5975235 GGGCTGGACC
5975245 CAGGCCTAACAAA
1 CAGGCCTAACAAA
5975258 CAGGCCTAACAAA
1 CAGGCCTAACAAA
*
5975271 TAGGCCTAA
1 CAGGCCTAA
5975280 ATTTTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.11
Consensus pattern (13 bp):
CAGGCCTAACAAA
Found at i:5976830 original size:37 final size:40
Alignment explanation
Indices: 5976739--5976874 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 40
5976729 ACTAGTTTGG
* *
5976739 CACCCAGTACCTCATCGAATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAAATCGAAGTAATAAGTTGA
** * **
5976779 CATACAGTGTCTCATCGGCTAAATCGAAGT-A-AA-TTGA
1 CACCCAGTGCCTCATCGAATAAATCGAAGTAATAAGTTGA
* * * *
5976816 CACCCAGTGCCTCATCGAATTAATTTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAAATCGAAGTAATAAGTTGA
**
5976857 CACCCAGTGTATCATCGA
1 CACCCAGTGCCTCATCGA
5976875 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 18 0.24
38 11 0.15
39 1 0.01
40 25 0.33
41 20 0.27
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAAATCGAAGTAATAAGTTGA
Found at i:5976858 original size:41 final size:40
Alignment explanation
Indices: 5976739--5976874 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 40
5976729 ACTAGTTTGG
* * *
5976739 CACCCAGTACCTCATCGAATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
** * ** *
5976779 CATACAGTGTCTCATCGGCTAAATCG-A--AGTAAATTGA
1 CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
*
5976816 CACCCAGTGCCTCATCGAATTAATTTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATTCGAAGTAGTAAATTGA
**
5976857 CACCCAGTGTATCATCGA
1 CACCCAGTGCCTCATCGA
5976875 CTCGAAGTCG
Statistics
Matches: 74, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 22 0.30
38 5 0.07
39 2 0.03
40 19 0.26
41 26 0.35
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
Found at i:5980477 original size:18 final size:19
Alignment explanation
Indices: 5980451--5980486 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5980441 TAGACTAGAT
*
5980451 TTAACTCCCT-AATTTTAC
1 TTAAATCCCTAAATTTTAC
5980469 TTAAATCCCTAAATTTTA
1 TTAAATCCCTAAATTTTA
5980487 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATCCCTAAATTTTAC
Found at i:5981204 original size:6 final size:6
Alignment explanation
Indices: 5981193--5981226 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5981183 GAGTCGTTAC
5981193 AATTAT AATTAT AATTAT AATTAT AATTAT AATT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATT
5981227 CTGTGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:5981319 original size:18 final size:18
Alignment explanation
Indices: 5981296--5981330 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5981286 ATTTAATATA
5981296 TTATATAAAATAAATTTT
1 TTATATAAAATAAATTTT
* *
5981314 TTATATATAATTAATTT
1 TTATATAAAATAAATTT
5981331 GTATTCTCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATAAAATAAATTTT
Found at i:5982296 original size:23 final size:22
Alignment explanation
Indices: 5982269--5982326 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
5982259 TAGTTCATGG
5982269 AAAAATTAAAAAATATCTTGA-AA
1 AAAAATTAAAAAATA-CTT-ATAA
* *
5982292 TAAAAA-TAAGAACTACTTATAA
1 -AAAAATTAAAAAATACTTATAA
5982314 AAAAATTAAAAAA
1 AAAAATTAAAAAA
5982327 AAAATAGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 6 0.21
22 10 0.36
23 7 0.25
24 5 0.18
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.24
Consensus pattern (22 bp):
AAAAATTAAAAAATACTTATAA
Found at i:5986318 original size:15 final size:15
Alignment explanation
Indices: 5986298--5986327 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5986288 AAACATAATA
5986298 AATTAAATATAAAAT
1 AATTAAATATAAAAT
5986313 AATTAAATATAAAAT
1 AATTAAATATAAAAT
5986328 TATATATTCC
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):
AATTAAATATAAAAT
Found at i:5989913 original size:42 final size:43
Alignment explanation
Indices: 5989837--5989920 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
5989827 ATTCTAAGAT
*
5989837 AAATAATAACTAACTAAAATAATAAGTATATATCAATTATTTA
1 AAATAATAACTAACTAAAATAATAAATATATATCAATTATTTA
* *
5989880 AAATAATAATTAATTAAAA-AATAAATATATATCAATTATTT
1 AAATAATAACTAACTAAAATAATAAATATATATCAATTATTT
5989921 TGAGAATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (43 bp):
AAATAATAACTAACTAAAATAATAAATATATATCAATTATTTA
Done.