Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2476
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: 62231
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12490 original size:44 final size:44
Alignment explanation
Indices: 12349--12646 Score: 213
Period size: 44 Copynumber: 6.9 Consensus size: 44
12339 ATTATACAGG
* * * *
12349 TCTTATCTCCCTGAGATTACAGGGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
* ** *
12395 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
12439 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGTAGA
* * ** * *
12483 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG--G--G-
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
* ** * * **
12522 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG--G-
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGTAGA
* * * * *
12563 TCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
*
12609 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA
12647 CACTATCCTA
Statistics
Matches: 196, Mismatches: 43, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
38 1 0.01
39 25 0.13
41 31 0.16
42 1 0.01
44 71 0.36
45 2 0.01
46 64 0.33
47 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
Found at i:12750 original size:174 final size:170
Alignment explanation
Indices: 12436--12768 Score: 458
Period size: 174 Copynumber: 1.9 Consensus size: 170
12426 TTGAAGCCAG
* *
12436 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTTGAGATT
* * * *
12501 ACAATGGAGCGGATTAAAGGGTCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGAATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
12566 TATTTCCCTG-AGATTACAGTGGAACAGACCAAAGAATTTC
131 TATTTCCCTGAAGA-TACAGTGGAACAGACCAAAGAATTTC
*
12606 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTTCC-TGA-AG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATC-TCCTTGAGA-
* * * *
12668 TTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCAT
64 TTACAATGGAGCGAA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACAT
*
12733 CAAGTCTTATTTCCCTGAAGATGCAGTGGAACAGAC
124 CAAGTCTTATTTCCCTGAAGATACAGTGGAACAGAC
12769 TGAAAACAAG
Statistics
Matches: 143, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
168 1 0.01
169 24 0.17
170 46 0.32
174 69 0.48
175 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTTGAGATT
ACAATGGAGCGAATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATTTCCCTGAAGATACAGTGGAACAGACCAAAGAATTTC
Found at i:13314 original size:16 final size:16
Alignment explanation
Indices: 13293--13342 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
13283 AAACCCATTA
13293 CAACAAACCTAAAACC
1 CAACAAACCTAAAACC
* *
13309 CAACAAACCCAACACC
1 CAACAAACCTAAAACC
13325 CAA-ATAACCTAACAACC
1 CAACA-AACCTAA-AACC
13342 C
1 C
13343 TAGCCCAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 1 0.04
16 23 0.82
17 4 0.14
ACGTcount: A:0.52, C:0.42, G:0.00, T:0.06
Consensus pattern (16 bp):
CAACAAACCTAAAACC
Found at i:14524 original size:3 final size:3
Alignment explanation
Indices: 14516--14541 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14506 GATTTAGTCC
14516 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
14542 CCTACTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:18259 original size:23 final size:23
Alignment explanation
Indices: 18227--18274 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
18217 ATATACATAT
*
18227 AAATATGAAAATATTCATTAAAA
1 AAATAAGAAAATATTCATTAAAA
* *
18250 AAATAAGAAAATATTCGTTTAAA
1 AAATAAGAAAATATTCATTAAAA
18273 AA
1 AA
18275 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (23 bp):
AAATAAGAAAATATTCATTAAAA
Found at i:19092 original size:12 final size:11
Alignment explanation
Indices: 19068--19098 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
19058 GTTTCTTCCC
19068 TTTTATTTGT-
1 TTTTATTTGTG
19078 TTTTATTTGTG
1 TTTTATTTGTG
19089 TTTTATTTGT
1 TTTTATTTGT
19099 ATGTAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (11 bp):
TTTTATTTGTG
Found at i:21550 original size:19 final size:21
Alignment explanation
Indices: 21515--21560 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
21505 ATGCATGTAT
21515 ATAAAAACATAAAGTATAAAA
1 ATAAAAACATAAAGTATAAAA
21536 ATAAAAA-AT-AAGTATAAAA
1 ATAAAAACATAAAGTATAAAA
21555 ATAAAA
1 ATAAAA
21561 GTAACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
ATAAAAACATAAAGTATAAAA
Found at i:23147 original size:132 final size:132
Alignment explanation
Indices: 22960--23245 Score: 421
Period size: 132 Copynumber: 2.2 Consensus size: 132
22950 TGCAACGTCG
* * * * * *
22960 GGGAGATAGGATTTG-TGATCTTCAACCTACTCCCCTGCTGTTCAGGGAGACAAGGCTTGGTGGC
1 GGGAGATAAGATCTGCT-ATCTTCAACCTACTACACTGCTGCTCAGGGAGACAAGGCTGGGTGGC
* * * *
23024 CTAAATCTGCTTCCTACTATCTTGGAAAGATAATATTTGTCGTCTTCGATCTGCTCTACTACTGC
65 CTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTGC
23089 TTA
130 TTA
* * *
23092 GGGAGATAAGATCTGCTATCTTCAACCTACTACACTGCTGCTCGGGGAGATAAGGCTGGGTGGCT
1 GGGAGATAAGATCTGCTATCTTCAACCTACTACACTGCTGCTCAGGGAGACAAGGCTGGGTGGCC
*
23157 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCT
66 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTGCT
23222 TA
131 TA
*
23224 GAGAGATAAGATCTGCTATCTT
1 GGGAGATAAGATCTGCTATCTT
23246 TACTGATCTG
Statistics
Matches: 138, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
132 137 0.99
133 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (132 bp):
GGGAGATAAGATCTGCTATCTTCAACCTACTACACTGCTGCTCAGGGAGACAAGGCTGGGTGGCC
TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATCTTCGATCTGCTCCACTACTGCT
TA
Found at i:23246 original size:44 final size:44
Alignment explanation
Indices: 23066--23245 Score: 116
Period size: 44 Copynumber: 4.1 Consensus size: 44
23056 ATATTTGTCG
* * *
23066 TCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGCTA
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCTA
* * * * ** * * * *
23110 TCTTCAACCTACTACACTGCTGCTCGGGGAGATAAG-GCTGGGTG
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATCT-GCTA
* * * * *
23154 GCTTAAATCTGCTTCCCACTA-T-CTTGGAAAGATAAGATTTG-TCA
1 TCTTCAATCTGC-T-CCACTACTGCTTAGAGAGATAAGATCTGCT-A
**
23198 TCTTTGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCTA
1 TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCTA
23242 TCTT
1 TCTT
23246 TACTGATCTG
Statistics
Matches: 99, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
42 6 0.06
43 5 0.05
44 80 0.81
45 4 0.04
46 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGCTA
Found at i:29760 original size:19 final size:21
Alignment explanation
Indices: 29725--29770 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
29715 ATGCATGTAT
29725 ATAAAAACATAAAGTATAAAA
1 ATAAAAACATAAAGTATAAAA
29746 ATAAAAA-AT-AAGTATAAAA
1 ATAAAAACATAAAGTATAAAA
29765 ATAAAA
1 ATAAAA
29771 GTAACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
ATAAAAACATAAAGTATAAAA
Found at i:30983 original size:24 final size:24
Alignment explanation
Indices: 30956--31002 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30946 TTCCATTACT
30956 ATTATTATTA-CATTATTTACTATC
1 ATTATTATTATCA-TATTTACTATC
*
30980 ATTATTATTATCATATTTTCTAT
1 ATTATTATTATCATATTTACTAT
31003 ACATATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATCATATTTACTATC
Found at i:30993 original size:12 final size:12
Alignment explanation
Indices: 30956--30993 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30946 TTCCATTACT
30956 ATTATTATTA-C
1 ATTATTATTATC
*
30967 ATTATTTACTATC
1 ATTA-TTATTATC
30980 ATTATTATTATC
1 ATTATTATTATC
30992 AT
1 AT
30994 ATTTTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 14 0.61
13 5 0.22
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:31224 original size:16 final size:16
Alignment explanation
Indices: 31189--31223 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
31179 TTTTTTTCAC
*
31189 TTTTATATACTTTATA
1 TTTTATATACTATATA
31205 TTTTATATA-TATATA
1 TTTTATATACTATATA
31220 TTTT
1 TTTT
31224 TTGTAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATATACTATATA
Found at i:33017 original size:19 final size:19
Alignment explanation
Indices: 32993--33039 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
32983 AACGTCTCTT
*
32993 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
33012 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
33031 TATGCATTA
1 TTTGCATTA
33040 AACACCGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:35916 original size:14 final size:14
Alignment explanation
Indices: 35882--35923 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
35872 AATGATGAGA
*
35882 TGAAAAATGAAATAG
1 TGAAAAATGAAA-AC
35897 TG-AAAATGAAAAC
1 TGAAAAATGAAAAC
35910 TGAAAAATGGAAAA
1 TGAAAAAT-GAAAA
35924 GTAAAATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 14 0.58
15 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (14 bp):
TGAAAAATGAAAAC
Found at i:37297 original size:89 final size:89
Alignment explanation
Indices: 37133--37686 Score: 666
Period size: 89 Copynumber: 6.2 Consensus size: 89
37123 GGCAGGTTGA
* * * *
37133 AAGAAAGCAGATATTGTCTTCACGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
37198 CCATACTGGTGGCGAAGTAGATCG
66 CCATACTGGTGGCGAAGTAGATCG
* *
37222 AAGATAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTC
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
37287 CCATACTGGTGGCGAAGTAGATCG
66 CCATACTGGTGGCGAAGTAGATCG
* * *
37311 ATGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCATGTCTTC
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
* * * *
37376 CTATATTGGTAGCGAAGTGGATCG
66 CCATACTGGTGGCGAAGTAGATCG
*** * * *
37400 AAGAT-GCAGATCTTGTCTTCCCATACTGGTG-GCAAAGTAGATCGAAGAAAGCAGATCTTGTCT
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGATAGCAGATCTTGTCT
*** * * * *
37463 TCATGTA-TTGTCGTGAAGTAGATCA
64 TCCCATACTGGTGGCGAAGTAGATCG
* * * * * * *
37488 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAAATCTTGTCTT
1 AAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
37552 CCCATACTGGTGGCGAAGTAGATCG
65 CCCATACTGGTGGCGAAGTAGATCG
* *
37577 AAGAAAGAAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
** * ** * *
37642 CTGTATTGGCAGTGAAGTAGATCA
66 CCATACTGGTGGCGAAGTAGATCG
*
37666 AAGATAGTAGATCTTGTCTTC
1 AAGATAGCAGATCTTGTCTTC
37687 CCATATCGGT
Statistics
Matches: 395, Mismatches: 63, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.00
88 71 0.18
89 321 0.81
90 1 0.00
91 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (89 bp):
AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCG
Found at i:37373 original size:133 final size:133
Alignment explanation
Indices: 37166--37714 Score: 805
Period size: 133 Copynumber: 4.1 Consensus size: 133
37156 GTATTGGCGT
*** * * *
37166 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGATAGCA
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCA
* * * * *
37231 AATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTG
65 GATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGAT-GCAGATCTTGTCTTCCCATACTG
37295 GTGGC
129 GTGGC
*
37300 GAAGTAGATCGATGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
* * *
37365 ATCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGT
66 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATACTGGT
37430 GGC
131 GGC
* * *
37433 AAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGTCGTGAAGTAGATCAAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
* * * *
37498 ATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGT
66 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATACTGGT
37563 GGC
131 GGC
*
37566 GAAGTAGATCGAAGAAAGAAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
* * * *
37631 ATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCCATA-TCG
66 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGAT-GCAGATCTTGTCTTCCCATACT-G
37695 GTGGC
129 GTGGC
37700 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
37715 TACAAGTCTT
Statistics
Matches: 379, Mismatches: 33, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
133 289 0.76
134 90 0.24
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (133 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAG
ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATGCAGATCTTGTCTTCCCATACTGGT
GGC
Found at i:37662 original size:222 final size:222
Alignment explanation
Indices: 37133--37686 Score: 743
Period size: 222 Copynumber: 2.5 Consensus size: 222
37123 GGCAGGTTGA
* * *
37133 AAGAAAGCAGATATTGTCTTCACGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
*
37198 CCATACTGGTGGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* * * *
37263 TCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGATGAAAGCAGATCTTGT
131 TCAAAGATAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAAATCTTGT
** * *
37328 CTTCATGTATTGGCGTGAAGTAGATCG
196 CTTCACATACTGGCGCGAAGTAGATCG
* * * * * * *
37355 AAGATAGCAGATCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * *
37419 CCCATACTGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGTCGTGAAGTAG
65 CCCATACTGGTGGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
* * * *
37484 ATCAAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAG-ATGCAAATCTTG
130 ATCAAAGATAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAAATCTTG
* *
37548 TCTTCCCATACTGGTGGCGAAGTAGATCG
195 TCTTCACATACTGG-CGCGAAGTAGATCG
*
37577 AAGAAAGAAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
** * ** * * *
37642 CTGTATTGGCAGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTC
66 CCATACTGGTGGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
37687 CCATATCGGT
Statistics
Matches: 283, Mismatches: 46, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
221 36 0.13
222 232 0.82
223 15 0.05
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (222 bp):
AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TCAAAGATAGCAGATCCTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAAATCTTGT
CTTCACATACTGGCGCGAAGTAGATCG
Found at i:39235 original size:24 final size:24
Alignment explanation
Indices: 39208--39254 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39198 TTCCATTACT
39208 ATTATTATTA-CATTATTTACTATC
1 ATTATTATTATCA-TATTTACTATC
*
39232 ATTATTATTATCATATTTTCTAT
1 ATTATTATTATCATATTTACTAT
39255 ACATATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATCATATTTACTATC
Found at i:39245 original size:12 final size:12
Alignment explanation
Indices: 39208--39245 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39198 TTCCATTACT
39208 ATTATTATTA-C
1 ATTATTATTATC
*
39219 ATTATTTACTATC
1 ATTA-TTATTATC
39232 ATTATTATTATC
1 ATTATTATTATC
39244 AT
1 AT
39246 ATTTTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 14 0.61
13 5 0.22
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:40849 original size:13 final size:13
Alignment explanation
Indices: 40831--40857 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40821 GTATACAATA
40831 TGTGTGTTTTTTT
1 TGTGTGTTTTTTT
40844 TGTGTGTTTTTTT
1 TGTGTGTTTTTTT
40857 T
1 T
40858 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (13 bp):
TGTGTGTTTTTTT
Found at i:46790 original size:19 final size:17
Alignment explanation
Indices: 46753--46786 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46743 TCATTTGCCC
46753 GTGATTTTTTCTTGAAA
1 GTGATTTTTTCTTGAAA
46770 GTGATTTTTTCTTGAAA
1 GTGATTTTTTCTTGAAA
46787 AAGTTTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
GTGATTTTTTCTTGAAA
Found at i:46793 original size:16 final size:17
Alignment explanation
Indices: 46755--46793 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
46745 ATTTGCCCGT
**
46755 GATTTTTTCTTGAAAGT
1 GATTTTTTCTTGAAAAA
46772 GATTTTTTCTTGAAAAA
1 GATTTTTTCTTGAAAAA
46789 G-TTTT
1 GATTTT
46794 CACGTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (17 bp):
GATTTTTTCTTGAAAAA
Found at i:48564 original size:21 final size:21
Alignment explanation
Indices: 48511--48565 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
48501 AATTTTGAAG
48511 CACGAAATTTTTTTTTAAAAA
1 CACGAAATTTTTTTTTAAAAA
*
48532 -ATGAAAGTTTTTTTTTAAAAA
1 CACGAAA-TTTTTTTTTAAAAA
48553 CACGAGAATTTTT
1 CACGA-AATTTTT
48566 AAACACGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 5 0.17
21 14 0.48
22 8 0.28
23 2 0.07
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (21 bp):
CACGAAATTTTTTTTTAAAAA
Found at i:48614 original size:17 final size:17
Alignment explanation
Indices: 48543--49063 Score: 245
Period size: 17 Copynumber: 29.8 Consensus size: 17
48533 TGAAAGTTTT
*
48543 TTTTTAAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
48561 TTTTT-AAACACGGAAA
1 TTTTTAAAACACGAAAA
**
48577 TTTCAAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
48594 TTTTTAAAACACGACAT
1 TTTTTAAAACACGAAAA
* *
48611 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAAAA
* * *
48628 TTTTTAAAACAAGACAT
1 TTTTTAAAACACGAAAA
* **
48645 TTTTTGAAACAC-AATT
1 TTTTTAAAACACGAAAA
**
48661 TTTTTCTTAA-A--AAAA
1 TTTTT-AAAACACGAAAA
* *
48676 --TTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
48691 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
48708 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
48725 TTTTCAAAACACGGAAAT
1 TTTTTAAAACAC-GAAAA
***
48743 TTTTTAGAAA-ACGATTTT
1 TTTTTA-AAACACGA-AAA
* * *
48761 TTTTTAAATCACCG-GAG
1 TTTTTAAAACA-CGAAAA
48778 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
48796 TCTTTAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
*
48813 TTTTTGAAAACACGAAGA
1 TTTTT-AAAACACGAAAA
* **
48831 TTTTTGAAACACGAATTT
1 TTTTTAAAACACGAA-AA
* *
48849 TTTTTGAAAATACGAAGATT
1 TTTTT-AAAACACGAA-A-A
** *
48869 TTTTTTTAACACGGAAA
1 TTTTTAAAACACGAAAA
* ***
48886 TTTTTGAAACACGGTCATTT
1 TTTTTAAAACAC-G--AAAA
48906 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* **
48924 TTTTTGAAAGACATG-ATT
1 TTTTT-AAA-ACACGAAAA
* *
48942 TTTTTGAAAATACGGAAA
1 TTTTT-AAAACACGAAAA
*
48960 TTTATAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
48977 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-T-AAAACACGAAAA
* * *
48998 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
* *
49015 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAAAA
* * *
49032 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
49049 TTTTTAAAAGCACGA
1 TTTTTAAAA-CACGA
49064 GGATTATTGA
Statistics
Matches: 378, Mismatches: 94, Indels: 62
0.71 0.18 0.12
Matches are distributed among these distances:
12 2 0.01
13 4 0.01
15 5 0.01
16 20 0.05
17 201 0.53
18 86 0.23
19 30 0.08
20 13 0.03
21 17 0.04
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.34
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:48699 original size:97 final size:97
Alignment explanation
Indices: 48582--48858 Score: 256
Period size: 97 Copynumber: 2.8 Consensus size: 97
48572 GGAAATTTCA
* * * * * *
48582 AAAACACGAAAATTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAAACA-AGACATT
1 AAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTCAAAACACAGAAATT
48646 TTTT-GAAACACAATTTTTTTCTTAAAAAAATTT
66 TTTTAGAAA-ACAATTTTTTT-TTAAAAAAATTT
* * *
48679 AAAATACGAGAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTCAAAACACGGAAATT
1 AAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTCAAAACACAGAAATT
* **
48744 TTTTAGAAAACGATTTTTTTTTAAATCACCGGAGTTTTT
66 TTTTAGAAAACAATTTTTTTTTAAA--A----A-AATTT
* * **
48783 GAAAACACGAAAATCTTTAAAACACCG-AAATTTTTGAAAACACGAAGATTTTTGAAACAC-GAA
1 -AAAACACGAAAATTTTTAAAACA-CGAAAATTTTT-AAAACACGAAAATTTTCAAAACACAGAA
* *
48846 TTTTTTTTGAAAA
63 ATTTTTTAGAAAA
48859 TACGAAGATT
Statistics
Matches: 148, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
97 55 0.37
98 19 0.13
99 5 0.03
103 1 0.01
104 3 0.02
105 42 0.28
106 23 0.16
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (97 bp):
AAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTCAAAACACAGAAATT
TTTTAGAAAACAATTTTTTTTTAAAAAAATTT
Found at i:48945 original size:38 final size:36
Alignment explanation
Indices: 48691--49045 Score: 134
Period size: 36 Copynumber: 9.9 Consensus size: 36
48681 AATACGAGAA
* **
48691 TTTTT-AAAACACGAAAATTTTT-AAAACACGA-AA
1 TTTTTGAAAACACGAAAATTTTTGAAAACATGATTT
* * *
48724 ATTTTCAAAACACGGAAATTTTTTAGAAAAC--GATTT
1 TTTTTGAAAACAC-GAAAATTTTT-GAAAACATGATTT
* * * * * ***
48760 TTTTTTAAATCACCG-GAGTTTTTGAAAACACGAAAA
1 TTTTTGAAAACA-CGAAAATTTTTGAAAACATGATTT
* * ***
48796 TCTTT-AAAACACCG-AAATTTTTGAAAACACGAAGA
1 TTTTTGAAAACA-CGAAAATTTTTGAAAACATGATTT
** *
48831 TTTTTG-AAACACGAATTTTTTTTGAAAATACGAAGATTT
1 TTTTTGAAAACACGAA-AATTTTTG-AAA-AC-ATGATTT
* * * *
48870 TTTTT--TAACACGGAAATTTTTGAAACACGGTCATTT
1 TTTTTGAAAACACGAAAATTTTTGAAA-AC-ATGATTT
48906 TTTTTGAAAACACGAAAATTTTTGAAAGACATGA-TT
1 TTTTTGAAAACACGAAAATTTTTGAAA-ACATGATTT
* * * *
48942 TTTTTGAAAATACGGAAATTTAT-AAAACACGAAAATTT
1 TTTTTGAAAACACGAAAATTTTTGAAAACATG---ATTT
* *
48980 TTTCTGAAAACAAGAAAATTTTTG-AAACACTAGA---
1 TTTTTGAAAACACGAAAATTTTTGAAAACA-T-GATTT
* *
49014 ATTTTGAAAACACGAAGATTTTTG-AAACATGA
1 TTTTTGAAAACACGAAAATTTTTGAAAACATGA
49046 GAATTTTTAA
Statistics
Matches: 248, Mismatches: 51, Indels: 47
0.72 0.15 0.14
Matches are distributed among these distances:
32 2 0.01
33 5 0.02
34 44 0.18
35 56 0.23
36 59 0.24
37 19 0.08
38 54 0.22
39 8 0.03
40 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTTTGAAAACATGATTT
Found at i:49020 original size:16 final size:16
Alignment explanation
Indices: 48999--49052 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
48989 ACAAGAAAAT
48999 TTTTGAAACACTAGAA
1 TTTTGAAACACTAGAA
* *
49015 TTTTGAAAACACGAAGAT
1 TTTTG-AAACAC-TAGAA
49033 TTTTGAAACA-TGAGAA
1 TTTTGAAACACT-AGAA
49049 TTTT
1 TTTT
49053 TAAAAGCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 12 0.39
17 11 0.35
18 8 0.26
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (16 bp):
TTTTGAAACACTAGAA
Found at i:49250 original size:17 final size:16
Alignment explanation
Indices: 49216--49266 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
49206 AAAATTATTT
49216 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
49232 AAAATCAAATTAAATTA
1 AAAAT-AAAATAAAATA
49249 AAAATATAAATATAAATA
1 AAAATA-AAATA-AAATA
49267 TGCATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 18 0.64
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:49410 original size:10 final size:9
Alignment explanation
Indices: 49395--49452 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 9
49385 ATTGAACCTC
49395 TTTTTTCTT
1 TTTTTTCTT
49404 GTTTTTTC--
1 -TTTTTTCTT
49412 TTTTTTC-T
1 TTTTTTCTT
*
49420 TTTTCTC-T
1 TTTTTTCTT
*
49428 CTTTTTCTT
1 TTTTTTCTT
49437 TTTTTCTCTT
1 TTTTT-TCTT
49447 TTTTTT
1 TTTTTT
49453 TGCTGGGCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 7 0.17
8 12 0.29
9 6 0.15
10 16 0.39
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:49415 original size:17 final size:16
Alignment explanation
Indices: 49393--49450 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 16
49383 GAATTGAACC
49393 TCTTTTTTCTTGTTTTT
1 TCTTTTTTCTT-TTTTT
*
49410 TCTTTTTTC-TTTTTC
1 TCTTTTTTCTTTTTTT
49425 TCTCTTTTTCTTTTTTT
1 TCT-TTTTTCTTTTTTT
49442 CTCTTTTTT
1 -TCTTTTTT
49451 TTTGCTGGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.19
16 7 0.19
17 19 0.53
18 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (16 bp):
TCTTTTTTCTTTTTTT
Found at i:49432 original size:16 final size:15
Alignment explanation
Indices: 49405--49453 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
49395 TTTTTTCTTG
49405 TTTTTTCT-TTTTTC
1 TTTTTTCTCTTTTTC
49419 TTTTTCTCTCTTTTTC
1 TTTTT-TCTCTTTTTC
49435 TTTTTTTCTCTTTTT-
1 -TTTTTTCTCTTTTTC
49450 TTTT
1 TTTT
49454 GCTGGGCTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.28
15 3 0.09
16 15 0.47
17 5 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCTCTTTTTC
Found at i:49599 original size:23 final size:23
Alignment explanation
Indices: 49571--49616 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
49561 TGCATTTGGG
49571 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
49594 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
49617 GCTACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.04, T:0.70
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTTTTTT
Found at i:49762 original size:17 final size:18
Alignment explanation
Indices: 49742--49812 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
49732 TTTTTTATTA
49742 TTTCTTTTCTTT-TTCTT
1 TTTCTTTTCTTTCTTCTT
49759 TTTC-TTTCTTTCTTCTT
1 TTTCTTTTCTTTCTTCTT
**
49776 CCTCTTTTC-TTCTTCCTT
1 TTTCTTTTCTTTCTT-CTT
*
49794 CTTCTTCCTTC-TTCTTCTT
1 TTTCTT--TTCTTTCTTCTT
49813 CAAAGTCTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.15
17 16 0.35
18 12 0.26
19 3 0.07
20 8 0.17
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTTTCTTTCTTCTT
Found at i:49776 original size:3 final size:3
Alignment explanation
Indices: 49743--49813 Score: 65
Period size: 3 Copynumber: 23.0 Consensus size: 3
49733 TTTTTATTAT
* * *
49743 TTC TT- TTC TTT TTC TTT TTC TTTC TTTC TTC TTC CTC TT- TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC TTC
49788 TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TT-C TTC TTC TT-C TTC TTC TTC TTC
49814 AAAGTCTAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 40 0.70
4 13 0.23
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:49783 original size:28 final size:28
Alignment explanation
Indices: 49752--49809 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
49742 TTTCTTTTCT
* *
49752 TTTTCTTTTTCTTTCTTTCTT-CTTCCTC
1 TTTTCTTCTTCCTTC-TTCTTCCTTCCTC
*
49780 TTTTCTTCTTCCTTCTTCTTCCTTCTTC
1 TTTTCTTCTTCCTTCTTCTTCCTTCCTC
49808 TT
1 TT
49810 CTTCAAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTCTTCTTCCTTCTTCTTCCTTCCTC
Found at i:49797 original size:10 final size:10
Alignment explanation
Indices: 49782--49810 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
49772 TCTTCCTCTT
49782 TTCTTCTTCC
1 TTCTTCTTCC
49792 TTCTTCTTCC
1 TTCTTCTTCC
49802 TTCTTCTTC
1 TTCTTCTTC
49811 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:49806 original size:34 final size:34
Alignment explanation
Indices: 49744--49810 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
49734 TTTTATTATT
* * *
49744 TCTTTTCTTTTTCTTTTTCTTTCTTTCTTCTTCC
1 TCTTTTCTTTTCCTTCTTCTTTCCTTCTTCTTCC
49778 TCTTTTCTTCTTCCTTCTTC-TTCCTTCTTCTTC
1 TCTTTTCTT-TTCCTTCTTCTTTCCTTCTTCTTC
49811 TTCAAAGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (34 bp):
TCTTTTCTTTTCCTTCTTCTTTCCTTCTTCTTCC
Found at i:49904 original size:10 final size:10
Alignment explanation
Indices: 49869--49918 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
49859 ACGCCGGTAC
49869 TCTT-TCTTT
1 TCTTCTCTTT
* *
49878 TCTTCTCCTC
1 TCTTCTCTTT
49888 T-TTCTCTTT
1 TCTTCTCTTT
49897 TCTTCTCTTT
1 TCTTCTCTTT
*
49907 TCTTCTTTTT
1 TCTTCTCTTT
49917 TC
1 TC
49919 CCTCGAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:49916 original size:19 final size:19
Alignment explanation
Indices: 49873--49915 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
49863 CGGTACTCTT
49873 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
49892 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
49909 TTCTTTT
1 -TCTTTT
49916 TTCCCTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:50201 original size:29 final size:29
Alignment explanation
Indices: 50169--50284 Score: 85
Period size: 30 Copynumber: 3.9 Consensus size: 29
50159 GTAATTTTTA
*
50169 GAAAATTTAGGATTAAAATGAAATTTAAT
1 GAAAATTTAGGGTTAAAATGAAATTTAAT
* *
50198 GAAAGTTTAGGGGTCT-AAGTGAAATTTAAAT
1 GAAAATTTA-GGGT-TAAAATGAAATTT-AAT
* * *
50229 -AAAGTTTAAGGGTCAAAATGAAATTT-AG
1 GAAAATTT-AGGGTTAAAATGAAATTTAAT
* *
50257 GAAAAGTTTAGGGGTCAAAATGCAATTT
1 GAAAA-TTTA-GGGTTAAAATGAAATTT
50285 TTATTTTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
28 1 0.01
29 12 0.17
30 53 0.75
31 5 0.07
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (29 bp):
GAAAATTTAGGGTTAAAATGAAATTTAAT
Found at i:50223 original size:30 final size:30
Alignment explanation
Indices: 50183--50284 Score: 127
Period size: 30 Copynumber: 3.4 Consensus size: 30
50173 ATTTAGGATT
50183 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAATGAAAGTTTAGGGGTC
* * *
50213 TAAGTGAAATTTAAAT-AAAGTTTAAGGGTC
1 AAAATGAAATTT-AATGAAAGTTTAGGGGTC
*
50243 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAATG-AAAGTTTAGGGGTC
*
50273 AAAATGCAATTT
1 AAAATGAAATTT
50285 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.02
30 57 0.93
31 3 0.05
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAATGAAAGTTTAGGGGTC
Found at i:50741 original size:54 final size:55
Alignment explanation
Indices: 50555--50772 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
50545 CACGTGAGCC
* *
50555 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
50610 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
50661 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
50715 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
50770 AAG
1 AAG
50773 TAGAAATTGA
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 52 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:50770 original size:14 final size:14
Alignment explanation
Indices: 50751--50785 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
50741 GAGTTGATTT
50751 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
50765 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
50779 TTGAAAA
1 TTGAAAA
50786 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:51018 original size:85 final size:87
Alignment explanation
Indices: 50874--51121 Score: 308
Period size: 85 Copynumber: 2.8 Consensus size: 87
50864 AATAGAAATT
* * *
50874 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
50939 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
50961 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
51024 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
51050 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
51114 GTTGATTT
64 GTTGATTT
51122 TTGAAAAACA
Statistics
Matches: 138, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 3 0.02
89 31 0.22
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:51067 original size:15 final size:16
Alignment explanation
Indices: 51034--51067 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51024 TTGATTTTTG
* *
51034 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
51050 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
51066 AA
1 AA
51068 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:51109 original size:91 final size:88
Alignment explanation
Indices: 50874--51128 Score: 324
Period size: 91 Copynumber: 2.9 Consensus size: 88
50864 AATAGAAATT
* * *
50874 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
50939 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
50961 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
51024 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
51050 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
51114 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
51129 ACAAAAATTA
Statistics
Matches: 145, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 32 0.22
88 3 0.02
89 28 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:51272 original size:123 final size:123
Alignment explanation
Indices: 51051--51369 Score: 548
Period size: 123 Copynumber: 2.6 Consensus size: 123
51041 TAGATTGAAA
* * * ** * *
51051 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACATAAACTAAAAATACCTCGGC--GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
51116 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
64 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
51176 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
51241 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
66 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
51299 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
51364 ATTTTT
66 ATTTTT
51370 TTTAAAAAAT
Statistics
Matches: 185, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 162 0.88
125 23 0.12
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (123 bp):
AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
Found at i:51834 original size:190 final size:192
Alignment explanation
Indices: 51209--52011 Score: 1531
Period size: 191 Copynumber: 4.2 Consensus size: 192
51199 GGCGTGCCCC
51209 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
51274 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
51339 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGA-TTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
51403 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
51468 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
51533 ACTCACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
51594 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
51659 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACT-AAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
51723 ACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAATTTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
*
51784 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAATAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
51849 ACCTCTTGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
*
51914 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
*
51976 GAGGCTCAACTTATTTCTCGCAATATGAGTTGATTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
52012 CCTTGGAAAG
Statistics
Matches: 602, Mismatches: 4, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
190 181 0.30
191 203 0.34
192 63 0.10
193 122 0.20
194 33 0.05
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (192 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:51854 original size:381 final size:385
Alignment explanation
Indices: 51209--52011 Score: 1533
Period size: 381 Copynumber: 2.1 Consensus size: 385
51199 GGCGTGCCCC
51209 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
51274 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
51339 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTG
51404 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
195 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
51469 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
260 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
*
51534 CTCACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
325 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
51594 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
51659 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACT-AAAATACCTCGGCGTGCCCCGAGGCTCA
66 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
51723 ACTCACTTCTCGCAATATGAGTTGA-TTTTTTT-AAAAATTTAAAAATACCTCAACGTGTCTTGA
131 ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
*
51786 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAATAAAAATTAAAAGGCTTAACTCAC
196 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
*
51851 CTCTTGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
261 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
51916 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
326 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
*
51976 GAGGCTCAACTTATTTCTCGCAATATGAGTTGATTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
52012 CCTTGGAAAG
Statistics
Matches: 413, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
381 182 0.44
382 77 0.19
383 53 0.13
384 68 0.16
385 33 0.08
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (385 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
Found at i:51929 original size:69 final size:68
Alignment explanation
Indices: 51838--52005 Score: 167
Period size: 70 Copynumber: 2.4 Consensus size: 68
51828 AAAAATTAAA
* * * **
51838 AGGCTTAACTCACCTCTTGCAATATGAGTCA-ATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTCATATTTAAAA-A-AAACTAAAAATACCTCAACGTG
51902 CCCCG
64 CCCCG
* * * *
51907 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAG-TCA-TATTTAAAAAAAACTAAAAATACCTCAACGTG
* **
51972 TCTTG
64 CCCCG
* *
51977 AGGCTCAACTTATTTCTCGCAATATGAGT
1 AGGCTCAACTCACTTCTCGCAATATGAGT
52006 TGATTTCCTT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
69 26 0.32
70 49 0.60
71 1 0.01
72 6 0.07
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (68 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTCATATTTAAAAAAAACTAAAAATACCTCAACGTGCC
CCG
Found at i:60051 original size:17 final size:16
Alignment explanation
Indices: 60031--60511 Score: 146
Period size: 17 Copynumber: 28.3 Consensus size: 16
60021 TGAAAGTTTT
60031 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGA-AA
60048 TTTTT---ACACGGAAA
1 TTTTTAAAACAC-GAAA
**
60062 TTTCAAAAAACACGAAA
1 TTT-TTAAAACACGAAA
*
60079 GTTTTTAAAACACGACAT
1 -TTTTTAAAACACGA-AA
*
60097 TTTTTGAAACACGAAA
1 TTTTTAAAACACGAAA
* *
60113 TTTTTTAAAACAAGACA
1 -TTTTTAAAACACGAAA
* *
60130 TTTTTGAAACAC-AATT
1 TTTTTAAAACACGAA-A
*
60146 TTTTCTTAAA-A--AAA
1 TTTT-TAAAACACGAAA
*
60160 --TTT-AAATACGAGAA
1 TTTTTAAAACACGA-AA
60174 TTTTTAAAACACGAAAA
1 TTTTTAAAACACG-AAA
60191 TTTTTAAAACACGAAAA
1 TTTTTAAAACACG-AAA
* *
60208 TTTTTGAAAC-GGAAA
1 TTTTTAAAACACGAAA
**
60223 TTTTTTAGAAA-ACGATTT
1 -TTTTTA-AAACACGA-AA
**
60241 TTTTTAAAATCACCGGAGT
1 TTTTTAAAA-CA-C-GAAA
60260 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACG-AAA
*
60278 TCTTTAAAACACCGAAA
1 TTTTTAAAACA-CGAAA
*
60295 TTTTGAAAAACACGAAGA
1 TTTT-TAAAACACGAA-A
*
60313 TTTTT-GAACACGAAA
1 TTTTTAAAACACGAAA
*
60328 TTTTTTTGAAAATACGAAGA
1 --TTTTT-AAAACACGAA-A
** *
60348 TTTTTTTTAACACGGAA
1 -TTTTTAAAACACGAAA
* **
60365 TTTTT-AAACAAGGTCATTTT
1 TTTTTAAAAC-ACG--A--AA
60385 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACG-AAA
* **
60403 TTTTTGAAAGACATGATT
1 TTTTT-AAA-ACACGAAA
*
60421 TTTTTGAAAAC-GGAAA
1 TTTTT-AAAACACGAAA
*
60437 TTTATAAAACACGAAA
1 TTTTTAAAACACGAAA
* *
60453 TTTTTTCTGAAACAAGAAAA
1 --TTTT-TAAAACACG-AAA
* *
60473 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGA-AA
*
60490 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAA-A
60507 TTTTT
1 TTTTT
60512 GAACATGGGA
Statistics
Matches: 350, Mismatches: 63, Indels: 102
0.68 0.12 0.20
Matches are distributed among these distances:
10 3 0.01
11 2 0.01
12 2 0.01
13 1 0.00
14 11 0.03
15 17 0.05
16 55 0.16
17 143 0.41
18 61 0.17
19 33 0.09
20 16 0.05
21 2 0.01
22 4 0.01
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (16 bp):
TTTTTAAAACACGAAA
Found at i:60241 original size:94 final size:93
Alignment explanation
Indices: 60080--60249 Score: 227
Period size: 94 Copynumber: 1.8 Consensus size: 93
60070 AACACGAAAG
* * * * *
60080 TTTTTAAAACACGACATTTTTTGAAACACGAAATTTTTTAAAACAAGACATTTTTGAAACACAAT
1 TTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACAAGAAATTTTTGAAACACAAT
60145 TTTTTCTTAAAAAAATTTAAATACGAGAA
66 TTTTT-TTAAAAAAATTTAAATACGAGAA
* * *
60174 TTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTTGAAAC-GGAAATTTTTTAGAAA-ACG
1 TTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACAAGAAA-TTTTT-GAAACACA
60237 ATTTTTTTTAAAA
64 ATTTTTTTTAAAA
60250 TCACCGGAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 9 0.14
94 53 0.80
95 4 0.06
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (93 bp):
TTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACAAGAAATTTTTGAAACACAAT
TTTTTTTAAAAAAATTTAAATACGAGAA
Found at i:60332 original size:15 final size:16
Alignment explanation
Indices: 60303--60332 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60293 AATTTTGAAA
60303 AACACGAAGATTTTTG
1 AACACGAAGATTTTTG
60319 AACACGAA-ATTTTT
1 AACACGAAGATTTTT
60333 TTGAAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (16 bp):
AACACGAAGATTTTTG
Found at i:60369 original size:35 final size:34
Alignment explanation
Indices: 60260--60369 Score: 89
Period size: 35 Copynumber: 3.1 Consensus size: 34
60250 TCACCGGAGT
* ** *
60260 TTTTTG-AAAACACGAAAATCTTTAAAACACCGAA
1 TTTTTGAAAAACACGAAGAT-TTTTGAACACGGAA
* *
60294 ATTTTGAAAAACACGAAGATTTTTGAACACGAAA
1 TTTTTGAAAAACACGAAGATTTTTGAACACGGAA
* *
60328 TTTTTTTG-AAAATACGAAGATTTTTTTTAACACGGAA
1 --TTTTTGAAAAACACGAAGA--TTTTTGAACACGGAA
60365 TTTTT
1 TTTTT
60370 AAACAAGGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
34 15 0.25
35 28 0.46
36 5 0.08
37 13 0.21
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (34 bp):
TTTTTGAAAAACACGAAGATTTTTGAACACGGAA
Found at i:61560 original size:15 final size:14
Alignment explanation
Indices: 61534--61593 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
61524 AGAAGACAAG
*
61534 GAAGAAGAAGGAAA
1 GAAGAAAAAGGAAA
61548 GAAGAAAAGAGG-AA
1 GAAGAAAA-AGGAAA
61562 GAAGAAAAAAGAGAAA
1 GAAG-AAAAAG-GAAA
*
61578 AAAGAAAAA-GAAA
1 GAAGAAAAAGGAAA
61591 GAA
1 GAA
61594 AAATAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 6 0.15
14 15 0.38
15 13 0.33
16 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAGGAAA
Found at i:61571 original size:16 final size:16
Alignment explanation
Indices: 61545--61596 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
61535 AAGAAGAAGG
*
61545 AAAGAAGAAAAGAGGAA
1 AAAGAA-AAAAGAGAAA
*
61562 GAAGAAAAAAGAGAAA
1 AAAGAAAAAAGAGAAA
*
61578 AAAGAAAAAGAAAGAAA
1 AAAGAAAAA-AGAGAAA
61595 AA
1 AA
61597 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGAGAAA
Found at i:61580 original size:25 final size:24
Alignment explanation
Indices: 61532--61596 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
61522 AGAGAAGACA
* *
61532 AGGAAGAAGAAGGAAAGAAGAAAAG
1 AGGAAGAAGAA-AAAAGAAAAAAAG
61557 AGGAAGAAGAAAAAAGAGAAAAAAG
1 AGGAAGAAGAAAAAAGA-AAAAAAG
**
61582 AAAAAGAAAGAAAAA
1 AGGAAG-AAGAAAAA
61597 TAAAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.15
25 21 0.62
26 8 0.24
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (24 bp):
AGGAAGAAGAAAAAAGAAAAAAAG
Found at i:61705 original size:17 final size:18
Alignment explanation
Indices: 61673--61706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61663 GCCCAAGCAA
*
61673 AAAAAAAGAAACAAGCCC
1 AAAAAAACAAACAAGCCC
61691 AAAAAAACAAA-AAGCC
1 AAAAAAACAAACAAGCC
61707 AAAGCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.21, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAACAAGCCC
Found at i:61742 original size:22 final size:22
Alignment explanation
Indices: 61726--61766 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
61716 AAAAGTAGCT
61726 AAAAAAGAAGAAGAAAGAAGAG
1 AAAAAAGAAGAAGAAAGAAGAG
61748 AAAAAAGAAGAAG-AAGAAG
1 AAAAAAGAAGAAGAAAGAAG
61767 CAGGCGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAGAAAGAAGAG
Found at i:61749 original size:12 final size:13
Alignment explanation
Indices: 61730--61765 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
61720 GTAGCTAAAA
61730 AAGAAGAAGAAAG
1 AAGAAGAAGAAAG
*
61743 AAG-AGAAAAAAG
1 AAGAAGAAGAAAG
61755 AAGAAGAAGAA
1 AAGAAGAAGAA
61766 GCAGGCGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAAG
Found at i:61914 original size:8 final size:8
Alignment explanation
Indices: 61895--61946 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
61885 CAGCCCAGCA
61895 AAAAAAAG
1 AAAAAAAG
*
61903 AGAAAAA-
1 AAAAAAAG
*
61910 AAGAAAAG
1 AAAAAAAG
*
61918 AGAAAAAG
1 AAAAAAAG
*
61926 AAATAAAG
1 AAAAAAAG
*
61934 AAAAACAG
1 AAAAAAAG
61942 AAAAA
1 AAAAA
61947 GAGGTTATTC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 5 0.15
8 29 0.85
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:61933 original size:16 final size:15
Alignment explanation
Indices: 61896--61946 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
61886 AGCCCAGCAA
61896 AAAAAAGAGAAAAA-
1 AAAAAAGAGAAAAAG
61910 AAGAAAAGAGAAAAAG
1 AA-AAAAGAGAAAAAG
61926 AAATAAAGA-AAAACAG
1 AAA-AAAGAGAAAA-AG
61942 AAAAA
1 AAAAA
61947 GAGGTTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 2 0.06
15 19 0.58
16 12 0.36
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAAGAGAAAAAG
Found at i:61933 original size:21 final size:22
Alignment explanation
Indices: 61897--61948 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
61887 GCCCAGCAAA
61897 AAAAAGAGAAAAAAAGAAAAGA-
1 AAAAA-AGAAAAAAAGAAAAGAC
* *
61919 GAAAAAGAAATAAAGAAAA-AC
1 AAAAAAGAAAAAAAGAAAAGAC
61940 AGAAAAAGA
1 A-AAAAAGA
61949 GGTTATTCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAAAAGAAAAGAC
Found at i:61943 original size:22 final size:21
Alignment explanation
Indices: 61898--61948 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
61888 CCCAGCAAAA
*
61898 AAAAGAGAAAAAAAGAAAAGAG
1 AAAA-AGAAAAAAAGAAAACAG
*
61920 AAAAAGAAATAAAGAAAAACAG
1 AAAAAGAAAAAAAG-AAAACAG
61942 AAAAAGA
1 AAAAAGA
61949 GGTTATTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAAAAGAAAACAG
Done.