Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 49 of 135
Found at i:12965430 original size:43 final size:43
Alignment explanation
Indices: 12965376--12965492 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
12965366 ATTTTCTCAA
*
12965376 CTCATTTCGAGTCACGAGTCTTCCTTTTAAATAAATTCTCATG
1 CTCATTACGAGTCACGAGTCTTCCTTTTAAATAAATTCTCATG
* *
12965419 CTCATTACGAGTCACGAGTCTTCTTTTTATATAAATTCTCATG
1 CTCATTACGAGTCACGAGTCTTCCTTTTAAATAAATTCTCATG
* * *
12965462 CTCATTCCAAGTCACGAGTCTTCCATTTAAA
1 CTCATTACGAGTCACGAGTCTTCCTTTTAAA
12965493 CATCAAGTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.38
Consensus pattern (43 bp):
CTCATTACGAGTCACGAGTCTTCCTTTTAAATAAATTCTCATG
Found at i:12967819 original size:17 final size:17
Alignment explanation
Indices: 12967797--12967834 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
12967787 CCTAGGAAAA
12967797 CACCCAAAAACCTTTAT
1 CACCCAAAAACCTTTAT
12967814 CACCCAAAAACCTTTAT
1 CACCCAAAAACCTTTAT
12967831 CACC
1 CACC
12967835 TTTATCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (17 bp):
CACCCAAAAACCTTTAT
Found at i:12968635 original size:23 final size:23
Alignment explanation
Indices: 12968606--12968889 Score: 397
Period size: 23 Copynumber: 12.3 Consensus size: 23
12968596 CTTATATATT
* *
12968606 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* * * *
12968629 TGATTAAATATTATTGAGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
12968652 TGCTTAAATATCAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
12968675 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
12968698 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12968721 TGATTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
12968744 TACTCAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
12968767 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
12968790 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
12968813 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12968836 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
12968859 TGATTAAATATCAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
12968882 TGGTTAAA
1 TGCTTAAA
12968890 GAATTAAGAT
Statistics
Matches: 234, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 234 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:12982823 original size:19 final size:19
Alignment explanation
Indices: 12982775--12982845 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
12982765 ATTTTAAAAT
*
12982775 CAAGTTAAAATGATTTTAA
1 CAAGTCAAAATGATTTTAA
*
12982794 CCAAGTCAAAATCATTTTAA
1 -CAAGTCAAAATGATTTTAA
*
12982814 CAAATCAAAATGATTTTCAAA
1 CAAGTCAAAATGATTTT--AA
12982835 CAAGTCAAAAT
1 CAAGTCAAAAT
12982846 TGCTCTAGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 15 0.34
20 17 0.39
21 12 0.27
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (19 bp):
CAAGTCAAAATGATTTTAA
Found at i:12982842 original size:21 final size:20
Alignment explanation
Indices: 12982765--12982845 Score: 92
Period size: 19 Copynumber: 4.0 Consensus size: 20
12982755 TTTTGCAACA
*
12982765 ATTTTAAAATCAAGTTAAAATG
1 ATTTT-AAA-CAAGTCAAAATG
* *
12982787 ATTTTAACCAAGTCAAAATC
1 ATTTTAAACAAGTCAAAATG
*
12982807 ATTTT-AACAAATCAAAATG
1 ATTTTAAACAAGTCAAAATG
12982826 ATTTTCAAACAAGTCAAAAT
1 ATTTT-AAACAAGTCAAAAT
12982846 TGCTCTAGGC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.32
20 15 0.30
21 14 0.28
22 5 0.10
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.32
Consensus pattern (20 bp):
ATTTTAAACAAGTCAAAATG
Found at i:13002386 original size:18 final size:19
Alignment explanation
Indices: 13002339--13002386 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
13002329 GAAGAAGCAG
13002339 GAGAAGAAGAAAGAAAAGTA
1 GAGAAGAA-AAAGAAAAGTA
13002359 GAGAAGGAAAAAGAAGAAG-A
1 GAGAA-GAAAAAGAA-AAGTA
13002379 G-GAAGAAA
1 GAGAAGAAA
13002387 TTGCCCCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.15
19 3 0.12
20 13 0.50
21 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (19 bp):
GAGAAGAAAAAGAAAAGTA
Found at i:13003347 original size:50 final size:50
Alignment explanation
Indices: 13003272--13003372 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
13003262 TGCAAGTGTT
13003272 AGAAAAATTATCTAGCCAAAGGCTATCACTACAAGAGTGTGTGTCGACGC
1 AGAAAAATTATCTAGCCAAAGGCTATCACTACAAGAGTGTGTGTCGACGC
13003322 AGAAAAATTATCTAGCCAAAGGCTATCACTACAAGAGTGTGTGTCGACGC
1 AGAAAAATTATCTAGCCAAAGGCTATCACTACAAGAGTGTGTGTCGACGC
13003372 A
1 A
13003373 ATTACATGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (50 bp):
AGAAAAATTATCTAGCCAAAGGCTATCACTACAAGAGTGTGTGTCGACGC
Found at i:13009473 original size:18 final size:19
Alignment explanation
Indices: 13009452--13009488 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13009442 TCGATACCAA
*
13009452 TTTA-AAAATATTGATACT
1 TTTATAAAATATCGATACT
13009470 TTTATAAAATATCGATACT
1 TTTATAAAATATCGATACT
13009489 CGTGGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (19 bp):
TTTATAAAATATCGATACT
Found at i:13011506 original size:20 final size:19
Alignment explanation
Indices: 13011483--13011541 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
13011473 AGTTAAAATT
13011483 ATTTTAACCAAGTCAGAATC
1 ATTTTAA-CAAGTCAGAATC
* * *
13011503 ATTTTAACAAATCAAAATG
1 ATTTTAACAAGTCAGAATC
*
13011522 ATTTTCAAACAAGTTAGAAT
1 ATTTT--AACAAGTCAGAAT
13011542 TGCTCCAGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.45
20 7 0.23
21 10 0.32
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (19 bp):
ATTTTAACAAGTCAGAATC
Found at i:13013722 original size:28 final size:28
Alignment explanation
Indices: 13013682--13013747 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
13013672 AATATTCTTC
13013682 CACTTAGACTATCCACAACTTTGACTTG
1 CACTTAGACTATCCACAACTTTGACTTG
* * * * *
13013710 CACTTGGACTATCCGCCAGTTTGGCTTG
1 CACTTAGACTATCCACAACTTTGACTTG
13013738 CACTTAGACT
1 CACTTAGACT
13013748 GTTTGGCACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (28 bp):
CACTTAGACTATCCACAACTTTGACTTG
Found at i:13014190 original size:12 final size:12
Alignment explanation
Indices: 13014173--13014197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13014163 CAAGATGTAA
13014173 CACCCCTAACCC
1 CACCCCTAACCC
13014185 CACCCCTAACCC
1 CACCCCTAACCC
13014197 C
1 C
13014198 TCTCCGTCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.68, G:0.00, T:0.08
Consensus pattern (12 bp):
CACCCCTAACCC
Found at i:13020028 original size:24 final size:24
Alignment explanation
Indices: 13020001--13020189 Score: 270
Period size: 24 Copynumber: 7.9 Consensus size: 24
13019991 ACAGACAATA
13020001 TTAGCTCTTACGAGCCCAGAACGG
1 TTAGCTCTTACGAGCCCAGAACGG
*
13020025 TTAGCTCTTACGAGCCTAGAACGG
1 TTAGCTCTTACGAGCCCAGAACGG
* ** *
13020049 TTAGCTCCTATAAGCCCAAAACGG
1 TTAGCTCTTACGAGCCCAGAACGG
* * *
13020073 TTAACTCTTATGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAACGG
13020097 TTAGCTCTTACGAGCCCAGAACGG
1 TTAGCTCTTACGAGCCCAGAACGG
* *
13020121 TTAGCTCTTACAAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAACGG
* *
13020145 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAACGG
13020169 TTAGCTCTTACGAGCCCAGAA
1 TTAGCTCTTACGAGCCCAGAA
13020190 TCAAAACAAC
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 146 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAACGG
Found at i:13023190 original size:15 final size:17
Alignment explanation
Indices: 13023169--13023206 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
13023159 ATACAAGACC
*
13023169 TTATATG-TAAAGTTTA
1 TTATATGATAAAATTTA
13023185 -TATATGATAAAATTTA
1 TTATATGATAAAATTTA
13023201 TTATAT
1 TTATAT
13023207 AACATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
TTATATGATAAAATTTA
Found at i:13023213 original size:14 final size:16
Alignment explanation
Indices: 13023170--13023214 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
13023160 TACAAGACCT
*
13023170 TATATG-TAAAGTTTA
1 TATATGATAAAATTTA
13023185 TATATGATAAAATTTA
1 TATATGATAAAATTTA
*
13023201 T-TAT-ATAACATTTA
1 TATATGATAAAATTTA
13023215 AATAATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 9 0.33
16 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (16 bp):
TATATGATAAAATTTA
Found at i:13029913 original size:41 final size:41
Alignment explanation
Indices: 13029810--13030177 Score: 320
Period size: 42 Copynumber: 8.9 Consensus size: 41
13029800 AAAGGTAAAA
* * * * *
13029810 CATTAGCGGCGCTTT-TCTTAATGCGCCGCAAAAGGTAAAG-
1 CATTAGCGGCGCTTTCACTCAA-GCGCCGCTAAAGGTCAGGT
* *
13029850 CATTAGCGG-GCTTTCCCTCAAGCGCCGCTAAAGGCCAGGT
1 CATTAGCGGCGCTTTCACTCAAGCGCCGCTAAAGGTCAGGT
* * * *
13029890 AATTAGCGGCGCTTTAACTCAAGCACCGCTAAAGGT-ATGAT
1 CATTAGCGGCGCTTTCACTCAAGCGCCGCTAAAGGTCA-GGT
* * * * * *
13029931 CATTAGCAGCGCTTTCCCTGAAGCGCCACGAAAAGGTCGGGT
1 CATTAGCGGCGCTTTCACTCAAGCGCCGC-TAAAGGTCAGGT
*
13029973 CATTAGCGGCGCTTTCATTCAAGCGCCGCTAAAGGT-AGGAT
1 CATTAGCGGCGCTTTCACTCAAGCGCCGCTAAAGGTCAGG-T
* * *
13030014 CATTTAGTGGCGCTTTCATTCAAGCGCCGCTAAAAGGTCGGGT
1 CA-TTAGCGGCGCTTTCACTCAAGCGCCGCT-AAAGGTCAGGT
* * *
13030057 CATTAGCGGCGCTTTTC-CTCAAGTGCCGCTAAAGTTCGGGT
1 CATTAGCGGCGC-TTTCACTCAAGCGCCGCTAAAGGTCAGGT
* *
13030098 CATTAGCGGCGCTTAT-ATATAAAGCGCCGCTAAAGAGTCAGGT
1 CATTAGCGGCGCTT-TCA-CTCAAGCGCCGCTAAAG-GTCAGGT
* *
13030141 CATTAGCGGCGCTTTTCTAAT-AAGCGTCGCTAAAGGT
1 CATTAGCGGCGC-TTTC-ACTCAAGCGCCGCTAAAGGT
13030178 GTGAATTAGC
Statistics
Matches: 269, Mismatches: 41, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
39 19 0.07
40 26 0.10
41 78 0.29
42 95 0.35
43 44 0.16
44 6 0.02
45 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (41 bp):
CATTAGCGGCGCTTTCACTCAAGCGCCGCTAAAGGTCAGGT
Found at i:13030068 original size:84 final size:83
Alignment explanation
Indices: 13029810--13030196 Score: 357
Period size: 84 Copynumber: 4.7 Consensus size: 83
13029800 AAAGGTAAAA
* * * * *
13029810 CATTAGCGGCGCTTTT--CTTAATGCGCCGCAAAAGGTA-AAGCATTAGCGG-GCTTTCCCTCAA
1 CATTAGCGGCGCTTTTCACTCAA-GCGCCGCTAAAGGTAGGATCATTAGCGGCGCTTTCACTCAA
*
13029871 GCGCCGCTAAAGGCCAGGT
65 GCGCCGCTAAAGGTCAGGT
* * * * * * *
13029890 AATTAGCGGCGC-TTTAACTCAAGCACCGCTAAAGGTATGATCATTAGCAGCGCTTTCCCTGAAG
1 CATTAGCGGCGCTTTTCACTCAAGCGCCGCTAAAGGTAGGATCATTAGCGGCGCTTTCACTCAAG
* * *
13029954 CGCCACGAAAAGGTCGGGT
66 CGCCGC-TAAAGGTCAGGT
* * *
13029973 CATTAGCGGCGC-TTTCATTCAAGCGCCGCTAAAGGTAGGATCATTTAGTGGCGCTTTCATTCAA
1 CATTAGCGGCGCTTTTCACTCAAGCGCCGCTAAAGGTAGGATCA-TTAGCGGCGCTTTCACTCAA
*
13030037 GCGCCGCTAAAAGGTCGGGT
65 GCGCCGCT-AAAGGTCAGGT
* * * * * *
13030057 CATTAGCGGCGCTTTTC-CTCAAGTGCCGCTAAAGTTCGGGTCATTAGCGGCGCTTAT-ATATAA
1 CATTAGCGGCGCTTTTCACTCAAGCGCCGCTAAAGGTAGGATCATTAGCGGCGCTT-TCA-CTCA
13030120 AGCGCCGCTAAAGAGTCAGGT
64 AGCGCCGCTAAAG-GTCAGGT
* *
13030141 CATTAGCGGCGCTTTTCTAAT-AAGCGTCGCTAAAGGT-GTGA--ATTAGCGGCGCTTTC
1 CATTAGCGGCGCTTTTC-ACTCAAGCGCCGCTAAAGGTAG-GATCATTAGCGGCGCTTTC
13030197 CCATAAGCGC
Statistics
Matches: 254, Mismatches: 38, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
79 3 0.01
80 24 0.09
81 13 0.05
82 18 0.07
83 76 0.30
84 101 0.40
85 18 0.07
86 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (83 bp):
CATTAGCGGCGCTTTTCACTCAAGCGCCGCTAAAGGTAGGATCATTAGCGGCGCTTTCACTCAAG
CGCCGCTAAAGGTCAGGT
Found at i:13032287 original size:42 final size:42
Alignment explanation
Indices: 13032170--13032290 Score: 215
Period size: 43 Copynumber: 2.9 Consensus size: 42
13032160 AGGACTGGAA
*
13032170 AATTTTAAACCCTTGTTCTGCTCTTACTACTATAGTTGATTG
1 AATTTTAAACCCTTGTTCTGCTCTTACTGCTATAGTTGATTG
*
13032212 AATTTTAAACCGTTGTTTCTGCTCTTACTGCTATAGTTGATTG
1 AATTTTAAACCCTTG-TTCTGCTCTTACTGCTATAGTTGATTG
13032255 AATTTTAAACCCTTGTTCTGCTCTTACTGCTATAGT
1 AATTTTAAACCCTTGTTCTGCTCTTACTGCTATAGT
13032291 CGGTTATGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
42 35 0.47
43 40 0.53
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.45
Consensus pattern (42 bp):
AATTTTAAACCCTTGTTCTGCTCTTACTGCTATAGTTGATTG
Found at i:13035208 original size:66 final size:66
Alignment explanation
Indices: 13035134--13035485 Score: 264
Period size: 66 Copynumber: 5.2 Consensus size: 66
13035124 ATTTAATTAT
*
13035134 TAATTATATTAAAGTAAATGATTATATTAAATTAAATATTTAATTATTTAATTATATTAAACTAA
1 TAATTATATTAAAGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAACTAA
13035199 A
66 A
* ** * * * ** ** * *
13035200 TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATT-AAT
1 TAATTATATTAAAGTAAATAATTATATTAAATTAAATATTTAATTATTTA-ATTAT--ATTAAAC
13035264 TAAA
63 TAAA
* * * * *
13035268 TATTTA-AGTTAAAGATTTAATATTTAATTATATTAAAGTAAATGA-TTATATTAAGTTAA-AAG
1 TAATTATA-TTAAAG---TAA-A--TAATTATATTAAATTAAAT-ATTTA-ATT-ATTTAATTAT
* * **
13035330 ATTTAATTATT
56 ATTAAACTAAA
* * * *
13035341 TAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTA
1 TAATTATATTAAAGTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAACTA
13035406 AA
65 AA
* * * *
13035408 TAATTATATTAAA-TTAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
1 TAATTATATTAAAGTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAACTA
13035472 AA
65 AA
13035474 TAATTATATTAA
1 TAATTATATTAA
13035486 GTTATTTAAT
Statistics
Matches: 221, Mismatches: 47, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
66 104 0.47
67 42 0.19
68 22 0.10
69 4 0.02
70 3 0.01
71 2 0.01
72 3 0.01
73 16 0.07
74 18 0.08
75 5 0.02
76 2 0.01
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (66 bp):
TAATTATATTAAAGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAACTAA
A
Found at i:13035221 original size:18 final size:18
Alignment explanation
Indices: 13035013--13035495 Score: 111
Period size: 18 Copynumber: 27.8 Consensus size: 18
13035003 TATCAGCTTG
13035013 ATTATAATTATTTAATTAT
1 ATTA-AATTATTTAATTAT
* **
13035032 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
13035050 ATTAAATTA-TTAATCAT
1 ATTAAATTATTTAATTAT
*
13035067 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
13035089 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
13035104 ATT-AA-TATTTAAGTTAAAAG
1 ATTAAATTATTTAA-TT---AT
*
13035124 ATTTAATTA-TTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
13035141 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
13035159 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
13035173 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
13035189 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
13035207 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
13035225 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
13035247 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
13035262 ATTAAA-TATTTAAGTTAAAG
1 ATTAAATTATTTAA-TT--AT
*
13035282 ATTTAA-TATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
13035299 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
13035317 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
13035330 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
13035348 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
13035366 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
13035379 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
13035397 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
13035415 ATTAAATTA-ATAATTAT
1 ATTAAATTATTTAATTAT
* **
13035432 ATT-AA-T-TTAAAAGAT
1 ATTAAATTATTTAATTAT
13035447 A-T-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
13035463 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
13035481 ATTAAGTTATTTAAT
1 ATTAAATTATTTAAT
13035496 CATGTTTAAT
Statistics
Matches: 333, Mismatches: 82, Indels: 99
0.65 0.16 0.19
Matches are distributed among these distances:
12 5 0.02
13 18 0.05
14 8 0.02
15 19 0.06
16 32 0.10
17 42 0.13
18 145 0.44
19 16 0.05
20 19 0.06
21 10 0.03
22 19 0.06
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTAAATTATTTAATTAT
Found at i:13035260 original size:158 final size:158
Alignment explanation
Indices: 13035012--13035370 Score: 625
Period size: 158 Copynumber: 2.3 Consensus size: 158
13035002 ATATCAGCTT
13035012 GATTATAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTAATCATGTTTAATTAT
1 GATT-TAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTAATCATGTTTAATTAT
13035077 GTATTTAATTATAAACACTATCGATTAATT-AATATTTAAGTTAAAAGATTTAAT-TATTAATTA
65 GTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTT-AAAGATTTAATAT-TTAATTA
13035140 TATTAAAGTAAATGATTATATTAAATT-AAA
128 TATTAAAGTAAATGATTATATTAAATTAAAA
*
13035170 TATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTAT
1 GATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTA-TTAATCATGTTTAATTAT
13035235 GTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAGATTTAATATTTAATTATA
65 GTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAGATTTAATATTTAATTATA
*
13035300 TTAAAGTAAATGATTATATTAAGTTAAAA
130 TTAAAGTAAATGATTATATTAAATTAAAA
* *
13035329 GATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAA
1 GATTTAATTATTTAATTATATTAAACTAAATAATTATATTAA
13035371 GTTAAAAGAT
Statistics
Matches: 192, Mismatches: 5, Indels: 7
0.94 0.02 0.03
Matches are distributed among these distances:
157 42 0.22
158 95 0.49
159 55 0.29
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (158 bp):
GATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTAATCATGTTTAATTATG
TATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAGATTTAATATTTAATTATAT
TAAAGTAAATGATTATATTAAATTAAAA
Found at i:13035396 original size:31 final size:31
Alignment explanation
Indices: 13035361--13035467 Score: 117
Period size: 31 Copynumber: 3.3 Consensus size: 31
13035351 AAAGTAAATG
13035361 ATTATATTAAGTTAAAAGATTTAATTATTTA
1 ATTATATTAAGTTAAAAGATTTAATTATTTA
* * *
13035392 ATTATATTAAAGTAAATAATTATATTAAATTA-ATA
1 ATTATATT-AAGTTAA-AA-GAT-TT-AATTATTTA
* *
13035427 ATTATATTAATTTAAAAGATATAATTATTTA
1 ATTATATTAAGTTAAAAGATTTAATTATTTA
13035458 ATTATATTAA
1 ATTATATTAA
13035468 ACTAAATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
30 5 0.08
31 21 0.34
32 8 0.13
33 4 0.06
34 7 0.11
35 12 0.19
36 5 0.08
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.47
Consensus pattern (31 bp):
ATTATATTAAGTTAAAAGATTTAATTATTTA
Found at i:13035437 original size:26 final size:26
Alignment explanation
Indices: 13035408--13035494 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
13035398 TTAAAGTAAA
*
13035408 TAATTATATTAAATTAATAATTATAT
1 TAATTATATTAAATAAATAATTATAT
* *
13035434 TAATT-TA--AAAGATATAATTAT-T
1 TAATTATATTAAATAAATAATTATAT
13035456 TAATTATATTAAACTAAATAATTATAT
1 TAATTATATTAAA-TAAATAATTATAT
13035483 TAAGTTAT-TTAA
1 TAA-TTATATTAA
13035495 TCATGTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
22 6 0.12
23 13 0.26
25 5 0.10
26 14 0.28
27 8 0.16
28 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (26 bp):
TAATTATATTAAATAAATAATTATAT
Found at i:13035441 original size:49 final size:49
Alignment explanation
Indices: 13035102--13035424 Score: 289
Period size: 49 Copynumber: 6.3 Consensus size: 49
13035092 CACTATCGAT
*
13035102 TAATTAATATTTAAGTTAAAAGATTTAATTA-TTAATTATATTAAAGTAAA
1 TAATT-ATA-TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
* * *
13035152 TGATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAACTAAA
1 TAATTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
* * ** *
13035200 TAATTATATTAAATTATTTAATCATG-TTTAATTATGTATTTA-ATTATAAACACTA
1 TAATTATATTAAATTA---AA--A-GATTTAATTATTTAATTATATTA-AAGTA-AA
* * * *
13035255 TCGATTA-ATTAAATATTTAAGTTAA-AGATTTAATATTTAATTATATTAAAGTAAA
1 T-AATTATATT-AA-A-TTAA---AAGA-TTTAATTATTTAATTATATTAAAGTAAA
* *
13035310 TGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
* *
13035359 TGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
13035408 TAATTATATTAAATTAA
1 TAATTATATTAAATTAA
13035425 TAATTATATT
Statistics
Matches: 225, Mismatches: 26, Indels: 45
0.76 0.09 0.15
Matches are distributed among these distances:
47 12 0.05
48 38 0.17
49 94 0.42
50 5 0.02
52 6 0.03
53 4 0.02
54 25 0.11
55 11 0.05
56 21 0.09
57 5 0.02
58 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (49 bp):
TAATTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
Found at i:13035503 original size:274 final size:272
Alignment explanation
Indices: 13035134--13035944 Score: 1242
Period size: 274 Copynumber: 3.0 Consensus size: 272
13035124 ATTTAATTAT
* * * *
13035134 TAATTATATTAAAGTAAATGATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAACTA
1 TAATTATATTAAA-TAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
13035198 AATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
65 AATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
13035263 TTAAATATTTAAGTT-AAAGATTTAA-TATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
130 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
13035326 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTT
195 AAAGATTTAATTATTTAATTATATTAAAGTAAAT-ATTATATTAA-TT-AAAGATTTAATTATTT
13035391 AATTATATTAAAGTAAA
257 AATTATATTAAAGT-AA
*
13035408 TAATTATATTAAATTAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAA
1 TAATTATATTAAATAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAA
* *
13035473 ATAATTATATTAAGTTATTTAATCATGTTTAATTTTGTATTTAATTATAAACACTATCGATTAAT
66 ATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAAT
13035538 TAAATATTTAAGTTTAAAAGATTTAATTATTT-ATTATATTAAAGTAAATGATTATATTAAGTTA
131 TAAATATTTAAG-TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
* *
13035602 AAAGATTTAATCATTTAATTATATTAAAGTAAATA--ATA-T-ATT-AA-A-TTAAATATTTAA-
195 AAAGATTTAATTATTTAATTATATTAAAGTAAATATTATATTAATTAAAGATTTAATTATTTAAT
13035659 T-TA-T----T--
260 TATATTAAAGTAA
* *
13035664 TAATTATATTAAGTAAATAAGTATATTAATTTAAAAGATAT-ATTATTTAATTATATTAAACTAA
1 TAATTATATTAAATAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAA
*
13035728 ATGATTATATTAAATTATTTTAATCATG-TT-ATTATGTATTTAATTATAAACACTATCGATTAA
66 ATAATTATATTAAATTA-TTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
*
13035791 TTAAATA-TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTCTATTAAGTTA
130 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
13035855 AAAGATTTAATTATTTAATTATATT-AAGTAAATCATTATATTAAATTAAAGATTTAATTATTTA
195 AAAGATTTAATTATTTAATTATATTAAAGTAAAT-ATTATATT-AATTAAAGATTTAATTATTTA
13035919 ATTATATTAAAG-AA
258 ATTATATTAAAGTAA
13035933 TAATTATATTAA
1 TAATTATATTAA
13035945 GTTAAAAGAT
Statistics
Matches: 495, Mismatches: 18, Indels: 53
0.87 0.03 0.09
Matches are distributed among these distances:
252 27 0.05
253 61 0.12
254 39 0.08
255 43 0.09
256 49 0.10
258 3 0.01
259 3 0.01
260 1 0.00
261 11 0.02
262 1 0.00
263 3 0.01
264 3 0.01
265 1 0.00
266 11 0.02
267 1 0.00
268 2 0.00
269 12 0.02
270 2 0.00
271 1 0.00
272 1 0.00
273 19 0.04
274 118 0.24
275 3 0.01
276 75 0.15
277 5 0.01
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (272 bp):
TAATTATATTAAATAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAA
ATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAAT
TAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAA
AAGATTTAATTATTTAATTATATTAAAGTAAATATTATATTAATTAAAGATTTAATTATTTAATT
ATATTAAAGTAA
Found at i:13035518 original size:66 final size:64
Alignment explanation
Indices: 13035341--13035520 Score: 182
Period size: 66 Copynumber: 2.7 Consensus size: 64
13035331 TTTAATTATT
* * * * *
13035341 TAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTA
1 TAATTATATTAAA-TTAATAATCATATTAA-TT-TAAGATTTAATTATTTAATTATATTAAACTA
13035406 AA
63 AA
* *
13035408 TAATTATATTAAATTAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAA
1 TAATTATATTAAATTAATAATCATATTAATTT--AAGATTTAATTATTTAATTATATTAAACTAA
13035473 A
64 A
* * * *
13035474 TAATTATATTAAGTTATTTAATCATGTTTAATTT-TGTATTTAATTAT
1 TAATTATATTAAATTA-ATAATCAT-ATTAATTTAAG-ATTTAATTAT
13035521 AAACACTATC
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
65 3 0.03
66 68 0.70
67 19 0.20
68 7 0.07
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (64 bp):
TAATTATATTAAATTAATAATCATATTAATTTAAGATTTAATTATTTAATTATATTAAACTAAA
Found at i:13035591 original size:227 final size:242
Alignment explanation
Indices: 13035315--13035954 Score: 784
Period size: 253 Copynumber: 2.7 Consensus size: 242
13035305 GTAAATGATT
13035315 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGA
1 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGA
13035380 TTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAATAATT-A-TA-TTAATT-TA
66 TTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAATAATTAATTATTTAATTATA
* * * * * *
13035441 -AAAG-ATATAATTAT-TTAA-TT-ATA-TTAAACTAAATAATTATATT-AAGT-TAT-TTA-AT
131 TAAAGTAAATAAGTATATTAATTTAAAAGATAAACTAAATAATTATATTAAACTAAATATTATAT
** *
13035496 CATGTT-TAAT-TTTGTATTTAATTATAAACACTATCGATTAATTAA
196 CAAATTATATTATTTGTATTTAATTATAAACACTATCGATTAATTAA
13035541 ATATTTAAGTTTAAAAGATTTAATTATTT-ATTATATTAAAGTAAATGATTATATTAAGTTAAAA
1 ATA-TTAAG-TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAA
* *
13035605 GATTTAATCATTTAATTATATTAAAGTAAATAA-TATATTAAATTAAATATTTAATTATTTAATT
64 GATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AATAATTAATTATTTAATT
* * * **
13035669 ATATTAAGTAAATAAGTATATTAATTTAAAAGATATATTATTTAATTATATTAAACTAAATGATT
128 ATATAAAGTAAATAAGTATATTAATTTAAAAGATAAACTAAATAATTATATTAAACTAAAT-ATT
*
13035734 ATATTAAATTATTTTAATCATGTTATTATGTATTTAATTATAAACACTATCGATTAATTAA
192 ATA-TCAA--A--TT-AT-A--TTATT-TGTATTTAATTATAAACACTATCGATTAATTAA
*
13035795 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTCTATTAAGTTAAAAGA
1 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGA
*
13035860 TTTAATTATTTAATTATATT-AAGTAAATCATTATATTAAATTAA-AGATTTAATTATTTAATTA
66 TTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAATA-A-TTAATTATTTAATTA
* *
13035923 TATTAAAG--AATAATTATATTAAGTTAAAAGAT
129 TA-TAAAGTAAATAAGTATATTAATTTAAAAGAT
13035955 TTAATTATAA
Statistics
Matches: 355, Mismatches: 24, Indels: 44
0.84 0.06 0.10
Matches are distributed among these distances:
226 14 0.04
227 78 0.22
228 20 0.06
229 2 0.01
230 6 0.02
231 2 0.01
232 3 0.01
233 8 0.02
234 4 0.01
235 2 0.01
236 2 0.01
237 15 0.04
238 3 0.01
239 2 0.01
241 3 0.01
242 1 0.00
243 2 0.01
247 2 0.01
249 1 0.00
250 1 0.00
251 1 0.00
252 53 0.15
253 90 0.25
254 40 0.11
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (242 bp):
ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGA
TTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAATAATTAATTATTTAATTATA
TAAAGTAAATAAGTATATTAATTTAAAAGATAAACTAAATAATTATATTAAACTAAATATTATAT
CAAATTATATTATTTGTATTTAATTATAAACACTATCGATTAATTAA
Found at i:13035603 original size:18 final size:18
Alignment explanation
Indices: 13035570--13035608 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13035560 TTAATTATTT
*
13035570 ATTATATTAAAGTAAATG
1 ATTATATTAAAGTAAAAG
13035588 ATTATATT-AAGTTAAAAG
1 ATTATATTAAAG-TAAAAG
13035606 ATT
1 ATT
13035609 TAATCATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (18 bp):
ATTATATTAAAGTAAAAG
Found at i:13035641 original size:17 final size:17
Alignment explanation
Indices: 13035621--13035653 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13035611 ATCATTTAAT
13035621 TATATTAAAGTAAATAA
1 TATATTAAAGTAAATAA
*
13035638 TATATTAAATTAAATA
1 TATATTAAAGTAAATA
13035654 TTTAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TATATTAAAGTAAATAA
Found at i:13035675 original size:17 final size:17
Alignment explanation
Indices: 13035608--13035722 Score: 50
Period size: 17 Copynumber: 7.2 Consensus size: 17
13035598 GTTAAAAGAT
*
13035608 TTAATCATTTAATTATA
1 TTAATTATTTAATTATA
* **
13035625 TTAAAGTAAATAA-TATA
1 TT-AATTATTTAATTATA
*
13035642 TTAA--A-TTAAATAT-
1 TTAATTATTTAATTATA
13035655 TTAATTATTTAATTATA
1 TTAATTATTTAATTATA
* ** *
13035672 TTAAGTAAATAAGTATA
1 TTAATTATTTAATTATA
* **
13035689 TTAA-T-TTAAAAGATA
1 TTAATTATTTAATTATA
13035704 -T-ATTATTTAATTATA
1 TTAATTATTTAATTATA
13035719 TTAA
1 TTAA
13035723 ACTAAATGAT
Statistics
Matches: 70, Mismatches: 18, Indels: 20
0.65 0.17 0.19
Matches are distributed among these distances:
13 8 0.11
14 6 0.09
15 13 0.19
16 11 0.16
17 26 0.37
18 6 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAATTATTTAATTATA
Found at i:13035861 original size:253 final size:254
Alignment explanation
Indices: 13035408--13035974 Score: 907
Period size: 253 Copynumber: 2.2 Consensus size: 254
13035398 TTAAAGTAAA
*
13035408 TAATTATATTAAATTAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTAA
1 TAATTATATT-AATAAATAATTATATTAATTTAAAAGATAT-ATTATTTAATTATATTAAACTAA
* *
13035473 ATAATTATATTAAGTTATTTAATCATGTTTAATTTTGTATTTAATTATAAACACTATCGATTAAT
64 ATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAAT
13035538 TAAATATTTAAGTTTAAAAGATTTAATTATTTATTATATTAAAGTAAATGATTATATTAAGTTAA
129 TAAATATTTAAGTTTAAAAGATTTAATTATTTATTATATTAAAGTAAATGATTATATTAAGTTAA
*
13035603 AAGATTTAATCATTTAATTATATTAAAGTAAAT-AATATATTAAATTAAATATTTAATTATT
194 AAGATTTAATCATTTAATTATATT-AAGTAAATCAATATATTAAATTAAAGATTTAATTATT
*
13035664 TAATTATATTAAGTAAATAAGTATATTAATTTAAAAGATATATTATTTAATTATATTAAACTAAA
1 TAATTATATTAA-TAAATAATTATATTAATTTAAAAGATATATTATTTAATTATATTAAACTAAA
*
13035729 TGATTATATTAAATTATTTTAATCATG-TT-ATTATGTATTTAATTATAAACACTATCGATTAAT
65 TAATTATATTAAATTA-TTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAAT
*
13035792 TAAATA-TTAAG-TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTCTATTAAGTTA
129 TAAATATTTAAGTTTAAAAGATTTAATTATTT-ATTATATTAAAGTAAATGATTATATTAAGTTA
* *
13035855 AAAGATTTAATTATTTAATTATATTAAGTAAATCATTATATTAAATTAAAGATTTAATTATT
193 AAAGATTTAATCATTTAATTATATTAAGTAAATCAATATATTAAATTAAAGATTTAATTATT
* *
13035917 TAATTATATTAA-AGAATAATTATATTAAGTTAAAAGAT-T-TAATTATAATTATATTAAA
1 TAATTATATTAATA-AATAATTATATTAATTTAAAAGATATATTATT-TAATTATATTAAA
13035975 GTCTAAATTT
Statistics
Matches: 293, Mismatches: 12, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
250 4 0.01
251 15 0.05
252 49 0.17
253 98 0.33
254 39 0.13
255 42 0.14
256 46 0.16
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (254 bp):
TAATTATATTAATAAATAATTATATTAATTTAAAAGATATATTATTTAATTATATTAAACTAAAT
AATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTA
AATATTTAAGTTTAAAAGATTTAATTATTTATTATATTAAAGTAAATGATTATATTAAGTTAAAA
GATTTAATCATTTAATTATATTAAGTAAATCAATATATTAAATTAAAGATTTAATTATT
Found at i:13035881 original size:17 final size:17
Alignment explanation
Indices: 13035861--13035928 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
13035851 GTTAAAAGAT
13035861 TTAATTATTTAATTATA
1 TTAATTATTTAATTATA
* ** *
13035878 TTAAGTAAATCATTATA
1 TTAATTATTTAATTATA
**
13035895 TTAA--A-TTAAAGAT-
1 TTAATTATTTAATTATA
13035908 TTAATTATTTAATTATA
1 TTAATTATTTAATTATA
13035925 TTAA
1 TTAA
13035929 AGAATAATTA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 2 0.05
16 6 0.16
17 21 0.57
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATTATTTAATTATA
Found at i:13036021 original size:17 final size:18
Alignment explanation
Indices: 13035999--13036050 Score: 88
Period size: 17 Copynumber: 2.9 Consensus size: 18
13035989 AAGTTAAAAG
13035999 ATTTAATTATTTAATTAT
1 ATTTAATTATTTAATTAT
*
13036017 ATTAAATT-TTTAATTAT
1 ATTTAATTATTTAATTAT
13036034 ATTTAATTATTTAATTA
1 ATTTAATTATTTAATTA
13036051 ATAAAATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATTATTTAATTAT
Found at i:13036024 original size:10 final size:8
Alignment explanation
Indices: 13035999--13036050 Score: 61
Period size: 8 Copynumber: 6.1 Consensus size: 8
13035989 AAGTTAAAAG
13035999 ATTTAATT
1 ATTTAATT
13036007 ATTTAATT
1 ATTTAATT
13036015 ATATTAAATT
1 AT-TT-AATT
13036025 -TTTAATTAT
1 ATTTAA-T-T
13036034 ATTTAATT
1 ATTTAATT
13036042 ATTTAATT
1 ATTTAATT
13036050 A
1 A
13036051 ATAAAATAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.05
8 23 0.59
9 5 0.13
10 9 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:13041667 original size:66 final size:66
Alignment explanation
Indices: 13041561--13041717 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
13041551 CAAATTGCTC
*
13041561 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
13041625 AA
65 AA
* ** *
13041627 AACTTAAAGAGGAGGTTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
13041692 C
66 A
* * *
13041693 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
13041718 GCAAGCGGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 1 0.01
66 79 0.99
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:13041720 original size:11 final size:11
Alignment explanation
Indices: 13041704--13041741 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
13041694 ACTTAAAGTG
13041704 GAGGCAGCAGC
1 GAGGCAGCAGC
13041715 GAGGCA--AGC
1 GAGGCAGCAGC
13041724 GGAGGCAGCAGC
1 -GAGGCAGCAGC
13041736 GAGGCA
1 GAGGCA
13041742 AGCGAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.12
10 6 0.25
11 12 0.50
12 3 0.12
ACGTcount: A:0.29, C:0.24, G:0.47, T:0.00
Consensus pattern (11 bp):
GAGGCAGCAGC
Found at i:13041729 original size:21 final size:21
Alignment explanation
Indices: 13041703--13041755 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
13041693 AACTTAAAGT
13041703 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
13041724 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
13041745 GAAGGAAGCAG
1 GGAGGCAGCAG
13041756 AGGCTACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.47, T:0.00
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:13045717 original size:35 final size:36
Alignment explanation
Indices: 13045649--13045719 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
13045639 TAACTACAGC
*
13045649 ATGTTTGGGGTTCGTGGTTGCCCCTCTCAACAATGTT
1 ATGTTTGGGGTTCGTGGCTG-CCCTCTCAACAATGTT
13045686 ATGTTTGGGGTTCGTGGCTG-CCTCTCAACAATGT
1 ATGTTTGGGGTTCGTGGCTGCCCTCTCAACAATGT
13045720 CATCTTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 14 0.42
37 19 0.58
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.37
Consensus pattern (36 bp):
ATGTTTGGGGTTCGTGGCTGCCCTCTCAACAATGTT
Found at i:13047584 original size:14 final size:14
Alignment explanation
Indices: 13047565--13047596 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13047555 TTTGGGAGTC
*
13047565 ACTTCAACAGTTAA
1 ACTTCAACAATTAA
13047579 ACTTCAACAATTAA
1 ACTTCAACAATTAA
13047593 ACTT
1 ACTT
13047597 TGGCATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (14 bp):
ACTTCAACAATTAA
Found at i:13049146 original size:17 final size:18
Alignment explanation
Indices: 13049113--13049147 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13049103 TATAATGTAG
*
13049113 TTTTTAAATAAATATTAA
1 TTTTTAAATAAAAATTAA
13049131 TTTTTAAA-AAAAATTAA
1 TTTTTAAATAAAAATTAA
13049148 ACTCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTTAAATAAAAATTAA
Found at i:13050149 original size:6 final size:6
Alignment explanation
Indices: 13050138--13050168 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
13050128 CACCCCTATC
*
13050138 CCGTCT CCGTCT CTGTCT CCGTCT CCGTCT C
1 CCGTCT CCGTCT CCGTCT CCGTCT CCGTCT C
13050169 TGGATTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.16, T:0.35
Consensus pattern (6 bp):
CCGTCT
Found at i:13052834 original size:23 final size:22
Alignment explanation
Indices: 13052790--13052841 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
13052780 GAATTCTTGT
* *
13052790 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGCT-AAA
13052813 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGCTAAA
13052835 TAAAATA
1 TAAAATA
13052842 GACTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 11 0.42
24 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCTAAA
Found at i:13056516 original size:17 final size:17
Alignment explanation
Indices: 13056490--13056524 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13056480 GGAGAACTTA
* *
13056490 TTCGTTGAGAGTTCTTG
1 TTCGTAGAGAATTCTTG
13056507 TTCGTAGAGAATTCTTG
1 TTCGTAGAGAATTCTTG
13056524 T
1 T
13056525 CAAGGTGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (17 bp):
TTCGTAGAGAATTCTTG
Found at i:13057158 original size:40 final size:40
Alignment explanation
Indices: 13057114--13057195 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
13057104 ATTTAACTAA
13057114 TAGAATTCAACTTTTGTAACTTTTACAATTTAGCCCTTTT
1 TAGAATTCAACTTTTGTAACTTTTACAATTTAGCCCTTTT
13057154 TAGAATTCAACTTTTGTAACTTTTACAATTTAGCCCTTTT
1 TAGAATTCAACTTTTGTAACTTTTACAATTTAGCCCTTTT
13057194 TA
1 TA
13057196 CTTAATTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (40 bp):
TAGAATTCAACTTTTGTAACTTTTACAATTTAGCCCTTTT
Found at i:13059920 original size:30 final size:31
Alignment explanation
Indices: 13059884--13059962 Score: 128
Period size: 30 Copynumber: 2.6 Consensus size: 31
13059874 ACCACCTAAG
13059884 ATACCCTTTC-GGTCTCACTTAGGCATACGA
1 ATACCCTTTCTGGTCTCACTTAGGCATACGA
13059914 ATACCC-TTCTGGTCTCACTTAGGCATACGA
1 ATACCCTTTCTGGTCTCACTTAGGCATACGA
*
13059944 ATACCC-TTCTAGTCTCACT
1 ATACCCTTTCTGGTCTCACT
13059963 CCTTGGCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 3 0.06
30 44 0.94
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (31 bp):
ATACCCTTTCTGGTCTCACTTAGGCATACGA
Found at i:13061690 original size:55 final size:55
Alignment explanation
Indices: 13061626--13061836 Score: 196
Period size: 56 Copynumber: 3.8 Consensus size: 55
13061616 TTTGATTCAA
* *
13061626 TATATCTCGGGTAGAGCTCGAATC-TGCTTACGTCTCGATTAGAGCGTAATGCTAT
1 TATAGCTCGGGTAGAGCTCGGA-CATGCTTACGTCTCGATTAGAGCGTAATGCTAT
* * * * * *
13061681 TTTAGCTCGGGTAGAGTTTTGGACATGCTTATGTATC-AGTTAAAGCGTAATGCTAT
1 TATAGCTCGGGTAGAG-CTCGGACATGCTTACGTCTCGA-TTAGAGCGTAATGCTAT
* * * * * * *
13061737 TATAGCTCGGGTATAGCTTTGGACATGTTTACATCTCGGTTAGAG-GTAAAGTTAT
1 TATAGCTCGGGTAGAGC-TCGGACATGCTTACGTCTCGATTAGAGCGTAATGCTAT
* *
13061792 TATAGCTTGGGTAGAGCTCTGG-CTTGCTTACGTCTCGATTAGAGC
1 TATAGCTCGGGTAGAGCTC-GGACATGCTTACGTCTCGATTAGAGC
13061837 ATAAGATTAT
Statistics
Matches: 123, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
54 19 0.15
55 41 0.33
56 63 0.51
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (55 bp):
TATAGCTCGGGTAGAGCTCGGACATGCTTACGTCTCGATTAGAGCGTAATGCTAT
Found at i:13061847 original size:55 final size:56
Alignment explanation
Indices: 13061650--13061836 Score: 218
Period size: 56 Copynumber: 3.4 Consensus size: 56
13061640 AGCTCGAATC
* *
13061650 TGCTTACGTCTCGATTAGAGCGTAATGCTATTTTAGCTCGGGTAGAGTTTTGGACA
1 TGCTTACGTCTCGATTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
* * * *
13061706 TGCTTATGTATC-AGTTAAAGCGTAATGCTATTATAGCTCGGGTATAGCTTTGGACA
1 TGCTTACGTCTCGA-TTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
* * * * * * * *
13061762 TGTTTACATCTCGGTTAGAG-GTAAAGTTATTATAGCTTGGGTAGAGCTCTGG-CT
1 TGCTTACGTCTCGATTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
13061816 TGCTTACGTCTCGATTAGAGC
1 TGCTTACGTCTCGATTAGAGC
13061837 ATAAGATTAT
Statistics
Matches: 107, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
54 18 0.17
55 28 0.26
56 61 0.57
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (56 bp):
TGCTTACGTCTCGATTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACA
Found at i:13063612 original size:56 final size:55
Alignment explanation
Indices: 13063537--13063735 Score: 213
Period size: 56 Copynumber: 3.6 Consensus size: 55
13063527 ATCTCCGATC
* * *
13063537 TGCTTACGTCTCAGTTAGAGCGTAATGTTATTATAGCTTGAGAAGAGTTTTGGACA
1 TGCTTACATCTCAGTTAGAGCGTAATGTTATTATAGCTTG-GTAGAGCTTTGGACA
* * * *
13063593 TGCTTACATCTCGGTTAGAGCATAATGCTATTGTAGCTCTGGTAGAGCTTTGGACA
1 TGCTTACATCTCAGTTAGAGCGTAATGTTATTATAGCT-TGGTAGAGCTTTGGACA
* * * * * *
13063649 TGATTATATCTCAGTTAGAGCGTAAAGTTATTATAGCTCGGGTAGAGCTCTGG-CT
1 TGCTTACATCTCAGTTAGAGCGTAATGTTATTATAGCT-TGGTAGAGCTTTGGACA
* *
13063704 TGCTTACGA-CTCGGTTAGAGCGTAAGGTTATT
1 TGCTTAC-ATCTCAGTTAGAGCGTAATGTTATT
13063736 TCAACTCAGG
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
55 27 0.22
56 91 0.76
57 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.35
Consensus pattern (55 bp):
TGCTTACATCTCAGTTAGAGCGTAATGTTATTATAGCTTGGTAGAGCTTTGGACA
Found at i:13078286 original size:22 final size:22
Alignment explanation
Indices: 13078261--13078314 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
13078251 CTATTTTGAT
13078261 ACTCTCTGTTTTGGCCATTTAA
1 ACTCTCTGTTTTGGCCATTTAA
13078283 ACTCTCTGTTTTGGCCATTTAA
1 ACTCTCTGTTTTGGCCATTTAA
*
13078305 ACTCTTTGTT
1 ACTCTCTGTT
13078315 AAACTCTCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (22 bp):
ACTCTCTGTTTTGGCCATTTAA
Found at i:13084830 original size:58 final size:58
Alignment explanation
Indices: 13084742--13084887 Score: 192
Period size: 58 Copynumber: 2.5 Consensus size: 58
13084732 ATATATTATA
* *
13084742 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
*
13084799 ATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
13084859 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
13084888 CATTAAAATT
Statistics
Matches: 80, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
57 1 0.01
58 49 0.61
59 12 0.15
60 10 0.12
61 8 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:13084838 original size:26 final size:26
Alignment explanation
Indices: 13084806--13084887 Score: 74
Period size: 32 Copynumber: 2.9 Consensus size: 26
13084796 CATATTATTT
13084806 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAATAATTA
* * * *
13084832 TGTTAAAATATAATTAAATAAATTAATATTTT
1 TATTAAATTAT-ATT---T-AA-TAATAATTA
13084864 TATTAAATTATATTTAATAATAAT
1 TATTAAATTATATTTAATAATAAT
13084888 CATTAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
26 15 0.35
27 5 0.12
28 1 0.02
30 1 0.02
31 5 0.12
32 16 0.37
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TATTAAATTATATTTAATAATAATTA
Found at i:13085026 original size:39 final size:44
Alignment explanation
Indices: 13084971--13085075 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
13084961 TTTCTTATGC
*
13084971 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
13085010 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
13085056 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
13085076 ACACCTCTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:13085074 original size:46 final size:44
Alignment explanation
Indices: 13084982--13085075 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
13084972 ATTACAGCAT
* *
13084982 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
13085026 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
13085072 CATT
1 CATT
13085076 ACACCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:13085078 original size:16 final size:16
Alignment explanation
Indices: 13085057--13085096 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
13085047 TGAATTACTG
13085057 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
13085073 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
13085089 ATTACAGC
1 ATTACAGC
13085097 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:13091997 original size:20 final size:20
Alignment explanation
Indices: 13091972--13092010 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
13091962 AATTATGTAG
13091972 TGTTGT-TTTTACATTATCTT
1 TGTTGTGTTTTA-ATTATCTT
13091992 TGTTGTGTTTTAATTATCT
1 TGTTGTGTTTTAATTATCT
13092011 GATCATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64
Consensus pattern (20 bp):
TGTTGTGTTTTAATTATCTT
Found at i:13105916 original size:27 final size:26
Alignment explanation
Indices: 13105886--13106005 Score: 116
Period size: 27 Copynumber: 4.5 Consensus size: 26
13105876 AGTTCTAATA
**
13105886 GACTCTCCACATTAGATAGTCCTGGTG
1 GACT-TCCACATTAGATAGTCCTGACG
* *
13105913 GACTTCTCACATTAGATAGTCTTGACA
1 GACTTC-CACATTAGATAGTCCTGACG
* *
13105940 GACCTCCTACATTAGATAGTTCTGACG
1 GACTTCC-ACATTAGATAGTCCTGACG
*
13105967 GACTTCCCACATTAAATAGTCCTTG-CG
1 GACTT-CCACATTAGATAGTCC-TGACG
*
13105994 AACTTCCACATT
1 GACTTCCACATT
13106006 TATAGTAATG
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
26 10 0.13
27 63 0.82
28 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (26 bp):
GACTTCCACATTAGATAGTCCTGACG
Found at i:13105931 original size:54 final size:55
Alignment explanation
Indices: 13105872--13105986 Score: 137
Period size: 54 Copynumber: 2.1 Consensus size: 55
13105862 TTCACCCAAC
* ** *
13105872 AGATAGTTC-TAATAGACTCTCC-ACATTAGATAGTCCTGGTGGACTTCTCACATT
1 AGATAGTTCTTAACAGAC-CTCCTACATTAGATAGTCCTGACGGACTTCCCACATT
* *
13105926 AGATAG-TCTTGACAGACCTCCTACATTAGATAGTTCTGACGGACTTCCCACATT
1 AGATAGTTCTTAACAGACCTCCTACATTAGATAGTCCTGACGGACTTCCCACATT
*
13105980 AAATAGT
1 AGATAGT
13105987 CCTTGCGAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
53 6 0.12
54 45 0.88
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (55 bp):
AGATAGTTCTTAACAGACCTCCTACATTAGATAGTCCTGACGGACTTCCCACATT
Found at i:13105987 original size:54 final size:54
Alignment explanation
Indices: 13105885--13105987 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
13105875 TAGTTCTAAT
** * *
13105885 AGACTCTCCACATTAGATAGTCCTGGTGGACTTCTCACATTAGATAGTCTTGAC
1 AGACTCTCCACATTAGATAGTCCTGACGGACTTCCCACATTAAATAGTCTTGAC
*
13105939 AGAC-CTCCTACATTAGATAGTTCTGACGGACTTCCCACATTAAATAGTC
1 AGACTCTCC-ACATTAGATAGTCCTGACGGACTTCCCACATTAAATAGTC
13105988 CTTGCGAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 4 0.09
54 39 0.91
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (54 bp):
AGACTCTCCACATTAGATAGTCCTGACGGACTTCCCACATTAAATAGTCTTGAC
Found at i:13108124 original size:12 final size:12
Alignment explanation
Indices: 13108109--13108143 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13108099 AAACTTTTGT
*
13108109 TTTTATTTTCTA
1 TTTTATTTTATA
*
13108121 TTTTATTTTATC
1 TTTTATTTTATA
13108133 TTTTATTTTAT
1 TTTTATTTTAT
13108144 GCTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:13108131 original size:17 final size:17
Alignment explanation
Indices: 13108109--13108143 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13108099 AAACTTTTGT
13108109 TTTTAT-TTTCTATTTTA
1 TTTTATCTTT-TATTTTA
13108126 TTTTATCTTTTATTTTA
1 TTTTATCTTTTATTTTA
13108143 T
1 T
13108144 GCTCTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:13115552 original size:12 final size:12
Alignment explanation
Indices: 13115535--13115569 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13115525 AAACTTTTGC
*
13115535 TTTTATTTTCTA
1 TTTTATTTTATA
*
13115547 TTTTATTTTATC
1 TTTTATTTTATA
13115559 TTTTATTTTAT
1 TTTTATTTTAT
13115570 TCTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:13115557 original size:17 final size:17
Alignment explanation
Indices: 13115535--13115570 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
13115525 AAACTTTTGC
13115535 TTTTAT-TTTCTATTTTA
1 TTTTATCTTT-TATTTTA
13115552 TTTTATCTTTTATTTTA
1 TTTTATCTTTTATTTTA
13115569 TT
1 TT
13115571 CTCTCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:13123636 original size:21 final size:24
Alignment explanation
Indices: 13123610--13123658 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 24
13123600 AAAGGCTATC
*
13123610 TACAAATTCA-ATCTT-T-AAGAT
1 TACAAAATCATATCTTCTAAAGAT
13123631 TACAAAATCATATCTTCTAAAGAT
1 TACAAAATCATATCTTCTAAAGAT
13123655 TACA
1 TACA
13123659 TATCAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 5 0.21
23 1 0.04
24 9 0.38
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (24 bp):
TACAAAATCATATCTTCTAAAGAT
Found at i:13129239 original size:25 final size:25
Alignment explanation
Indices: 13129205--13129262 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
13129195 GTGACATCGC
13129205 TGGCTGCAACTCCAAGCTGATCTTG
1 TGGCTGCAACTCCAAGCTGATCTTG
13129230 TGGCTGCAACTCCAAGCTGATCTTG
1 TGGCTGCAACTCCAAGCTGATCTTG
13129255 TGGCTGCA
1 TGGCTGCA
13129263 TTATTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28
Consensus pattern (25 bp):
TGGCTGCAACTCCAAGCTGATCTTG
Found at i:13130542 original size:3 final size:3
Alignment explanation
Indices: 13130536--13130590 Score: 85
Period size: 3 Copynumber: 18.0 Consensus size: 3
13130526 CTTCTTTATG
13130536 CTT CTT CTT CTT CTT CTT CTT -TT CCTT CTT CTT CTT CTT CTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT C-TT
13130582 CTT CTT CTT
1 CTT CTT CTT
13130591 GTCTTTGTGC
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:13140743 original size:21 final size:24
Alignment explanation
Indices: 13140717--13140765 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 24
13140707 AAAGGCTATC
*
13140717 TACAAATTCA-ATC-TCT-AAGAT
1 TACAAAATCATATCTTCTAAAGAT
13140738 TACAAAATCATATCTTCTAAAGAT
1 TACAAAATCATATCTTCTAAAGAT
13140762 TACA
1 TACA
13140766 TATCAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 3 0.12
24 9 0.38
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (24 bp):
TACAAAATCATATCTTCTAAAGAT
Found at i:13151478 original size:18 final size:18
Alignment explanation
Indices: 13151455--13151513 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
13151445 CAATCTACTA
13151455 ATGCTCATACGAGCCAGT
1 ATGCTCATACGAGCCAGT
* * *
13151473 ATGCTCAAACAAGCTAGT
1 ATGCTCATACGAGCCAGT
*
13151491 ATGCTC-TAATGAGCCAGT
1 ATGCTCAT-ACGAGCCAGT
13151509 ATGCT
1 ATGCT
13151514 ATTTCTTCCG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (18 bp):
ATGCTCATACGAGCCAGT
Found at i:13158432 original size:18 final size:18
Alignment explanation
Indices: 13158419--13158521 Score: 109
Period size: 18 Copynumber: 5.7 Consensus size: 18
13158409 ATGCTCTTAT
13158419 GAGCTAGTATGCTCAAAC
1 GAGCTAGTATGCTCAAAC
* * *
13158437 AAGCCAGTATGCTTAAAC
1 GAGCTAGTATGCTCAAAC
*
13158455 GAGCTAGTATGCTCAAAT
1 GAGCTAGTATGCTCAAAC
* *
13158473 GAGCTAATATGCTCAAAA
1 GAGCTAGTATGCTCAAAC
*
13158491 GAGGCT-GCATGCTCAAAC
1 GA-GCTAGTATGCTCAAAC
* *
13158509 GAACCAGTATGCT
1 GAGCTAGTATGCT
13158522 ATTTCTTCCG
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
17 1 0.01
18 64 0.94
19 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (18 bp):
GAGCTAGTATGCTCAAAC
Found at i:13158503 original size:54 final size:54
Alignment explanation
Indices: 13158403--13158521 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
13158393 CTCTTGCGAT
** * * * *
13158403 CTAGTAATGCTCTTATGAGCTAGTATGCTCAAACAAGCCAGTATGCTTAAACGAG
1 CTAGT-ATGCTCAAATGAGCTAATATGCTCAAACAAGCCAGCATGCTCAAACGAA
* *
13158458 CTAGTATGCTCAAATGAGCTAATATGCTCAAA-AGAGGCTGCATGCTCAAACGAA
1 CTAGTATGCTCAAATGAGCTAATATGCTCAAACA-AGCCAGCATGCTCAAACGAA
*
13158512 CCAGTATGCT
1 CTAGTATGCT
13158522 ATTTCTTCCG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
53 1 0.02
54 48 0.89
55 5 0.09
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (54 bp):
CTAGTATGCTCAAATGAGCTAATATGCTCAAACAAGCCAGCATGCTCAAACGAA
Found at i:13160384 original size:6 final size:6
Alignment explanation
Indices: 13160364--13160447 Score: 63
Period size: 6 Copynumber: 14.7 Consensus size: 6
13160354 TAAATTGATC
* ** *
13160364 TAAATT T-ATTT TAAATT TAAATT TATCCTTT TAAATT TAAATT T-ACTT
1 TAAATT TAAATT TAAATT TAAATT TA--AATT TAAATT TAAATT TAAATT
*
13160412 TAAATT TAAATT T-AA-T TAAATT TGAA-T T-AATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
13160448 ACTTAATATT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.07
5 16 0.26
6 37 0.61
8 4 0.07
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:13160397 original size:20 final size:18
Alignment explanation
Indices: 13160364--13160425 Score: 92
Period size: 17 Copynumber: 3.4 Consensus size: 18
13160354 TAAATTGATC
13160364 TAAATTTA-TTTTAAATT
1 TAAATTTACTTTTAAATT
13160381 TAAATTTATCCTTTTAAATT
1 TAAATTTA--CTTTTAAATT
13160401 TAAATTTAC-TTTAAATT
1 TAAATTTACTTTTAAATT
13160418 TAAATTTA
1 TAAATTTA
13160426 ATTAAATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
17 24 0.57
18 1 0.02
20 17 0.40
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATTTACTTTTAAATT
Found at i:13160428 original size:11 final size:11
Alignment explanation
Indices: 13160342--13160447 Score: 56
Period size: 11 Copynumber: 9.4 Consensus size: 11
13160332 ATTAAGCTTC
*
13160342 TAAAATTAAGTT
1 TAAATTTAA-TT
* *
13160354 TAAA-TTGATC
1 TAAATTTAATT
*
13160364 TAAATTTATTT
1 TAAATTTAATT
13160375 TAAATTTAAATT
1 TAAATTT-AATT
**
13160387 TATCCTTTTAAATT
1 TA--AATTT-AATT
*
13160401 TAAATTTACTT
1 TAAATTTAATT
13160412 TAAATTTAAATT
1 TAAATTT-AATT
*
13160424 T-AATTAAATT
1 TAAATTTAATT
*
13160434 TGAA-TTAATT
1 TAAATTTAATT
13160444 TAAA
1 TAAA
13160448 ACTTAATATT
Statistics
Matches: 73, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
10 18 0.25
11 29 0.40
12 16 0.22
14 10 0.14
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:13161226 original size:23 final size:24
Alignment explanation
Indices: 13161200--13161250 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
13161190 GTTAAGGACG
* *
13161200 AAAAGAAAAAGATTTTTTA-AATA
1 AAAAGAAAAACATTTTTAAGAATA
**
13161223 AAAATCAAAACATTTTTAAGAATA
1 AAAAGAAAAACATTTTTAAGAATA
13161247 AAAA
1 AAAA
13161251 AAGGAAAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (24 bp):
AAAAGAAAAACATTTTTAAGAATA
Found at i:13161246 original size:24 final size:23
Alignment explanation
Indices: 13161206--13161250 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
13161196 GACGAAAAGA
* *
13161206 AAAAGATTTTTTAAATAAAAATC
1 AAAACATTTTTAAAATAAAAATC
13161229 AAAACATTTTTAAGAATAAAAA
1 AAAACATTTTTAA-AATAAAAA
13161251 AAGGAAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAACATTTTTAAAATAAAAATC
Found at i:13162077 original size:30 final size:31
Alignment explanation
Indices: 13162052--13162290 Score: 234
Period size: 29 Copynumber: 8.1 Consensus size: 31
13162042 AAAAATTGTA
*
13162052 TTTTGACCCCAAAACTTCTCTAAAATTACA-
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
* * * **
13162082 TTTTAACCCTAAAACTTATCCCAAATTACAT
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
*
13162113 TTTTGACCCTAAAACTTCTC-AAAATTACA-
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
* *
13162142 TTTTAACCCCAAAACTTCT-AAAAATTCCAT
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
**
13162172 TTTTGACCCTGAAACTTC-C-AAAATTACAT
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
* *
13162201 ATTT-ACCCC-AAACTTC-CAAAAATTTCAT
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
*
13162229 TTTTAACCCC-AAACTTC-CAAAAATTACAT
1 TTTTGACCCCAAAACTTCTCAAAAATTACAT
* *
13162258 TTTTGACCCTAAAAC-TCTC-AGAATTACCAT
1 TTTTGACCCCAAAACTTCTCAAAAATTA-CAT
13162288 TTT
1 TTT
13162291 ACCCCTAGAT
Statistics
Matches: 177, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
27 8 0.05
28 16 0.09
29 76 0.43
30 59 0.33
31 18 0.10
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (31 bp):
TTTTGACCCCAAAACTTCTCAAAAATTACAT
Found at i:13162370 original size:87 final size:85
Alignment explanation
Indices: 13162157--13162436 Score: 259
Period size: 87 Copynumber: 3.2 Consensus size: 85
13162147 ACCCCAAAAC
*
13162157 TTCTAAAAATT-CCATTTTTGACCCTGAAACTTCCAAAATTA-CATATTTACCCCAAACTTCCAA
1 TTCTAAAAATTACCATTTTTGACCCTGAAAC-TCCAAAATTACCAT-TTTACCCCAGA-TTCCAA
* *
13162220 AAATTTCATTTTTAACCCCAA--A
63 AAATCTCATTTTT-ATCCCAATTA
* * * *
13162242 CTTCCAAAAATTA-CATTTTTGACCCTAAAACTCTCAGAATTACCATTTTACCCCTAGATGTCTA
1 -TTCTAAAAATTACCATTTTTGACCCTGAAACTC-CAAAATTACCATTTTACCCC-AGAT-TCCA
*
13162306 AAAATCCCATTTTTGATCCCAATTA
62 AAAATCTCATTTTT-ATCCCAATTA
* *
13162331 TTCTAAAAATTACCA-TTTTG-CCCTCGAAAGTCCAAAATTACCATTTTACCCCCGGATATCCAA
1 TTCTAAAAATTACCATTTTTGACCCT-GAAACTCCAAAATTACCATTTTA-CCCCAGAT-TCCAA
* * *
13162394 AAAGTCTCATTTTTATCTCGATTC
63 AAA-TCTCATTTTTATCCCAATTA
* *
13162418 TTTTAAAAATTACCGTTTT
1 TTCTAAAAATTACCATTTT
13162437 ATCCCCAAAT
Statistics
Matches: 160, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
85 2 0.01
86 43 0.27
87 75 0.47
88 37 0.23
89 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (85 bp):
TTCTAAAAATTACCATTTTTGACCCTGAAACTCCAAAATTACCATTTTACCCCAGATTCCAAAAA
TCTCATTTTTATCCCAATTA
Found at i:13173035 original size:92 final size:92
Alignment explanation
Indices: 13172607--13173458 Score: 1019
Period size: 92 Copynumber: 9.2 Consensus size: 92
13172597 AGATCAAAAT
*
13172607 AACATTAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
13172672 TTGTAGTAAGAGCAAGA-GAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
13172698 AACATCAAT-TCTATCCTCTTGAAGTTGTAATAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
*
13172762 ATGTAGTAAGAGCAAGATGAAGCAT-A
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* ** * *
13172788 AACATCAATTCCTATCCTCTTGAAGTTGTAGT-AA-TTTAATATCAAGTGTTTATCTCTC--AAG
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
* ** *** * *
13172849 ATAGTAACACAGAATGAGCAAGAAG-ATGA
66 -TTGTAGTA-AGAGCAAG-ATGAAGCATCA
* * * **
13172878 AACATCAATCCCTATCTTCTTGAA-TCGTAGTAAAGTT-G-TAGTAAGTCTTGGATATCAAGTCT
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTT---TATC-TCTCT
* ** * *
13172940 TATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCA
62 GA--AGT-TGTAG-T-AAG--AG--CAAGATGAAGCATCA
*
13172980 AACATCAATCCCTATCTTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
13173045 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * * * * *
13173072 AATATCAATTCCTCTCCTCTTGAAGTTGTAATAAAGTTGGATAGCAAGTCTTTGTCTCTCTAAAG
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
13173137 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
*
13173164 AACATCAATATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGGGTAGCAAGTCTTTATCTCTCT
1 AACATC-A-ATCCCTATCCTCTTGAAGTTGTAGTAAAGTT--GGATAGCAAGTCTTTATCTCTCT
*
13173229 GAAGTTGTAGTAAGAGCTAGATGAAGCATCA
62 GAAGTTGTAGTAAGAGCAAGATGAAGCATCA
*
13173260 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
13173325 TTGTAGTAAGAGCAAGAT-AAGGCATCA
66 TTGTAGTAAGAGCAAGATGAA-GCATCA
* *
13173352 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGCTGGATAGCAAGTCTTTATCTCTCTTTGA
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC--TGA
* *
13173417 AGTTGTAGTAAGAGCAGGATGAAGCCTC-
64 AGTTGTAGTAAGAGCAAGATGAAGCATCA
* *
13173445 GACATCAAACCCTA
1 AACATCAATCCCTA
13173459 CTTTTGAGAA
Statistics
Matches: 654, Mismatches: 72, Indels: 68
0.82 0.09 0.09
Matches are distributed among these distances:
87 3 0.00
88 4 0.01
89 41 0.06
90 111 0.17
91 39 0.06
92 217 0.33
93 14 0.02
94 86 0.13
95 4 0.01
96 59 0.09
97 3 0.00
98 6 0.01
99 1 0.00
100 1 0.00
101 9 0.01
102 33 0.05
103 12 0.02
104 1 0.00
105 10 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (92 bp):
AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG
TTGTAGTAAGAGCAAGATGAAGCATCA
Found at i:13173269 original size:188 final size:186
Alignment explanation
Indices: 13172614--13173441 Score: 1130
Period size: 188 Copynumber: 4.4 Consensus size: 186
13172604 AATAACATTA
13172614 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
1 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
13172679 AAGAGCAAGA-GAAGCATCAAACATCAATT-CTATCCTCTTGAAGTTGTAATAAAGTTGGATAGC
66 AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAATAAAGTTGGATAGC
*
13172742 AAGTCTTTATCTCTCTGAAGATGTAGTAAGAGCAAGATGAAGCAT-AAACATCAAT
131 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAAT
** * * * *
13172797 -T-CCTATCCTCTTGAAGTTGTAGT-AA-TTTAATATCAAGTGTTTATCTCTC--AAGATAGTAA
1 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAG-TTGTAG
* *** * * * * *
13172856 CACAGAATGAGCAAGAAG-ATGAAACATCAATCCCTATCTTCTTGAATCGTAGTAAAGTTGTAGT
65 TA-AGAGCAAG-ATGAAGCATCAAACATCAATTCCTATCCTCTTGAA--GTTGT-AA----TA--
*
13172920 AAGTCTTGGATATCAAGTC-TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACA
119 AAG--TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACA
13172984 TC-A-
182 TCAAT
*
13172987 ATCCCTATCTTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
1 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
* *
13173052 AAGAGCAAGATGAAGCATCAAATATCAATTCCTCTCCTCTTGAAGTTGTAATAAAGTTGGATAGC
66 AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAATAAAGTTGGATAGC
* *
13173117 AAGTCTTTGTCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAAT
131 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAAT
*
13173173 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGGGTAGCAAGTCTTTATCTCTCTGAAGTTGTA
1 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTT--GGATAGCAAGTCTTTATCTCTCTGAAGTTGTA
* *
13173238 GTAAGAGCTAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATA
64 GTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAATAAAGTTGGATA
13173303 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGAT-AAGGCATCAAACATCAAT
129 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAA-GCATCAAACATCAAT
*
13173361 -T-CCTATCCTCTTGAAGTTGTAGTAAAGCTGGATAGCAAGTCTTTATCTCTCTTTGAAGTTGTA
1 ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC--TGAAGTTGTA
*
13173424 GTAAGAGCAGGATGAAGC
64 GTAAGAGCAAGATGAAGC
13173442 CTCGACATCA
Statistics
Matches: 564, Mismatches: 49, Indels: 61
0.84 0.07 0.09
Matches are distributed among these distances:
177 3 0.01
178 5 0.01
179 25 0.04
180 15 0.03
181 38 0.07
182 1 0.00
183 17 0.03
184 68 0.12
185 4 0.01
186 83 0.15
187 5 0.01
188 147 0.26
190 3 0.01
191 42 0.07
192 45 0.08
193 7 0.01
194 48 0.09
195 5 0.01
196 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (186 bp):
ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAATAAAGTTGGATAGC
AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAAT
Found at i:13173292 original size:280 final size:277
Alignment explanation
Indices: 13172607--13173458 Score: 1154
Period size: 280 Copynumber: 3.1 Consensus size: 277
13172597 AGATCAAAAT
* *
13172607 AACATTAATCCCTATCCTCTTGAAGTTGTAGTAAAGTT--GGATAGCAAGTCTTTATCTCTCTGA
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGGGTAGCAAGTCTTTATCTCTCTGA
*
13172670 AGTTGTAGTAAGAGCAAGA-GAAGCATCAAACATCAATT-CTATCCTCTTGAAGTTGTAATAAAG
66 AGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAG
*
13172733 TTGGATAGCAAGTCTTTATCTCTCTGAAGATGTAGTAAGAGCAAGATGAAGCAT-AAACATCAAT
131 TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAAT
** * * * **
13172797 TCCTATCCTCTTGAAGTTGTAGT-AA-TTTAATATCAAGTGTTTATCTCTC-AAGATAGTAACAC
196 TCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTAAG-TTGTAGTA-
*** * *
13172859 AGAATGAGCAAGAAG-ATGA
259 AGAGCAAG-ATGAAGCATCA
* * *
13172878 AACATCAATCCCTATCTTCTTGAA-TCGTAGTAAAGTTGTAGTAAGTCTTGGATATCAAGTC-TT
1 AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTG--G---G----GG-TAGCAAGTCTTT
* *
13172941 ATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATCCCTATCTTCTTGAAGT
56 ATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGT
13173006 TGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATC
121 TGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATC
* * * *
13173071 AAATATCAATTCCTCTCCTCTTGAAGTTGTAATAAAGTTGGATAGCAAGTCTTTGTCTCTCTAAA
186 AAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT-AA
13173136 GTTGTAGTAAGAGCAAGATGAAGCATCA
250 GTTGTAGTAAGAGCAAGATGAAGCATCA
13173164 AACATCAATATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGGGTAGCAAGTCTTTATCTCTCT
1 AACATC-A-ATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGGGTAGCAAGTCTTTATCTCTCT
*
13173229 GAAGTTGTAGTAAGAGCTAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
64 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
13173294 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGAT-AAGGCATCAAACATC
129 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAA-GCATCAAACATC
*
13173358 AATTCCTATCCTCTTGAAGTTGTAGTAAAGCTGGATAGCAAGTCTTTATCTCTCTTTGAAGTTGT
193 AATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC--T-AAGTTGT
* *
13173423 AGTAAGAGCAGGATGAAGCCTC-
255 AGTAAGAGCAAGATGAAGCATCA
* *
13173445 GACATCAAACCCTA
1 AACATCAATCCCTA
13173459 CTTTTGAGAA
Statistics
Matches: 513, Mismatches: 41, Indels: 46
0.86 0.07 0.08
Matches are distributed among these distances:
270 12 0.02
271 22 0.04
277 1 0.00
279 16 0.03
280 185 0.36
281 37 0.07
282 54 0.11
283 76 0.15
284 31 0.06
285 7 0.01
286 33 0.06
287 7 0.01
288 19 0.04
289 13 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (277 bp):
AACATCAATCCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGGGTAGCAAGTCTTTATCTCTCTGA
AGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAG
TTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAAT
TCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTAAGTTGTAGTAAG
AGCAAGATGAAGCATCA
Found at i:13173745 original size:17 final size:17
Alignment explanation
Indices: 13173723--13173803 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
13173713 TAAATTGATC
*
13173723 TAAATTTATTTTAATTT
1 TAAATTTATTTTAAATT
13173740 TAAATTTATTTTTTAAAATT
1 TAAATTTA--TTTT-AAATT
*
13173760 TAAATTTACTTTAAATT
1 TAAATTTATTTTAAATT
*
13173777 TAAATTTA-ATTAAATT
1 TAAATTTATTTTAAATT
* *
13173793 TGAATTAATTT
1 TAAATTTATTT
13173804 AAAACTTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.24
17 22 0.41
18 3 0.06
19 4 0.07
20 12 0.22
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:13173764 original size:6 final size:6
Alignment explanation
Indices: 13173723--13173806 Score: 54
Period size: 6 Copynumber: 14.7 Consensus size: 6
13173713 TAAATTGATC
* * ** *
13173723 TAAATT T-ATTT TAATTT TAAATT TATTTTT TAAAATT TAAATT T-ACTT
1 TAAATT TAAATT TAAATT TAAATT TA-AATT T-AAATT TAAATT TAAATT
*
13173771 TAAATT TAAATT T-AA-T TAAATT TGAA-T T-AATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
13173807 ACTTAATATT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.07
5 16 0.26
6 34 0.56
7 6 0.10
8 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TAAATT
Found at i:13173787 original size:11 final size:11
Alignment explanation
Indices: 13173756--13173806 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
13173746 TATTTTTTAA
13173756 AATTTAAATTT
1 AATTTAAATTT
*
13173767 ACTTTAAATTT
1 AATTTAAATTT
*
13173778 AAATTT-AATTA
1 -AATTTAAATTT
*
13173789 AATTTGAA-TT
1 AATTTAAATTT
13173799 AATTTAAA
1 AATTTAAA
13173807 ACTTAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 13 0.39
11 16 0.48
12 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:13174646 original size:21 final size:21
Alignment explanation
Indices: 13174622--13174661 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13174612 CATTGAATAA
13174622 TTTAATAA-ATATTAATAATGT
1 TTTAATAATA-ATTAATAATGT
*
13174643 TTTAGTAATAATTAATAAT
1 TTTAATAATAATTAATAAT
13174662 AATAATAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTAATAATAATTAATAATGT
Found at i:13175762 original size:59 final size:59
Alignment explanation
Indices: 13175640--13175949 Score: 324
Period size: 58 Copynumber: 5.3 Consensus size: 59
13175630 AGAAATTGTA
* * * * **
13175640 TTTTGACCCCCAAACTTCTCCAAAATTACATTTTAACCTTGAAACTTCTCCTAAATTACAT
1 TTTTAACCCCGAAACTTC-CAAAAATTACATTTTAACCTCGAAACTTC-CAAAAATTACAT
* *
13175701 TTTTAACCTCGAAACTTCCAAAAATTACATTTTAACCTTGAAACTTCCAAAAATTACAT
1 TTTTAACCCCGAAACTTCCAAAAATTACATTTTAACCTCGAAACTTCCAAAAATTACAT
* * * * * *
13175760 TTTTGACCCCAAAACTTTCGAAAATTACATTTTACCCTCG-AACTTCCAAAAATTCCAT
1 TTTTAACCCCGAAACTTCCAAAAATTACATTTTAACCTCGAAACTTCCAAAAATTACAT
* * * * * *
13175818 TTTTAACCTCGAAACTTCTC-GAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCA-
1 TTTTAACCCCGAAACTTC-CAAAAATTACATTTTAACCTCGAAACTTCCAAAAATTACAT
* * * *
13175876 TTTTAACCCC-AAACTTCCAAAAATTTCATTTATGACC-CCAAACTTCCAAAAATTTCAT
1 TTTTAACCCCGAAACTTCCAAAAATTACATTT-TAACCTCGAAACTTCCAAAAATTACAT
*
13175934 TTTTGACCCCGAAACT
1 TTTTAACCCCGAAACT
13175950 CTCGAAATTA
Statistics
Matches: 214, Mismatches: 29, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
56 1 0.00
57 36 0.17
58 68 0.32
59 66 0.31
60 28 0.13
61 15 0.07
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
TTTTAACCCCGAAACTTCCAAAAATTACATTTTAACCTCGAAACTTCCAAAAATTACAT
Found at i:13175833 original size:58 final size:58
Alignment explanation
Indices: 13175640--13175995 Score: 310
Period size: 58 Copynumber: 6.1 Consensus size: 58
13175630 AGAAATTGTA
* * * * * ** *
13175640 TTTTGACCCCCAAACTTCTCCAAAATTACATTTTAACCTTGAAACTTCTCCTAAATTACAT
1 TTTTAACCCCGAAACTT-TCGAAAATTACATTTTACCCTCG-AACTTC-CAAAAATTCCAT
* * * * * *
13175701 TTTTAACCTCGAAACTTCCAAAAATTACATTTTAACCTTGAAACTTCCAAAAATTACAT
1 TTTTAACCCCGAAACTTTCGAAAATTACATTTTACCCTCG-AACTTCCAAAAATTCCAT
* *
13175760 TTTTGACCCCAAAACTTTCGAAAATTACATTTTACCCTCGAACTTCCAAAAATTCCAT
1 TTTTAACCCCGAAACTTTCGAAAATTACATTTTACCCTCGAACTTCCAAAAATTCCAT
* * *
13175818 TTTTAACCTCGAAACTTCTCG-AAATTACATTTTTACCCCCAAACTTCCAAAAATTCCA-
1 TTTTAACCCCGAAACTT-TCGAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTCCAT
* * * * *
13175876 TTTTAACCCC-AAACTTCCAAAAATTTCATTTATGACCC-CAAACTTCCAAAAATTTCAT
1 TTTTAACCCCGAAACTTTCGAAAATTACATTT-T-ACCCTCGAACTTCCAAAAATTCCAT
* * * * * *
13175934 TTTTGACCCCGAAACTCTCG-AAATTACCATTTCACCCTAGGA-TGTCCAAAAATCCCAT
1 TTTTAACCCCGAAACTTTCGAAAATTA-CATTTTACCCTCGAACT-TCCAAAAATTCCAT
13175992 TTTT
1 TTTT
13175996 GATCTCGATT
Statistics
Matches: 249, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
56 4 0.02
57 37 0.15
58 83 0.33
59 83 0.33
60 28 0.11
61 14 0.06
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (58 bp):
TTTTAACCCCGAAACTTTCGAAAATTACATTTTACCCTCGAACTTCCAAAAATTCCAT
Found at i:13175958 original size:29 final size:30
Alignment explanation
Indices: 13175640--13175949 Score: 289
Period size: 29 Copynumber: 10.5 Consensus size: 30
13175630 AGAAATTGTA
* *
13175640 TTTTGACCCCCAAACTTCTCCAAAATTACA-
1 TTTTGACCCCGAAACTTC-CAAAAATTACAT
* ** **
13175670 TTTTAACCTTGAAACTTCTCCTAAATTACAT
1 TTTTGACCCCGAAACTTC-CAAAAATTACAT
* *
13175701 TTTTAACCTCGAAACTTCCAAAAATTACA-
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* **
13175730 TTTTAACCTTGAAACTTCCAAAAATTACAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* * *
13175760 TTTTGACCCCAAAACTTTCGAAAATTACA-
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
*
13175789 TTTT-ACCCTCG-AACTTCCAAAAATTCCAT
1 TTTTGACCC-CGAAACTTCCAAAAATTACAT
* * *
13175818 TTTTAACCTCGAAACTTCTC-GAAATTACAT
1 TTTTGACCCCGAAACTTC-CAAAAATTACAT
* *
13175848 TTTT-ACCCCCAAACTTCCAAAAATTCCA-
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* *
13175876 TTTTAACCCC-AAACTTCCAAAAATTTCAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
* *
13175905 TTATGACCCC-AAACTTCCAAAAATTTCAT
1 TTTTGACCCCGAAACTTCCAAAAATTACAT
13175934 TTTTGACCCCGAAACT
1 TTTTGACCCCGAAACT
13175950 CTCGAAATTA
Statistics
Matches: 239, Mismatches: 30, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
28 40 0.17
29 98 0.41
30 83 0.35
31 18 0.08
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTTGACCCCGAAACTTCCAAAAATTACAT
Found at i:13175982 original size:87 final size:87
Alignment explanation
Indices: 13175713--13175993 Score: 272
Period size: 87 Copynumber: 3.2 Consensus size: 87
13175703 TTAACCTCGA
* **
13175713 AACTTCCAAAAATTACATTT-TAACCTTGAAACTTCCAAAAATTACATTTTTGACCCCAAAACTT
1 AACTTCCAAAAATTCCATTTATAACCTCCAAACTTCCAAAAATTACATTTTTGACCCCAAAAC-T
* *
13175777 TCGAAAATTA-CATTTTACCCTCG
65 TCG-AAATTACCATTTAACCCTAG
* * * *
13175800 AACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCTC-GAAATTACATTTTT-ACCCCCAAACT
1 AACTTCCAAAAATTCCATTTATAACCTCCAAACTTC-CAAAAATTACATTTTTGACCCCAAAACT
* *
13175863 TCCAAAAATT-CCATTTTAACCCCA-
65 T-C-GAAATTACCA-TTTAACCCTAG
* * * *
13175887 AACTTCCAAAAATTTCATTTATGACC-CCAAACTTCCAAAAATTTCATTTTTGACCCCGAAACTC
1 AACTTCCAAAAATTCCATTTATAACCTCCAAACTTCCAAAAATTACATTTTTGACCCCAAAACT-
*
13175951 TCGAAATTACCATTTCACCCTAG
65 TCGAAATTACCATTTAACCCTAG
* *
13175974 GA-TGTCCAAAAATCCCATTT
1 AACT-TCCAAAAATTCCATTT
13175994 TTGATCTCGA
Statistics
Matches: 161, Mismatches: 21, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
85 1 0.01
86 36 0.22
87 88 0.55
88 35 0.22
89 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTATAACCTCCAAACTTCCAAAAATTACATTTTTGACCCCAAAACTT
CGAAATTACCATTTAACCCTAG
Found at i:13176127 original size:28 final size:28
Alignment explanation
Indices: 13176071--13176130 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
13176061 AATTTTTCCA
* * *
13176071 AAAATTACCATTTTTCCCTCGTAAGTCC
1 AAAATTACCATTTTACCCCCGGAAGTCC
13176099 AAAATTACCATTTTACCCCCGGACA-TCC
1 AAAATTACCATTTTACCCCCGGA-AGTCC
13176127 AAAA
1 AAAA
13176131 AGTCTTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.30, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGGAAGTCC
Found at i:13176129 original size:146 final size:146
Alignment explanation
Indices: 13175954--13176263 Score: 342
Period size: 146 Copynumber: 2.1 Consensus size: 146
13175944 GAAACTCTCG
* * ** * *
13175954 AAATTACCATTTCACCCTAGGATGTCCAAAAA-TCCCATTT-TTGATCTCGATTTTTCTAAAAAT
1 AAATTACCATTTTACCCCAGGACATCCAAAAAGTCCCATTTATTGATCTCGATTCTTCCAAAAAT
* * * *
13176017 TATCGTTTTGCCCTC-GA-TTGTCTAAAATGTCATTTCTAACCCAAAATTTTTCCAAAAATTACC
66 TATCATTTTACCCGCAGACAT-T-TAAAATGTCATTTCTAACCC-AAA-TTTTCCAAAAATTACC
*
13176080 ATTTTTCCCTCGTA-AGTCCA
127 ATTTTGCCCTCG-AGAGTCCA
* *** *
13176100 AAATTACCATTTTACCCCCGGACATCCAAAAAGTCTTGTTTATTGATCTCGATTCTTCCGAAAAT
1 AAATTACCATTTTACCCCAGGACATCCAAAAAGTCCCATTTATTGATCTCGATTCTTCCAAAAAT
* * * *
13176165 TATCATTTTATCCGCAGACATTTAAAATGTTATTTCTAACCCAAATTTTCCCAAAATTATCATTT
66 TATCATTTTACCCGCAGACATTTAAAATGTCATTTCTAACCCAAATTTTCCAAAAATTACCATTT
*
13176230 TGCCCTCGAGAGTCTA
131 TGCCCTCGAGAGTCCA
*
13176246 AAATTACCATTTTGCCCC
1 AAATTACCATTTTACCCC
13176264 TGGGTATTCA
Statistics
Matches: 137, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
145 1 0.01
146 74 0.54
147 8 0.06
148 50 0.36
149 3 0.02
150 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (146 bp):
AAATTACCATTTTACCCCAGGACATCCAAAAAGTCCCATTTATTGATCTCGATTCTTCCAAAAAT
TATCATTTTACCCGCAGACATTTAAAATGTCATTTCTAACCCAAATTTTCCAAAAATTACCATTT
TGCCCTCGAGAGTCCA
Found at i:13176164 original size:148 final size:146
Alignment explanation
Indices: 13175994--13176263 Score: 348
Period size: 148 Copynumber: 1.8 Consensus size: 146
13175984 AATCCCATTT
* * * * * *
13175994 TTGATCTCGATTTTTCTAAAAATTATCGTTTTGCCCTC-GA-TTGTCTAAAATGTCATTTCTAAC
1 TTGATCTCGATTCTTCCAAAAATTATCATTTTACCCGCAGACAT-T-TAAAATGTCATTTCTAAC
*
13176057 CCAAAATTTTTCCAAAAATTACCATTTTTCCCTCGTA-AGTCCAAAATTACCATTTTACCCCCGG
64 CC-AAA-TTTTCCAAAAATTACCATTTTGCCCTCG-AGAGTCCAAAATTACCATTTTACCCCCGG
13176121 ACATCCAAAAAGTCTTGTTTA
126 ACATCCAAAAAGTCTTGTTTA
* * *
13176142 TTGATCTCGATTCTTCCGAAAATTATCATTTTATCCGCAGACATTTAAAATGTTATTTCTAACCC
1 TTGATCTCGATTCTTCCAAAAATTATCATTTTACCCGCAGACATTTAAAATGTCATTTCTAACCC
* * * *
13176207 AAATTTTCCCAAAATTATCATTTTGCCCTCGAGAGTCTAAAATTACCATTTTGCCCC
66 AAATTTTCCAAAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTTACCCC
13176264 TGGGTATTCA
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
145 1 0.01
146 47 0.45
147 3 0.03
148 50 0.48
149 3 0.03
150 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.38
Consensus pattern (146 bp):
TTGATCTCGATTCTTCCAAAAATTATCATTTTACCCGCAGACATTTAAAATGTCATTTCTAACCC
AAATTTTCCAAAAATTACCATTTTGCCCTCGAGAGTCCAAAATTACCATTTTACCCCCGGACATC
CAAAAAGTCTTGTTTA
Found at i:13185123 original size:39 final size:39
Alignment explanation
Indices: 13185073--13185677 Score: 377
Period size: 39 Copynumber: 15.5 Consensus size: 39
13185063 TTGAAGATTT
* * *
13185073 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAAACATC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * ** * *
13185112 CAATCTTTTACCCCGAGCTTAGGGCAAATCACCATCAAC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * **
13185151 CAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCATC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * * * * * *
13185190 CGATGTTTTACCCCGAGCTTGGGGTAGA-T-CATTGTCAGC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCA--ATCATC
* * * * * *
13185229 CAATCTCTTACCCCGAGCCTCGGGCAGATTGTAACCTTT
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* ** * * *
13185268 CAATCTTTTACCCCGAGCTTAGGGCAGATCACCATTAGC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * * **
13185307 CAATCTCTTACCCCAAGCTTGGGGTAGATTGCAGCCATC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * * * ** * *
13185346 CGATCTTTTACCCCGAGGTTGGGGCAGATCACCATCAGC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * * * **
13185385 CAATCTCTTACCCAGAGCTTGGGGTAGATTGTAGCCATC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * * * * ** * *
13185424 CGATCTTTTACCTCGAGCCTAGGGCAAATCACCATCAAC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * *
13185463 CAATCTCTTACCTCGAGCTTAGGGCAGATTGCAGTCATT
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * ** * ** * *
13185502 CGATCTTTTACCTTGAGCTTGGGGCAGATCACTATCACC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * ** *
13185541 CAATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCTTC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * ** * *
13185580 CAATCTTTTACCTCGAGCTTAGGGCAGATCACCATCAAC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* * * *
13185619 TAATCTCTTACCTCGAACTTAGGGCAGATTGCAGTCATC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
* *
13185658 CGATCTTTTACCCCGAGCTT
1 CAATCTCTTACCCCGAGCTT
13185678 GAGGTAGATC
Statistics
Matches: 405, Mismatches: 157, Indels: 8
0.71 0.28 0.01
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 401 0.99
40 1 0.00
41 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAATCATC
Found at i:13185357 original size:156 final size:156
Alignment explanation
Indices: 13185073--13185734 Score: 860
Period size: 156 Copynumber: 4.2 Consensus size: 156
13185063 TTGAAGATTT
* *
13185073 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAAACATCCAATCTTTTACCCCGAGCTTAGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATCCAATCTTTTACCCCGAGCTTAGGGCA
* * * *
13185138 AATCACCATCAACCAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCATCCGATGTTTTACCC
66 AATCACCATCAACCAATCTCTTACCCCAAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCC
* ***
13185203 CGAGCTTGGGGTAGATCATTGTCAGC
131 CGAGCTTGGGGCAGATCACCATCAGC
* * *
13185229 CAATCTCTTACCCCGAGCCTCGGGCAGATTGTAACCTTTCAATCTTTTACCCCGAGCTTAGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATCCAATCTTTTACCCCGAGCTTAGGGCA
* * * * *
13185294 GATCACCATTAGCCAATCTCTTACCCCAAGCTTGGGGTAGATTGCAGCCATCCGATCTTTTACCC
66 AATCACCATCAACCAATCTCTTACCCCAAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCC
*
13185359 CGAGGTTGGGGCAGATCACCATCAGC
131 CGAGCTTGGGGCAGATCACCATCAGC
* * * * * * *
13185385 CAATCTCTTACCCAGAGCTTGGGGTAGATTGTAGCCATCCGATCTTTTACCTCGAGCCTAGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATCCAATCTTTTACCCCGAGCTTAGGGCA
* * * * *
13185450 AATCACCATCAACCAATCTCTTACCTCGAGCTTAGGGCAGATTGCAGTCATTCGATCTTTTACCT
66 AATCACCATCAACCAATCTCTTACCCCAAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCC
* * *
13185515 TGAGCTTGGGGCAGATCACTATCACC
131 CGAGCTTGGGGCAGATCACCATCAGC
* * * *
13185541 CAATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCTTCCAATCTTTTACCTCGAGCTTAGGGCA
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATCCAATCTTTTACCCCGAGCTTAGGGCA
* * * *
13185606 GATCACCATCAACTAATCTCTTACCTCGAA-CTTAGGGCAGATTGCAGTCATCCGATCTTTTACC
66 AATCACCATCAACCAATCTCTTACC-CCAAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACC
* * *
13185670 CCGAGCTTGAGGTAGATCACCACCAGC
130 CCGAGCTTGGGGCAGATCACCATCAGC
* * *
13185697 CAATCTCTTA-CCTGAAGCCTGAGGAAGATTGTAACCAT
1 CAATCTCTTACCCCG-AGCCTGGGGCAGATTGTAACCAT
13185735 TCGATCTCTT
Statistics
Matches: 437, Mismatches: 67, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
155 3 0.01
156 433 0.99
157 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (156 bp):
CAATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATCCAATCTTTTACCCCGAGCTTAGGGCA
AATCACCATCAACCAATCTCTTACCCCAAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCC
CGAGCTTGGGGCAGATCACCATCAGC
Found at i:13185709 original size:78 final size:78
Alignment explanation
Indices: 13185073--13185708 Score: 761
Period size: 78 Copynumber: 8.2 Consensus size: 78
13185063 TTGAAGATTT
* ** *
13185073 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAAACATCCAATCTTTTACCCCGAGCTTAGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
* *
13185138 AATCACCATCAAC
66 GATCACCATCAGC
* * * *
13185151 CAATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCATCCGATGTTTTACCCCGAGCTTGGGGTA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
***
13185216 GATCATTGTCAGC
66 GATCACCATCAGC
* * * * * * *
13185229 CAATCTCTTACCCCGAGCCTCGGGCAGATTGTAACCTTTCAATCTTTTACCCCGAGCTTAGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
*
13185294 GATCACCATTAGC
66 GATCACCATCAGC
* * * *
13185307 CAATCTCTTACCCCAAGCTTGGGGTAGATTGCAGCCATCCGATCTTTTACCCCGAGGTTGGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
13185372 GATCACCATCAGC
66 GATCACCATCAGC
* * * * *
13185385 CAATCTCTTACCCAGAGCTTGGGGTAGATTGTAGCCATCCGATCTTTTACCTCGAGCCTAGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
* *
13185450 AATCACCATCAAC
66 GATCACCATCAGC
* * * * ** *
13185463 CAATCTCTTACCTCGAGCTTAGGGCAGATTGCAGTCATTCGATCTTTTACCTTGAGCTTGGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
* *
13185528 GATCACTATCACC
66 GATCACCATCAGC
* * * * * *
13185541 CAATCTCTTACCCCGAGCCTAGGGCAGATTGTAGCCTTCCAATCTTTTACCTCGAGCTTAGGGCA
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
*
13185606 GATCACCATCAAC
66 GATCACCATCAGC
* * * * * *
13185619 TAATCTCTTACCTCGAACTTAGGGCAGATTGCAGTCATCCGATCTTTTACCCCGAGCTT-GAGGT
1 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAG-GGC
*
13185683 AGATCACCACCAGC
65 AGATCACCATCAGC
13185697 CAATCTCTTACC
1 CAATCTCTTACC
13185709 TGAAGCCTGA
Statistics
Matches: 473, Mismatches: 84, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
77 1 0.00
78 472 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (78 bp):
CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTAGGGCA
GATCACCATCAGC
Found at i:13187863 original size:30 final size:30
Alignment explanation
Indices: 13187768--13187947 Score: 242
Period size: 30 Copynumber: 6.0 Consensus size: 30
13187758 CTCAAGAGGT
**
13187768 CCCTCAAACTTTTCCAAAATTACA-TTCGAC
1 CCCT-AAACTTTTCCAAAATTACATTTTAAC
* * *
13187798 CCCTAAAATTTTTCAAAATCACATTTTAA-
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
13187827 CCCTAAACTTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
*
13187857 CCCTAAACTTTTTCAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
13187887 CCCTAAAC-TTTCCTAAAATTACATTTTAA-
1 CCCTAAACTTTTCC-AAAATTACATTTTAAC
*
13187916 CCCTCAAACTTTTCCAAAATCACATTTTAAC
1 CCCT-AAACTTTTCCAAAATTACATTTTAAC
13187947 C
1 C
13187948 TCGGATTCTC
Statistics
Matches: 133, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
29 50 0.38
30 77 0.58
31 6 0.05
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.36
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:13189253 original size:24 final size:24
Alignment explanation
Indices: 13189202--13189256 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
13189192 TCTTTTAGTT
*
13189202 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* *
13189226 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
13189250 AAACTCT
1 AAACTCT
13189257 TATTACTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:13191236 original size:24 final size:24
Alignment explanation
Indices: 13191185--13191239 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
13191175 TCTTTTAGTT
*
13191185 AAACTCTGTTTATTTGCTTCAATT
1 AAACTCTGTTTATTTGCTTCAATC
* * *
13191209 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGCTTCAATC
13191233 AAACTCT
1 AAACTCT
13191240 TATTACTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTATTTGCTTCAATC
Found at i:13201582 original size:33 final size:33
Alignment explanation
Indices: 13201538--13201605 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
13201528 TTGTCGTGAG
13201538 ACCACTAGAATTGGAATTAAAGTCATTACCAAA
1 ACCACTAGAATTGGAATTAAAGTCATTACCAAA
*
13201571 ACCACTGGAATTGGAATTAAAGTCATTACCAAA
1 ACCACTAGAATTGGAATTAAAGTCATTACCAAA
13201604 AC
1 AC
13201606 ACTTGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (33 bp):
ACCACTAGAATTGGAATTAAAGTCATTACCAAA
Found at i:13205720 original size:13 final size:14
Alignment explanation
Indices: 13205702--13205731 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13205692 GTCAATGCAA
13205702 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
13205715 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
13205729 TCA
1 TCA
13205732 ATGTATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:13216116 original size:44 final size:44
Alignment explanation
Indices: 13216053--13216148 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
13216043 ACAGATAATT
*
13216053 CTATCGTATATCGATCCCACAAGGAAATGGGTTCTTGATCTTAA
1 CTATCGGATATCGATCCCACAAGGAAATGGGTTCTTGATCTTAA
* *
13216097 CTATCGGATATCGATCCCACGAGGAAATGGGTTCTTGATGTTAA
1 CTATCGGATATCGATCCCACAAGGAAATGGGTTCTTGATCTTAA
*
13216141 CTGTCGGA
1 CTATCGGA
13216149 GCAATTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (44 bp):
CTATCGGATATCGATCCCACAAGGAAATGGGTTCTTGATCTTAA
Found at i:13216261 original size:13 final size:14
Alignment explanation
Indices: 13216243--13216272 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13216233 ATCAATGCAA
13216243 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
13216256 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
13216270 TCA
1 TCA
13216273 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:13221757 original size:26 final size:27
Alignment explanation
Indices: 13221708--13221800 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
13221698 TAAGATGACT
* *
13221708 ATATAAAA-AATTTCAATAAATAAAAAA
1 ATATAAAATAATTTAAAT-ATTAAAAAA
*
13221735 ATATAAAATTA-TTAAATATTAAAATAA
1 ATATAAAATAATTTAAATATTAAAA-AA
*
13221762 A-ATAAAATAATTTAAATTTTTAAAAAA
1 ATATAAAATAATTTAAA-TATTAAAAAA
* *
13221789 TTAAAAAATAAT
1 ATATAAAATAAT
13221801 ATGGGCGGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 14 0.26
27 23 0.43
28 17 0.31
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATAAAATAATTTAAATATTAAAAAA
Found at i:13221765 original size:36 final size:36
Alignment explanation
Indices: 13221711--13221794 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
13221701 GATGACTATA
**
13221711 TAAAAAATTTCAAT-AAATAAAAAAATATAAAATTAT
1 TAAAAAATTAAAATAAAATAAAAAAAT-TAAAATTAT
* * * *
13221747 T-AAATATTAAAATAAAATAAAATAATTTAAATTTT
1 TAAAAAATTAAAATAAAATAAAAAAATTAAAATTAT
13221782 TAAAAAATTAAAA
1 TAAAAAATTAAAA
13221795 AATAATATGG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
35 17 0.44
36 22 0.56
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (36 bp):
TAAAAAATTAAAATAAAATAAAAAAATTAAAATTAT
Found at i:13223246 original size:51 final size:49
Alignment explanation
Indices: 13223116--13223271 Score: 210
Period size: 50 Copynumber: 3.2 Consensus size: 49
13223106 ATAAAATATT
* * *
13223116 TGAAC-AAACAATATAAATAAATATTTATATTTATGTAAAACACCAAATC
1 TGAACAAAACAATTTAAATAAATATTTATTTTTAT-TAAAACACCAGATC
* *
13223165 TGAATAGAACAATTTAAATAAATATTTATTTTTATATAAAACACCAGATC
1 TGAACAAAACAATTTAAATAAATATTTATTTTTAT-TAAAACACCAGATC
*
13223215 TGAACAAAAGCAATTTAAATAAATATTTA-TTTT-TTAAAGCACCAGATC
1 TGAACAAAA-CAATTTAAATAAATATTTATTTTTATTAAAACACCAGATC
13223263 TGAACAAAA
1 TGAACAAAA
13223272 TAATCTAGAT
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
48 22 0.23
49 5 0.05
50 50 0.52
51 19 0.20
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (49 bp):
TGAACAAAACAATTTAAATAAATATTTATTTTTATTAAAACACCAGATC
Found at i:13224675 original size:11 final size:11
Alignment explanation
Indices: 13224661--13224690 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
13224651 AGTTTTTTAA
13224661 TATATTTTAGT
1 TATATTTTAGT
13224672 TATATTTTAGT
1 TATATTTTAGT
13224683 TATATTTT
1 TATATTTT
13224691 TAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TATATTTTAGT
Found at i:13224873 original size:23 final size:23
Alignment explanation
Indices: 13224828--13224899 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 23
13224818 AAAATATTTA
* *
13224828 AAATTAAAAT-TAAAATTAGAAGG
1 AAATTAAAATAAAAAATGA-AAGG
13224851 AAATTAAAATAAAAAATGAAAGG
1 AAATTAAAATAAAAAATGAAAGG
13224874 AGAATTATAAAAAATAAAAAATGAAA
1 A-AA-T-T--AAAATAAAAAATGAAA
13224900 ATAGCAAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 15 0.37
24 8 0.20
25 1 0.02
26 1 0.02
28 16 0.39
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (23 bp):
AAATTAAAATAAAAAATGAAAGG
Found at i:13227644 original size:22 final size:23
Alignment explanation
Indices: 13227610--13227656 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
13227600 AAATTTATGT
13227610 TATTAAAATAAAAT-ATAAAAATA
1 TATTAAAATAAAATAAT-AAAATA
*
13227633 TATTCAAA-AAAATAATAAAATA
1 TATTAAAATAAAATAATAAAATA
13227655 TA
1 TA
13227657 AAAAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TATTAAAATAAAATAATAAAATA
Found at i:13231559 original size:17 final size:17
Alignment explanation
Indices: 13231510--13231568 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
13231500 CTAATTAGAA
* *
13231510 TTTTTATTATAAGGATT
1 TTTTTATAATAAAGATT
* *
13231527 TTTATTCTAAT-TAGATT
1 TTT-TTATAATAAAGATT
13231544 TTTTTATAATAAAGATT
1 TTTTTATAATAAAGATT
*
13231561 ATTTTATA
1 TTTTTATA
13231569 TGATTGAGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 6 0.18
17 22 0.67
18 5 0.15
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58
Consensus pattern (17 bp):
TTTTTATAATAAAGATT
Found at i:13247769 original size:20 final size:21
Alignment explanation
Indices: 13247733--13247782 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
13247723 TCATTAAGCT
*
13247733 TTAATT-AATCATTTTTA-ATC
1 TTAATTAAATCATATTTACA-C
13247753 TTAATTAAATC-TATTTACAC
1 TTAATTAAATCATATTTACAC
13247773 TTAATATAAA
1 TTAAT-TAAA
13247783 CCATGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTAAATCATATTTACAC
Found at i:13250866 original size:13 final size:14
Alignment explanation
Indices: 13250848--13250877 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13250838 GTCAACGTAA
13250848 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
13250861 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
13250875 TCA
1 TCA
13250878 ATGCACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:13253232 original size:23 final size:24
Alignment explanation
Indices: 13253202--13253251 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
13253192 TAATCATCAC
13253202 TTATCAAACCATATTGTGT-TTTT
1 TTATCAAACCATATTGTGTCTTTT
*
13253225 TTATCAAATCATATTGTGTCTTTT
1 TTATCAAACCATATTGTGTCTTTT
13253249 TTA
1 TTA
13253252 ATTCACCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (24 bp):
TTATCAAACCATATTGTGTCTTTT
Found at i:13257018 original size:18 final size:18
Alignment explanation
Indices: 13256992--13257034 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
13256982 GGAAATTTAT
* *
13256992 GAAACAGTTGTTATCAAA
1 GAAAAAGTTATTATCAAA
13257010 GAAAAAGTTATTATCAAA
1 GAAAAAGTTATTATCAAA
13257028 GAAAAAG
1 GAAAAAG
13257035 AAATTGTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (18 bp):
GAAAAAGTTATTATCAAA
Found at i:13270462 original size:21 final size:22
Alignment explanation
Indices: 13270438--13270479 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
13270428 GATTATACTT
13270438 GTATTGATAG-AACTTGCACAA
1 GTATTGATAGAAACTTGCACAA
* *
13270459 GTATTGGTAGAAATTTGCACA
1 GTATTGATAGAAACTTGCACA
13270480 GTTTCTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (22 bp):
GTATTGATAGAAACTTGCACAA
Found at i:13297064 original size:9 final size:9
Alignment explanation
Indices: 13297050--13297092 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
13297040 GGGCAGTGTC
13297050 TTCTTCTTT
1 TTCTTCTTT
*
13297059 TTCTTCCTT
1 TTCTTCTTT
*
13297068 CTCTTCTTT
1 TTCTTCTTT
13297077 CTTCTTCTTT
1 -TTCTTCTTT
13297087 TTCTTC
1 TTCTTC
13297093 AATACCCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:13298767 original size:24 final size:24
Alignment explanation
Indices: 13298740--13298786 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
13298730 TGTAAAAACT
13298740 AAAGA-AACAAATTAA-AGTAAAATA
1 AAAGACAA-AAATTAACAG-AAAATA
13298764 AAAGACAAAAATTAACAGAAAAT
1 AAAGACAAAAATTAACAGAAAAT
13298787 TGTAATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.70, C:0.06, G:0.09, T:0.15
Consensus pattern (24 bp):
AAAGACAAAAATTAACAGAAAATA
Found at i:13306488 original size:23 final size:22
Alignment explanation
Indices: 13306436--13306489 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
13306426 TAGGGAGAAA
*
13306436 ACAT-ATGTTCTTTCTAGTACT
1 ACATCATGTTCTTTCTAGTACC
* *
13306457 ATCAACATGTTCTTTCCTATTACC
1 A-CATCATGTTCTTT-CTAGTACC
13306481 ACATCATGT
1 ACATCATGT
13306490 AGTCTTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 2 0.08
23 16 0.62
24 7 0.27
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (22 bp):
ACATCATGTTCTTTCTAGTACC
Found at i:13309343 original size:6 final size:6
Alignment explanation
Indices: 13309334--13309369 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
13309324 TATATTATCA
* *
13309334 TGAGAT TGAGAT TGAGAT TGTGAT TGAGAC TGAGAT
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT
13309370 ATACTTGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (6 bp):
TGAGAT
Found at i:13316731 original size:17 final size:16
Alignment explanation
Indices: 13316711--13316759 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
13316701 CATATCTCCT
13316711 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTT-A
*
13316728 TTGTCACTGCATTTGTA
1 TTGTCATTGCATTT-TA
*
13316745 TTGTCATTGTATTTT
1 TTGTCATTGCATTTT
13316760 CATTTGTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.55
Consensus pattern (16 bp):
TTGTCATTGCATTTTA
Found at i:13317866 original size:26 final size:26
Alignment explanation
Indices: 13317810--13317866 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
13317800 AGCATTGCAC
* * **
13317810 CCAGAATTGTCGCTGCAGGAACCTGT
1 CCAGAATTATCACTGCAGGAAAATGT
* *
13317836 TCAGAATTATCACTGCATGAAAATGT
1 CCAGAATTATCACTGCAGGAAAATGT
13317862 CCAGA
1 CCAGA
13317867 GTGTCGCTGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (26 bp):
CCAGAATTATCACTGCAGGAAAATGT
Found at i:13331868 original size:15 final size:15
Alignment explanation
Indices: 13331849--13331888 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
13331839 TAACCAGTAG
13331849 AAAGAGAAGGAAGAA
1 AAAGAGAAGGAAGAA
*
13331864 GAAGAGAAGGAAGAA
1 AAAGAGAAGGAAGAA
13331879 AAAGAAGAAG
1 AAAG-AGAAG
13331889 AGAATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGGAAGAA
Found at i:13342763 original size:22 final size:23
Alignment explanation
Indices: 13342733--13342775 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
13342723 TAAAGTGGGT
13342733 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
13342756 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
13342776 TGGACATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:13352152 original size:203 final size:203
Alignment explanation
Indices: 13351803--13352209 Score: 762
Period size: 203 Copynumber: 2.0 Consensus size: 203
13351793 TTTCTAAACA
13351803 TCCAAATAAACTCGTAAGCGAAAAACTACCCCTTAACCTCAGATCTCAAAACATCGCCAAAAGTT
1 TCCAAATAAACTCGTAAGCGAAAAACTACCCCTTAACCTCAGATCTCAAAACATCGCCAAAAGTT
13351868 AACCCAATCACGTGCATAAGGTCCTTTTTATCACATTCCGAAGGACTAGGACCAATTTTAAGCAA
66 AACCCAATCACGTGCATAAGGTCCTTTTTATCACATTCCGAAGGACTAGGACCAATTTTAAGCAA
*
13351933 GGATGGCGACCAAATCAGCTTTAGCTAGCTATGTTCCTTTGCCACCAAAAATCGATCAAACACAA
131 GGATGGCGACCAAATCAGCTTTAGCTAGCTACGTTCCTTTGCCACCAAAAATCGATCAAACACAA
13351998 TAACTTGC
196 TAACTTGC
*
13352006 TCCAAATAAACTTGTAAGCGAAAAACTACCCCTTAACCTCAGATCTCAAAACATCGCCAAAAGTT
1 TCCAAATAAACTCGTAAGCGAAAAACTACCCCTTAACCTCAGATCTCAAAACATCGCCAAAAGTT
13352071 AACCCAATCACGTGCATAAGGTCCTTTTTATCACATTCC-AGAGGACTAGGACCAATTTTAAGCA
66 AACCCAATCACGTGCATAAGGTCCTTTTTATCACATTCCGA-AGGACTAGGACCAATTTTAAGCA
* *
13352135 AGGATGGCGACCAAATCAGCTTTAGCTAGCTACGTTCCTTTGCCACTAAAAATTGATCAAACACA
130 AGGATGGCGACCAAATCAGCTTTAGCTAGCTACGTTCCTTTGCCACCAAAAATCGATCAAACACA
13352200 ATAACTTGC
195 ATAACTTGC
13352209 T
1 T
13352210 TACAAAACTA
Statistics
Matches: 199, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
202 1 0.01
203 198 0.99
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (203 bp):
TCCAAATAAACTCGTAAGCGAAAAACTACCCCTTAACCTCAGATCTCAAAACATCGCCAAAAGTT
AACCCAATCACGTGCATAAGGTCCTTTTTATCACATTCCGAAGGACTAGGACCAATTTTAAGCAA
GGATGGCGACCAAATCAGCTTTAGCTAGCTACGTTCCTTTGCCACCAAAAATCGATCAAACACAA
TAACTTGC
Done.