Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 21 of 24
Found at i:3452253 original size:58 final size:58
Alignment explanation
Indices: 3452101--3452254 Score: 143
Period size: 58 Copynumber: 2.7 Consensus size: 58
3452091 GCTTTATAAA
* * * *
3452101 ATCCAAGT-CATTAGATCATGGTAAATGACCT-AATGACATCAAAATACATGAAACAAT
1 ATCCAAGTCCA-TAGATCATGGTAAATAACCTAAATGGCATCAAAATACATAAAACAAC
** * * * * * **
3452158 ATAAAAATCCTTAGATCATGGAAAATAAAC-AACATGGCATCAAAATTCATAAAATTAC
1 ATCCAAGTCCATAGATCATGGTAAATAACCTAA-ATGGCATCAAAATACATAAAACAAC
*
3452216 ATCCAAGTCCATGGATCATGGTAAATAACCTAAATGGCA
1 ATCCAAGTCCATAGATCATGGTAAATAACCTAAATGGCA
3452255 GTAAAATGTG
Statistics
Matches: 73, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
57 22 0.30
58 49 0.67
59 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (58 bp):
ATCCAAGTCCATAGATCATGGTAAATAACCTAAATGGCATCAAAATACATAAAACAAC
Found at i:3453269 original size:20 final size:20
Alignment explanation
Indices: 3453244--3453297 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
3453234 AGTCAACCTT
3453244 CTATGTATCGATACAAATAC
1 CTATGTATCGATACAAATAC
3453264 CTATGTATCGATACAAATAC
1 CTATGTATCGATACAAATAC
3453284 CTATGTATCGATAC
1 CTATGTATCGATAC
3453298 TTTGAGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (20 bp):
CTATGTATCGATACAAATAC
Found at i:3454668 original size:61 final size:61
Alignment explanation
Indices: 3454573--3454695 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
3454563 AGATAAAGTA
3454573 AGCGAGGTTGGAACAACAACCAGTTCGGATCATGTGAAGGCGCCAATAATCAGAGATACTG
1 AGCGAGGTTGGAACAACAACCAGTTCGGATCATGTGAAGGCGCCAATAATCAGAGATACTG
3454634 AGCGAGGTTGGAACAACAACCAGTTCGGATCATGTGAAGGCGCCAATAATCAGAGATACTG
1 AGCGAGGTTGGAACAACAACCAGTTCGGATCATGTGAAGGCGCCAATAATCAGAGATACTG
3454695 A
1 A
3454696 TGTAGACACC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.18
Consensus pattern (61 bp):
AGCGAGGTTGGAACAACAACCAGTTCGGATCATGTGAAGGCGCCAATAATCAGAGATACTG
Found at i:3455039 original size:13 final size:13
Alignment explanation
Indices: 3455021--3455045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3455011 CATAGAGTGT
3455021 TGTATCGATACAA
1 TGTATCGATACAA
3455034 TGTATCGATACA
1 TGTATCGATACA
3455046 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3455043 original size:33 final size:33
Alignment explanation
Indices: 3455001--3455067 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3454991 TTCAACGATT
3455001 TGTATCGATACATAGAGTGTTGTATCGATACAA
1 TGTATCGATACATAGAGTGTTGTATCGATACAA
*** *
3455034 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAGAGTGTTGTATCGATACAA
3455067 T
1 T
3455068 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAGAGTGTTGTATCGATACAA
Found at i:3455126 original size:13 final size:13
Alignment explanation
Indices: 3455108--3455132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3455098 ATCACTTAAA
3455108 TGTATCGATACAT
1 TGTATCGATACAT
3455121 TGTATCGATACA
1 TGTATCGATACA
3455133 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3455197 original size:52 final size:52
Alignment explanation
Indices: 3455141--3455321 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
3455131 CACTGATCTT
* *
3455141 TGTATCGATACATGCAGGCAAAGTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3455193 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
3455245 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3455297 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3455322 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3459462 original size:10 final size:10
Alignment explanation
Indices: 3459447--3459473 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3459437 TGCTAACTAA
3459447 GTTTTTGTTT
1 GTTTTTGTTT
3459457 GTTTTTGTTT
1 GTTTTTGTTT
3459467 GTTTTTG
1 GTTTTTG
3459474 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:3469168 original size:1 final size:1
Alignment explanation
Indices: 3469162--3469278 Score: 90
Period size: 1 Copynumber: 117.0 Consensus size: 1
3469152 GGCGTCCTCC
* ** * ** ** *
3469162 AAAAAAAAAAAAACAAAAAAAATGAAAAAACAAAAAAAAATGAATGAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
3469227 CAAAACAAAAAAAAAAACAAAAACAAAAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3469279 GGGGGTCCGG
Statistics
Matches: 87, Mismatches: 29, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 87 1.00
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:3469189 original size:17 final size:16
Alignment explanation
Indices: 3469162--3469278 Score: 128
Period size: 17 Copynumber: 6.8 Consensus size: 16
3469152 GGCGTCCTCC
3469162 AAAAAAAAAAAAACAA
1 AAAAAAAAAAAAACAA
*
3469178 AAAAAATGAAAAAACAA
1 AAAAAA-AAAAAAACAA
3469195 AAAAAAATGAATGAAAA-AA
1 AAAAAAA--AA--AAAACAA
*
3469214 AAAACAAAAAAAACAA
1 AAAAAAAAAAAAACAA
3469230 AACAAAAAAAAAAACAA
1 AA-AAAAAAAAAAACAA
3469247 AAACAAAAAAAAAACAA
1 AAA-AAAAAAAAAACAA
3469264 ACAAAAACAAAAAAA
1 A-AAAAA-AAAAAAA
3469279 GGGGGTCCGG
Statistics
Matches: 87, Mismatches: 4, Indels: 18
0.80 0.04 0.17
Matches are distributed among these distances:
15 4 0.05
16 11 0.13
17 49 0.56
18 11 0.13
19 8 0.09
20 4 0.05
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAAAACAA
Found at i:3469212 original size:43 final size:43
Alignment explanation
Indices: 3469165--3469275 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
3469155 GTCCTCCAAA
* ** **
3469165 AAAAAAAAAACAAAAAAAATGAAAA-AACAAAAAAAAA-TGAATG
1 AAAAAAAAAACAAAAAAAA-CAAAACAA-AAAAAAAAACAAAAAC
3469208 AAAAAAAAAACAAAAAAAACAAAACAAAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAAAACAAAACAAAAAAAAAAACAAAAAC
3469251 AAAAAAAAAACAAACAAAAACAAAA
1 AAAAAAAAAACAAA-AAAAACAAAA
3469276 AAAGGGGGTC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
42 13 0.22
43 37 0.62
44 10 0.17
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.03
Consensus pattern (43 bp):
AAAAAAAAAACAAAAAAAACAAAACAAAAAAAAAAACAAAAAC
Found at i:3470775 original size:30 final size:29
Alignment explanation
Indices: 3470720--3471031 Score: 182
Period size: 30 Copynumber: 10.3 Consensus size: 29
3470710 TCACCCTTCA
* *
3470720 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
3470749 AAAGCCCACAAGTCGGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
3470778 GAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
3470806 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
3470836 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
3470865 AAAGTCCACAACTCCGTGACACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
3470895 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TCTTTTTC
** * * *
3470930 TTTTTCAGCCCACAAGTCAGTGGCAAC-CTTTA
1 ----AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
3470962 AAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
3470991 AAAAGCCCACAAGTCAGTGGCATATTTCTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
3471021 TAAAGCCCACA
1 -AAAGCCCACA
3471032 CAAGTTGGTG
Statistics
Matches: 223, Mismatches: 46, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
27 20 0.09
28 23 0.10
29 53 0.24
30 81 0.36
32 3 0.01
33 2 0.01
34 18 0.08
35 23 0.10
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:3470821 original size:27 final size:27
Alignment explanation
Indices: 3470779--3470831 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3470769 ATTTTTTTCG
*
3470779 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
3470806 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
3470832 TTCCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:3470825 original size:57 final size:57
Alignment explanation
Indices: 3470746--3470856 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
3470736 TGGCATTTTT
* * ** *
3470746 TTCAAAGCCCACAAGTCGGTGGCA-TTTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCG-AAGCCCACAAGTCAGTGGCAACC
*
3470803 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCA
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCAGTGGCA
3470857 TCTTTTCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 41 0.87
58 6 0.13
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (57 bp):
TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCAGTGGCAACC
Found at i:3471034 original size:32 final size:30
Alignment explanation
Indices: 3470998--3471122 Score: 126
Period size: 32 Copynumber: 4.0 Consensus size: 30
3470988 TTCAAAAGCC
* *
3470998 CACAAGTCAGTGGCATATTTCTCTAAAGCCCA
1 CACAAGTCGGTGGCA-A-CTCTCTAAAGCCCA
* * *
3471030 CACAAGTTGGTGGCAACCCCCTCAAAGCCCA
1 CACAAGTCGGTGGCAACTCTCT-AAAGCCCA
*
3471061 CACAAGTCGATGGCAACCCTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAA--CTCTCTAAAGCCCA
*
3471093 CACAAGTCGGTGGCAACCCTTCT-AAGCCCA
1 CACAAGTCGGTGGCAACTC-TCTAAAGCCCA
3471123 ATATAGCTGG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 12 0.15
31 26 0.33
32 36 0.46
33 4 0.05
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.18
Consensus pattern (30 bp):
CACAAGTCGGTGGCAACTCTCTAAAGCCCA
Found at i:3471060 original size:31 final size:32
Alignment explanation
Indices: 3471018--3471111 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
3471008 TGGCATATTT
*
3471018 CTCTAAAGCCCACACAAGTTGGTGGCAACCCC
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCCC
* *
3471050 CTC-AAAGCCCACACAAGTCGATGGCAACCCT
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCCC
3471081 CTCTAAAGCCCACACAAGTCGGTGGCAACCC
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCC
3471112 TTCTAAGCCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
31 28 0.49
32 29 0.51
ACGTcount: A:0.30, C:0.38, G:0.18, T:0.14
Consensus pattern (32 bp):
CTCTAAAGCCCACACAAGTCGGTGGCAACCCC
Found at i:3471177 original size:49 final size:49
Alignment explanation
Indices: 3471115--3472317 Score: 1543
Period size: 49 Copynumber: 24.7 Consensus size: 49
3471105 GCAACCCTTC
* *
3471115 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
3471164 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
3471213 TAAGTCCAATGTAGCGGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
3471256 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * * * *
3471308 TAAGTCCAATGTAGCTGGCGTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471357 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471406 TAAGACCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471455 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471503 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
3471546 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * * *
3471598 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
3471647 TAAGTACAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
3471696 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CATCTT
* *
3471745 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471794 TAAGACCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471843 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3471891 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
3471934 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * * *
3471986 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3472035 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * * *
3472084 TAAGTCCAATGTAGCTGGCCTCGACTCAGTACATTGGCA-CTTGCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CATCTT
*
3472133 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
3472181 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
3472230 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * *
3472282 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
3472318 ACATCATTTT
Statistics
Matches: 1004, Mismatches: 115, Indels: 67
0.85 0.10 0.06
Matches are distributed among these distances:
43 117 0.12
45 3 0.00
48 128 0.13
49 584 0.58
50 12 0.01
51 2 0.00
52 158 0.16
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:3471641 original size:290 final size:291
Alignment explanation
Indices: 3471115--3472317 Score: 1754
Period size: 290 Copynumber: 4.1 Consensus size: 291
3471105 GCAACCCTTC
* * * * * *
3471115 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
*
3471180 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCGGGCCTTGAATCAGCAC
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
3471245 ATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTA
131 ATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT-CATCTTTA
* *
3471310 AGTCCAATGTAGCTGGCGTTGACTCAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGG
194 AGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGG
*
3471375 CCTTGAATCAGCATATTGGCACC-TTT-ATCTT
259 CCTTGAATCAGCATATCGGCACCTTTTCATCTT
* * * * * *
3471406 TAAGACCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
* *
3471471 GGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
*
3471535 ATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTA
131 ATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT-CATCTTTA
*
3471600 AGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTACAATATAGCTGG
194 AGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGG
*
3471665 CCTTGAATCAGCATATTGGCA-CTTTT-ATCTT
259 CCTTGAATCAGCATATCGGCACCTTTTCATCTT
* *
3471696 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCATTAAGCCCAATATAGC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-CACCATTAAGTCCAATATAGC
* * * *
3471760 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGCCCTGAATCAGCA
65 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
* * *
3471825 TATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TCAC
130 CATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCAT
*
3471888 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T-----TTAAGTCCAATATA
189 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATA
3471947 GCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
254 GCTGGCCTTGAATCAGCATATCGGCACCTTTT-CATCTT
*
3471986 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
* * * * *
3472051 GGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCTGGCCTCGACTCAGTAC
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
*
3472116 ATTGGCACTTGCACCATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-ATC
131 ATT-G-----GCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
* *
3472179 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAG
190 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAG
3472244 CTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
255 CTGGCCTTGAATCAGCATATCGGCACCTTTT-CATCTT
*
3472282 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
3472318 ACATCATTTT
Statistics
Matches: 839, Mismatches: 46, Indels: 49
0.90 0.05 0.05
Matches are distributed among these distances:
287 38 0.05
288 5 0.01
289 36 0.04
290 447 0.53
291 132 0.16
292 2 0.00
293 45 0.05
294 1 0.00
295 1 0.00
296 90 0.11
297 42 0.05
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (291 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
ATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTCATCTTTAAG
TCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCC
TTGAATCAGCATATCGGCACCTTTTCATCTT
Found at i:3471842 original size:388 final size:388
Alignment explanation
Indices: 3471110--3472317 Score: 2024
Period size: 388 Copynumber: 3.1 Consensus size: 388
3471100 CGGTGGCAAC
* * *
3471110 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATA
1 CCTT-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATA
* *
3471175 TAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGTAGCGGGCCTTGA
59 TAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGA
*
3471237 ATCAGCACATTGGCACC-T-----TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
124 CTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-
*
3471296 CTTTTCCATCTTTAAGTCCAATGTAGCTGGCGTTGACTCAGCACATTGGCACCTT-CACCATTAA
188 CTTTT--ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCATTAA
3471360 GCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGC
250 GCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGC
3471425 CCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT
315 CCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT
3471490 GGCACCTCA
380 GGCACCTCA
3471499 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
3471564 CCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
66 CCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
*
3471629 CATTGGCACCTTCACCATTAAGTACAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATC
131 CATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATC
3471694 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCACCATTAAGCCCAATATAG
196 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCACCATTAAGCCCAATATAG
3471759 CTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGCCCTGAATCAGC
261 CTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGCCCTGAATCAGC
3471824 ATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCA
326 ATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCA
3471887 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
3471952 CCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
66 CCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
3472017 CATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATC
131 CATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATC
* * *
3472082 TTTAAGTCCAATGTAGCTGGCCTCGACTCAGTACATTGGCACTTGCACCATTAAGTCC-ATATAG
196 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCACCATTAAGCCCAATATAG
* * * *
3472146 CTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGC
261 CTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGCCCTGAATCAGC
* * *
3472211 ACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTC
326 ATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC---T-
3472276 CA
387 CA
* *
3472278 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
3472318 ACATCATTTT
Statistics
Matches: 784, Mismatches: 21, Indels: 26
0.94 0.03 0.03
Matches are distributed among these distances:
382 43 0.05
384 2 0.00
385 45 0.06
386 1 0.00
387 128 0.16
388 476 0.61
389 4 0.01
390 6 0.01
391 79 0.10
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (388 bp):
CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
CCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
CATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATC
TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCACCATTAAGCCCAATATAG
CTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATAGCTGGCCCTGAATCAGC
ATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCA
Found at i:3472357 original size:56 final size:53
Alignment explanation
Indices: 3471931--3472365 Score: 349
Period size: 49 Copynumber: 8.6 Consensus size: 53
3471921 ACATTGGCAC
* *
3471931 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
3471983 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
3472032 CATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-TTT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * * * * *
3472081 CTTTAAGTCCAATGTAGCTGGCCTCGACTCAGTACATTGGCA-C--TT-GCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
3472130 CATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
3472178 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* *
3472227 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
3472279 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCATTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACA-C-CTTTTC-TCAT
* * * *
3472335 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
3472366 ACATATTGGC
Statistics
Matches: 322, Mismatches: 46, Indels: 26
0.82 0.12 0.07
Matches are distributed among these distances:
48 41 0.13
49 164 0.51
50 2 0.01
52 81 0.25
53 1 0.00
54 5 0.02
56 28 0.09
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
Found at i:3473200 original size:33 final size:33
Alignment explanation
Indices: 3473163--3473229 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3473153 TTCAACGATT
3473163 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3473196 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3473229 T
1 T
3473230 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3473201 original size:13 final size:13
Alignment explanation
Indices: 3473183--3473207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3473173 CATAAAATGT
3473183 TGTATCGATACAA
1 TGTATCGATACAA
3473196 TGTATCGATACA
1 TGTATCGATACA
3473208 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3473288 original size:13 final size:13
Alignment explanation
Indices: 3473270--3473294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3473260 ATTACTCAAA
3473270 TGTATCGATACAT
1 TGTATCGATACAT
3473283 TGTATCGATACA
1 TGTATCGATACA
3473295 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3473396 original size:52 final size:52
Alignment explanation
Indices: 3473303--3473426 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
3473293 CACTGATCTT
*
3473303 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3473354 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3473406 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
3473427 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3481511 original size:30 final size:30
Alignment explanation
Indices: 3481475--3481531 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3481465 CCTTTGCACC
3481475 AAAAAAAAACAAAAAAAAACAAAAAAAACA
1 AAAAAAAAACAAAAAAAAACAAAAAAAACA
* *
3481505 AAAAAAAAACAAAAAATAGCAAAAAAA
1 AAAAAAAAACAAAAAAAAACAAAAAAA
3481532 TAGAAGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (30 bp):
AAAAAAAAACAAAAAAAAACAAAAAAAACA
Found at i:3481531 original size:1 final size:1
Alignment explanation
Indices: 3481475--3481520 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
3481465 CCTTTGCACC
* * * *
3481475 AAAAAAAAACAAAAAAAAACAAAAAAAACAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3481521 TAGCAAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3481534 original size:11 final size:10
Alignment explanation
Indices: 3481474--3481531 Score: 82
Period size: 10 Copynumber: 5.8 Consensus size: 10
3481464 TCCTTTGCAC
3481474 CAAAAAAAAA
1 CAAAAAAAAA
3481484 CAAAAAAAAA
1 CAAAAAAAAA
3481494 C-AAAAAAAA
1 CAAAAAAAAA
3481503 CAAAAAAAAAA
1 C-AAAAAAAAA
* *
3481514 CAAAAAATAG
1 CAAAAAAAAA
3481524 CAAAAAAA
1 CAAAAAAA
3481532 TAGAAGGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
9 9 0.21
10 25 0.58
11 9 0.21
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:3482897 original size:28 final size:28
Alignment explanation
Indices: 3482747--3484610 Score: 2468
Period size: 28 Copynumber: 64.6 Consensus size: 28
3482737 AATATTCATT
* *
3482747 CCTTTCAAAGCCCACAAATCAATGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3482775 TCTTTTCAAAGCCCACAAATCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3482804 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3482833 TCCTTTTAAAGCCCACGCAAGTCAGTGGTAC
1 -CCTTTCAAAGCCCA--CAAGTCAGTGGCAC
* *
3482864 CTTTTCAAAGCCCACGAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3482892 TCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3482920 CCTTGCGAAGCCCACGAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3482948 CCTTTCAAAGCCCACAAGATTCGGTGGTAAC
1 CCTTTCAAAGCCCACAAG--TCAGTGG-CAC
* *
3482979 TCTTTTCAAAGCCCATAAGTCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483008 CCTTCCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483036 CCTTTTCAAAGCCCACGCAAGTAAGTGGCAC
1 CC-TTTCAAAGCCCA--CAAGTCAGTGGCAC
3483067 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3483095 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483123 CCTTTCAGAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483151 CCTTTCGAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3483179 CCTTGCGAAGCCCACACAAGTCAATGGCAC
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCAC
* *
3483209 TCCTTTTAAAGCCCACGCAAGTCAATGGCAC
1 -CCTTTCAAAGCCCA--CAAGTCAGTGGCAC
* *
3483240 CCTTTCAAAGCCCACGAGTCAATGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483268 TCTTTCAAAGCCCACAAGTCCACAAGTCAGTGGCAC
1 CCTTTCAAAG----C----CCACAAGTCAGTGGCAC
3483304 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483332 CCTTTTCAAAGCCCACACAAGTAAGTGGCAC
1 CC-TTTCAAAG-CC-CACAAGTCAGTGGCAC
3483363 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3483391 TCTTTTCAAAGCCCACAAGTTAGTGGCAT
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483420 CCTTTCAAAACCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3483448 CATTTCAAAGCCCGCAAATCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3483476 TCTTTTCAAAGCCCGCAAATCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483505 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483534 CCTTTTCAAAGCCCACGCAAGTAAGTGGCAC
1 CC-TTTCAAAGCCCA--CAAGTCAGTGGCAC
3483565 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3483593 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483621 CCTTTCGAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483649 CCTTTTCAAAGCCCACGCAAGTAAGTGGCAC
1 CC-TTTCAAAGCCCA--CAAGTCAGTGGCAC
*
3483680 CCTTTCAAAGCCCACAAATCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483708 CCTTTCAAAGCCCACGCAAGTAAGTGGCAC
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCAC
*
3483738 CCTTTCAAAGCCCACAAATCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483766 CCTTTCAAAGCCCACGAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483794 TCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3483822 TCTTTTCAAAGCCCACAAGTTAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483851 CCTTTCAGAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3483879 CCTTTCGAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3483907 CCTTGCGAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3483935 TCTTTCAAAGTCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3483963 CCTTTCAAAGCCCACACAAGTCAGTGGCAC
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCAC
*
3483993 TCCTTTTAAAGCCCACGCAAGTCAGTGGCAC
1 -CCTTTCAAAGCCCA--CAAGTCAGTGGCAC
* * *
3484024 CTTTTCAAAACCCACGAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
** *
3484052 TTTTTCAAAGCCCACAAGTTAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
3484080 CCTTGCGAAGCCCACGAGTTAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
**
3484108 CCTTTCAAAGCCCACAAGAGTTGGTGGCAAC
1 CCTTTCAAAGCCCAC-A-AGTCAGTGGC-AC
*
3484139 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484168 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3484196 CCTTTTCGAAGCCCACGCAAGTAAGTGGCAC
1 CC-TTTCAAAGCCCA--CAAGTCAGTGGCAC
3484227 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484255 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3484283 TCTTTTCAAAGCCCACAAGTTAGTGGCAT
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484312 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* *
3484340 CCTTTCAAAGCCCGCAAATCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3484368 TCTTTTCAAAGCCCACAAGTCAGTGGCAC
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3484397 CCTTTCAAAGCCCACAAGTGAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484425 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
3484453 TCTTTTCAAAGCCCACAAGTTAGTGGCAT
1 -CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484482 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484510 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484538 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
3484566 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAGCCCACAAGTCAGTGGCAC
*
3484594 TCTTTTCAAAGCCCACA
1 -CCTTTCAAAGCCCACA
3484611 CGAGTTGGTG
Statistics
Matches: 1643, Mismatches: 140, Indels: 104
0.87 0.07 0.06
Matches are distributed among these distances:
28 938 0.57
29 327 0.20
30 183 0.11
31 139 0.08
32 32 0.02
36 24 0.01
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.20
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:3483275 original size:173 final size:168
Alignment explanation
Indices: 3482748--3484610 Score: 2436
Period size: 173 Copynumber: 10.8 Consensus size: 168
3482738 ATATTCATTC
* * * * *
3482748 CTTTCAAAGCCCACAAATCAATGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
* * *
3482813 AGCCCACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGGTACCTTTTCAAAGCCCA
64 AGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA
* * *
3482878 CGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACC
126 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * *
3482921 CTTGCGAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGATTCGGTGGTAACTCTTTTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG--TCAGTGG-CAC-CCTTTC
* *
3482986 AAAGCCCATAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCA
62 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCA
* *
3483051 CGCAAGTAAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
126 --CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3483096 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAG
1 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * * *
3483161 CCCACAAGTCAGTGGCACCCTTGCGAAGCCCACACAAGTCAATGGCACTCCTTTTAAAGCCCACG
66 CCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCA--
* * *
3483226 CAAGTCAATGGCACCCTTTCAAAGCCCACGAGTCAATGGCACT
126 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
3483269 CTTTCAAAGCCCACAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
1 CTTTCAAAG----C----CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
3483334 TTTTCAAAGCCCACACAAGTAAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
58 -TTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
* * *
3483399 AAGCCCACAAGTTAGTGGCATCCTTTCAAAACCCACAAGTCAGTGGCAC-
119 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * *
3483448 CATTTCAAAGCCCGCAAATCAGTGGCACTCTTTTCAAAGCCCGCAAATCAGTGGCACTCTTTTCA
1 C-TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
*
3483513 AAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACGCAAGTAAGTGGCACCCTTTCAAAGCCC
63 AAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCC
*
3483578 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
125 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3483622 CTTTCGAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACGCAAGTAAGTGGCACCCTTTCA
1 CTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCA
* *
3483687 AAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACGCAAGTAAGTGGCACCCTTTCAAAGCCCA
63 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA
* *
3483752 CAAATCAGTGGCACCCTTTCAAAGCCCACGAGTCAGTGGCACT
126 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3483795 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGA
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
* * *
3483860 GCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCACAAG
65 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
* * *
3483925 TCAGTGGCACTCTTTCAAAGTCCACAAGTCAGTGGCACC
130 TCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3483964 CTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGGCACCTTTT
1 CTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTT
* * ** * * *
3484029 CAAAACCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAAGTTAGTGGCACCCTTGCGAAGCCCA
61 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA
* * **
3484094 CGAGTTAGTGGCACCCTTTCAAAGCCCACAAGAGTTGGTGGCAACT
126 CAAGTCAGTGGCACCCTTTCAAAGCCCAC-A-AGTCAGTGGC-ACT
*
3484140 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCGA
1 C-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAA
*
3484205 AGCCCACGCAAGTAAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
64 AGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
* *
3484270 AAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA-T
127 AAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
3484312 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCGCAAATCAGTGGCACTCTTTTCAA
1 -CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAA
*
3484377 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTGAGTGGCACCCTTTCAAAGCCCACAA
64 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
* *
3484442 GTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA-T
129 GTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACT
3484482 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
1 -CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
*
3484547 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
65 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACA
3484611 CGAGTTGGTG
Statistics
Matches: 1513, Mismatches: 131, Indels: 95
0.87 0.08 0.05
Matches are distributed among these distances:
169 126 0.08
170 168 0.11
171 131 0.09
172 143 0.09
173 467 0.31
174 87 0.06
175 209 0.14
176 20 0.01
177 9 0.01
179 1 0.00
180 44 0.03
181 46 0.03
182 35 0.02
183 4 0.00
184 23 0.02
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.20
Consensus pattern (168 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:3483303 original size:36 final size:36
Alignment explanation
Indices: 3483251--3483323 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
3483241 CTTTCAAAGC
* *
3483251 CCACGAGTCAATGGCACTCTTTCAAAGCCCACAAGT
1 CCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGT
*
3483287 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
1 CCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGT
3483323 C
1 C
3483324 AGTGGCACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (36 bp):
CCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGT
Found at i:3483470 original size:85 final size:84
Alignment explanation
Indices: 3483287--3484610 Score: 1874
Period size: 85 Copynumber: 15.4 Consensus size: 84
3483277 GCCCACAAGT
3483287 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACACAA
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAG-CC-CACAA
*
3483352 GTAAGTGGCACCCTTTCAAAGC
63 GTCAGTGGCACCCTTTCAAAGC
* * * *
3483374 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAACCCACAAGT
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
*
3483439 CAGTGGCACCATTTCAAAGC
65 CAGTGGCACCCTTTCAAAGC
* * * * * *
3483459 CCGCAAATCAGTGGCACTCTTTTCAAAGCCCGCAAATCAGTGGCACTCTTTTCAAAGCCCACAAG
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAG
3483524 TCAGTGGCACCCTTTTCAAAGC
64 TCAGTGGCACCC-TTTCAAAGC
*
3483546 CCACGCAAGTAAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
1 CCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
3483611 TCAGTGGCACCCTTTCGAAGC
64 TCAGTGGCACCCTTTCAAAGC
*
3483632 CCACAAGTCAGTGGCACCCTTTTCAAAGCCCACGCAAGTAAGTGGCACCCTTTCAAAGCCCACAA
1 CCACAAGTCAGTGGCACCC-TTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAA
*
3483697 ATCAGTGGCACCCTTTCAAAGC
63 GTCAGTGGCACCCTTTCAAAGC
* * *
3483719 CCACGCAAGTAAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACGAG
1 CCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
3483784 TCAGTGGCACTCTTTCAAAGC
64 TCAGTGGCACCCTTTCAAAGC
* * *
3483805 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGT
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
*
3483870 CAGTGGCACCCTTTCGAAGC
65 CAGTGGCACCCTTTCAAAGC
* * * *
3483890 CCACAAGTCAGTGGCACCCTTGCGAAGCCCACAAGTCAGTGGCACTCTTTCAAAGTCCACAAGTC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
3483955 AGTGGCACCCTTTCAAAGCC
66 AGTGGCACCCTTTCAAAG-C
* * * *
3483975 CACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAACCCACG
1 C-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACA
**
3484040 AGTCAGTGGCACTTTTTCAAAGC
62 AGTCAGTGGCACCCTTTCAAAGC
* * * * *
3484063 CCACAAGTTAGTGGCACCCTTGCGAAGCCCACGAGTTAGTGGCACCCTTTCAAAGCCCACAAGAG
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC-A-AG
** *
3484128 TTGGTGGCAACTCTTTTCAAAGC
64 TCAGTGGC-AC-CCTTTCAAAGC
*
3484151 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCGAAGCCCACGCAA
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCA--CAA
*
3484216 GTAAGTGGCACCCTTTCAAAGC
63 GTCAGTGGCACCCTTTCAAAGC
*
3484238 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGT
* *
3484303 TAGTGGCATCCTTTCAAAGC
65 CAGTGGCACCCTTTCAAAGC
* * *
3484323 CCACAAGTCAGTGGCACCCTTTCAAAGCCCGCAAATCAGTGGCACTCTTTTCAAAGCCCACAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGT
3484388 CAGTGGCACCCTTTCAAAGC
65 CAGTGGCACCCTTTCAAAGC
* *
3484408 CCACAAGTGAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGT
* *
3484473 TAGTGGCATCCTTTCAAAGC
65 CAGTGGCACCCTTTCAAAGC
3484493 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
3484558 AGTGGCACCCTTTCAAAGC
66 AGTGGCACCCTTTCAAAGC
*
3484577 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
1 CCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACA
3484611 CGAGTTGGTG
Statistics
Matches: 1114, Mismatches: 98, Indels: 52
0.88 0.08 0.04
Matches are distributed among these distances:
84 164 0.15
85 399 0.36
86 126 0.11
87 211 0.19
88 121 0.11
89 91 0.08
90 1 0.00
91 1 0.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (84 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
AGTGGCACCCTTTCAAAGC
Found at i:3485249 original size:20 final size:20
Alignment explanation
Indices: 3485220--3485291 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
3485210 TTTTTACCCT
3485220 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
3485240 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* * *
3485260 AATGTATCGATATATTCTAC
1 AATGTATCGATACATTTTTC
3485280 AATGTATCGATA
1 AATGTATCGATA
3485292 TATTATGTCT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:3488256 original size:17 final size:17
Alignment explanation
Indices: 3488205--3488256 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
3488195 ATATATTAAT
*
3488205 TATTATTTTT-TAAAAA
1 TATTATTTTTATTAAAA
*
3488221 TTTGTATTTATTAATTAAAA
1 TAT-TATTT-TT-ATTAAAA
3488241 TATTATTTTTATTAAA
1 TATTATTTTTATTAAA
3488257 TTTATATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 2 0.07
17 11 0.38
18 4 0.14
19 5 0.17
20 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTATTTTTATTAAAA
Found at i:3488258 original size:36 final size:37
Alignment explanation
Indices: 3488182--3488264 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
3488172 GAATTTGATT
*
3488182 AATTTATATTTATATATATTAATTATTATTTTTTAAA
1 AATTTATATTTATATATATTAAATATTATTTTTTAAA
* *
3488219 AATTTGTATTTAT-TA-ATTAAAATATTA-TTTTTATTA
1 AATTTATATTTATATATATT-AAATATTATTTTTTA-AA
3488255 AATTTATATT
1 AATTTATATT
3488265 AATTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 9 0.22
36 19 0.47
37 12 0.30
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (37 bp):
AATTTATATTTATATATATTAAATATTATTTTTTAAA
Found at i:3488698 original size:14 final size:14
Alignment explanation
Indices: 3488674--3488740 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
3488664 AGATAAAATA
3488674 AAAATTATAAATATT
1 AAAATT-TAAATATT
3488689 AAAATTTAAATATT
1 AAAATTTAAATATT
** *
3488703 AATTTTATTAAATGTT
1 AA-AAT-TTAAATATT
3488719 AAAATTTAAATATT
1 AAAATTTAAATATT
*
3488733 AATATTTA
1 AAAATTTA
3488741 TTTAAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
14 25 0.58
15 8 0.19
16 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:3488721 original size:30 final size:31
Alignment explanation
Indices: 3488681--3488742 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
3488671 ATAAAAATTA
3488681 TAAATATTAAAATTTAAATATTAAT-TTTAT
1 TAAATATTAAAATTTAAATATTAATATTTAT
*
3488711 TAAATGTTAAAATTTAAATATTAATATTTAT
1 TAAATATTAAAATTTAAATATTAATATTTAT
3488742 T
1 T
3488743 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
TAAATATTAAAATTTAAATATTAATATTTAT
Found at i:3488770 original size:20 final size:21
Alignment explanation
Indices: 3488747--3488792 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
3488737 TTTATTTAAA
*
3488747 AAAATTATTAT-ATTAAGATT
1 AAAATTATTATAATAAAGATT
* *
3488767 AAAA-AATTATAATAAATATT
1 AAAATTATTATAATAAAGATT
3488787 AAAATT
1 AAAATT
3488793 TAATATTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATTATTATAATAAAGATT
Found at i:3491787 original size:37 final size:36
Alignment explanation
Indices: 3491742--3491829 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 36
3491732 TGGATTGACG
*
3491742 CTGCCACCCAAATTCTAACAATCATAGT-GAATTGGC
1 CTGCCACCCAAATACTAACAATCATAGTAG-ATTGGC
3491778 ACTGCCACCCAAATACTAACAATCATAGTAGATTGGC
1 -CTGCCACCCAAATACTAACAATCATAGTAGATTGGC
*
3491815 CAAGCCACCCAAATA
1 C-TGCCACCCAAATA
3491830 TTACTTGTCG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
36 1 0.02
37 45 0.96
38 1 0.02
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (36 bp):
CTGCCACCCAAATACTAACAATCATAGTAGATTGGC
Found at i:3495798 original size:6 final size:7
Alignment explanation
Indices: 3495778--3495804 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3495768 AGATATGGAG
3495778 ATGAAAA
1 ATGAAAA
3495785 ATGAAAA
1 ATGAAAA
3495792 ATGAAAA
1 ATGAAAA
3495799 ATGAAA
1 ATGAAA
3495805 CAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:3495872 original size:5 final size:6
Alignment explanation
Indices: 3495855--3495879 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3495845 TTTTGCCACA
3495855 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
3495880 TGCTTGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3495947 original size:48 final size:48
Alignment explanation
Indices: 3495895--3496041 Score: 181
Period size: 48 Copynumber: 3.1 Consensus size: 48
3495885 GCTAAGTTAA
3495895 CTTTCATCCATGTTTTTTGTCACA-CGACCCATGCTTTTATC-TTTTGTT
1 CTTTCATCCATGTTTTTTGTCACATC-ACCCATGCTTTTATCATTTT-TT
** *
3495943 CTTTCATCCATGTTTTTTGTCTTATCACCCATGTTTTTATCATTTTTT
1 CTTTCATCCATGTTTTTTGTCACATCACCCATGCTTTTATCATTTTTT
* * * ** *
3495991 CTTTCATCCATGTTTTTTGTAATACCACTTATGCTTTTATTATTTTTT
1 CTTTCATCCATGTTTTTTGTCACATCACCCATGCTTTTATCATTTTTT
3496039 CTT
1 CTT
3496042 ACAAGCTATC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
48 82 0.94
49 5 0.06
ACGTcount: A:0.16, C:0.21, G:0.07, T:0.56
Consensus pattern (48 bp):
CTTTCATCCATGTTTTTTGTCACATCACCCATGCTTTTATCATTTTTT
Found at i:3495953 original size:27 final size:27
Alignment explanation
Indices: 3495923--3496007 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
3495913 GTCACACGAC
*
3495923 CCATGCTTTTATCTTTTGTTCTTTCAT
1 CCATGTTTTTATCTTTTGTTCTTTCAT
*
3495950 CCATG----T-T-TTTTG-TCTTATCAC
1 CCATGTTTTTATCTTTTGTTCTT-TCAT
3495971 CCATGTTTTTATCATTTT-TTCTTTCAT
1 CCATGTTTTTATC-TTTTGTTCTTTCAT
3495998 CCATGTTTTT
1 CCATGTTTTT
3496008 TGTAATACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
22 1 0.02
23 1 0.02
25 1 0.02
26 1 0.02
27 18 0.38
28 8 0.17
ACGTcount: A:0.13, C:0.21, G:0.07, T:0.59
Consensus pattern (27 bp):
CCATGTTTTTATCTTTTGTTCTTTCAT
Found at i:3495965 original size:20 final size:22
Alignment explanation
Indices: 3495936--3495980 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3495926 TGCTTTTATC
*
3495936 TTTTGTTCTT-TCATCCATGTT
1 TTTTGTTCTTATCACCCATGTT
3495957 TTTTG-TCTTATCACCCATGTT
1 TTTTGTTCTTATCACCCATGTT
3495978 TTT
1 TTT
3495981 ATCATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.11, C:0.20, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTTGTTCTTATCACCCATGTT
Found at i:3501906 original size:17 final size:17
Alignment explanation
Indices: 3501884--3501918 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3501874 TTGCTATATA
3501884 TTTTTT-ATTCTTTTCTT
1 TTTTTTCATT-TTTTCTT
3501901 TTTTTTCATTTTTTCTT
1 TTTTTTCATTTTTTCTT
3501918 T
1 T
3501919 AACCAATTTT
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:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCATTTTTTCTT
Found at i:3502084 original size:16 final size:16
Alignment explanation
Indices: 3502063--3502094 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3502053 AATTAAAATA
*
3502063 TAACTTAATAATAATT
1 TAACTTAACAATAATT
3502079 TAACTTAACAATAATT
1 TAACTTAACAATAATT
3502095 AAAGATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TAACTTAACAATAATT
Found at i:3503257 original size:16 final size:16
Alignment explanation
Indices: 3503238--3503268 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3503228 TTCTAAATCA
3503238 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
*
3503254 TTTTATATTTAAATT
1 TTTTAAATTTAAATT
3503269 ATTAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAATTTAAATTT
Found at i:3503745 original size:11 final size:10
Alignment explanation
Indices: 3503726--3503801 Score: 58
Period size: 10 Copynumber: 8.1 Consensus size: 10
3503716 ATTAATAATT
3503726 TATATATTTA
1 TATATATTTA
*
3503736 TATCATATTTT
1 TAT-ATATTTA
3503747 TATATATTTA
1 TATATATTTA
3503757 TAT-TA--TA
1 TATATATTTA
3503764 TA-A-ATTT-
1 TATATATTTA
*
3503771 TA-ATATATA
1 TATATATTTA
*
3503780 CATATATTTA
1 TATATATTTA
3503790 TATTATATTTA
1 TA-TATATTTA
3503801 T
1 T
3503802 GTCATATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
6 1 0.02
7 7 0.13
8 4 0.08
9 3 0.06
10 19 0.37
11 18 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATATTTA
Found at i:3503749 original size:21 final size:21
Alignment explanation
Indices: 3503724--3503809 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
3503714 AGATTAATAA
3503724 TTTATATATTTATATCATATT
1 TTTATATATTTATATCATATT
*
3503745 TTTATATATTTATATTATATAAAT
1 TTTATATATTTATATCATAT---T
* *
3503769 TTTA-ATATATACAT-ATATT
1 TTTATATATTTATATCATATT
* *
3503788 TATATTATATTTATGTCATATT
1 TTTA-TATATTTATATCATATT
3503810 ATATTTTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.08
21 26 0.50
22 9 0.17
23 8 0.15
24 5 0.10
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (21 bp):
TTTATATATTTATATCATATT
Found at i:3503784 original size:25 final size:26
Alignment explanation
Indices: 3503733--3503784 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
3503723 ATTTATATAT
* * **
3503733 TTATATCATATTTTTATATATTTATA
1 TTATATCAAATTTTAATATATACATA
3503759 TTATAT-AAATTTTAATATATACATA
1 TTATATCAAATTTTAATATATACATA
3503784 T
1 T
3503785 ATTTATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATCAAATTTTAATATATACATA
Found at i:3506533 original size:11 final size:11
Alignment explanation
Indices: 3506513--3506543 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3506503 CTTTCACACC
3506513 TTTTTT-TTTT
1 TTTTTTCTTTT
3506523 TTTTTTCTTTT
1 TTTTTTCTTTT
3506534 TTTTTTCTTT
1 TTTTTTCTTT
3506544 GAATTTGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:3508145 original size:34 final size:34
Alignment explanation
Indices: 3508102--3508166 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
3508092 TTAAAAATAT
*
3508102 ATAAAATTATATTAATTTTATACGAGTTAATCTA
1 ATAAAATTATATTAATTTTACACGAGTTAATCTA
*
3508136 ATAAAATTATATTAATTTTACATGAGTTAAT
1 ATAAAATTATATTAATTTTACACGAGTTAAT
3508167 TTATCCTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (34 bp):
ATAAAATTATATTAATTTTACACGAGTTAATCTA
Found at i:3509861 original size:14 final size:14
Alignment explanation
Indices: 3509827--3509863 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3509817 TTTTTAAAAT
*
3509827 TAAAAAAATTTAAA
1 TAAAATAATTTAAA
3509841 TAAAATAATTTAAA
1 TAAAATAATTTAAA
*
3509855 TATAATAAT
1 TAAAATAAT
3509864 ATATCAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATAATTTAAA
Found at i:3510456 original size:34 final size:34
Alignment explanation
Indices: 3510413--3510478 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
3510403 GACATGACAA
*
3510413 TAATAAAATAAGTTGGTGACTATGAAAATTTTAG
1 TAATAAAATAAGTTGGTAACTATGAAAATTTTAG
*
3510447 TAATAAAATAAGTTGGTAATTATGAAAATTTT
1 TAATAAAATAAGTTGGTAACTATGAAAATTTT
3510479 CTTCTTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (34 bp):
TAATAAAATAAGTTGGTAACTATGAAAATTTTAG
Found at i:3511049 original size:19 final size:18
Alignment explanation
Indices: 3511005--3511051 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 18
3510995 AATATTTTAA
3511005 ATTTAATTATAAAAATAT
1 ATTTAATTATAAAAATAT
3511023 AATATTAATATATAAATAATAT
1 -AT-TTAAT-TATAAA-AATAT
3511045 -TTTAATT
1 ATTTAATT
3511052 TTTTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.04
19 7 0.28
20 6 0.24
21 6 0.24
22 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAATTATAAAAATAT
Found at i:3511458 original size:17 final size:18
Alignment explanation
Indices: 3511426--3511460 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3511416 ATTTATATTT
3511426 TAAAATTTATTAAAAAAC
1 TAAAATTTATTAAAAAAC
3511444 TAAAA-TTATTTAAAAAA
1 TAAAATTTA-TTAAAAAA
3511461 TAATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATTTATTAAAAAAC
Found at i:3511591 original size:16 final size:17
Alignment explanation
Indices: 3511572--3511606 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3511562 ATAAAATTAA
3511572 ATATAAATAAATAT-AT
1 ATATAAATAAATATCAT
*
3511588 ATATAAATTAATATCAT
1 ATATAAATAAATATCAT
3511605 AT
1 AT
3511607 TTAACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAAATAAATATCAT
Found at i:3512096 original size:24 final size:26
Alignment explanation
Indices: 3512060--3512109 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3512050 AATAAACATC
*
3512060 ATATAATATATTTAA-ACATA-ATTA
1 ATATAATACATTTAATACATATATTA
*
3512084 ATATGATACATTTAATACATATATTA
1 ATATAATACATTTAATACATATATTA
3512110 TATTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 5 0.23
26 4 0.18
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATAATACATTTAATACATATATTA
Found at i:3512839 original size:32 final size:30
Alignment explanation
Indices: 3512800--3512872 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
3512790 ATTAAAAATA
*
3512800 ATAAATAAAAGCTATCGATTAATATTTTTATT
1 ATAAATAAAA-AT-TCGATTAATATTTTTATT
*
3512832 ATAAATAATAAATTTGATTAATATTTTTATT
1 ATAAATAA-AAATTCGATTAATATTTTTATT
*
3512863 AAATAATAAA
1 ATA-AATAAA
3512873 TTTGATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 20 0.56
32 14 0.39
33 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
ATAAATAAAAATTCGATTAATATTTTTATT
Found at i:3512875 original size:29 final size:31
Alignment explanation
Indices: 3512816--3512878 Score: 112
Period size: 29 Copynumber: 2.1 Consensus size: 31
3512806 AAAAGCTATC
3512816 GATTAATATTTTTATTATAAATAATAAATTT
1 GATTAATATTTTTATTATAAATAATAAATTT
3512847 GATTAATATTTTTA-T-TAAATAATAAATTT
1 GATTAATATTTTTATTATAAATAATAAATTT
3512876 GAT
1 GAT
3512879 AATTTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (31 bp):
GATTAATATTTTTATTATAAATAATAAATTT
Found at i:3514816 original size:2 final size:2
Alignment explanation
Indices: 3514809--3514837 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3514799 CCATTGGAAG
3514809 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3514838 AGAAATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3523528 original size:15 final size:16
Alignment explanation
Indices: 3523496--3523536 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3523486 AAGGTAGTTA
3523496 TAAATTAAA-TTACAT
1 TAAATTAAATTTACAT
*
3523511 TAAATTAAATTTA-TT
1 TAAATTAAATTTACAT
3523526 TAAATTTAAAT
1 TAAA-TTAAAT
3523537 ATAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTAAATTTACAT
Found at i:3523697 original size:18 final size:18
Alignment explanation
Indices: 3523676--3523734 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
3523666 TATTTTTTAA
3523676 AAATTTAATAATTTTATT
1 AAATTTAATAATTTTATT
* *
3523694 AAATTTTA-AATTTTAAAT
1 AAATTTAATAATTTT-ATT
3523712 AAA-TTAAT-ATTTT-TT
1 AAATTTAATAATTTTATT
3523727 AATATTTA
1 AA-ATTTA
3523735 TATTATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 17 0.52
18 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTTAATAATTTTATT
Found at i:3523791 original size:17 final size:17
Alignment explanation
Indices: 3523771--3523830 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
3523761 ATACTTTTAA
*
3523771 TATAAAATTATTTAATT
1 TATAAAATTATATAATT
*
3523788 TATAAAAATATATAATT
1 TATAAAATTATATAATT
* *
3523805 AATATATATTATATAA-T
1 TATA-AAATTATATAATT
3523822 TATAAAATT
1 TATAAAATT
3523831 TATTAAGCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 4 0.11
17 22 0.63
18 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAAAATTATATAATT
Found at i:3523906 original size:18 final size:19
Alignment explanation
Indices: 3523879--3523927 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
3523869 AAAAATTTTG
3523879 ATTT-ATTTTTTAAAT-AA
1 ATTTAATTTTTTAAATCAA
*
3523896 ATTTAATTTTTT-ATTCAA
1 ATTTAATTTTTTAAATCAA
*
3523914 ATTTATTTTTTTAA
1 ATTTAATTTTTTAA
3523928 TTATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTAATTTTTTAAATCAA
Found at i:3523921 original size:17 final size:17
Alignment explanation
Indices: 3523879--3523924 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
3523869 AAAAATTTTG
3523879 ATTTATTTTTTAAATAA
1 ATTTATTTTTTAAATAA
*
3523896 ATTTAATTTTTT-ATTCAA
1 ATTT-ATTTTTTAAAT-AA
3523914 ATTTATTTTTT
1 ATTTATTTTTT
3523925 TAATTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTATTTTTTAAATAA
Found at i:3523949 original size:18 final size:18
Alignment explanation
Indices: 3523903--3523950 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
3523893 TAAATTTAAT
*
3523903 TTTTTATTCAAA-T-TTA
1 TTTTTATTTAAATTATTA
3523919 -TTTT-TTT-AATTATTA
1 TTTTTATTTAAATTATTA
3523934 TTTTTATTTAAATTATT
1 TTTTTATTTAAATTATT
3523951 TTAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
13 2 0.08
14 3 0.12
15 7 0.27
16 4 0.15
17 3 0.12
18 7 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTATTTAAATTATTA
Found at i:3523970 original size:19 final size:18
Alignment explanation
Indices: 3523939--3523986 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3523929 TATTATTTTT
*
3523939 ATTTAAAT-TATTTTAAA
1 ATTTAAATAAATTTTAAA
*
3523956 ATATTAAATAAATTTTTAA
1 AT-TTAAATAAATTTTAAA
*
3523975 ATTTGAATAAAT
1 ATTTAAATAAAT
3523987 AGTTTCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.08
18 15 0.58
19 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTTAAATAAATTTTAAA
Found at i:3532175 original size:2 final size:2
Alignment explanation
Indices: 3532170--3532205 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
3532160 TTCTTTAGTG
3532170 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
3532206 CATGTATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3532194 original size:21 final size:21
Alignment explanation
Indices: 3532170--3532214 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3532160 TTCTTTAGTG
*
3532170 TATATATATAATATATATATA
1 TATATATATAATATACATATA
* *
3532191 TATATATATACTATACATGTA
1 TATATATATAATATACATATA
3532212 TAT
1 TAT
3532215 CTAATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATATATAATATACATATA
Found at i:3534519 original size:19 final size:18
Alignment explanation
Indices: 3534495--3534539 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3534485 TATATAAATA
3534495 TAAATATAATAAAAATTAT
1 TAAATATAATAAAAATT-T
*
3534514 TAAATAT-ATTAAAATTT
1 TAAATATAATAAAAATTT
*
3534531 TAAACATAA
1 TAAATATAA
3534540 AAGTAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATATAATAAAAATTT
Found at i:3536969 original size:24 final size:24
Alignment explanation
Indices: 3536937--3536984 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3536927 AATTCTCCAT
3536937 GATGCATATAATGCTGTATCAATG
1 GATGCATATAATGCTGTATCAATG
3536961 GATGCATATAATGCTGTATCAATG
1 GATGCATATAATGCTGTATCAATG
3536985 AATGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (24 bp):
GATGCATATAATGCTGTATCAATG
Found at i:3536995 original size:24 final size:24
Alignment explanation
Indices: 3536944--3536995 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3536934 CATGATGCAT
* * *
3536944 ATAATGCTGTATCAATGGATGCAT
1 ATAATGCTGTATCAATGAATGAAA
3536968 ATAATGCTGTATCAATGAATGAAA
1 ATAATGCTGTATCAATGAATGAAA
3536992 ATAA
1 ATAA
3536996 CAGACTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (24 bp):
ATAATGCTGTATCAATGAATGAAA
Found at i:3538120 original size:30 final size:31
Alignment explanation
Indices: 3538086--3538146 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
3538076 TATTTTATTT
**
3538086 TTTAAAAAATTAATCTAATAAT-TTTAAATA
1 TTTAAAAAATTAAGATAATAATATTTAAATA
* *
3538116 TTTAATAAATTCAGATAATAATATTTAAATA
1 TTTAAAAAATTAAGATAATAATATTTAAATA
3538147 ATAAATAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTAAAAAATTAAGATAATAATATTTAAATA
Found at i:3539217 original size:16 final size:16
Alignment explanation
Indices: 3539196--3539226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3539186 TTCAAATTCT
3539196 AATAATATATAATATA
1 AATAATATATAATATA
*
3539212 AATAATATATTATAT
1 AATAATATATAATAT
3539227 TATAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATATATAATATA
Found at i:3539478 original size:16 final size:17
Alignment explanation
Indices: 3539440--3539481 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3539430 CTCCTCTTTC
3539440 TTTTA-TTT-TTTTAGT
1 TTTTATTTTATTTTAGT
3539455 TTTGTATTTTATTTTA-T
1 TTT-TATTTTATTTTAGT
3539472 TTTTATTTTA
1 TTTTATTTTA
3539482 AGATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 9 0.38
17 7 0.29
18 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTTATTTTAGT
Found at i:3540347 original size:32 final size:32
Alignment explanation
Indices: 3540280--3540340 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
3540270 AATATAATTA
** *
3540280 ATATAAAATATTTAATGTATATATTTATTTGT
1 ATATAAAATATTTAAAATATATATATATTTGT
*
3540312 ATATAAAAT-TTTAAAATATTTATATATTT
1 ATATAAAATATTTAAAATATATATATATTT
3540341 TTTATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
ATATAAAATATTTAAAATATATATATATTTGT
Found at i:3541618 original size:2 final size:2
Alignment explanation
Indices: 3541611--3541653 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3541601 ATAAAATCAT
3541611 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3541653 T
1 T
3541654 TCCAAGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3543249 original size:19 final size:19
Alignment explanation
Indices: 3543196--3543266 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
3543186 TAAGTTAAAT
* *
3543196 TATTTTATTTTAAATTAATT
1 TATTTTA-TTTAAAATAATA
* *
3543216 TAGTTTGA-TTGAAATAATA
1 TA-TTTTATTTAAAATAATA
3543235 -ATTTTATATTAAAATAATA
1 TATTTTAT-TTAAAATAATA
3543254 TATTTTATTTAAA
1 TATTTTATTTAAA
3543267 TTTAATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 4 0.10
18 1 0.02
19 23 0.56
20 9 0.22
21 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TATTTTATTTAAAATAATA
Found at i:3543287 original size:21 final size:21
Alignment explanation
Indices: 3543263--3543302 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3543253 ATATTTTATT
3543263 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTA-AAAATATA
3543284 TAAATATTAATTAAAAATA
1 TAAATATTAATTAAAAATA
3543303 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATTAAAAATATA
Found at i:3543311 original size:22 final size:22
Alignment explanation
Indices: 3543259--3543311 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3543249 TAATATATTT
3543259 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATTAATTATAAAA
*
3543280 TATATAAATATTAATTA-AAAA
1 TATTTAAATATTAATTATAAAA
*
3543301 TAATTTTAATA
1 T-ATTTAAATA
3543312 AAATAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAAATATTAATTATAAAA
Found at i:3543329 original size:16 final size:16
Alignment explanation
Indices: 3543283--3543331 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3543273 TATAAAATAT
3543283 ATAAATATTAATTAAA
1 ATAAATATTAATTAAA
*
3543299 A-ATAATTTTAA-TAAA
1 ATA-AATATTAATTAAA
*
3543314 ATAAATAATAATTAAA
1 ATAAATATTAATTAAA
3543330 AT
1 AT
3543332 TTAAATAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATATTAATTAAA
Found at i:3543811 original size:18 final size:19
Alignment explanation
Indices: 3543782--3543820 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3543772 ATTATATATC
3543782 TTTTTTATATAAATATTTA
1 TTTTTTATATAAATATTTA
*
3543801 TTTTTTA-ATAATTATTTA
1 TTTTTTATATAAATATTTA
3543819 TT
1 TT
3543821 ATAATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTATATAAATATTTA
Found at i:3544201 original size:23 final size:22
Alignment explanation
Indices: 3544175--3544235 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 22
3544165 ATCGTATTCG
3544175 TATTATTTTTTTATATTATATCA
1 TATTATTTTTTTATATTATAT-A
* *
3544198 TATT-TTATGTTATATT-T-TA
1 TATTATTTTTTTATATTATATA
3544217 -ATTA-TTTTTTATATTATAT
1 TATTATTTTTTTATATTATAT
3544236 TTGTATCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
18 12 0.39
19 2 0.06
20 2 0.06
21 1 0.03
22 10 0.32
23 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTTTTATATTATATA
Found at i:3544226 original size:11 final size:12
Alignment explanation
Indices: 3544190--3544237 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
3544180 TTTTTTTATA
*
3544190 TTATATCATATT
1 TTATATTATATT
*
3544202 TTATGTTATATT
1 TTATATTATATT
*
3544214 TTA-ATTATTTT
1 TTATATTATATT
3544225 TTATATTATATT
1 TTATATTATATT
3544237 T
1 T
3544238 GTATCATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATATTATATT
Found at i:3544488 original size:13 final size:13
Alignment explanation
Indices: 3544470--3544495 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3544460 ACGTGTTATA
3544470 TTTATATTATATT
1 TTTATATTATATT
3544483 TTTATATTATATT
1 TTTATATTATATT
3544496 ATATATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:3544886 original size:22 final size:21
Alignment explanation
Indices: 3544840--3544892 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3544830 TTTATAATTT
*
3544840 TTATATGATTTTTATTTATTTAA
1 TTATAT-A-TTTTATTTATTGAA
*
3544863 TTTTATATTTTATTTATGTGAA
1 TTATATATTTTATTTAT-TGAA
3544885 TTATATAT
1 TTATATAT
3544893 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 11 0.42
23 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (21 bp):
TTATATATTTTATTTATTGAA
Found at i:3545036 original size:13 final size:12
Alignment explanation
Indices: 3544998--3545041 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
3544988 AATTTAAAAT
3544998 TTTAATATTATAA
1 TTTAATATTAT-A
*
3545011 TTATATTATTATA
1 TT-TAATATTATA
3545024 TTTAATGATTATA
1 TTTAAT-ATTATA
3545037 TTTAA
1 TTTAA
3545042 ATAAGTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 16 0.59
14 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTAATATTATA
Found at i:3545073 original size:16 final size:18
Alignment explanation
Indices: 3545054--3545094 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3545044 AAGTATAATT
3545054 ATTAATAAA-ATA-AAAA
1 ATTAATAAATATATAAAA
*
3545070 ATTATAAAAATATATAAAA
1 ATTA-ATAAATATATAAAA
3545089 ATTAAT
1 ATTAAT
3545095 TTTCTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 4 0.20
19 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAATAAATATATAAAA
Found at i:3545239 original size:26 final size:27
Alignment explanation
Indices: 3545185--3545252 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 27
3545175 CCACAATTTG
3545185 TTTGTAAAAAATGGTAGTTACTTTGTA
1 TTTGTAAAAAATGGTAGTTACTTTGTA
* *
3545212 TTTGTAAAAAATGGTAGTT-TTTTTTA
1 TTTGTAAAAAATGGTAGTTACTTTGTA
*
3545238 TTTGTCAAAAATGGT
1 TTTGTAAAAAATGGT
3545253 GGCATGTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (27 bp):
TTTGTAAAAAATGGTAGTTACTTTGTA
Found at i:3545362 original size:13 final size:13
Alignment explanation
Indices: 3545346--3545379 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3545336 CCTCTCAAGC
3545346 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
* *
3545359 ATCCTTATCTTGT
1 ATCCCTCTCTTGT
3545372 ATCCCTCT
1 ATCCCTCT
3545380 TCAATTCTTT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (13 bp):
ATCCCTCTCTTGT
Found at i:3549721 original size:24 final size:26
Alignment explanation
Indices: 3549668--3549722 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3549658 TGGGTGGCTA
* *
3549668 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAACCACCCATTGTGTTT
3549694 GTCAACAAAAACCA-CCATT-TGTTT
1 GTCAACAAAAACCACCCATTGTGTTT
3549718 GTCAA
1 GTCAA
3549723 AAATGGTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 10 0.37
25 4 0.15
26 13 0.48
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (26 bp):
GTCAACAAAAACCACCCATTGTGTTT
Found at i:3549766 original size:24 final size:25
Alignment explanation
Indices: 3549715--3549775 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
3549705 CCACCATTTG
* *
3549715 TTTGTCAAAAATGGTGGTTTCTTTTTA
1 TTTGTCAAAAATGGTGG--TCATGTTA
3549742 TTTGTCAAAAATGGTGG-CATGTTA
1 TTTGTCAAAAATGGTGGTCATGTTA
3549766 TTTGTCAAAA
1 TTTGTCAAAA
3549776 TTTGTGACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 15 0.47
27 17 0.53
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
TTTGTCAAAAATGGTGGTCATGTTA
Found at i:3551091 original size:14 final size:14
Alignment explanation
Indices: 3551054--3551092 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
3551044 TAGAGTCTGT
3551054 AATTTAAAATAAAAA
1 AATTT-AAATAAAAA
3551069 AATTATAAATAAAAA
1 AATT-TAAATAAAAA
3551084 AATTTAAAT
1 AATTTAAAT
3551093 TTTATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 17 0.74
16 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTTAAATAAAAA
Found at i:3551140 original size:19 final size:19
Alignment explanation
Indices: 3551116--3551152 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3551106 AAAAATAATT
3551116 ATATAAAATAATAATTATA
1 ATATAAAATAATAATTATA
* *
3551135 ATATAATATTATAATTAT
1 ATATAAAATAATAATTAT
3551153 TATTTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAAATAATAATTATA
Found at i:3551145 original size:13 final size:13
Alignment explanation
Indices: 3551117--3551221 Score: 52
Period size: 14 Copynumber: 7.7 Consensus size: 13
3551107 AAAATAATTA
*
3551117 TATAAAATAATAAT
1 TATAATATAAT-AT
3551131 TATAATATAATAT
1 TATAATATAATAT
* *
3551144 TATAATTATTATTT
1 TATAA-TATAATAT
* * *
3551158 TATATTTTATATTT
1 TATAATATA-ATAT
* *
3551172 TTTATTATTAATATT
1 TATAATA-TAATA-T
3551187 TATAAT-TAATAT
1 TATAATATAATAT
*
3551199 T-TATTATAATTAAT
1 TATAATATAA-T-AT
3551213 TATAATATA
1 TATAATATA
3551222 TTTATTATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
11 3 0.04
12 5 0.07
13 15 0.21
14 34 0.49
15 13 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATAATATAATAT
Found at i:3551148 original size:22 final size:22
Alignment explanation
Indices: 3551123--3551230 Score: 59
Period size: 21 Copynumber: 5.1 Consensus size: 22
3551113 ATTATATAAA
3551123 ATAATAATTATAATATAATATT
1 ATAATAATTATAATATAATATT
* ** *
3551145 ATAATTATTATTTTAT-ATTTT
1 ATAATAATTATAATATAATATT
* ** *
3551166 ATATTTTTTATTAT-TAATATT
1 ATAATAATTATAATATAATATT
*
3551187 -T-ATAA-T-TAATAT-TTATT
1 ATAATAATTATAATATAATATT
*
3551204 ATAATTAATTATAATATATTTATT
1 ATAA-TAATTATAATATA-ATATT
3551228 ATA
1 ATA
3551231 TTTTTAATTA
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
17 7 0.11
18 3 0.05
19 2 0.03
20 5 0.08
21 20 0.31
22 19 0.30
24 8 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAATAATTATAATATAATATT
Found at i:3551185 original size:16 final size:16
Alignment explanation
Indices: 3551143--3551212 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 16
3551133 TAATATAATA
*
3551143 TTATAATT-AT-TATT
1 TTATAATTAATATTTT
* *
3551157 TTATATTTTATATTTT
1 TTATAATTAATATTTT
*
3551173 TTATTATTAATA---T
1 TTATAATTAATATTTT
*
3551186 TTATAATTAATATTTA
1 TTATAATTAATATTTT
3551202 TTATAATTAAT
1 TTATAATTAAT
3551213 TATAATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 12 0.27
14 7 0.16
15 2 0.05
16 23 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATAATTAATATTTT
Found at i:3551238 original size:20 final size:21
Alignment explanation
Indices: 3551176--3551238 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
3551166 ATATTTTTTA
*
3551176 TTATTAATATTTATAATTAATAT
1 TTATT-ATATTTTTAA-TAATAT
3551199 TTATTATAATTAATTATAAT-ATAT
1 TTATTAT-ATT--TT-TAATAATAT
3551223 TTATTATATTTTTAAT
1 TTATTATATTTTTAAT
3551239 TATAATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
20 4 0.11
21 2 0.06
22 2 0.06
23 11 0.31
24 11 0.31
25 2 0.06
26 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTATATTTTTAATAATAT
Found at i:3551560 original size:17 final size:16
Alignment explanation
Indices: 3551527--3551560 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3551517 TTGAAAATTA
3551527 TTATTTAATAATAAAT
1 TTATTTAATAATAAAT
*
3551543 TTATTTATATAATTAAT
1 TTATTTA-ATAATAAAT
3551560 T
1 T
3551561 ATATAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTTAATAATAAAT
Found at i:3551763 original size:22 final size:21
Alignment explanation
Indices: 3551738--3551797 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
3551728 AAAAATAAAA
3551738 ATATATTGTTAT-ATTAATATTT
1 ATATATT-TTATAATTAA-ATTT
3551760 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
* *
3551781 AAATAATTTTTTAATTA
1 ATAT-ATTTTATAATTA
3551798 TTAAATATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.32
22 23 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:3552380 original size:25 final size:23
Alignment explanation
Indices: 3552307--3552380 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 23
3552297 TTTAAATTTT
*
3552307 ATTAATTT--TTAATTGTTTTTAA
1 ATTAATTTAATTAATT-TTCTTAA
* * *
3552329 ATTAATTTTATTTATTTTCTT-T
1 ATTAATTTAATTAATTTTCTTAA
3552351 A-TAATTTAAATTAATTATTCTTAA
1 ATTAATTT-AATTAATT-TTCTTAA
3552375 ATTAAT
1 ATTAAT
3552381 AATTTTGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 6 0.15
22 15 0.38
23 9 0.22
24 6 0.15
25 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (23 bp):
ATTAATTTAATTAATTTTCTTAA
Found at i:3552692 original size:18 final size:18
Alignment explanation
Indices: 3552671--3552714 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3552661 AGATTTGGTC
3552671 AATTTTAATTATTTTTTT
1 AATTTTAATTATTTTTTT
3552689 AATTATT-ATTATTTTTTT
1 AATT-TTAATTATTTTTTT
3552707 AATGTTTA
1 AAT-TTTA
3552715 TGGCAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
AATTTTAATTATTTTTTT
Found at i:3554159 original size:24 final size:26
Alignment explanation
Indices: 3554108--3554171 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
3554098 AATTCAATTT
*
3554108 ATTTTTCTATTATATAATATATATTA
1 ATTTTTATATTATATAATATATATTA
3554134 ATTTTTATATT-TAT-ATAT-TATGTA
1 ATTTTTATATTATATAATATATAT-TA
*
3554158 ATTTTTATAATATA
1 ATTTTTATATTATA
3554172 AAAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 3 0.09
24 16 0.47
25 5 0.15
26 10 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTTATATTATATAATATATATTA
Found at i:3555597 original size:40 final size:37
Alignment explanation
Indices: 3555553--3555647 Score: 92
Period size: 36 Copynumber: 2.6 Consensus size: 37
3555543 TAACTTGAAT
*
3555553 TATTATTTAAATAATAAAATATTTTTAATTTAATTATAA
1 TATTATTTAAATAATAAAATATTTTTAATTT-TTTA-AA
3555592 -A-TA-TT-AAT-ATAAAAATAATTTTTAATTTTTTAAA
1 TATTATTTAAATAAT-AAAAT-ATTTTTAATTTTTTAAA
*
3555626 TATTATTTTAATTAATAAAATA
1 TATTA-TTTAAATAATAAAATA
3555648 GATTTTAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
34 4 0.09
35 12 0.26
36 15 0.33
37 2 0.04
38 4 0.09
39 7 0.15
40 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
TATTATTTAAATAATAAAATATTTTTAATTTTTTAAA
Found at i:3555598 original size:18 final size:18
Alignment explanation
Indices: 3555577--3555644 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
3555567 TAAAATATTT
3555577 TTAATTTAATTATAAATA
1 TTAATTTAATTATAAATA
* ** * *
3555595 TTAATATAAAAATAATTT
1 TTAATTTAATTATAAATA
3555613 TTAATTT--TT-TAAATA
1 TTAATTTAATTATAAATA
*
3555628 TTATTTTAATTAATAAA
1 TTAATTTAATT-ATAAA
3555645 ATAGATTTTA
Statistics
Matches: 35, Mismatches: 11, Indels: 7
0.66 0.21 0.13
Matches are distributed among these distances:
15 10 0.29
17 2 0.06
18 19 0.54
19 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTTAATTATAAATA
Found at i:3556188 original size:21 final size:21
Alignment explanation
Indices: 3556164--3556207 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3556154 GTTTTTATTG
* *
3556164 TTTTTTTATCAATTCAAAGAA
1 TTTTTTTACCAATTCAAAAAA
*
3556185 TTTTTTTACCAATTTAAAAAA
1 TTTTTTTACCAATTCAAAAAA
3556206 TT
1 TT
3556208 CTTGGTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTTTTACCAATTCAAAAAA
Found at i:3557884 original size:23 final size:22
Alignment explanation
Indices: 3557839--3557880 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3557829 AATTTTTATT
3557839 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
*
3557861 TAAATATTAA-TATTAAAATA
1 TAAAT-TTAATTATAAAAATA
3557881 ATATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:3557947 original size:26 final size:26
Alignment explanation
Indices: 3557900--3557962 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
3557890 TATTTTTAAT
*
3557900 AAAATTATAAATAATAAAATTAATTTT
1 AAAATTA-AAATAATAAAATTAATTTA
* * *
3557927 TAAATTAAATTAATTAAATTAATTTA
1 AAAATTAAAATAATAAAATTAATTTA
3557953 AAAATTAAAA
1 AAAATTAAAA
3557963 AATTCAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATTAAAATAATAAAATTAATTTA
Found at i:3557971 original size:26 final size:26
Alignment explanation
Indices: 3557907--3557973 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
3557897 AATAAAATTA
* **
3557907 TAAAT-AATAAAATTAATTTTTAAAT
1 TAAATAAATTAAATTAATTTAAAAAT
*
3557932 TAAATTAATTAAATTAATTTAAAAAT
1 TAAATAAATTAAATTAATTTAAAAAT
3557958 TAAA-AAATTCAAATTA
1 TAAATAAATT-AAATTA
3557974 CAACCTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAATAAATTAAATTAATTTAAAAAT
Found at i:3558142 original size:27 final size:28
Alignment explanation
Indices: 3558103--3558187 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 28
3558093 ATTAACAAAT
3558103 AAATATTAAATATATAATTTAAATTTAA-A
1 AAATATT--ATATATAATTTAAATTTAATA
* *
3558132 AAATATTATATATAATATATATTTAATA
1 AAATATTATATATAATTTAAATTTAATA
*
3558160 AAA-A-TATATTTAATTTAATATTATAATA
1 AAATATTATATATAATTTAA-ATT-TAATA
3558188 TCTAATATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
26 11 0.23
27 21 0.44
28 9 0.19
29 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATATTATATATAATTTAAATTTAATA
Found at i:3558665 original size:11 final size:12
Alignment explanation
Indices: 3558626--3558666 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
3558616 ATATTATAAA
3558626 AATATTATATTAT
1 AATATTAT-TTAT
3558639 AAT-TTATTTAT
1 AATATTATTTAT
3558650 AAATATTATTT-T
1 -AATATTATTTAT
3558662 AATAT
1 AATAT
3558667 CTGAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.35
12 8 0.31
13 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATTATTTAT
Found at i:3559035 original size:19 final size:19
Alignment explanation
Indices: 3559009--3559053 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3558999 ATAATGGATA
3559009 AAAAATAAGTAAA-AAATAC
1 AAAAATAA-TAAACAAATAC
* *
3559028 ATAAATAATAAACTAATAC
1 AAAAATAATAAACAAATAC
3559047 AAAAATA
1 AAAAATA
3559054 TTATTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAAATAATAAACAAATAC
Found at i:3560360 original size:28 final size:31
Alignment explanation
Indices: 3560319--3560390 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
3560309 CCTTTTAATT
3560319 TAATACAATTAATAAC-T-TTT-ATTATTATA
1 TAATA-AATTAATAACATATTTCATTATTATA
3560348 TAATAAATTAATAACTATATTTCATTATTATA
1 TAATAAATTAATAAC-ATATTTCATTATTATA
*
3560380 TAATTAATTAA
1 TAATAAATTAA
3560391 AATAAGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 10 0.26
29 5 0.13
30 1 0.03
31 3 0.08
32 19 0.50
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
TAATAAATTAATAACATATTTCATTATTATA
Found at i:3562476 original size:22 final size:22
Alignment explanation
Indices: 3562436--3562489 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
3562426 TAAAATTATG
*
3562436 AAAT-AATTTTATTATTTAATAT
1 AAATAAATTTTATGATTTAA-AT
*
3562458 AAATAAATTTTATGA-TTAAGT
1 AAATAAATTTTATGATTTAAAT
3562479 -AATAAATTTTA
1 AAATAAATTTTA
3562490 AAAGATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
22 8 0.28
23 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AAATAAATTTTATGATTTAAAT
Found at i:3562654 original size:17 final size:17
Alignment explanation
Indices: 3562632--3562664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3562622 TCAAAAAATA
3562632 ATAAATATAAATTTTAC
1 ATAAATATAAATTTTAC
*
3562649 ATAAATATAATTTTTA
1 ATAAATATAAATTTTA
3562665 TTATTTTAAA
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAATATAAATTTTAC
Found at i:3562658 original size:26 final size:27
Alignment explanation
Indices: 3562603--3562659 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
3562593 CAAATATTAT
*
3562603 TAATAAATTATAAATTCTTTCAAAAAA
1 TAATAAATTATAAATTCTTACAAAAAA
*
3562630 TAATAAA-TATAAATT-TTACATAAATA
1 TAATAAATTATAAATTCTTACA-AAAAA
3562656 TAAT
1 TAAT
3562660 TTTTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 4 0.15
26 16 0.59
27 7 0.26
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATAAATTATAAATTCTTACAAAAAA
Found at i:3562833 original size:21 final size:20
Alignment explanation
Indices: 3562800--3562839 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3562790 ATATTTAATT
3562800 ATTAATTTTAATTTCATTAC
1 ATTAATTTTAATTTCATTAC
*
3562820 ATTAATTATTAATTTTATTA
1 ATTAATT-TTAATTTCATTA
3562840 ATATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTAATTTTAATTTCATTAC
Found at i:3562845 original size:27 final size:26
Alignment explanation
Indices: 3562794--3562871 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 26
3562784 AAACATATAT
3562794 TTAATTATTAATTTTAATT--TCATTACA
1 TTAATTATTAATTTT-ATTAAT-ATTA-A
3562821 TTAATTATTAATTTTATTAATATTAA
1 TTAATTATTAATTTTATTAATATTAA
* * *
3562847 -T-ATTTTTAATTTTACTAAAATTAA
1 TTAATTATTAATTTTATTAATATTAA
3562871 T
1 T
3562872 CGTGCATTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
24 20 0.44
25 1 0.02
26 4 0.09
27 19 0.42
28 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (26 bp):
TTAATTATTAATTTTATTAATATTAA
Found at i:3562846 original size:15 final size:16
Alignment explanation
Indices: 3562820--3562856 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3562810 ATTTCATTAC
3562820 ATTAATTATTAAT-TTT
1 ATTAA-TATTAATATTT
3562836 ATTAATATTAATATTT
1 ATTAATATTAATATTT
3562852 -TTAAT
1 ATTAAT
3562857 TTTACTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTAATATTAATATTT
Found at i:3565335 original size:23 final size:23
Alignment explanation
Indices: 3565309--3565360 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
3565299 TTAAAAAATA
3565309 AAATAATTATAATAT-AAATATAT
1 AAATAATTAT-ATATCAAATATAT
*
3565332 AAAT-A-TATATATCAAATTTAT
1 AAATAATTATATATCAAATATAT
3565353 ATAATAAT
1 A-AATAAT
3565361 AATTAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 4 0.17
23 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATAATTATATATCAAATATAT
Done.