Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 188 of 208
Found at i:57494367 original size:89 final size:89
Alignment explanation
Indices: 57494132--57494414 Score: 449
Period size: 89 Copynumber: 3.1 Consensus size: 89
57494122 GCCAATACAT
* *
57494132 GAAGACAAGATCTATTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTC
1 GAAGGCAAGATCTATTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG--TTTT-
57494197 CTTCGATCTGCTTCGCCACCAGTATGG
63 CTTCGATCTGCTTCGCCACCAGTATGG
*
57494224 GAAGGCAAGATCTATTTTTCTTCAATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GAAGGCAAGATCTA-TTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
* *
57494289 TTGATCAGCTTCGCCACCAGTATGG
65 TCGATCTGCTTCGCCACCAGTATGG
* * * *
57494314 GAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGGCAAGATCTATTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
57494379 CGATCTGCTTCGCCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
57494403 GAAGGCAAGATC
1 GAAGGCAAGATC
57494415 GATGGCCGAT
Statistics
Matches: 178, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
89 81 0.46
90 38 0.21
91 4 0.02
92 13 0.07
93 42 0.24
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GAAGGCAAGATCTATTTTCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
CGATCTGCTTCGCCACCAGTATGG
Found at i:57494412 original size:45 final size:45
Alignment explanation
Indices: 57494003--57494414 Score: 329
Period size: 45 Copynumber: 9.2 Consensus size: 45
57493993 GAGTAACTGG
** * * *
57494003 CAAGATCTATTTTCCTTCGATCTACTTC-ACGCCAGTACATGAAGA
1 CAAGATCTGCTTT-CTTCGATCTACTTCGCCACCAGTACAGGAAGA
**
57494048 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGA
1 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTACAGGAAGA
* * *
57494093 CAAGATCTGCTCTCTTTGATCTACTTCATGCCA--A-TACATGAAGA
1 CAAGATCTGCTTTCTTCGATCTACTTC--GCCACCAGTACAGGAAGA
** * * * *
57494137 CAAGATCTATTTTCTTCGATCTACTTC-ACGCCAATACATGAAGA
1 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTACAGGAAGA
* ** *
57494181 CAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGG
1 CAAGATCTGC--TTT-CTTCGATCTACTTCGCCACCAGTACAGGAAGA
** * * * *
57494229 CAAGATCTATTTTTCTTCAATCTACTTC-ACGCCAGTACATGAAGA
1 CAAGATCT-GCTTTCTTCGATCTACTTCGCCACCAGTACAGGAAGA
* * ** *
57494274 CAAGATCTGTTTTCTTTGATC-AGCTTCGCCACCAGTATGGGAAGG
1 CAAGATCTGCTTTCTTCGATCTA-CTTCGCCACCAGTACAGGAAGA
* * * *
57494319 CAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGAAGA
1 CAAGATCTGCTT-TCTTCGATCTACTTCGCCACCAGTACAGGAAGA
* ** *
57494363 CAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGG
1 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTACAGGAAGA
57494408 CAAGATC
1 CAAGATC
57494415 GATGGCCGAT
Statistics
Matches: 289, Mismatches: 61, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
41 1 0.00
43 2 0.01
44 111 0.38
45 121 0.42
46 16 0.06
47 20 0.07
48 18 0.06
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (45 bp):
CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTACAGGAAGA
Found at i:57496446 original size:44 final size:44
Alignment explanation
Indices: 57496397--57496636 Score: 219
Period size: 44 Copynumber: 5.4 Consensus size: 44
57496387 GTGGAAAAGC
57496397 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* * * * * * * * *
57496441 AGATCAAATATACCAGATCTTATCTTCCTATACTGGTGGCGAAGC
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
* * * * *
57496486 AGATCGAAGAAAACAAATCTTATATTCATGTGCTGGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* * * *** * *
57496530 AGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGC
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGT
** *
57496575 AGATCAAAGAAAGTAAATCTTGTCTTCATGTACTGGCGTGAAGT
1 AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
* *
57496619 AGATCAGAGATAACAGAT
1 AGATCAAAGAAAACAGAT
57496637 GAACGCCATC
Statistics
Matches: 145, Mismatches: 49, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
44 79 0.54
45 66 0.46
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (44 bp):
AGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
Found at i:57496532 original size:89 final size:89
Alignment explanation
Indices: 57496376--57496636 Score: 378
Period size: 89 Copynumber: 2.9 Consensus size: 89
57496366 AGTTATCGTT
* *
57496376 TTCCCATACTGGTGGAAAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGT
1 TTCCCATACTGGTGGAGAAGCAGATCAAAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGT
* *
57496441 AGATCAAATATACCAGATCTTATC
66 AGATCAAAGATACCAGATCTTACC
* * * * * *
57496465 TTCCTATACTGGTGGCGAAGCAGATCGAAGAAAACAAATCTTATATTCATGTGCTGGCGTGAAGT
1 TTCCCATACTGGTGGAGAAGCAGATCAAAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGT
*
57496530 AGATCAAAGATACCAGATCTTGCC
66 AGATCAAAGATACCAGATCTTACC
* **
57496554 TTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAAATCTTGTCTTCATGTACTGGCGTGAAGT
1 TTCCCATACTGGTGGAGAAGCAGATCAAAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGT
* *
57496619 AGATCAGAGATAACAGAT
66 AGATCAAAGATACCAGAT
57496637 GAACGCCATC
Statistics
Matches: 151, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 151 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (89 bp):
TTCCCATACTGGTGGAGAAGCAGATCAAAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGT
AGATCAAAGATACCAGATCTTACC
Found at i:57500094 original size:20 final size:20
Alignment explanation
Indices: 57500069--57500108 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57500059 TTCATCTCAT
57500069 GCATCGCATCATATACATTA
1 GCATCGCATCATATACATTA
* *
57500089 GCATCGTATTATATACATTA
1 GCATCGCATCATATACATTA
57500109 TAGACCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
GCATCGCATCATATACATTA
Found at i:57500970 original size:36 final size:36
Alignment explanation
Indices: 57500930--57501001 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
57500920 GCAAGAAACA
57500930 CTTAATCTGGAATCCACTAGGGTTTTGGGATAGTTC
1 CTTAATCTGGAATCCACTAGGGTTTTGGGATAGTTC
*
57500966 CTTAATCTGGAATTCACTAGGGTTTTGGGATAGTTC
1 CTTAATCTGGAATCCACTAGGGTTTTGGGATAGTTC
57501002 TACCTAGGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (36 bp):
CTTAATCTGGAATCCACTAGGGTTTTGGGATAGTTC
Found at i:57502168 original size:14 final size:14
Alignment explanation
Indices: 57502146--57502184 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
57502136 AACATATACG
*
57502146 AATAAATATTTGCA
1 AATAAATATATGCA
*
57502160 AATATATATATGCA
1 AATAAATATATGCA
57502174 AATACAATATA
1 AATA-AATATA
57502185 ACAGTAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (14 bp):
AATAAATATATGCA
Found at i:57502386 original size:16 final size:17
Alignment explanation
Indices: 57502352--57502397 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
57502342 GAATAAAGGA
*
57502352 AAAATATATATAA-TAT
1 AAAATATATAAAAGTAT
57502368 AAAATATATAAAAGT-T
1 AAAATATATAAAAGTAT
* *
57502384 AAAAAAAATAAAAG
1 AAAATATATAAAAG
57502398 AATGTATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAATATATAAAAGTAT
Found at i:57502534 original size:2 final size:2
Alignment explanation
Indices: 57502529--57502556 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57502519 GAAAAAAAAC
57502529 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57502557 CAAAGAACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57508094 original size:41 final size:42
Alignment explanation
Indices: 57507989--57508100 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 42
57507979 ATTGTTTATA
* *
57507989 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTG
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATCATTGATTGAG
* * * * *
57508032 AAAGGGTTACTATGTGTTGATTCC-TCGTATCATTGATT-AG
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTGAG
57508072 AAGGCGGTTGCTAAGTGCTGATTCCACCG
1 AAGG-GGTTGCTAAGTGCTGATTCCACCG
57508101 GGATCCTTTG
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
40 4 0.07
41 29 0.53
42 19 0.35
43 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTGAG
Found at i:57508143 original size:18 final size:18
Alignment explanation
Indices: 57508120--57508156 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
57508110 GAACATGAGG
57508120 TGGTTGCTAAGTGTTGAT
1 TGGTTGCTAAGTGTTGAT
57508138 TGGTTGCTAAGTGTTGAT
1 TGGTTGCTAAGTGTTGAT
57508156 T
1 T
57508157 CCACCGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.46
Consensus pattern (18 bp):
TGGTTGCTAAGTGTTGAT
Found at i:57508156 original size:62 final size:62
Alignment explanation
Indices: 57508077--57508194 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
57508067 ATTAGAAGGC
*
57508077 GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATGAGGTGGTTGCTAAGTGTTGATT
1 GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATAAGGTGGTTGCTAAGTGTTGATT
*
57508139 GGTTGCTAAGTGTTGATTCCACCGGGATCCTTTGAACATAAGGTGGTTGCTAAGTG
1 GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATAAGGTGGTTGCTAAGTG
57508195 CTAATTCCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (62 bp):
GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATAAGGTGGTTGCTAAGTGTTGATT
Found at i:57511414 original size:3 final size:3
Alignment explanation
Indices: 57511408--57511478 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
57511398 ATTATTTAGT
57511408 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57511456 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
57511479 GCATTTAATC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:57513620 original size:5 final size:5
Alignment explanation
Indices: 57513606--57513637 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
57513596 CTAAAACAAT
57513606 AAAT- AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
57513638 ATATAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:57518077 original size:6 final size:6
Alignment explanation
Indices: 57518068--57518103 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
57518058 TCTTGTTGCT
57518068 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
1 ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA
57518104 TGGAGTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGCAA
Found at i:57519172 original size:108 final size:106
Alignment explanation
Indices: 57518940--57519286 Score: 540
Period size: 108 Copynumber: 3.3 Consensus size: 106
57518930 NNNNNNNCCG
*
57518940 CAGCACCCAAAATTTTTTTTATTTTGTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGA
1 CAGCACCCAAAATTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGA
57519005 AATTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGC
66 AA-TTTTTTTTAAA-TTGTACTGGGTGCCGGCCATTGACAGGC
*
57519048 CAGCACCCAAAATTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACATGAAAAAAAAAG
1 CAGCACCCAAAATTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACG-AAAAAAAAG
57519113 AAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGC
65 AAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGC
* *
57519155 CAACACCCAAAATTTTTTTTA-TTTTTTCGTATATTTATATCTGACTTTGACACGAAAAAAAAGT
1 CAGCACCCAAAATTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAG-
* * *
57519219 AAATTTTTTTT-TACTGT--TGGGTGCCGGCCATTGACAAGC
65 AAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGC
* *
57519258 CAGCACCCAAATTTTTTTTTTCTTTTTTT
1 CAGCACCCAAA-ATTTTTTTTATTTTTTT
57519287 ATTTTTCGTA
Statistics
Matches: 224, Mismatches: 11, Indels: 11
0.91 0.04 0.04
Matches are distributed among these distances:
103 31 0.14
104 8 0.04
105 19 0.08
106 42 0.19
107 48 0.21
108 64 0.29
109 12 0.05
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (106 bp):
CAGCACCCAAAATTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGA
AATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGC
Found at i:57519910 original size:20 final size:20
Alignment explanation
Indices: 57519873--57519915 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
57519863 GGTATTGTAA
57519873 AAATATTAAAAACTTAAATAT
1 AAATATTAAAAACTTAAAT-T
*
57519894 AAATATT-AAATCTTAAATT
1 AAATATTAAAAACTTAAATT
57519913 AAA
1 AAA
57519916 ATGTAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 7 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTAAAAACTTAAATT
Found at i:57520460 original size:52 final size:52
Alignment explanation
Indices: 57520379--57520478 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
57520369 CCTATATTTG
* * *
57520379 ATTAAAAAAAATTTTAGGTGCTAGAACACTGATGGCCGACACCCCTTTCAAA
1 ATTAAAAAAAAATTGAGGTGCTAGAACACTAATGGCCGACACCCCTTTCAAA
* *
57520431 ATTAAAAAAAAATTGGGGTGCT-GAGACACTAATGGCCGGCACCCCTTT
1 ATTAAAAAAAAATTGAGGTGCTAGA-ACACTAATGGCCGACACCCCTTT
57520479 ATATGGTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.05
52 40 0.95
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (52 bp):
ATTAAAAAAAAATTGAGGTGCTAGAACACTAATGGCCGACACCCCTTTCAAA
Found at i:57520491 original size:52 final size:52
Alignment explanation
Indices: 57520356--57520493 Score: 127
Period size: 52 Copynumber: 2.6 Consensus size: 52
57520346 TAACATATTG
* * * * *
57520356 ATGGCTGGCACCCCCTATATTTGATTAAAAAAAATTTTAGGTGCTAGAACACTG
1 ATGGCCGGCA-CCCCTTTATATG-TTAAAAAAAATTTGAGGTGCTAGAACACTA
* ** * *
57520410 ATGGCCGACACCCCTTTCA-AAATTAAAAAAAAATTGGGGTGCT-GAGACACTA
1 ATGGCCGGCACCCCTTT-ATATGTTAAAAAAAATTTGAGGTGCTAGA-ACACTA
57520462 ATGGCCGGCACCCCTTTATATGGTTAAAAAAA
1 ATGGCCGGCACCCCTTTATAT-GTTAAAAAAA
57520494 TAAATTTTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
51 3 0.04
52 40 0.60
53 15 0.22
54 9 0.13
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (52 bp):
ATGGCCGGCACCCCTTTATATGTTAAAAAAAATTTGAGGTGCTAGAACACTA
Found at i:57530710 original size:18 final size:18
Alignment explanation
Indices: 57530668--57530710 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57530658 TGAGCAAATG
57530668 TTTTTTCATTCTTTACGA
1 TTTTTTCATTCTTTACGA
*
57530686 TTCTTTCATTCTTTTA-GA
1 TTTTTTCATTC-TTTACGA
57530704 TTTTTTC
1 TTTTTTC
57530711 TGCCAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.14, C:0.16, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTCATTCTTTACGA
Found at i:57531664 original size:7 final size:7
Alignment explanation
Indices: 57531639--57531680 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
57531629 AGTGATGTGA
57531639 AAAAATG
1 AAAAATG
57531646 AAAAGATG
1 AAAA-ATG
57531654 -AAAATG
1 AAAAATG
57531660 AAAAATG
1 AAAAATG
57531667 AAAAA-G
1 AAAAATG
57531673 TAAAAATG
1 -AAAAATG
57531681 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:57531678 original size:21 final size:21
Alignment explanation
Indices: 57531639--57531680 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57531629 AGTGATGTGA
*
57531639 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
57531660 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
57531681 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:57534015 original size:132 final size:132
Alignment explanation
Indices: 57533002--57533997 Score: 1521
Period size: 132 Copynumber: 7.6 Consensus size: 132
57532992 GGAGCAGGTT
* *
57533002 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCTGTAATTCTATCTCCAT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * *
57533067 GGGCAACAGTGGAATAGATTGAAGATTACAGATGTTATCCCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
57533132 AA
131 AG
* *
57533134 GATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
57533199 GGGCAGCAGTGGAATAGATTAAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
57533264 AG
131 AG
* * * *
57533266 GATAGCGGATTTTACTTCTCTGAGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * *
57533331 AGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
57533396 AG
131 AG
**
57533398 GATGGCAAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
57533463 GGGC-GACAGTGGAATAGATTAAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 GGGCAG-CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
57533527 AAG
130 AAG
* * *
57533530 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACCTCACT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
57533595 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
57533660 AT
131 AG
*
57533662 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCCATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
*
57533727 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCT-CC----C--TAG-GGAGTAGATCG
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-
57533784 AA-
130 AAG
57533786 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * *
57533851 GGGCAGCAGTGGAATAGATTGAATATTACAGATTTTATCTCCCT-AGACAGTAGTGGAGTAGATC
66 GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATC
57533915 GAA-
130 -AAG
** * * * * *
57533918 GATGGTAGATTTTACCTCTCTGAGGTTATAGTAGAGTATATTGAAGCCAGTAATTCTAACTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
57533983 GGTCGGCAGTGGAAT
66 GGGCAGCAGTGGAAT
57533998 CAATCGAAGA
Statistics
Matches: 800, Mismatches: 53, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
124 111 0.14
125 7 0.01
127 1 0.00
129 1 0.00
131 6 0.01
132 673 0.84
133 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
AG
Found at i:57534063 original size:44 final size:44
Alignment explanation
Indices: 57534000--57534156 Score: 235
Period size: 44 Copynumber: 3.6 Consensus size: 44
57533990 AGTGGAATCA
*
57534000 ATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
1 ATCGAAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
* *
57534044 ATCGAAAAAAGTAGATCTTGTCTTCATGTATTGGCGTGGAGTAG
1 ATCGAAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
* *
57534088 ATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
1 ATCGAAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
* *
57534132 ATC-AAAGAGAGTAGATCTTGTCTTC
1 ATCGAAA-AAAGCAGATCTTGTCTTC
57534157 CCATACTGGT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 2 0.02
44 100 0.98
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (44 bp):
ATCGAAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
Found at i:57534940 original size:13 final size:14
Alignment explanation
Indices: 57534922--57534954 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
57534912 AAAGGGGGGA
57534922 TCGAAAGAAAAGAT
1 TCGAAAGAAAAGAT
*
57534936 T-GAAAGAACAGAT
1 TCGAAAGAAAAGAT
57534949 TCGAAA
1 TCGAAA
57534955 ATTTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (14 bp):
TCGAAAGAAAAGAT
Found at i:57535709 original size:18 final size:17
Alignment explanation
Indices: 57535681--57535728 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
57535671 GCATTGTATC
* *
57535681 ATTATTATTATATTATT
1 ATTATTTTTATATCATT
*
57535698 CATTGTTTTTATCATCATT
1 -ATTATTTTTAT-ATCATT
57535717 ATTATTTTTATA
1 ATTATTTTTATA
57535729 CACTTACACG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 19 0.76
19 5 0.20
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTATTTTTATATCATT
Found at i:57538538 original size:18 final size:18
Alignment explanation
Indices: 57538515--57538550 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57538505 CTCTATTATA
* *
57538515 TAGGCTTTTGCTTTTGCT
1 TAGGCTTATGCTATTGCT
57538533 TAGGCTTATGCTATTGCT
1 TAGGCTTATGCTATTGCT
57538551 AGCTATTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (18 bp):
TAGGCTTATGCTATTGCT
Found at i:57565872 original size:46 final size:43
Alignment explanation
Indices: 57565820--57566053 Score: 226
Period size: 46 Copynumber: 5.6 Consensus size: 43
57565810 TTTGAGTACT
57565820 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG---TAGCTACACTTA
**
57565866 TCTGATCAAGAAACAAAGTGATAAGT-G--GT---TACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
**
57565903 TCTGATCAAGAAACAAAGTGATAA---GT-G--GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
*
57565940 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG--T-AGCTACACTTA
**
57565986 TCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG--TAGCTACACTTA
*
57566031 TCTGATTAAG-GAC-AAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
57566054 AGGTCATATG
Statistics
Matches: 166, Mismatches: 10, Indels: 27
0.82 0.05 0.13
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 61 0.37
40 3 0.02
41 1 0.01
43 11 0.07
44 1 0.01
45 21 0.13
46 66 0.40
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (43 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
Found at i:57565899 original size:37 final size:37
Alignment explanation
Indices: 57565858--57565968 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
57565848 TAGTTTTAGC
57565858 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
*
57565895 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
** *
57565932 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
57565969 AGCTTCAGCT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
Found at i:57573246 original size:24 final size:24
Alignment explanation
Indices: 57573231--57573282 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
57573221 AATCAAATTC
57573231 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
57573255 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
57573279 AAAT
1 AAAT
57573283 CTTCTAGAAA
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:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:57574682 original size:61 final size:62
Alignment explanation
Indices: 57574576--57574695 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 62
57574566 AAACTTTTAG
* *
57574576 AATTAGAACTAAAATGACAAATTATTCTAAATTTTAAGGGCTAAATTTCTTGAATTTTTTCA
1 AATTAGAACTAAAATGACAAATTATTCTAAATATCAAGGGCTAAATTTCTTGAATTTTTTCA
* * *
57574638 AATTAGAATTAAAATGA-AATATT-TTGTAAATATCAAGGGCTAAATTTGTTGAATTTTT
1 AATTAGAACTAAAATGACAA-ATTATTCTAAATATCAAGGGCTAAATTTCTTGAATTTTT
57574696 AGATTTATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 33 0.63
62 19 0.37
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (62 bp):
AATTAGAACTAAAATGACAAATTATTCTAAATATCAAGGGCTAAATTTCTTGAATTTTTTCA
Found at i:57577013 original size:63 final size:64
Alignment explanation
Indices: 57576914--57577049 Score: 193
Period size: 63 Copynumber: 2.1 Consensus size: 64
57576904 AGCTTCAGAT
*
57576914 GAAGCAGTTCCTAATCCTAATGGCGCAGAAGACAAGCCTCAAAC-CGTGCCTGATAAAGTAAAG
1 GAAGCAGCTCCTAATCCTAATGGCGCAGAAGACAAGCCTCAAACGCGTGCCTGATAAAGTAAAG
* *
57576977 GAAGCAGCTCCTAATCCTAATGGCTCAGAGGACAAGCCTCAAACTGTGGTCGTGCCTGATAAAGT
1 GAAGCAGCTCCTAATCCTAATGGCGCAGAAGACAAGCCTCAAAC----G-CGTGCCTGATAAAGT
57577042 AAAG
61 AAAG
57577046 GAAG
1 GAAG
57577050 AAGAAGTCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
63 41 0.64
69 23 0.36
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (64 bp):
GAAGCAGCTCCTAATCCTAATGGCGCAGAAGACAAGCCTCAAACGCGTGCCTGATAAAGTAAAG
Found at i:57592352 original size:16 final size:17
Alignment explanation
Indices: 57592331--57592368 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
57592321 TATATTTATG
*
57592331 TATTTA-AATTTTATTT
1 TATTTATAATTTAATTT
57592347 TATTTATAATTTAATTT
1 TATTTATAATTTAATTT
*
57592364 AATTT
1 TATTT
57592369 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTATAATTTAATTT
Found at i:57593164 original size:16 final size:15
Alignment explanation
Indices: 57593142--57593203 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
57593132 TTTACTTATT
57593142 ATAATATATAATATA
1 ATAATATATAATATA
*
57593157 AT-ATATATACTTAATA
1 ATAATATATA-AT-ATA
* *
57593173 ATGAAGATATAATATT
1 AT-AATATATAATATA
57593189 ATAATATTATAATAT
1 ATAATA-TATAATAT
57593204 TTATTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
14 7 0.19
15 6 0.16
16 17 0.46
17 1 0.03
18 6 0.16
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAATATATAATATA
Found at i:57593193 original size:8 final size:8
Alignment explanation
Indices: 57593180--57593204 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
57593170 ATAATGAAGA
57593180 TATAATAT
1 TATAATAT
57593188 TATAATAT
1 TATAATAT
57593196 TATAATAT
1 TATAATAT
57593204 T
1 T
57593205 TATTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATAATAT
Found at i:57599309 original size:17 final size:15
Alignment explanation
Indices: 57599285--57599323 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
57599275 TTTTCTTTTC
*
57599285 TTTCTTTTTCTCCTTG
1 TTTCTTTTTATCC-TG
57599301 TTTCGTTTTTATCCTG
1 TTTC-TTTTTATCCTG
57599317 TTTCTTT
1 TTTCTTT
57599324 CTATTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 10 0.48
17 8 0.38
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (15 bp):
TTTCTTTTTATCCTG
Found at i:57608699 original size:15 final size:15
Alignment explanation
Indices: 57608652--57608701 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
57608642 CAATTCAAAT
*
57608652 AATCAATATATATTC
1 AATCAATATAAATTC
57608667 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
57608684 AATCAATATAAATTC
1 AATCAATATAAATTC
57608699 AAT
1 AAT
57608702 AAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:57610200 original size:105 final size:105
Alignment explanation
Indices: 57610001--57610210 Score: 253
Period size: 105 Copynumber: 2.0 Consensus size: 105
57609991 TTTATAAAAA
* * * * **
57610001 AAAGGTTAATATACTAATTGGTACTTGAGATTAATTTCAATGTTCAATTTAATATTTGTTTTTTT
1 AAAGGCTAATATACTAATCGGTACTTAAGATCAATTTCAATGTTCAATTTAATATTTGTACTTTT
* * ** * *
57610066 TTTCTAATTTAGCACTAAGTTTGGTTTTAATGTTCAAATT
66 TTCCCAATTTAGCACTAAACTTGGCTTTAATGATCAAATT
* *
57610106 AAAGGCTAATATACTACTCGGTACTTAAGATCAATTTCAATGTTCAATTTGATATTTG-ACTTTT
1 AAAGGCTAATATACTAATCGGTACTTAAGATCAATTTCAATGTTCAATTTAATATTTGTACTTTT
*
57610170 TTCCCAATTT-GTTACTTAAACTTGGCTTTAATGATCAAATT
66 TTCCCAATTTAG-CAC-TAAACTTGGCTTTAATGATCAAATT
57610211 GGTACTTAAG
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
103 1 0.01
104 14 0.16
105 73 0.83
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (105 bp):
AAAGGCTAATATACTAATCGGTACTTAAGATCAATTTCAATGTTCAATTTAATATTTGTACTTTT
TTCCCAATTTAGCACTAAACTTGGCTTTAATGATCAAATT
Found at i:57614677 original size:20 final size:20
Alignment explanation
Indices: 57614652--57614689 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57614642 TTAATAAATA
*
57614652 ACATTATAATTATATGACAG
1 ACATTATAACTATATGACAG
57614672 ACATTATAACTATATGAC
1 ACATTATAACTATATGAC
57614690 TACGGGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (20 bp):
ACATTATAACTATATGACAG
Found at i:57614828 original size:67 final size:67
Alignment explanation
Indices: 57614720--57614855 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
57614710 ACACTAATCA
57614720 ATGTTTTGATTTGTATAAAATAATGATTAAAATTTTATCAAACACTTATTTAATACGAAATCAAG
1 ATGTTTTGATTTGTATAAAATAATGATTAAAATTTTATCAAACACTTATTTAATACGAAATCAAG
57614785 TC
66 TC
57614787 ATGTTTTGATTTGTATAAAATAATGATTAAAATTTTATCAAACACTTATTTAATACGAAATCAAG
1 ATGTTTTGATTTGTATAAAATAATGATTAAAATTTTATCAAACACTTATTTAATACGAAATCAAG
57614852 TC
66 TC
57614854 AT
1 AT
57614856 ATAACTCTAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (67 bp):
ATGTTTTGATTTGTATAAAATAATGATTAAAATTTTATCAAACACTTATTTAATACGAAATCAAG
TC
Found at i:57616152 original size:16 final size:15
Alignment explanation
Indices: 57616131--57616162 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
57616121 GAGTTATTCG
57616131 TGTGTTCAAATTATAT
1 TGTGTTCAAATT-TAT
57616147 TGTGTTCAAATTTAT
1 TGTGTTCAAATTTAT
57616162 T
1 T
57616163 TTATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
TGTGTTCAAATTTAT
Found at i:57616752 original size:98 final size:98
Alignment explanation
Indices: 57616583--57616773 Score: 346
Period size: 98 Copynumber: 1.9 Consensus size: 98
57616573 ACAATAAAAC
*
57616583 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
57616648 TAGAATCCCAAACTCGGAATATTTCCTTTACTT
66 TAGAATCCCAAACTCGGAATATTTCCTTTACTT
* *
57616681 TAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
*
57616746 TAGAATCTCAAACTCGGAATATTTCCTT
66 TAGAATCCCAAACTCGGAATATTTCCTT
57616774 CATGATTTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
TAGAATCCCAAACTCGGAATATTTCCTTTACTT
Found at i:57619296 original size:44 final size:44
Alignment explanation
Indices: 57618984--57619432 Score: 136
Period size: 44 Copynumber: 10.2 Consensus size: 44
57618974 TATCTTGGAA
* * * *
57618984 AGATAAGATTCGCCGTCTTCGATCTACTCCACTATTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*** * * * * *
57619028 AGATAAGA-TCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * *
57619072 AGACAAGGCTT-AGTGGCTTAAATCCGCTTTCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC--TCCACTACTGCTTAGG-G
* * * *
57619116 AGATAAGATTCGCCGTCTTCGATCTGCTCTATTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*** * * * * *
57619160 AGATAAGA-TCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *** * * *
57619204 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
57619248 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * * * *
57619292 AGATAAGA-TCTACAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 AGATAAGATTC-ACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *** * * * *
57619336 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCTCACTA--ACTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC-TC-CACTACTGCTTAGG-G
* *
57619380 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
57619424 AGATAAGAT
1 AGATAAGAT
57619433 CTGAAATCTT
Statistics
Matches: 274, Mismatches: 101, Indels: 60
0.63 0.23 0.14
Matches are distributed among these distances:
42 16 0.06
43 26 0.09
44 202 0.74
45 14 0.05
46 16 0.06
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:57619458 original size:132 final size:132
Alignment explanation
Indices: 57618744--57619442 Score: 1105
Period size: 132 Copynumber: 5.3 Consensus size: 132
57618734 TGGATGCGAC
* * * * * * *
57618744 CTGCTCCACTACTGCTTAGAGAAATAAGATCTACAATCTTCAACTTTCTTCGCTACTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
* * *
57618809 GGAAAAGGCTTGGTGGC-TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
57618873 AT
131 AT
* * * *
57618875 TTGTTCCACTACTACTTAGAGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
* * *
57618940 AAACAAGGCTTGGTAGCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
57619005 AT
131 AT
* *
57619007 CTACTCCACTATTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
* * *
57619072 AGACAAGGCTTAGTGGCTTAAATCCGCTTTCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
57619137 AT
131 AT
* *
57619139 CTGCTCTATTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
*
57619204 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
57619269 AT
131 AT
* * *
57619271 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
* *
57619336 AGACAAGGCTTGGTGGCTTAAATCTGCTTCTCACTAACTTGGAAAGATAAGATTCGCCGTCTTCG
66 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
57619401 AT
131 AT
57619403 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-AATCTT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTT
57619443 TAGTCTGCCT
Statistics
Matches: 523, Mismatches: 43, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
131 69 0.13
132 453 0.87
133 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTACTCCGCTGCTGCTCAGGG
AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCG
AT
Found at i:57627782 original size:19 final size:20
Alignment explanation
Indices: 57627745--57627782 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
57627735 TATAAGAAAA
*
57627745 CTTTACTATAAATTAAATTC
1 CTTTACTATAAAATAAATTC
*
57627765 CTTTA-TATAAAATGAATT
1 CTTTACTATAAAATAAATT
57627783 ACAAATACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (20 bp):
CTTTACTATAAAATAAATTC
Found at i:57631028 original size:98 final size:98
Alignment explanation
Indices: 57630859--57631049 Score: 346
Period size: 98 Copynumber: 1.9 Consensus size: 98
57630849 ACAATAAAAC
*
57630859 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
57630924 TAGAATCCCAAACTCGGAATATTTCCTTTACTT
66 TAGAATCCCAAACTCGGAATATTTCCTTTACTT
* *
57630957 TAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
*
57631022 TAGAATCTCAAACTCGGAATATTTCCTT
66 TAGAATCCCAAACTCGGAATATTTCCTT
57631050 CATGATTTTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
TAGAATCCCAAACTCGGAATATTTCCTTTACTT
Found at i:57635419 original size:28 final size:27
Alignment explanation
Indices: 57635369--57635424 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
57635359 CTTTTATTAA
*
57635369 TTTAATTTTAAATAAAATTAAAATCATG
1 TTTAATTTTAAATAAAATGAAAA-CATG
*
57635397 TTTAATATTTAATTAAAA-GAAAACATG
1 TTTAAT-TTTAAATAAAATGAAAACATG
57635424 T
1 T
57635425 CTACCCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 10 0.40
29 10 0.40
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (27 bp):
TTTAATTTTAAATAAAATGAAAACATG
Found at i:57637630 original size:19 final size:20
Alignment explanation
Indices: 57637608--57637646 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
57637598 AAAATGATAA
*
57637608 TTATATTTAATTATT-TTTT
1 TTATAGTTAATTATTCTTTT
*
57637627 TTATAGTTAGTTATTCTTTT
1 TTATAGTTAATTATTCTTTT
57637647 ATAACAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TTATAGTTAATTATTCTTTT
Found at i:57651249 original size:39 final size:39
Alignment explanation
Indices: 57651195--57651271 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
57651185 TAGAAGTGGT
57651195 ATATTCATTGTTCATAATTACGGCACTAGTAAAATCTAA
1 ATATTCATTGTTCATAATTACGGCACTAGTAAAATCTAA
57651234 ATATTCATTGTTCATAATTACGGCACTAGTAAAATCTA
1 ATATTCATTGTTCATAATTACGGCACTAGTAAAATCTA
57651272 TCTCATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (39 bp):
ATATTCATTGTTCATAATTACGGCACTAGTAAAATCTAA
Found at i:57653044 original size:20 final size:20
Alignment explanation
Indices: 57653016--57653060 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
57653006 CCTAGCTGTT
* *
57653016 AGAAGAAGAAGCAGAAGAGA
1 AGAAAAAGAAGAAGAAGAGA
* *
57653036 AGAAAAAGAATAATAAGAGA
1 AGAAAAAGAAGAAGAAGAGA
57653056 AGAAA
1 AGAAA
57653061 TGGATATACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAAGAAGAAGAGA
Found at i:57654401 original size:19 final size:20
Alignment explanation
Indices: 57654377--57654421 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
57654367 CTAGGGGTTC
*
57654377 ACACATAT-GGTTTGCATAT
1 ACACATATAGGTTTACATAT
57654396 ACACATATAGGGTTTACATAT
1 ACACATATA-GGTTTACATAT
57654417 ACACA
1 ACACA
57654422 AGTATGTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
21 15 0.65
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ACACATATAGGTTTACATAT
Found at i:57654515 original size:23 final size:22
Alignment explanation
Indices: 57654485--57654528 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
57654475 GTTCGCATAC
*
57654485 TACAATATGA-AGGTTTTGCATG
1 TACAATAT-ATAGGGTTTGCATG
57654507 TACACATATATAGGGTTTGCAT
1 TACA-ATATATAGGGTTTGCAT
57654529 AATAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (22 bp):
TACAATATATAGGGTTTGCATG
Found at i:57654529 original size:46 final size:46
Alignment explanation
Indices: 57654473--57654631 Score: 108
Period size: 46 Copynumber: 3.3 Consensus size: 46
57654463 GGAACAGTTC
* *
57654473 GGGTTCGCATACT-ACA-ATATGAAGGTTTTGCATGTACACATATATA
1 GGGTTCGCATAATAACATATAT-AAGG-TTTGCATATACACATATATA
* *
57654519 GGGTTTGCATAATAACATGTATAAGGTTTGCATATACACATGTATATATA
1 GGGTTCGCATAATAACATATATAAGGTTTGCATATACAC----ATATATA
* * ** * *
57654569 GAGAGTTTGCATAGATAA-ACATGCAGGGTTCGCATATACACATATATA
1 G-G-GTTCGCATA-ATAACATATATAAGGTTTGCATATACACATATATA
* *
57654617 GGTTTCGCATCATAA
1 GGGTTCGCATAATAA
57654632 ACATTTTTGG
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
45 4 0.04
46 29 0.32
47 8 0.09
48 11 0.12
50 8 0.09
51 1 0.01
52 26 0.29
53 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (46 bp):
GGGTTCGCATAATAACATATATAAGGTTTGCATATACACATATATA
Found at i:57654559 original size:23 final size:23
Alignment explanation
Indices: 57654494--57654564 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
57654484 CTACAATATG
* *
57654494 AAGGTTTTGCATGTACACATATAT
1 AAGG-TTTGCATATACACATGTAT
*
57654518 AGGGTTTGCATAATA-ACATGTAT
1 AAGGTTTGCAT-ATACACATGTAT
57654541 AAGGTTTGCATATACACATGTAT
1 AAGGTTTGCATATACACATGTAT
57654564 A
1 A
57654565 TATAGAGAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.07
23 33 0.80
24 5 0.12
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (23 bp):
AAGGTTTGCATATACACATGTAT
Found at i:57654577 original size:52 final size:50
Alignment explanation
Indices: 57654512--57654616 Score: 124
Period size: 52 Copynumber: 2.1 Consensus size: 50
57654502 GCATGTACAC
* * *
57654512 ATATATAGGGTTTGCATA-AT-AACATGTATAAGGTTTGCATATACACATGT
1 ATATATAGGGTTTGCATAGATAAACATG--CAAGGTTCGCATATACACATAT
*
57654562 ATATATAGAGAGTTTGCATAGATAAACATGCAGGGTTCGCATATACACATAT
1 ATATATAG-G-GTTTGCATAGATAAACATGCAAGGTTCGCATATACACATAT
57654614 ATA
1 ATA
57654617 GGTTTCGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
50 8 0.17
51 1 0.02
52 30 0.64
53 2 0.04
54 6 0.13
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (50 bp):
ATATATAGGGTTTGCATAGATAAACATGCAAGGTTCGCATATACACATAT
Found at i:57654623 original size:23 final size:22
Alignment explanation
Indices: 57654597--57654651 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
57654587 ACATGCAGGG
*
57654597 TTCGCATATACACATATATAGGT
1 TTCGCATATAAACAT-TATAGGT
* *
57654620 TTCGCATCATAAACATTTTTGGT
1 TTCGCAT-ATAAACATTATAGGT
57654643 TT-GCATATA
1 TTCGCATATA
57654652 TAAACATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 3 0.11
22 4 0.14
23 14 0.50
24 7 0.25
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCGCATATAAACATTATAGGT
Found at i:57654803 original size:13 final size:13
Alignment explanation
Indices: 57654775--57654818 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
57654765 AACCTTATAA
57654775 GGTTCTGCATAT-G
1 GGTTC-GCATATGG
57654788 GGTTCGCATATGG
1 GGTTCGCATATGG
*
57654801 GGTTCGCTTATGAG
1 GGTTCGCATATG-G
57654815 GGTT
1 GGTT
57654819 TGCCTATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 6 0.21
13 17 0.61
14 5 0.18
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (13 bp):
GGTTCGCATATGG
Found at i:57659548 original size:10 final size:10
Alignment explanation
Indices: 57659511--57659559 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
57659501 TGCAACACGT
57659511 GAAAACAACAA
1 GAAAA-AACAA
* *
57659522 GGACAAACAGA
1 GAAAAAACA-A
57659533 GCAAAAAACAA
1 G-AAAAAACAA
57659544 GAAAAAACAA
1 GAAAAAACAA
57659554 GAAAAA
1 GAAAAA
57659560 GAAACAGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 19 0.59
11 7 0.22
12 6 0.19
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (10 bp):
GAAAAAACAA
Found at i:57659551 original size:22 final size:20
Alignment explanation
Indices: 57659511--57659559 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
57659501 TGCAACACGT
* *
57659511 GAAAACAACAAGGACAAACAGA
1 GAAAA-AACAAGAAAAAACA-A
57659533 GCAAAAAACAAGAAAAAACAA
1 G-AAAAAACAAGAAAAAACAA
57659554 GAAAAA
1 GAAAAA
57659560 GAAACAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 2 0.08
22 13 0.54
23 4 0.17
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (20 bp):
GAAAAAACAAGAAAAAACAA
Found at i:57660412 original size:18 final size:20
Alignment explanation
Indices: 57660391--57660461 Score: 56
Period size: 24 Copynumber: 3.4 Consensus size: 20
57660381 TATTTAGTCA
57660391 ATTTT-TGTTAACT-TTATT
1 ATTTTATGTTAACTATTATT
*
57660409 ATTTTAATGTTATCTATTATT
1 ATTTT-ATGTTAACTATTATT
*
57660430 ATTATTATTATTATTACTATTATT
1 ATT-TTA-TGTTA--ACTATTATT
57660454 ATTATTAT
1 ATT-TTAT
57660462 TATTANNNNN
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
18 5 0.12
20 7 0.16
21 9 0.21
22 6 0.14
23 1 0.02
24 15 0.35
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTTTATGTTAACTATTATT
Found at i:57660429 original size:3 final size:3
Alignment explanation
Indices: 57660404--57660466 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
57660394 TTTGTTAACT
* * *
57660404 TTA TTA TT- TTA ATG TTA TCTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
57660449 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
57660467 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:57661270 original size:112 final size:111
Alignment explanation
Indices: 57660999--57661297 Score: 476
Period size: 112 Copynumber: 2.7 Consensus size: 111
57660989 GGCACACAGA
57660999 ATTT-GGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCAACCAAAT
1 ATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCAACCAAAT
*
57661063 AGCTAAATATCC-TTTCAAAAATTTTAAAATAAGGCAATGTTTTGC
66 AGCTAAATATCCTTTTAAAAAATTTTAAAATAAGGCAATGTTTTGC
* * *
57661108 GTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAAT
1 ATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCAACCAAAT
* *
57661173 GGCTAAATATCCTTTTAAAAAATTTTCGAAATAAGGCAATGTTTTGC
66 AGCTAAATATCCTTTTAAAAAATTTT-AAAATAAGGCAATGTTTTGC
* * *
57661220 ATTTGGGAAATTCGAGAAAACGTGTCCTAAGGTGCTGGGTGTCGATTTTTCTCATTTAACCGAAT
1 ATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCAACCAAAT
* *
57661285 TGCCAAATATCCT
66 AGCTAAATATCCT
57661298 CTTGAATTTC
Statistics
Matches: 173, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
109 3 0.02
110 69 0.40
111 12 0.07
112 89 0.51
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (111 bp):
ATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCATTCAACCAAAT
AGCTAAATATCCTTTTAAAAAATTTTAAAATAAGGCAATGTTTTGC
Found at i:57662010 original size:34 final size:34
Alignment explanation
Indices: 57661964--57662034 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
57661954 TGCCACTGAG
57661964 TTGAACTATTATAAACATATTAATTGCTACTGTA
1 TTGAACTATTATAAACATATTAATTGCTACTGTA
* * *
57661998 TTGAACTGTTATAAGCATATTGATTGCTACTGTA
1 TTGAACTATTATAAACATATTAATTGCTACTGTA
57662032 TTG
1 TTG
57662035 TTCTATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (34 bp):
TTGAACTATTATAAACATATTAATTGCTACTGTA
Found at i:57662048 original size:34 final size:34
Alignment explanation
Indices: 57661964--57662055 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
57661954 TGCCACTGAG
57661964 TTGAACTATTATAAA-CATATTAATTGCTACTGTA
1 TTGAACTATTA-AAAGCATATTAATTGCTACTGTA
* * *
57661998 TTGAACTGTTATAAGCATATTGATTGCTACTGTA
1 TTGAACTATTAAAAGCATATTAATTGCTACTGTA
**
57662032 TTGTTCTATTAAAAGCATAATTAA
1 TTGAACTATTAAAAGCAT-ATTAA
57662056 ATACTATCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 2 0.04
34 42 0.88
35 4 0.08
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (34 bp):
TTGAACTATTAAAAGCATATTAATTGCTACTGTA
Found at i:57663482 original size:33 final size:36
Alignment explanation
Indices: 57663436--57663517 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 36
57663426 AAAAAAATAT
*
57663436 TATTTATTATATTATT-AA-TTTGACAT-TTGAATAA
1 TATTTATTATATTATTAAATTTTGA-ATATTGAAAAA
*
57663470 T-TTTATTTTATTATTAAATTTTGAATATTGAAAAA
1 TATTTATTATATTATTAAATTTTGAATATTGAAAAA
57663505 TATTTATTATATT
1 TATTTATTATATT
57663518 TAAGCTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.32
34 5 0.12
35 13 0.32
36 10 0.24
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (36 bp):
TATTTATTATATTATTAAATTTTGAATATTGAAAAA
Found at i:57663941 original size:17 final size:19
Alignment explanation
Indices: 57663921--57663964 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
57663911 AATAATTGTA
57663921 AAAAATTAT-A-AATTAAT
1 AAAAATTATCATAATTAAT
57663938 AAAAATTATCGATAATTAAT
1 AAAAATTATC-ATAATTAAT
57663958 AAAAATT
1 AAAAATT
57663965 CTTACAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
19 1 0.04
20 14 0.58
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATTATCATAATTAAT
Found at i:57664855 original size:36 final size:34
Alignment explanation
Indices: 57664805--57664879 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 34
57664795 AATATAATAG
* *
57664805 ATAAATATTTTTC-AATATTCAAAATTTAATAATAAA
1 ATAAAAATTATTCAAATA-TCAAAA--TAATAATAAA
*
57664841 ATAAAAATTATTCAAATATCAAAATAATAATATA
1 ATAAAAATTATTCAAATATCAAAATAATAATAAA
57664875 ATAAA
1 ATAAA
57664880 TAATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 14 0.40
36 17 0.49
37 4 0.11
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (34 bp):
ATAAAAATTATTCAAATATCAAAATAATAATAAA
Found at i:57664858 original size:23 final size:23
Alignment explanation
Indices: 57664832--57664885 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
57664822 TTCAAAATTT
*
57664832 AATAATAAAATAAAAAT-TATTCA
1 AATAATAAAATAAAAATATAAT-A
*
57664855 AAT-ATCAAAATAATAATATAATA
1 AATAAT-AAAATAAAAATATAATA
57664878 AATAATAA
1 AATAATAA
57664886 TTTTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 2 0.08
23 19 0.73
24 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AATAATAAAATAAAAATATAATA
Found at i:57665121 original size:22 final size:23
Alignment explanation
Indices: 57665068--57665123 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
57665058 TTAAATTAAA
* * *
57665068 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
57665091 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
57665113 ATTAAAATTAA
1 ATTAAAATTAA
57665124 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:57665136 original size:16 final size:16
Alignment explanation
Indices: 57665099--57665138 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
57665089 TTAATAAAAT
* *
57665099 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
57665115 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
57665131 TAAAATTA
1 TAAAATTA
57665139 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:57665217 original size:59 final size:61
Alignment explanation
Indices: 57665148--57665327 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
57665138 ATCAAATTAT
*
57665148 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
57665213 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
57665276 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
57665328 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:57665244 original size:9 final size:9
Alignment explanation
Indices: 57665211--57665238 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57665201 TTTATCAAAT
57665211 TATTAATTG
1 TATTAATTG
57665220 TATTAATTG
1 TATTAATTG
57665229 TATTAATTG
1 TATTAATTG
57665238 T
1 T
57665239 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:57665248 original size:68 final size:68
Alignment explanation
Indices: 57665127--57665297 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
57665117 AAATTAATTG
*
57665127 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
57665190 TGA
66 TGA
57665193 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
57665258 TGA
66 TGA
57665261 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
57665298 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:57665360 original size:59 final size:63
Alignment explanation
Indices: 57665127--57665363 Score: 230
Period size: 68 Copynumber: 3.8 Consensus size: 63
57665117 AAATTAATTG
* *
57665127 TTAGTAAAATTATCAAATTATTAATTGTTAATT-GTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGT-AAA-TATCAAATTATTAATTG-T-ATTATTATTAATTGTTGTAACAAAATCTAACATTT
57665191 GA
62 GA
*
57665193 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAA--TATCAAATTATTAATTGTATT-A-T-TATTAATTGTTGTAACAAAATCTAACATT
57665258 TGA
61 TGA
57665261 TTAGTAAATTTATCAAATTATTAATTG------TATTAATTGTTGTAACAAAATCTAACATTTGA
1 TTAGTAAA--TATCAAATTATTAATTGTATTATTATTAATTGTTGTAACAAAATCTAACATTTGA
*
57665320 TTAGTAAA-A-CAAACTTGA-T-ATTTTATTATTATT-ATT-TTGTAACA
1 TTAGTAAATATCAAA-TT-ATTAATTGTATTATTATTAATTGTTGTAACA
57665364 CTAGTCAAGG
Statistics
Matches: 155, Mismatches: 3, Indels: 33
0.81 0.02 0.17
Matches are distributed among these distances:
55 7 0.05
56 4 0.03
57 1 0.01
59 47 0.30
60 3 0.02
61 4 0.03
64 3 0.02
65 4 0.03
66 23 0.15
68 59 0.38
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (63 bp):
TTAGTAAATATCAAATTATTAATTGTATTATTATTAATTGTTGTAACAAAATCTAACATTTGA
Found at i:57665441 original size:23 final size:24
Alignment explanation
Indices: 57665394--57665439 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
57665384 AAATAAACTT
57665394 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
57665418 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
57665440 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:57666177 original size:11 final size:13
Alignment explanation
Indices: 57666161--57666194 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
57666151 AATTTTACGG
57666161 AAAAATTTCG-T-
1 AAAAATTTCGTTC
57666172 AAAAATTTCGTTC
1 AAAAATTTCGTTC
57666185 AAAAATTTCG
1 AAAAATTTCG
57666195 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:57667304 original size:33 final size:33
Alignment explanation
Indices: 57667262--57667413 Score: 136
Period size: 33 Copynumber: 4.5 Consensus size: 33
57667252 AATATGAAGG
57667262 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
57667295 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CAT-T---GGT
*
57667338 GGTTGCTAAGTGCTGATT-CCC--C-CAAT-G-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
57667365 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
57667398 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
57667414 CTCCACCATA
Statistics
Matches: 97, Mismatches: 6, Indels: 32
0.72 0.04 0.24
Matches are distributed among these distances:
27 18 0.19
28 4 0.04
31 3 0.03
32 2 0.02
33 37 0.38
34 3 0.03
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
40 1 0.01
41 2 0.02
42 1 0.01
43 20 0.21
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:57667443 original size:103 final size:103
Alignment explanation
Indices: 57667261--57667462 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
57667251 GAATATGAAG
* * *
57667261 GGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGACTCCACCATATCTTT
*
57667326 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAT
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAT
57667364 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGACTCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGACTCCACCATATCTTT
*
57667429 GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
57667463 AAATCACTGG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (103 bp):
GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGACTCCACCATATCTTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAT
Found at i:57670821 original size:11 final size:12
Alignment explanation
Indices: 57670793--57670826 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
57670783 GCCCAAACGT
57670793 CGAAATTTTTGAA
1 CGAAATTTTT-AA
57670806 CGAAATTTTT-A
1 CGAAATTTTTAA
57670817 CGAAATTTTT
1 CGAAATTTTT
57670827 CAGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:57672929 original size:75 final size:75
Alignment explanation
Indices: 57672789--57672935 Score: 172
Period size: 75 Copynumber: 2.0 Consensus size: 75
57672779 ATATTAGAGA
**
57672789 GGCCTACTTATATTTTTAGGAGAGCTAAAATACATATACAAAGGGAAAAATTGCAAAAATCTTAA
1 GGCCTACTTATATTTTTAGGAGAGCTAAAATACATATACAAAGGGAAAAATTGCAAAAAAATTAA
57672854 ACCTTGGGGG
66 ACCTTGGGGG
* * * * * * *
57672864 GGCCTACTTATATTTTTGGGA-AGGCTACAGTATATTTACAAA-GGATTAAATTGTAAAAAAATT
1 GGCCTACTTATATTTTTAGGAGA-GCTAAAATACATATACAAAGGGA-AAAATTGCAAAAAAATT
*
57672927 AAACTTTGG
64 AAACCTTGG
57672936 AGGGCAATGC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
74 4 0.07
75 56 0.93
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (75 bp):
GGCCTACTTATATTTTTAGGAGAGCTAAAATACATATACAAAGGGAAAAATTGCAAAAAAATTAA
ACCTTGGGGG
Found at i:57673015 original size:19 final size:19
Alignment explanation
Indices: 57672991--57673029 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
57672981 TGATCCTTAG
57672991 CGAAATTATTAACCCATAA
1 CGAAATTATTAACCCATAA
57673010 CGAAATTATTAACCCATAA
1 CGAAATTATTAACCCATAA
57673029 C
1 C
57673030 ATTATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (19 bp):
CGAAATTATTAACCCATAA
Found at i:57673033 original size:16 final size:17
Alignment explanation
Indices: 57672994--57673034 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
57672984 TCCTTAGCGA
57672994 AATTATTAACCCATAAC
1 AATTATTAACCCATAAC
57673011 GAAATTATTAACCCATAAC
1 --AATTATTAACCCATAAC
57673030 -ATTAT
1 AATTAT
57673035 CATATTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
19 17 0.77
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (17 bp):
AATTATTAACCCATAAC
Found at i:57689475 original size:46 final size:46
Alignment explanation
Indices: 57689414--57689681 Score: 349
Period size: 46 Copynumber: 5.6 Consensus size: 46
57689404 TTTGAGTACT
* *
57689414 TCTGATCAGGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
57689460 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
57689506 TCTGATCAAGTGACAATTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
57689558 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
57689610 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
57689656 TCTGATCAAGAGACAAAG-GATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
57689682 GCTACACTTA
Statistics
Matches: 205, Mismatches: 11, Indels: 13
0.90 0.05 0.06
Matches are distributed among these distances:
45 8 0.04
46 104 0.51
52 93 0.45
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:57689535 original size:98 final size:92
Alignment explanation
Indices: 57689414--57689718 Score: 342
Period size: 98 Copynumber: 3.3 Consensus size: 92
57689404 TTTGAGTACT
* * *
57689414 TCTGATCAGGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGT
57689479 GATAAGTGATAGCTTCAGCTACACTTA
66 GATAAGTGATAGCTTCAGCTACACTTA
*
57689506 TCTGATCAAGTGACAATTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGAGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
57689571 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 C------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
** *
57689610 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAG-
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGT
57689674 GATAA--G-T-G-----GCTACACTTA
66 GATAAGTGATAGCTTCAGCTACACTTA
*
57689692 TCTGATCAAGAAACAAAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
57689719 GCTACACTTA
Statistics
Matches: 191, Mismatches: 10, Indels: 34
0.81 0.04 0.14
Matches are distributed among these distances:
82 35 0.18
87 1 0.01
88 1 0.01
89 1 0.01
91 5 0.03
92 17 0.09
98 88 0.46
104 43 0.23
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (92 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGATAGCTTCAGCTACACTTA
Found at i:57689724 original size:37 final size:37
Alignment explanation
Indices: 57689646--57689773 Score: 222
Period size: 37 Copynumber: 3.5 Consensus size: 37
57689636 GATAGCTTTA
*
57689646 GCTACACTTATCTGATCAAGAGACAAAG-GATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
57689682 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
57689719 GCTACACTTATCTGATCAAGAAATAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
57689756 GCTACACTTATCTGATCA
1 GCTACACTTATCTGATCA
57689774 GGGACAGTGA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 27 0.31
37 61 0.69
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:57695938 original size:16 final size:17
Alignment explanation
Indices: 57695906--57695939 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
57695896 TATGTACATT
57695906 TTATTTATTTAAAAAAA
1 TTATTTATTTAAAAAAA
57695923 TTATTT-TTTGAAAAAAA
1 TTATTTATTT-AAAAAAA
57695940 AATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTATTTATTTAAAAAAA
Found at i:57704804 original size:2 final size:2
Alignment explanation
Indices: 57704793--57704826 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
57704783 CTTTATAATA
57704793 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57704827 CCCACTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57705799 original size:3 final size:3
Alignment explanation
Indices: 57705791--57705823 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
57705781 ACTAAATTGT
57705791 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57705824 AAGAAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57706225 original size:27 final size:29
Alignment explanation
Indices: 57706177--57706230 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
57706167 GATTTGACAA
57706177 AAAAATGTAAATTTAAAAGTTAAAATATG
1 AAAAATGTAAATTTAAAAGTTAAAATATG
57706206 AAAAAT-TAAA-TTAAAAGTTAAAATA
1 AAAAATGTAAATTTAAAAGTTAAAATA
57706231 AGTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 15 0.60
28 4 0.16
29 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAAATGTAAATTTAAAAGTTAAAATATG
Found at i:57709018 original size:16 final size:17
Alignment explanation
Indices: 57708999--57709035 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
57708989 AATAAATAAA
57708999 TATTATTTAAAA-TTAT
1 TATTATTTAAAATTTAT
57709015 TATT-TTTAAAATTTAT
1 TATTATTTAAAATTTAT
57709031 TATTA
1 TATTA
57709036 AAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:57709148 original size:16 final size:16
Alignment explanation
Indices: 57709111--57709156 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
57709101 ATATGTATTT
57709111 TTAATAATATTTAAAA
1 TTAATAATATTTAAAA
* *
57709127 TT-ATAATATTTTATA
1 TTAATAATATTTAAAA
57709142 TTAATAAT-TTTAAAA
1 TTAATAATATTTAAAA
57709157 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATAATATTTAAAA
Found at i:57709981 original size:14 final size:15
Alignment explanation
Indices: 57709964--57709992 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57709954 ATACTATTTT
57709964 AAAATTA-ATAAATA
1 AAAATTATATAAATA
57709978 AAAATTATATAAATA
1 AAAATTATATAAATA
57709993 TATAAAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATTATATAAATA
Found at i:57718392 original size:17 final size:17
Alignment explanation
Indices: 57718360--57718394 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57718350 CATTTCACTA
**
57718360 TTTTGTCTTTTGTATTT
1 TTTTGTCTTTCATATTT
57718377 TTTTGTCTTTCATATTT
1 TTTTGTCTTTCATATTT
57718394 T
1 T
57718395 GCATACATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGTCTTTCATATTT
Found at i:57723133 original size:23 final size:24
Alignment explanation
Indices: 57723102--57723151 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
57723092 AATTTTGTGT
* * *
57723102 CTATCTGTAATATCTCGAAAATTA
1 CTATCTGTAATACCCCGAAAATAA
57723126 CTAT-TGTAATACCCCGAAAATAA
1 CTATCTGTAATACCCCGAAAATAA
57723149 CTA
1 CTA
57723152 CAGTAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (24 bp):
CTATCTGTAATACCCCGAAAATAA
Found at i:57723157 original size:23 final size:23
Alignment explanation
Indices: 57723108--57723157 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
57723098 GTGTCTATCT
* * * **
57723108 GTAATATCTCGAAAATTACTATT
1 GTAATACCCCGAAAATAACTACA
57723131 GTAATACCCCGAAAATAACTACA
1 GTAATACCCCGAAAATAACTACA
57723154 GTAA
1 GTAA
57723158 GAAAGTAGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (23 bp):
GTAATACCCCGAAAATAACTACA
Found at i:57726719 original size:33 final size:33
Alignment explanation
Indices: 57726674--57726757 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
57726664 CTACCATGGT
* *
57726674 CCAACCATGGTCTTACATTCATAATGCCATAAC
1 CCAACTATGGTCTTACATTCAGAATGCCATAAC
* * * *
57726707 CCAATTATGGTCTTTTCA-TCAGAATGTCATAGC
1 CCAACTATGGTC-TTACATTCAGAATGCCATAAC
57726740 CCAACTATGGTCTTACAT
1 CCAACTATGGTCTTACAT
57726758 ATAAACACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.10
33 33 0.80
34 4 0.10
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (33 bp):
CCAACTATGGTCTTACATTCAGAATGCCATAAC
Found at i:57726760 original size:101 final size:101
Alignment explanation
Indices: 57726585--57726824 Score: 336
Period size: 101 Copynumber: 2.4 Consensus size: 101
57726575 AATTCATCCT
* ** * * *
57726585 TTACATTCGTAGTGCCATAACTTAGTCATGGTATTATCATCAAAATGCCATAGCCCAGCTATGGT
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGT
*
57726650 TTTACATATAAACACTACCATGGTCCAACCATGGTC
66 CTTACATATAAACACTACCATGGTCCAACCATGGTC
* * * * *
57726686 TTACATTCATAATGCCATAACCCAATTATGGTCTTTTCATCAGAATGTCATAGCCCAACTATGGT
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGT
* *
57726751 CTTACATATAAACACTGCCATGGTCTAACCATGGTC
66 CTTACATATAAACACTACCATGGTCCAACCATGGTC
**
57726787 TTATGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATC
57726825 CGTCAATTCA
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 120 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (101 bp):
TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAACTATGGT
CTTACATATAAACACTACCATGGTCCAACCATGGTC
Found at i:57729945 original size:39 final size:39
Alignment explanation
Indices: 57729883--57730051 Score: 239
Period size: 39 Copynumber: 4.3 Consensus size: 39
57729873 CATGTTTTGA
* * * *
57729883 GTATTGTGATATATTCTTGAATGTTATGTGATTAAATAT
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* *
57729922 GTATTGTGATATATGTTTAAATGTTATGTGATTGTATGT
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* **
57729961 GTATCGTGATATATGCTTAAATGTTACATGATTATATGT
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
*
57730000 GTACTGTGATATATGCTTAAATGTTATGTGATTATATGT
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
*
57730039 GTAATGTGATATA
1 GTATTGTGATATA
57730052 CGATTAAAAG
Statistics
Matches: 114, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 114 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.47
Consensus pattern (39 bp):
GTATTGTGATATATGCTTAAATGTTATGTGATTATATGT
Found at i:57731618 original size:18 final size:17
Alignment explanation
Indices: 57731587--57731622 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
57731577 ATATATAATG
*
57731587 AAAAGAAATCAACAAAT
1 AAAAGAAATAAACAAAT
57731604 AAAAGTAAATAAACAAAT
1 AAAAG-AAATAAACAAAT
57731622 A
1 A
57731623 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAGAAATAAACAAAT
Found at i:57731840 original size:38 final size:39
Alignment explanation
Indices: 57731784--57731870 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 39
57731774 TAAGTAATCA
* * *
57731784 TATACATATATATGTATGTAACTATCATAAAATA-AAAG
1 TATACATATAGATATATGTAACAATCATAAAATATAAAG
* **
57731822 TATATATATAGATATATGTATGAATCATAAAATATAAAG
1 TATACATATAGATATATGTAACAATCATAAAATATAAAG
* *
57731861 AACACATATA
1 TATACATATA
57731871 TAAAATACAT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
38 28 0.72
39 11 0.28
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (39 bp):
TATACATATAGATATATGTAACAATCATAAAATATAAAG
Found at i:57731968 original size:25 final size:25
Alignment explanation
Indices: 57731911--57731968 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
57731901 GTAAGTGTAC
* *
57731911 ATATATAT-TACAAAAAGTATGTGT
1 ATATATATATACAAAAAATATATGT
*
57731935 GTA-AGTATATACAAAAAATATATGT
1 ATATA-TATATACAAAAAATATATGT
57731960 ATATATATA
1 ATATATATA
57731969 AAAAAACGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 1 0.04
24 5 0.19
25 20 0.74
26 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.36
Consensus pattern (25 bp):
ATATATATATACAAAAAATATATGT
Found at i:57731984 original size:22 final size:23
Alignment explanation
Indices: 57731940--57731984 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
57731930 TGTGTGTAAG
* *
57731940 TATATACAAAAAATATATGTATA
1 TATATACAAAAAACATATATATA
*
57731963 TATATA-AAAAAACGTATATATA
1 TATATACAAAAAACATATATATA
57731985 AGGGCAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
TATATACAAAAAACATATATATA
Found at i:57732055 original size:3 final size:3
Alignment explanation
Indices: 57731994--57732038 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
57731984 AAGGGCAATT
* * *
57731994 ATA ATA ATG ATA ATA ATA ATA ATA ATA AAA ATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
57732039 TTATTAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:57732973 original size:17 final size:17
Alignment explanation
Indices: 57732951--57732990 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
57732941 GACGTGCGGC
*
57732951 GCGGCGTCAGAACGGTG
1 GCGGCGACAGAACGGTG
*
57732968 GCGGCGACAGAATGGTG
1 GCGGCGACAGAACGGTG
57732985 GCGGCG
1 GCGGCG
57732991 CCCGGCTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.50, T:0.10
Consensus pattern (17 bp):
GCGGCGACAGAACGGTG
Found at i:57734331 original size:17 final size:17
Alignment explanation
Indices: 57734309--57734342 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57734299 ATAGACAAAT
57734309 ATTAAAATTAAAAATTA
1 ATTAAAATTAAAAATTA
57734326 ATTAAAATTAAAAATTA
1 ATTAAAATTAAAAATTA
57734343 GCTCTATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAAATTAAAAATTA
Found at i:57736373 original size:15 final size:15
Alignment explanation
Indices: 57736353--57736382 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57736343 TTTGGCTTGC
57736353 ATGCAAGTATTATTT
1 ATGCAAGTATTATTT
*
57736368 ATGCAATTATTATTT
1 ATGCAAGTATTATTT
57736383 TTTAATGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (15 bp):
ATGCAAGTATTATTT
Found at i:57761010 original size:53 final size:52
Alignment explanation
Indices: 57760873--57761203 Score: 199
Period size: 53 Copynumber: 6.2 Consensus size: 52
57760863 CCACTTTAAA
* *
57760873 ATTTATAATAAAAAATTGGATGCTGTAACACTGATGACCGACACCCTTGTACCAG
1 ATTTA-AA-AAAAAATTGGGTGCTGGAACACTGATGACCGACACCC-TGTACCAG
* * * *
57760928 A-TTAAAAAAAATTTGGGTGTTAGG-ACACTGATGACCGGCACTCCAGTACCAG
1 ATTTAAAAAAAAATTGGGTGCT-GGAACACTGATGACCGACAC-CCTGTACCAG
* * *
57760980 ATTTAAAAAAAAATTGAGTGCTGGAACACTGAT-AGCTGACACCCTTGTACTAG
1 ATTTAAAAAAAAATTGGGTGCTGGAACACTGATGA-CCGACACCC-TGTACCAG
* * * * * * * * * *
57761033 ATTTTTAAAAAAAATTAGTTGTTAGG-GCAATAATGGCCAACACTCTTGTACCAG
1 A-TTTAAAAAAAAATTGGGTGCT-GGAACACTGATGACCGACAC-CCTGTACCAG
** * * *
57761087 A-TTAAAAAAAAATTTGGGTGCT-GAGACACTGATGGTCGGCACCCCAGTACCAA
1 ATTTAAAAAAAAA-TTGGGTGCTGGA-ACACTGATGACCGACA-CCCTGTACCAG
* * * * * *
57761140 ATTTGAAAAAAAATTGGGTGTTGGGACACTGATTGTCAG-CACCCTTGTACCAA
1 ATTTAAAAAAAAATTGGGTGCTGGAACACTGA-TGACCGACACCC-TGTACCAG
*
57761193 ATTTTAAAAAA
1 ATTTAAAAAAA
57761204 TAATAAAATT
Statistics
Matches: 211, Mismatches: 47, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
51 1 0.00
52 54 0.26
53 100 0.47
54 52 0.25
55 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (52 bp):
ATTTAAAAAAAAATTGGGTGCTGGAACACTGATGACCGACACCCTGTACCAG
Found at i:57761108 original size:107 final size:105
Alignment explanation
Indices: 57760873--57761120 Score: 261
Period size: 107 Copynumber: 2.3 Consensus size: 105
57760863 CCACTTTAAA
* *
57760873 ATTTATAATAAAAAATTGGATGCTGTAACACTGATGACCGACACCCTTGTACCAGATTAAAAAAA
1 ATTTA-AA-AAAAAATTGGGTGCTGGAACACTGATGACCGACACCCTTGTACCAGATTAAAAAAA
* * * **
57760938 ATTTGGGTGTTAGGACACTGATGACCGGCACTCCAGTACCAG
64 ATTTAGGTGTTAGGACAATAATGACCAACACTCCAGTACCAG
* * *
57760980 ATTTAAAAAAAAATTGAGTGCTGGAACACTGAT-AGCTGACACCCTTGTACTAGATTTTTAAAAA
1 ATTTAAAAAAAAATTGGGTGCTGGAACACTGATGA-CCGACACCCTTGTACCAGA---TTAAAAA
* * * **
57761044 AAA-TTAGTTGTTAGGGCAATAATGGCCAACACTCTTGTACCAG
62 AAATTTAGGTGTTAGGACAATAATGACCAACACTCCAGTACCAG
57761087 A-TTAAAAAAAAATTTGGGTGCT-GAGACACTGATG
1 ATTTAAAAAAAAA-TTGGGTGCTGGA-ACACTGATG
57761121 GTCGGCACCC
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
104 1 0.01
105 40 0.34
106 15 0.13
107 52 0.44
108 10 0.08
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (105 bp):
ATTTAAAAAAAAATTGGGTGCTGGAACACTGATGACCGACACCCTTGTACCAGATTAAAAAAAAT
TTAGGTGTTAGGACAATAATGACCAACACTCCAGTACCAG
Found at i:57761136 original size:160 final size:158
Alignment explanation
Indices: 57760913--57761203 Score: 406
Period size: 160 Copynumber: 1.8 Consensus size: 158
57760903 CTGATGACCG
* *
57760913 ACACCCTTGTACCAGATTAAAAAAAATTTGGGTGTTAGGACACTGATGACCGGCACTCCAGTACC
1 ACACCCTTGTACCAGATTAAAAAAAATTTGGGTGTGAGGACACTGATGACCGGCACCCCAGTACC
* * * *
57760978 AGATTTAAAAAAAAATTGAGTGCTGGAACACTGATAG-CTGACACCCTTGTACTAGATTTTTAAA
66 AAATTTAAAAAAAAATTGAGTGCTGGAACACTGATAGTCAG-CACCCTTGTACCA-AATTTTAAA
57761042 AAAAATTAGTTGTTAGGGCAATAATGGCCA
129 AAAAATTAGTTGTTAGGGCAATAATGGCCA
* **
57761072 ACACTCTTGTACCAGATTAAAAAAAAATTTGGGTGCTGA-GACACTGATGGTCGGCACCCCAGTA
1 ACACCCTTGTACCAGATT-AAAAAAAATTTGGGTG-TGAGGACACTGATGACCGGCACCCCAGTA
* * * * *
57761136 CCAAATTTGAAAAAAAATTGGGTGTTGGGACACTGATTGTCAGCACCCTTGTACCAAATTTTAAA
64 CCAAATTTAAAAAAAAATTGAGTGCTGGAACACTGATAGTCAGCACCCTTGTACCAAATTTTAAA
57761201 AAA
129 AAA
57761204 TAATAAAATT
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
159 28 0.24
160 83 0.72
161 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (158 bp):
ACACCCTTGTACCAGATTAAAAAAAATTTGGGTGTGAGGACACTGATGACCGGCACCCCAGTACC
AAATTTAAAAAAAAATTGAGTGCTGGAACACTGATAGTCAGCACCCTTGTACCAAATTTTAAAAA
AAATTAGTTGTTAGGGCAATAATGGCCA
Found at i:57762931 original size:19 final size:19
Alignment explanation
Indices: 57762909--57762954 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
57762899 ATAGATAGAT
*
57762909 TATAAAAATATGTATATTA
1 TATAAAAATATATATATTA
* *
57762928 TATATATATATATATATTA
1 TATAAAAATATATATATTA
57762947 TATAAAAA
1 TATAAAAA
57762955 CACATGTATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATAAAAATATATATATTA
Found at i:57763035 original size:16 final size:15
Alignment explanation
Indices: 57763008--57763045 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
57762998 TAAATGAGCA
*
57763008 AATAACAATAACAAT
1 AATAATAATAACAAT
57763023 AATTAATAATAACAAT
1 AA-TAATAATAACAAT
57763039 AATAATA
1 AATAATA
57763046 TGAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:57764403 original size:55 final size:56
Alignment explanation
Indices: 57764313--57764460 Score: 149
Period size: 55 Copynumber: 2.7 Consensus size: 56
57764303 TAGACTAAGG
* * * **
57764313 GGGTGCCGGCCATCAGTGTCCTAGCA-CCTTTTTTTTTAAAAAAAAAT-TGGTACAA
1 GGGTGCCGGCCATCAGTGGCCCAACACCCTAATTTTTT-AAAAAAAATCTGGTACAA
** * ** * *
57764368 GGGTGTTGGTCATCAGTGGCTTAACACCC-AATTTTTTTAAAAAAATCTGGTACTA
1 GGGTGCCGGCCATCAGTGGCCCAACACCCTAATTTTTTAAAAAAAATCTGGTACAA
*
57764423 GGGTGCCGGCCATCAGTGTCCCAACACCCTAATTTTTT
1 GGGTGCCGGCCATCAGTGGCCCAACACCCTAATTTTTT
57764461 TTTTAAATTT
Statistics
Matches: 74, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
54 8 0.11
55 56 0.76
56 10 0.14
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (56 bp):
GGGTGCCGGCCATCAGTGGCCCAACACCCTAATTTTTTAAAAAAAATCTGGTACAA
Found at i:57764537 original size:55 final size:55
Alignment explanation
Indices: 57764410--57764537 Score: 143
Period size: 55 Copynumber: 2.3 Consensus size: 55
57764400 TTTTTTAAAA
* ** * *
57764410 AAATCTGGTACTAGGGTGCCGGCCATCAGTGTCCCAACACCCTAATTTTTTTTTT
1 AAATCTGGTACAAGGGTGAAGGCCATCAGTGTCCCAACACCCAAATGTTTTTTTT
* * * *
57764465 AAATTTGATA-AATGGGTGAAGGCCATTAGTGTCCCAGCACCCAAAATGTTTTTTTT
1 AAATCTGGTACAA-GGGTGAAGGCCATCAGTGTCCCAACACCC-AAATGTTTTTTTT
57764521 -AATCTGGTACAAGGGTG
1 AAATCTGGTACAAGGGTG
57764538 TCAGCCATCA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
54 1 0.02
55 45 0.76
56 13 0.22
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (55 bp):
AAATCTGGTACAAGGGTGAAGGCCATCAGTGTCCCAACACCCAAATGTTTTTTTT
Found at i:57776114 original size:27 final size:27
Alignment explanation
Indices: 57776084--57776149 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
57776074 ACGCCAATAG
57776084 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* * **
57776111 CATTGGCGGCAGCAATGGTGCCAATGC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
57776138 CATTGGCGGCAC
1 CATTGGCGGCAC
57776150 TATTCGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.30, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:57776386 original size:3 final size:3
Alignment explanation
Indices: 57776378--57776456 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
57776368 TATTAGTTTG
57776378 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57776426 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
57776457 GTTGTTGTTG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:57776461 original size:3 final size:3
Alignment explanation
Indices: 57776455--57776489 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
57776445 ATTATTATTA
57776455 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
57776490 AGTATTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:57776708 original size:26 final size:26
Alignment explanation
Indices: 57776679--57776731 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
57776669 TTTTAGTGTG
*
57776679 TATTATTTTGAGTATAAAATTATTAA
1 TATTATTTTGAGTATAAAATTAATAA
57776705 TATTATTTTGAGTATAAAATTAATAA
1 TATTATTTTGAGTATAAAATTAATAA
57776731 T
1 T
57776732 TTTAGTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATTATTTTGAGTATAAAATTAATAA
Found at i:57776727 original size:62 final size:60
Alignment explanation
Indices: 57776645--57776761 Score: 207
Period size: 62 Copynumber: 1.9 Consensus size: 60
57776635 GTTAGTTAGT
*
57776645 TATTATTTTTAGTAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
1 TATTATTTTGAGTAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
57776705 TATTATTTTGAGTATAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATT
1 TATTATTTTGAG--TAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATT
57776762 TTTTTTAAGT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
60 11 0.20
62 43 0.80
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (60 bp):
TATTATTTTGAGTAAAATTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAA
Found at i:57777365 original size:18 final size:18
Alignment explanation
Indices: 57777322--57777366 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
57777312 TTGACATGGT
*
57777322 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
**
57777340 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
57777358 TGGTGGCGA
1 TGGTGGCGA
57777367 TCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.49, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:57780489 original size:18 final size:18
Alignment explanation
Indices: 57780466--57780614 Score: 106
Period size: 18 Copynumber: 8.7 Consensus size: 18
57780456 CTTCCCTCTT
57780466 CTTCTTTTCTTTTCTTTC
1 CTTCTTTTCTTTTCTTTC
57780484 CTTC-TTTC-TTTCTTT-
1 CTTCTTTTCTTTTCTTTC
* * *
57780499 TTTCTTCTCTTTTCCTTTT
1 CTTCTTTTCTTTT-CTTTC
57780518 CTTCTTCTTC-TTTCTTT-
1 CTTCTT-TTCTTTTCTTTC
57780535 C-T-TTTT-TTTTCTCTT-
1 CTTCTTTTCTTTTCT-TTC
* *
57780550 CTCCTTTCCTTTTCTTTC
1 CTTCTTTTCTTTTCTTTC
57780568 CTTCTTTT-TCTTTCTTTC
1 CTTCTTTTCT-TTTCTTTC
*
57780586 CTCTCCTTTC-TTTCTTTC
1 CT-TCTTTTCTTTTCTTTC
*
57780604 TTTC-TTTCTTT
1 CTTCTTTTCTTT
57780615 CCCTCTCCTT
Statistics
Matches: 106, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
14 7 0.07
15 8 0.08
16 15 0.14
17 18 0.17
18 43 0.41
19 13 0.12
20 2 0.02
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTCTTTTCTTTTCTTTC
Done.