Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 26 of 52
Found at i:4289488 original size:86 final size:84
Alignment explanation
Indices: 4289334--4289517 Score: 194
Period size: 86 Copynumber: 2.2 Consensus size: 84
4289324 GATAAAGTGT
* * *
4289334 TGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAATGTAAGCTACTGCCAAAAAA
1 TGTATCGATACATTGTATCGATACATAAGTTTTGTATCGATACAATGCAAGCAACTGCC-AAAAA
* *
4289399 TGTATCAATACATTACTCAAA
65 TGTATCAATACACTA-TAAAA
* * *
4289420 TGTATCGATACATTGTATCGATACACTAA-TCTTTGTATCGATAC-ATGCAGGCAAATTTGCC-C
1 TGTATCGATACATTGTATCGATACA-TAAGT-TTTGTATCGATACAATGCAAGC-AA-CTGCCAA
* *
4289482 AGATGTATCGATACACTATAAAA
62 AAATGTATCAATACACTATAAAA
*
4289505 TATATCGATACAT
1 TGTATCGATACAT
4289518 GCAGGTAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
85 16 0.19
86 46 0.55
87 17 0.20
88 4 0.05
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (84 bp):
TGTATCGATACATTGTATCGATACATAAGTTTTGTATCGATACAATGCAAGCAACTGCCAAAAAT
GTATCAATACACTATAAAA
Found at i:4289496 original size:52 final size:52
Alignment explanation
Indices: 4289453--4289581 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
4289443 CACTAATCTT
4289453 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
4289505 TATATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
4289557 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4289582 TCATATTTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:4294076 original size:19 final size:19
Alignment explanation
Indices: 4294052--4294107 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4294042 TGTATCGATG
* **
4294052 CATTGTATCAATACATGTT
1 CATTGTATCGATACATGGA
*
4294071 CATTGTATCGATATATGGA
1 CATTGTATCGATACATGGA
4294090 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
4294108 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGGA
Found at i:4300930 original size:31 final size:31
Alignment explanation
Indices: 4300893--4300972 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
4300883 GATACATTGA
*
4300893 AAAATGTATTGATACATTTGGAAAAAAAAAC
1 AAAATGTATCGATACATTTGGAAAAAAAAAC
* * ** **
4300924 AGAATGTATCGATACATCTGGGTAAAATGAC
1 AAAATGTATCGATACATTTGGAAAAAAAAAC
4300955 AAAATGTATCGATACATT
1 AAAATGTATCGATACATT
4300973 GAAGAATGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (31 bp):
AAAATGTATCGATACATTTGGAAAAAAAAAC
Found at i:4301796 original size:48 final size:48
Alignment explanation
Indices: 4301725--4302089 Score: 407
Period size: 48 Copynumber: 7.6 Consensus size: 48
4301715 AGAGGAGTGC
** * * * *
4301725 CAATGTGCCAATTCAATGCCAACGACATCGAGTTAAGGGAATAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* *
4301773 CAATGTGCTGATTTAAGGCCAACGACATTTAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* *
4301821 CAATGTGCTGATTCAAGGCCAACGACAATGAGCTGAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* * * * * *
4301869 CAATGTGTTGATTCAAGGCCAGCAAAATTGAGCTAA--TAAAGGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* * *
4301915 CAATGTGCTGATTTAAGGCCAACAACATTGAACTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* * *
4301963 CAATATGTTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* * * *
4302011 CAATGTGCTGATTCAAGGCTAGCGACATT-AGACTTAA-AGATGAAAGT-GC
1 CAATGTGCTGATTCAAGGCCAACGACATTGAG-C-TAAGGGA--AAAGTGGA
* *
4302060 CAATGTGCTGATTCAAGGCTAGCGACATTG
1 CAATGTGCTGATTCAAGGCCAACGACATTG
4302090 GACTTAAAGA
Statistics
Matches: 272, Mismatches: 38, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
46 39 0.14
47 2 0.01
48 193 0.71
49 33 0.12
50 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
Found at i:4301943 original size:142 final size:142
Alignment explanation
Indices: 4301768--4302029 Score: 443
Period size: 142 Copynumber: 1.8 Consensus size: 142
4301758 TAAGGGAATA
* * * *
4301768 GTGGACAATGTGCTGATTTAAGGCCAACGACATTTAGCTAAGGGAAAAGTGGACAATGTGCTGAT
1 GTGGACAATGTGCTGATTTAAGGCCAACAACATTGAACTAAGGGAAAAGTGGACAATATGCTGAT
* *
4301833 TCAAGGCCAACGACAATGAGCTGAGGGAAAAGTGGACAATGTGTTGATTCAAGGCCAGCAAAATT
66 TCAAGGCCAACGACAATGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCCAGCAAAATT
4301898 GAGCTAATAAAG
131 GAGCTAATAAAG
*
4301910 GTGGACAATGTGCTGATTTAAGGCCAACAACATTGAACTAAGGGAAAAGTGGACAATATGTTGAT
1 GTGGACAATGTGCTGATTTAAGGCCAACAACATTGAACTAAGGGAAAAGTGGACAATATGCTGAT
* *
4301975 TCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGC
66 TCAAGGCCAACGACAATGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGC
4302030 TAGCGACATT
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
142 111 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.21
Consensus pattern (142 bp):
GTGGACAATGTGCTGATTTAAGGCCAACAACATTGAACTAAGGGAAAAGTGGACAATATGCTGAT
TCAAGGCCAACGACAATGAGCTAAGGGAAAAGTGGACAATGTGCTGATTCAAGGCCAGCAAAATT
GAGCTAATAAAG
Found at i:4302209 original size:95 final size:94
Alignment explanation
Indices: 4302062--4302383 Score: 380
Period size: 95 Copynumber: 3.4 Consensus size: 94
4302052 GAAAGTGCCA
* **** * *
4302062 ATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGGTGGAGGTGCCAATATGTTGATTCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCA
* * *
4302127 AGGTC-GACAATATTGGACTTAAAGTTATCG
66 AGGCCAG-CGATATTGGACTTAAAGGT-TCG
* * * *
4302157 ATGTG-TCGATTCAAGGCCAACTACATTGGACTTAATGATGACAAAGGCGCCAATATGCTAATTC
1 ATGTGCT-GATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
* * *
4302221 AAGGCCAGTGATATTGGACTTAAAGGTGCAA
65 AAGGCCAGCGATATTGGACTTAAAGGTTC-G
* * *
4302252 ATGTGCTGATTCAAGGCCAGCGACATTAGAATTAAAGATGACAAAGGCGCTAATATGCTGATTCA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCA
4302317 AGGCCAGCGATATTGGACTTAAAGGTGT-G
66 AGGCCAGCGATATTGGACTTAAAGGT-TCG
*
4302346 AATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 -ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
4302384 GTGCCAATGT
Statistics
Matches: 191, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
94 2 0.01
95 187 0.98
96 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (94 bp):
ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGGTTCG
Found at i:4302243 original size:52 final size:52
Alignment explanation
Indices: 4302164--4302338 Score: 170
Period size: 52 Copynumber: 3.5 Consensus size: 52
4302154 TCGATGTGTC
* * * *
4302164 GATTCAAGGCCAACTACATTGGACTTAATGATGACAAAGGCGCCAATATGCT
1 GATTCAAGGCCAGCGATATTGGACTTAATGATGACAAAGGCGCAAATATGCT
* * * *
4302216 AATTCAAGGCCAGTGATATTGGAC----T--T---AAAGGTGCAAATGTGCT
1 GATTCAAGGCCAGCGATATTGGACTTAATGATGACAAAGGCGCAAATATGCT
* * * * *
4302259 GATTCAAGGCCAGCGACATTAGAATTAAAGATGACAAAGGCGCTAATATGCT
1 GATTCAAGGCCAGCGATATTGGACTTAATGATGACAAAGGCGCAAATATGCT
4302311 GATTCAAGGCCAGCGATATTGGACTTAA
1 GATTCAAGGCCAGCGATATTGGACTTAA
4302339 AGGTGTGAAT
Statistics
Matches: 94, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
43 33 0.35
46 1 0.01
48 1 0.01
49 1 0.01
52 58 0.62
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (52 bp):
GATTCAAGGCCAGCGATATTGGACTTAATGATGACAAAGGCGCAAATATGCT
Found at i:4302265 original size:43 final size:43
Alignment explanation
Indices: 4302212--4302412 Score: 222
Period size: 43 Copynumber: 4.5 Consensus size: 43
4302202 GGCGCCAATA
* *
4302212 TGCTAATTCAAGGCCAGTGATATTGGACTTAAAGGTGCAAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCAAATG
* * * * *
4302255 TGCTGATTCAAGGCCAGCGACATTAGAATTAAAGATGACAAAGGCGCTAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG-C--A------AATG
**
4302307 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGTGAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCAAATG
*
4302350 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCAAATG
*
4302393 TGCTGATTTAAGGCCAGCGA
1 TGCTGATTCAAGGCCAGCGA
4302413 CATTAGGCTA
Statistics
Matches: 132, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
43 94 0.71
44 1 0.01
46 1 0.01
52 36 0.27
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (43 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCAAATG
Found at i:4302341 original size:22 final size:22
Alignment explanation
Indices: 4302316--4302384 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
4302306 ATGCTGATTC
4302316 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
* * *
4302338 AAGG--TGTGA-ATGTGCTGA-TTC
1 AAGGCCAGCGATAT-TG--GACTTA
4302359 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
4302381 AAGG
1 AAGG
4302385 TGCCAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.25
Consensus pattern (22 bp):
AAGGCCAGCGATATTGGACTTA
Found at i:4302540 original size:32 final size:32
Alignment explanation
Indices: 4302432--4302633 Score: 236
Period size: 30 Copynumber: 6.5 Consensus size: 32
4302422 AAGAAGGAAA
* * *
4302432 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
1 TGCCACCGACTTGTGTGGGC-TTTGAGAAGGGT
* *
4302465 TGCCACTGACTTGTGTGGGCTTTG-G-AGGGG
1 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
** * *
4302495 TGCCACTAACTTGTGTGGACTTTAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
* *
4302527 TGCCACCGGCTTGTGTGGGCTTTG-G-AGGGG
1 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
*
4302557 TGCCACTGACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
4302589 TGCCACCGACTTGTGTGGGCTTTGA-AAGGG-
1 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
*
4302619 TGCCACCAACTTGTG
1 TGCCACCGACTTGTG
4302634 GGATTTCAAA
Statistics
Matches: 145, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
30 64 0.44
31 8 0.06
32 55 0.38
33 18 0.12
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
Found at i:4302543 original size:62 final size:62
Alignment explanation
Indices: 4302432--4302633 Score: 289
Period size: 62 Copynumber: 3.2 Consensus size: 62
4302422 AAGAAGGAAA
* *
4302432 TGCCACCAACTTGTGTGGGCTTTTGAA-AAAGGTTGCCACTGACTTGTGTGGGCTTTGGAGGGG
1 TGCCACCAACTTGTGTGGGC-TTT-AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAGGGG
* * *
4302495 TGCCACTAACTTGTGTGGACTTTAAGAAGGGTTGCCACCGGCTTGTGTGGGCTTTGGAGGGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAGGGG
** * * *
4302557 TGCCACTGACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAGGGG
4302619 TGCCACCAACTTGTG
1 TGCCACCAACTTGTG
4302634 GGATTTCAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
61 2 0.02
62 105 0.84
63 18 0.14
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (62 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAGGGG
Found at i:4302635 original size:28 final size:28
Alignment explanation
Indices: 4302445--4302897 Score: 361
Period size: 28 Copynumber: 15.5 Consensus size: 28
4302435 CACCAACTTG
*
4302445 TGTGGGCTTTTGAAAAAGGTTGCCACTGACTT
1 TGTGGGC-TTTG--AAAGGATGCCACTGAC-T
* * * *
4302477 GTGTGGGCTTTGGAGGGGTGCCACTAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
4302506 TGTGTGGACTTTAAGAAGGGTTGCCACCGGCTT
1 TGTG-GG-CTTT--GAAAGGATGCCACTGAC-T
* * *
4302539 GTGTGGGCTTTGGAGGGGTGCCACTGACTT
1 -TGTGGGCTTTGAAAGGATGCCACTGAC-T
* *
4302569 GTGTGGGCTTTGAGAAGGGTTGCCACCGACTT
1 -TGTGGGCTTTGA-AA-GGATGCCACTGAC-T
* **
4302601 GTGTGGGCTTTGAAAGGGTGCCACCAACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
4302630 TGTGGGATTTCAAAGTGTATTCCATTGACT
1 TGTGGGCTTTGAAAG-G-ATGCCACTGACT
* *
4302660 TATGGTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GATGCCACTGACT
* * *
4302689 TGTGGGCTTTGAAGGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
4302717 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
4302745 TGTGAGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
4302773 TGTGAGCTTTGAAATGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
4302801 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
4302829 TGTGGGCTTTGAAA-AATTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
4302857 TGTGGGCTTTGAAAGGATACCATTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
4302885 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
4302898 GAGATGAACG
Statistics
Matches: 351, Mismatches: 55, Indels: 33
0.80 0.13 0.08
Matches are distributed among these distances:
27 1 0.00
28 192 0.55
29 23 0.07
30 69 0.20
31 6 0.02
32 46 0.13
33 10 0.03
34 4 0.01
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:4304164 original size:17 final size:17
Alignment explanation
Indices: 4304144--4304211 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
4304134 CATCTGGACC
*
4304144 TTTTTTTGTTTGTTTG-
1 TTTTTTTGTTTTTTTGT
*
4304160 TTTTTGT-TTTTTTTGT
1 TTTTTTTGTTTTTTTGT
4304176 CTTTTTCTTGGTTTTTTTGT
1 -TTTTT-TT-GTTTTTTTGT
*
4304196 TTTTTTGGTTTTTTTG
1 TTTTTTTGTTTTTTTG
4304212 GGTACAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
15 7 0.16
16 6 0.14
17 14 0.33
18 2 0.05
19 5 0.12
20 9 0.21
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTGT
Found at i:4304171 original size:8 final size:8
Alignment explanation
Indices: 4304144--4304211 Score: 66
Period size: 8 Copynumber: 8.0 Consensus size: 8
4304134 CATCTGGACC
4304144 TTTTTTTG
1 TTTTTTTG
*
4304152 TTTGTTTG
1 TTTTTTTG
4304160 TTTTTGTT-
1 TTTTT-TTG
*
4304168 TTTTTTGTC
1 TTTTTT-TG
4304177 TTTTTCTTGG
1 TTTTT-TT-G
4304187 TTTTTTTG
1 TTTTTTTG
4304195 TTTTTTTGG
1 TTTTTTT-G
4304204 TTTTTTTG
1 TTTTTTTG
4304212 GGTACAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
7 1 0.02
8 26 0.51
9 18 0.35
10 6 0.12
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (8 bp):
TTTTTTTG
Found at i:4304191 original size:11 final size:9
Alignment explanation
Indices: 4304146--4304210 Score: 76
Period size: 9 Copynumber: 6.8 Consensus size: 9
4304136 TCTGGACCTT
4304146 TTTTTGTTTG
1 TTTTT-TTTG
4304156 TTTGTTTTTG
1 TTT-TTTTTG
4304166 TTTTTTTTG
1 TTTTTTTTG
4304175 TCTTTTTCTTG
1 T-TTTTT-TTG
*
4304186 GTTTTTTTG
1 TTTTTTTTG
*
4304195 TTTTTTTGG
1 TTTTTTTTG
4304204 TTTTTTT
1 TTTTTTT
4304211 GGGTACAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
9 24 0.49
10 20 0.41
11 5 0.10
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:4317189 original size:71 final size:71
Alignment explanation
Indices: 4317088--4317223 Score: 204
Period size: 71 Copynumber: 1.9 Consensus size: 71
4317078 ACACTGAAAA
* *
4317088 ATGTATCAATACATCTGGAAAAAAAGACAGAATGTATCGATATATTGGAA-AATGTATCGATACA
1 ATGTATCAATACATCTGGAAAAAAAGACAGAATGTATCGATACATT-AAAGAATGTATCGATACA
4317152 TTCACAC
65 TTCACAC
* *
4317159 ATGTATCGATACATCTAGG-TAAAAAGACAGAATGTATCGATACATTAAAGAATGTATCGATACA
1 ATGTATCAATACATCT-GGAAAAAAAGACAGAATGTATCGATACATTAAAGAATGTATCGATACA
4317223 T
65 T
4317224 CTAGGTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
70 2 0.03
71 55 0.93
72 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (71 bp):
ATGTATCAATACATCTGGAAAAAAAGACAGAATGTATCGATACATTAAAGAATGTATCGATACAT
TCACAC
Found at i:4317193 original size:51 final size:51
Alignment explanation
Indices: 4317138--4317234 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
4317128 TATATTGGAA
* *
4317138 AATGTATCGATACATTCACA-CATGTATCGATACATCTAGGTAAAAAGACAG
1 AATGTATCGATACATT-AAAGAATGTATCGATACATCTAGGTAAAAAGACAG
4317189 AATGTATCGATACATTAAAGAATGTATCGATACATCTAGGTAAAAA
1 AATGTATCGATACATTAAAGAATGTATCGATACATCTAGGTAAAAA
4317235 ATGTGACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (51 bp):
AATGTATCGATACATTAAAGAATGTATCGATACATCTAGGTAAAAAGACAG
Found at i:4322637 original size:28 final size:28
Alignment explanation
Indices: 4322594--4323010 Score: 336
Period size: 28 Copynumber: 14.2 Consensus size: 28
4322584 GTCAATACGA
*
4322594 CACCTTTTCAAAGCCCACAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
* * * * *
4322622 CATCTTTTCAGAGCCCACAAGTCAATGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
* * * *
4322650 AAACCCTTTTCAAAGCCCATATGTCAGTGG
1 -CACCC-TTTCAAAGCCCACAAGTTAGTGG
* * * *
4322680 CATCCTCTCAAAGCCTACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
* *
4322708 CATCCTTTCAAAGCCCACAAGTAAGTGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
*
4322736 CACCCCTTT--AAGCCTACACAAGTTGGTGG
1 CA-CCCTTTCAAAGCC--CACAAGTTAGTGG
* *
4322765 CAACCTCTCTCAAAGCCCACAAGTTAGTAG
1 C-ACC-CTTTCAAAGCCCACAAGTTAGTGG
*
4322795 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
*
4322823 CACCCTTTCTAAGCCCACAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
** *
4322851 CACTTTTTGAAA-CCCACAAGTTAGTGG
1 CACCCTTTCAAAGCCCACAAGTTAGTGG
*
4322878 CACCCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCCTTTCAAAG-CC-CACAAGTTAGTGG
* **
4322908 CAACCTTCTCTAAAGCCCACACAGGTCGGTGG
1 CACCCTT-TC-AAAGCCCACA-A-GTTAGTGG
* *
4322940 CAACCCTTTTAAAGCCCACACAAGTTGGTGG
1 C-ACCCTTTCAAAG-CC-CACAAGTTAGTGG
* *
4322971 CAACCTTCTCTAAAGCCCACACAAGTTGGTGG
1 CACCCTT-TC-AAAG-CC-CACAAGTTAGTGG
4323003 CAACCCTT
1 C-ACCCTT
4323011 CTAAACCCAA
Statistics
Matches: 320, Mismatches: 47, Indels: 39
0.79 0.12 0.10
Matches are distributed among these distances:
27 29 0.09
28 125 0.39
29 29 0.09
30 62 0.19
31 18 0.06
32 43 0.13
33 14 0.04
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
CACCCTTTCAAAGCCCACAAGTTAGTGG
Found at i:4322679 original size:58 final size:57
Alignment explanation
Indices: 4322596--4322991 Score: 223
Period size: 58 Copynumber: 6.8 Consensus size: 57
4322586 CAATACGACA
* * * *
4322596 CCTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAGAGCCCACAAGTCAATGGAAAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAATGG-AAC
* * * * * *
4322654 CCTTTTCAAAGCCCATATGTCAGTGGCATCCTCTCAAAGCCTACAAGTCAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAATGGAAC
* * ** ***
4322711 CC-TTTCAAAGCCCACAAGTAAGTGGCA-CCCCTTTAAGCCTACACAAGTTGGTGGCAA-
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCC--CACAAGTCAATGG-AAC
* * * * * * *
4322768 CCTCTCTCAAAGCCCACAAGTTAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCT-TTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAATGGAAC
* * * * * * * *
4322826 CC-TTTCTAAGCCCACAAGTTAGTGGCA-CTTTTTGAAA-CCCACAAGTTAGTGGCAC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATC-CTCTCAAAGCCCACAAGTCAATGGAAC
** * **
4322881 CC-TTTCAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACACAGGTCGGTGGCAAC
1 CCTTTTCAAAG-CC-CACAAGTCAGTGGCATCC-TCTC-AAAGCCCACA-A-GTCAATGG-AAC
** *
4322944 CCTTTT-AAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACA
1 CCTTTTCAAAG-CC-CACAAGTCAGTGGCATCC-TCTC-AAAGCCCACA
4322992 CAAGTTGGTG
Statistics
Matches: 276, Mismatches: 44, Indels: 31
0.79 0.13 0.09
Matches are distributed among these distances:
55 36 0.13
56 52 0.19
57 30 0.11
58 63 0.23
59 25 0.09
60 14 0.05
61 1 0.00
62 6 0.02
63 46 0.17
64 3 0.01
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (57 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAATGGAAC
Found at i:4322802 original size:87 final size:84
Alignment explanation
Indices: 4322601--4322896 Score: 321
Period size: 86 Copynumber: 3.5 Consensus size: 84
4322591 CGACACCTTT
* * * * * *
4322601 TCAAAGCCCACAAGTTAGTGGCATCTTTTCAGAGCCCACAAGTCAA-TGGAAACCCTTTTCAAAG
1 TCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGT-AAGTGG-CACCC-CTTCTAAG
* * *
4322665 CCCATATGTCAGTGGCA-TCCTC
63 CCCACAAGTTAGTGGCACT-CTC
* * *
4322687 TCAAAGCCTACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTAAGTGGCACCCCTT-TAAGCCT
1 TCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTAAGTGGCACCCCTTCTAAGCC-
*
4322751 ACACAAGTTGGTGGCAACCTCTC
65 -CACAAGTTAGTGGC-A-CTCTC
* * *
4322774 TCAAAGCCCACAAGTTAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCTAAGCCC
1 TCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTAAGTGGCACCCCTTCTAAGCCC
* *
4322839 ACAAGTTAGTGGCACTTTT
66 ACAAGTTAGTGGCACTCTC
*
4322858 TGAAA-CCCACAAGTTAGTGGCACCCTTTCAAAGCCCACA
1 TCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACA
4322897 CAAGTTGGTG
Statistics
Matches: 181, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
83 38 0.21
84 9 0.05
85 17 0.09
86 56 0.31
87 54 0.30
88 7 0.04
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (84 bp):
TCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTAAGTGGCACCCCTTCTAAGCCC
ACAAGTTAGTGGCACTCTC
Found at i:4322806 original size:115 final size:113
Alignment explanation
Indices: 4322594--4323009 Score: 374
Period size: 115 Copynumber: 3.6 Consensus size: 113
4322584 GTCAATACGA
* * *** *
4322594 CACCTTTTCAAAGCCCACAAGTTAGTGGCATCT-TTTCAGAGCC-CACAAGTCAATGGAAACCCT
1 CACCCTTTCAAAGCCCACAAGTTAGTGGCACCTCTTT-A-AGCCACACAAGTTGGTGGCAACCC-
* * * * * * *
4322657 TTTCAAAGCCCATATGTCAGTGGCATCCTCTCAAAGCCTACAAGTCAGTGG
63 TCTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGG
* * *
4322708 CATCCTTTCAAAGCCCACAAGTAAGTGGCACCCCTTTAAGCCTACACAAGTTGGTGGCAACCTCT
1 CACCCTTTCAAAGCCCACAAGTTAGTGGCACCTCTTTAAGCC-ACACAAGTTGGTGGCAACC-CT
* *
4322773 CTCAAAGCCCACAAGTTAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGG
64 CTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGG
* * * * *
4322823 CACCCTTTCTAAGCCCACAAGTTAGTGGCA-CTTTTTGAAACC-CACAAGTTAGTGGC-ACCCTT
1 CACCCTTTCAAAGCCCACAAGTTAGTGGCACCTCTTT-AAGCCACACAAGTTGGTGGCAACCCTC
* *
4322885 TCAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACACAGGTCGGTGG
65 TCAAAG-CC-CACAAGTTAGTGGCAACCTT-TC-AAAGCCCACA-A-GTCAGTGG
* * *
4322940 CAACCCTTTTAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCA
1 C-ACCCTTTCAAAG-CC-CACAAGTTAGTGGC-ACC-TCT-TTAAG-CCACACAAGTTGGTGGCA
4323005 ACCCT
59 ACCCT
4323010 TCTAAACCCA
Statistics
Matches: 245, Mismatches: 36, Indels: 30
0.79 0.12 0.10
Matches are distributed among these distances:
111 8 0.03
112 5 0.02
113 34 0.14
114 35 0.14
115 101 0.41
116 2 0.01
117 8 0.03
118 10 0.04
119 2 0.01
120 13 0.05
121 1 0.00
122 1 0.00
123 4 0.02
124 3 0.01
125 13 0.05
126 5 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (113 bp):
CACCCTTTCAAAGCCCACAAGTTAGTGGCACCTCTTTAAGCCACACAAGTTGGTGGCAACCCTCT
CAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGG
Found at i:4322892 original size:143 final size:146
Alignment explanation
Indices: 4322651--4322991 Score: 390
Period size: 143 Copynumber: 2.3 Consensus size: 146
4322641 AGTCAATGGA
* * * * * *
4322651 AACCCTTTTCAAAGCCCATATGTCAGTGGCATCCTCTCAAAGCCTACAAGTCAGTGGCATCCTTT
1 AACCC-TTTCAAAGCCCACAAGTCAGTGGCAACCTTTCTAAGCCCACAAGTCAGTGGCATCCTTT
*
4322716 CAAAGCCCACAAGTAAGTGGCACCCCTTTAAGCCTACACAAGTTGGTGGCAACC-TCTCTCAAAG
65 CAAAGCCCACAAGTAAGTGGCACCCCTTTAAGCCCACACAAGTTGGTGGCAACCTTCTCT-AAAG
*
4322780 CCCACA-A-GTTAGTAGC
129 CCCACACAGGTCAGTAGC
* * *
4322796 -ACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCTAAGCCCACAAGTTAGTGGCA-CTTTTT
1 AACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCTAAGCCCACAAGTCAGTGGCATC-CTTT
* *
4322859 GAAA-CCCACAAGTTAGTGGCA-CCCTTTCAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAA
65 CAAAGCCCACAAGTAAGTGGCACCCCTTT--AAGCCCACACAAGTTGGTGGCAACCTTCTCTAAA
* *
4322922 GCCCACACAGGTCGGTGGC
128 GCCCACACAGGTCAGTAGC
* **
4322941 AACCCTTTTAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACA
1 AACCCTTTCAAAG-CC-CACAAGTCAGTGGCAACCTT-TCT-AAGCCCACA
4322992 CAAGTTGGTG
Statistics
Matches: 167, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
141 6 0.04
142 17 0.10
143 86 0.51
144 10 0.06
145 6 0.04
146 11 0.07
147 2 0.01
148 17 0.10
149 3 0.02
150 9 0.05
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (146 bp):
AACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCTAAGCCCACAAGTCAGTGGCATCCTTTC
AAAGCCCACAAGTAAGTGGCACCCCTTTAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCC
CACACAGGTCAGTAGC
Found at i:4322959 original size:63 final size:61
Alignment explanation
Indices: 4322596--4323019 Score: 263
Period size: 63 Copynumber: 7.2 Consensus size: 61
4322586 CAATACGACA
* * * *** *
4322596 CCTTTTCAAAG-CC-CACAAGTTAGTGGCATCTTTTC-AGAGCCCACA-AGTCAATGGAAAC
1 CCTTTT-AAAGCCCACACAAGTTAGTGGCAACCTTTCTAAAGCCCACACAGTTGGTGGCAAC
* * * * * * ** *
4322654 CCTTTTCAAAG-CC-CATATGTCAGTGGCATCCTCTC-AAAGCCTACA-AGTCAGTGGC-AT
1 CCTTTT-AAAGCCCACACAAGTTAGTGGCAACCTTTCTAAAGCCCACACAGTTGGTGGCAAC
* * * * *
4322711 CCTTTCAAAG-CC-CACAAGTAAGTGGCACCCCTT-T-AAGCCTACACAAGTTGGTGGCAAC
1 CCTTTTAAAGCCCACACAAGTTAGTGGCAACCTTTCTAAAGCCCACAC-AGTTGGTGGCAAC
* * * * **
4322769 CTCTCTCAAAG-CC-CACAAGTTAGTAGCACCCTTTC-AAAGCCCACA-AGTCAGTGGC-AC
1 C-CTTTTAAAGCCCACACAAGTTAGTGGCAACCTTTCTAAAGCCCACACAGTTGGTGGCAAC
* *
4322826 CCTTTCT-AAG-CC-CACAAGTTAGTGGC-A-CTTTTTGAAA-CCCACA-AGTTAGTGGC-AC
1 CCTTT-TAAAGCCCACACAAGTTAGTGGCAACCTTTCT-AAAGCCCACACAGTTGGTGGCAAC
* * *
4322881 CCTTTCAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACACAGGTCGGTGGCAAC
1 CCTTTTAAAGCCCACACAAGTTAGTGGCAACCTT-TCTAAAGCCCACACA-GTTGGTGGCAAC
*
4322944 CCTTTTAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAAC
1 CCTTTTAAAGCCCACACAAGTTAGTGGCAACCTT-TCTAAAGCCCACAC-AGTTGGTGGCAAC
*
4323007 CCTTCTAAA-CCCA
1 CCTTTTAAAGCCCA
4323020 ATGTCGCTAT
Statistics
Matches: 304, Mismatches: 41, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
54 4 0.01
55 34 0.11
56 47 0.15
57 30 0.10
58 57 0.19
59 34 0.11
60 16 0.05
61 1 0.00
62 11 0.04
63 69 0.23
64 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTAGTGGCAACCTTTCTAAAGCCCACACAGTTGGTGGCAAC
Found at i:4324771 original size:20 final size:20
Alignment explanation
Indices: 4324748--4324820 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4324738 ACAATTCAAA
4324748 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4324768 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4324789 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4324809 GTATCGATACAT
1 GTATCGATACAT
4324821 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4324792 original size:21 final size:21
Alignment explanation
Indices: 4324766--4324841 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
4324756 ACATGTTGCA
4324766 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4324787 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
4324807 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
4324828 ATGTATCGATACAT
1 ATGTATCGATACAT
4324842 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4324799 original size:41 final size:41
Alignment explanation
Indices: 4324748--4324841 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
4324738 ACAATTCAAA
*
4324748 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4324789 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4324830 GTATCGATACAT
1 GTATCGATACAT
4324842 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:4324898 original size:13 final size:13
Alignment explanation
Indices: 4324880--4324905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4324870 TACAGCAAGT
4324880 ATGTATCGATACA
1 ATGTATCGATACA
4324893 ATGTATCGATACA
1 ATGTATCGATACA
4324906 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4328987 original size:15 final size:15
Alignment explanation
Indices: 4328967--4328997 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4328957 TAAAAATGAA
*
4328967 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4328982 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4328997 C
1 C
4328998 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4331090 original size:20 final size:21
Alignment explanation
Indices: 4331012--4331089 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
4331002 ATGTCCAAAA
*
4331012 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
4331032 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
4331056 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
4331077 TGTATCGATACAT
1 TGTATCGATACAT
4331090 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:4331094 original size:13 final size:13
Alignment explanation
Indices: 4331076--4331114 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4331066 ACATTTTTTG
4331076 TTGTATCGATACA
1 TTGTATCGATACA
4331089 TTGTATCGATACA
1 TTGTATCGATACA
*
4331102 CTGTATCGATACA
1 TTGTATCGATACA
4331115 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4333621 original size:20 final size:20
Alignment explanation
Indices: 4333598--4333670 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4333588 ACAATTCAAA
4333598 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4333618 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4333639 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4333659 GTATCGATACAT
1 GTATCGATACAT
4333671 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4333642 original size:21 final size:21
Alignment explanation
Indices: 4333616--4333691 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
4333606 ACATGTTGCA
4333616 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4333637 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
4333657 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
4333678 TTGTATCGATACAT
1 ATGTATCGATACAT
4333692 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4333649 original size:41 final size:41
Alignment explanation
Indices: 4333598--4333691 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
4333588 ACAATTCAAA
*
4333598 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
4333639 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4333680 GTATCGATACAT
1 GTATCGATACAT
4333692 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:4333748 original size:13 final size:13
Alignment explanation
Indices: 4333730--4333755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4333720 TACAGCAAGT
4333730 ATGTATCGATACA
1 ATGTATCGATACA
4333743 ATGTATCGATACA
1 ATGTATCGATACA
4333756 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4336104 original size:21 final size:21
Alignment explanation
Indices: 4336080--4336122 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4336070 TAGGGCCTCC
4336080 CTTATTCTTCTT-CTTCTCTTT
1 CTTA-TCTTCTTCCTTCTCTTT
* *
4336101 CTTATCTTGTTCCTTGTCTTT
1 CTTATCTTCTTCCTTCTCTTT
4336122 C
1 C
4336123 AAAGATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.63
Consensus pattern (21 bp):
CTTATCTTCTTCCTTCTCTTT
Found at i:4337302 original size:28 final size:30
Alignment explanation
Indices: 4337265--4337320 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4337255 TTAATAACCC
*
4337265 AACAACAGTAAC-A-ACATTACGAACAAAA
1 AACAACAGTAACGACACATTAAGAACAAAA
*
4337293 AACAATAGTAACGACACATTAAGAACAA
1 AACAACAGTAACGACACATTAAGAACAA
4337321 GACAGAGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 1 0.04
30 12 0.50
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.12
Consensus pattern (30 bp):
AACAACAGTAACGACACATTAAGAACAAAA
Found at i:4343200 original size:32 final size:33
Alignment explanation
Indices: 4343139--4343201 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
4343129 CAACCAGATG
*
4343139 TATCAATACATATTGCTTAGTATTGATACATTA
1 TATCAATACATATTGCTTAGTATCGATACATTA
* * *
4343172 TATCGATACATGTT-CTTGGTATCGATACAT
1 TATCAATACATATTGCTTAGTATCGATACAT
4343202 AGTAAATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (33 bp):
TATCAATACATATTGCTTAGTATCGATACATTA
Found at i:4344798 original size:12 final size:12
Alignment explanation
Indices: 4344781--4344805 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4344771 ACAATTTTTG
4344781 TGTATCGATACA
1 TGTATCGATACA
4344793 TGTATCGATACA
1 TGTATCGATACA
4344805 T
1 T
4344806 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:4344799 original size:31 final size:31
Alignment explanation
Indices: 4344761--4344823 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
4344751 TTACAAGCCA
**
4344761 ATGTATCGATACAATTTTTG-TGTATCGATAC
1 ATGTATCGATAC-ATACTTGCTGTATCGATAC
4344792 ATGTATCGATACATACTTGCTGTATCGATAC
1 ATGTATCGATACATACTTGCTGTATCGATAC
4344823 A
1 A
4344824 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (31 bp):
ATGTATCGATACATACTTGCTGTATCGATAC
Found at i:4344890 original size:20 final size:20
Alignment explanation
Indices: 4344865--4344937 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4344855 CAACTTTTTT
4344865 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
4344885 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
4344906 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
4344926 ATGTATCGATAC
1 ATGTATCGATAC
4344938 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:4344903 original size:41 final size:41
Alignment explanation
Indices: 4344844--4344937 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
4344834 CTGCCAAGAA
*
4344844 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
4344885 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
4344926 ATGTATCGATAC
1 ATGTATCGATAC
4344938 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:4344919 original size:21 final size:21
Alignment explanation
Indices: 4344844--4344919 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
4344834 CTGCCAAGAA
* *
4344844 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
4344865 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
4344885 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
4344906 ATGTATCGATACAT
1 ATGTATCGATACAT
4344920 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:4350091 original size:154 final size:153
Alignment explanation
Indices: 4349780--4350159 Score: 480
Period size: 154 Copynumber: 2.5 Consensus size: 153
4349770 GTTTCATAGA
* * * * *
4349780 AAAATTATGAAAATACTCCTAAAAGATACCTTCGACATAGAAGTACCTGATACCCTTAAAGGATT
1 AAAATTATGAAAATAC-CTTTAAGGATACCTTCGACGTAGAAGTACCTGATACCCTTAAAGGACT
* ** * * *
4349845 TAAAAAAGGTTTAAGACCGGATAAACCTGTCCTGTATGCCTACCTTTGGCATAAAAGCAGACCTA
65 T-AAAAAGGTTTAAGACCGGATAAACCTATCCTAAATGCCTACATTTGGCATAAAAGCAAACCGA
* *
4349910 GTGACGACCTAAAAGTTGGTTCTAG
129 GTGACAACCTAAAAGTTGGTTCCAG
* * *
4349935 AAAATTATGAAAATACCTTTAGAGGATACCTTCGACGTAGAAGTACCTAATACCCCTAAGGGACT
1 AAAATTATGAAAATACCTTTA-AGGATACCTTCGACGTAGAAGTACCTGATACCCTTAAAGGACT
* *
4350000 TAAAAAGGTTTAAGA-TGGAATGAACCTATCCTAAATGCCCT-CATTTGGCATAAAAGCAAACCC
65 TAAAAAGGTTTAAGACCGG-ATAAACCTATCCTAAATG-CCTACATTTGGCATAAAAGCAAA-CC
*
4350063 GA-TGACAACCTAGGAA-TTGGTTCCAG
127 GAGTGACAACCTA-AAAGTTGGTTCCAG
*
4350089 AAAATTATGAAAATGCCTTTAAGGGATACCTTCGACGTAGAAGTACCTGATACCCTTAAAGGACT
1 AAAATTATGAAAATACCTTTAA-GGATACCTTCGACGTAGAAGTACCTGATACCCTTAAAGGACT
4350154 TAAAAA
65 TAAAAA
4350160 TGATGATAAA
Statistics
Matches: 196, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
153 3 0.02
154 131 0.67
155 62 0.32
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (153 bp):
AAAATTATGAAAATACCTTTAAGGATACCTTCGACGTAGAAGTACCTGATACCCTTAAAGGACTT
AAAAAGGTTTAAGACCGGATAAACCTATCCTAAATGCCTACATTTGGCATAAAAGCAAACCGAGT
GACAACCTAAAAGTTGGTTCCAG
Found at i:4352557 original size:28 final size:29
Alignment explanation
Indices: 4352517--4352591 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
4352507 GGAATAAAGC
*
4352517 CGGGGTTGGAGTATCCTCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCTCTCGAGAAATAA
4352545 CGGGGTTGGAGTATCC-C-CGATGAAATAA
1 CGGGGTTGGAGTATCCTCTCGA-GAAATAA
* *
4352573 CGAGGTTAGAGTATCCTCT
1 CGGGGTTGGAGTATCCTCT
4352592 ATTGTGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 36 0.90
29 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCTCTCGAGAAATAA
Found at i:4352710 original size:53 final size:52
Alignment explanation
Indices: 4352577--4352756 Score: 157
Period size: 52 Copynumber: 3.4 Consensus size: 52
4352567 AAATAACGAG
* * * *
4352577 GTTAGAGTATCCTCTATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATTGGA
1 GTTAGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTTGAG-AATAAAATCGGA
* ** * * * *
4352629 GTTGGAGTATCCCCGATTAAAGGGAAATTTGGTGTTTTGAGAATAAAACCGGG
1 GTTAGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTTGAGAATAAAATCGGA
** * *
4352682 GTTAGAGTATCCCCGATTGTGGAAAAATTAATGTTTTAAAAATAAAATCGGA
1 GTTAGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAGAATAAAATCGGA
* * *
4352734 GTTGGAATATCCCCAATTGTGGA
1 GTTAGAGTATCCCCGATTGTGGA
4352757 GAATCGAGAA
Statistics
Matches: 100, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
52 59 0.59
53 31 0.31
54 10 0.10
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (52 bp):
GTTAGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAGAATAAAATCGGA
Found at i:4355134 original size:13 final size:13
Alignment explanation
Indices: 4355116--4355141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4355106 ACAAAGATCC
4355116 ATGTATCGATACA
1 ATGTATCGATACA
4355129 ATGTATCGATACA
1 ATGTATCGATACA
4355142 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4355137 original size:33 final size:33
Alignment explanation
Indices: 4355095--4355161 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4355085 AAAATTTCCA
***
4355095 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4355128 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4355161 A
1 A
4355162 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4355205 original size:19 final size:18
Alignment explanation
Indices: 4355181--4355248 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
4355171 CAGTAGCTAA
4355181 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
4355200 TTATGTAACGATAC--A-
1 TTATGTATCGATACAAAC
4355215 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4355232 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4355249 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4355225 original size:32 final size:32
Alignment explanation
Indices: 4355184--4355246 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4355174 TAGCTAATTA
*
4355184 TGTATCGATACAATACTTATGTAACGATACAT
1 TGTATCGATACAAAACTTATGTAACGATACAT
*
4355216 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTAACGATACA
4355247 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTAACGATACAT
Found at i:4355572 original size:20 final size:19
Alignment explanation
Indices: 4355522--4355574 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4355512 TTGCATAGAT
*
4355522 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
* * *
4355541 TCACTATATCGATACATGC
1 ACATTGTATCGATACATGC
4355560 ACAATTGTATCGATA
1 AC-ATTGTATCGATA
4355575 TATGAAACTG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:4355646 original size:13 final size:13
Alignment explanation
Indices: 4355624--4355686 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
4355614 GATACATGGC
*
4355624 ACATTATATCGAT
1 ACATTGTATCGAT
4355637 ACATTGTATCGAT
1 ACATTGTATCGAT
*
4355650 ACA-TG----G-C
1 ACATTGTATCGAT
4355657 ACATTGTATCGAT
1 ACATTGTATCGAT
*
4355670 CCATTGTATCGAT
1 ACATTGTATCGAT
4355683 ACAT
1 ACAT
4355687 GATGAATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
12 3 0.08
13 30 0.77
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:4355649 original size:33 final size:33
Alignment explanation
Indices: 4355607--4355687 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
4355597 CTACCACTGT
4355607 TTGTATCGATACATGGCACATTATATCGATACA
1 TTGTATCGATACATGGCACATTATATCGATACA
* *
4355640 TTGTATCGATACATGGCACATTGTATCGATCCA
1 TTGTATCGATACATGGCACATTATATCGATACA
4355673 TTGTATCGATACATG
1 TTGTATCGATACATG
4355688 ATGAATTGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGGCACATTATATCGATACA
Found at i:4355662 original size:20 final size:20
Alignment explanation
Indices: 4355607--4355669 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
4355597 CTACCACTGT
4355607 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
*
4355627 TTATATCG----AT---ACA
1 TTGTATCGATACATGGCACA
4355640 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
4355660 TTGTATCGAT
1 TTGTATCGAT
4355670 CCATTGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
13 10 0.29
16 2 0.06
17 2 0.06
20 20 0.59
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:4355701 original size:33 final size:33
Alignment explanation
Indices: 4355607--4355708 Score: 136
Period size: 33 Copynumber: 3.1 Consensus size: 33
4355597 CTACCACTGT
**
4355607 TTGTATCGATACATGGCACATTATATCGATACA
1 TTGTATCGATACATGGCACATTGCATCGATACA
* *
4355640 TTGTATCGATACATGGCACATTGTATCGATCCA
1 TTGTATCGATACATGGCACATTGCATCGATACA
4355673 TTGTATCGATACATGATG-A-ATTGCATCGATACA
1 TTGTATCGATACATG--GCACATTGCATCGATACA
4355706 TTG
1 TTG
4355709 CTTCAAACGG
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
33 61 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGGCACATTGCATCGATACA
Found at i:4355755 original size:19 final size:20
Alignment explanation
Indices: 4355731--4355768 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4355721 ATAATTTAAA
4355731 ATGAA-TGTATCGATACATT
1 ATGAATTGTATCGATACATT
4355750 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
4355769 AGCTACAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:4359328 original size:20 final size:20
Alignment explanation
Indices: 4359282--4359355 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
4359272 ATCCCAATGA
***
4359282 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
4359303 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
4359323 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
4359343 TATGTATCGATAC
1 CATGTATCGATAC
4359356 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:4361797 original size:13 final size:13
Alignment explanation
Indices: 4361779--4361816 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4361769 ATAATCCCCC
4361779 TGTATCGATACAG
1 TGTATCGATACAG
*
4361792 TGTATCGATACAT
1 TGTATCGATACAG
4361805 TGTATCGATACA
1 TGTATCGATACA
4361817 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:4363917 original size:15 final size:15
Alignment explanation
Indices: 4363897--4363927 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4363887 ATTTCGTTTG
*
4363897 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4363912 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4363927 G
1 G
4363928 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4368011 original size:13 final size:13
Alignment explanation
Indices: 4367993--4368018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4367983 CAATTTTTTG
4367993 TGTATCGATACAT
1 TGTATCGATACAT
4368006 TGTATCGATACAT
1 TGTATCGATACAT
4368019 ATTTTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4368029 original size:32 final size:33
Alignment explanation
Indices: 4367973--4368036 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
4367963 TACAAGCCAA
*
4367973 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
4368006 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
4368037 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:4368030 original size:19 final size:19
Alignment explanation
Indices: 4367973--4368036 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
4367963 TACAAGCCAA
*
4367973 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
4367993 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
4368006 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
4368025 TGTATCGATACA
1 TGTATCGATACA
4368037 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:4368113 original size:20 final size:20
Alignment explanation
Indices: 4368067--4368140 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
4368057 ATCCCAATGA
***
4368067 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
4368088 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
4368108 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
4368128 TATGTATCGATAC
1 CATGTATCGATAC
4368141 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:4369212 original size:20 final size:20
Alignment explanation
Indices: 4369187--4369261 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
4369177 TTTAATCTAG
*
4369187 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
4369207 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
4369227 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
4369247 ATGTATCGATACATT
1 ATGTATCGATACATT
4369262 CGGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:4369285 original size:31 final size:31
Alignment explanation
Indices: 4369247--4369312 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
4369237 ACATTCTTCA
*
4369247 ATGTATCGATACATTCGGTCTTTTTACCTAG
1 ATGTATCGATACATTCGGTCTTTTTACCCAG
* *
4369278 ATGTATCGATACATTCTGTCTTTTTTCCCAG
1 ATGTATCGATACATTCGGTCTTTTTACCCAG
4369309 ATGT
1 ATGT
4369313 GTAGATACGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (31 bp):
ATGTATCGATACATTCGGTCTTTTTACCCAG
Found at i:4369320 original size:31 final size:31
Alignment explanation
Indices: 4369247--4369320 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
4369237 ACATTCTTCA
* *
4369247 ATGTATCGATACATTCGGTCTTTTTACCTAG
1 ATGTATAGATACATTCGGTCTTTTTACCCAG
* * *
4369278 ATGTATCGATACATTCTGTCTTTTTTCCCAG
1 ATGTATAGATACATTCGGTCTTTTTACCCAG
*
4369309 ATGTGTAGATAC
1 ATGTATAGATAC
4369321 GTTTTTCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (31 bp):
ATGTATAGATACATTCGGTCTTTTTACCCAG
Found at i:4381267 original size:20 final size:20
Alignment explanation
Indices: 4381242--4381296 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4381232 TTGCCAAGGA
4381242 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
4381262 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
4381282 TTTGTATCGATACAT
1 AATGTATCGATACAT
4381297 CTGGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:4386482 original size:21 final size:22
Alignment explanation
Indices: 4386443--4386486 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4386433 TTTTTAACCA
* *
4386443 TTTATCAAGGGGGAGAATTTTT
1 TTTATCAAGAGGGAAAATTTTT
4386465 TTTATCAA-AGGGAAAATTTTT
1 TTTATCAAGAGGGAAAATTTTT
4386486 T
1 T
4386487 AACGAGAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTATCAAGAGGGAAAATTTTT
Found at i:4387172 original size:13 final size:13
Alignment explanation
Indices: 4387150--4387179 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4387140 GATACATGGC
4387150 ACATTATATCGAT
1 ACATTATATCGAT
*
4387163 ACATTGTATCGAT
1 ACATTATATCGAT
4387176 ACAT
1 ACAT
4387180 GATGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:4387193 original size:33 final size:33
Alignment explanation
Indices: 4387133--4387202 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
4387123 ATATCACTAT
*
4387133 TTGTATCGATACATGGCACATTATATCGATACA
1 TTGTATCGATACATGGCACATTATATCGATAAA
*
4387166 TTGTATCGATACATGATG-A-ATTGTATCGATAAA
1 TTGTATCGATACATG--GCACATTATATCGATAAA
4387199 TTGT
1 TTGT
4387203 TTCAAACGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGGCACATTATATCGATAAA
Found at i:4389288 original size:166 final size:166
Alignment explanation
Indices: 4388995--4389563 Score: 618
Period size: 166 Copynumber: 3.4 Consensus size: 166
4388985 TTAGATAAAT
* * * * *
4388995 TTTAAAAATTTTAAATCAAGAAAAATCCCCTTGAAAACATTTACGGAGTAGAAAACTCTGTTTTT
1 TTTAAAAATTTAAAACCAAGAAAAATCCCCCT-AAAACATTTACGAAGTAGAAAACTCTGTATTT
* * * * *
4389060 TGAAAACA-ATGGCT-TTTCAAGG-AAAAAATTAAAAACTCATGAAAACAAATGCATTTTTGAAA
65 TGAAAACATAGGGATATTTAAAGGAAAAAAATTAAAAACTCATGCAAACAAATGAATTTTTGAAA
4389122 ACTAATTTAATATGAAAAAATTAAATATATTTGATGAA
130 ACTAATTTAATATGAAAAAA-TAAATATATTTGATGAA
* * *
4389160 TTTAAAAATTGAAAACCAAGAAAAATCCCCCTAAAAACATTTACGAAGTACAAAACTTTGTATTT
1 TTTAAAAATTTAAAACCAAGAAAAATCCCCCT-AAAACATTTACGAAGTAGAAAACTCTGTATTT
*
4389225 TGAAAACATA-GG-TATTTAAAGGAAAAAAATTCAAAACTCATGCAAACAAATGAATTTTTGAAA
65 TGAAAACATAGGGATATTTAAAGGAAAAAAATTAAAAACTCATGCAAACAAATGAATTTTTGAAA
* * * *
4389288 ATTAATTTCATATGAAATAAATATATATATTTGATAAA
130 ACTAATTTAATATGAAA-AAATAAATATATTTGATGAA
* * *
4389326 TTTTAAAAATTAAAAACCAAGAAAAATCCCCCTAAAACATTTATGGAA-TAGAAAACTCTATATT
1 -TTTAAAAATTTAAAACCAAGAAAAATCCCCCTAAAACATTTA-CGAAGTAGAAAACTCTGTATT
* * * * * *
4389390 TTG-ATA-ATAGGGAAATTTTAA-GAAAAAAATATTAAAACTCATGCAAATAAATGAATTTTTAA
64 TTGAAAACATAGGGATATTTAAAGGAAAAAAAT-TAAAAACTCATGCAAACAAATGAATTTTTGA
* **
4389452 AAACTGATTTAATAGTGATTAAAT-AATAATATTTGATGAA
128 AAACTAATTTAATA-TGAAAAAATAAAT-ATATTTGATGAA
* * * * * * * * *
4389492 TTTTAAAATTTATAAACCAAGAAAAATCCCCTCAAAAAAACTTATGGAGAAGAAAACCCTGTAAT
1 TTTAAAAATTTA-AAACCAAGAAAAATCCCC-CTAAAACATTTACGAAGTAGAAAACTCTGTATT
4389557 TTGAAAA
64 TTGAAAA
4389564 TAGGAGGAAT
Statistics
Matches: 342, Mismatches: 47, Indels: 27
0.82 0.11 0.06
Matches are distributed among these distances:
164 4 0.01
165 98 0.29
166 174 0.51
167 64 0.19
168 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (166 bp):
TTTAAAAATTTAAAACCAAGAAAAATCCCCCTAAAACATTTACGAAGTAGAAAACTCTGTATTTT
GAAAACATAGGGATATTTAAAGGAAAAAAATTAAAAACTCATGCAAACAAATGAATTTTTGAAAA
CTAATTTAATATGAAAAAATAAATATATTTGATGAA
Found at i:4389623 original size:166 final size:165
Alignment explanation
Indices: 4389074--4389661 Score: 452
Period size: 166 Copynumber: 3.5 Consensus size: 165
4389064 AACAATGGCT
* * * * * * *
4389074 TTTCAAGGAAAAAAT-TAAAAACTCATGAAAACAAATGCATTTTTGAAAACT-AATTTAATATGA
1 TTTCAAGAAAAAAATATTAAAACTCATAAAAATAAATGAATTTTTAAAAACTGAA-TTAATAAGA
* * * * *
4389137 A-AAAATTAAATATATTTGATGAA-TTTAAAAATTGAAAACCAAGAAAAATCCCCCTAAAAACAT
65 ATTAAA-TATA-ATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCC-AAAAAAAC
* * ** * * *
4389200 TTA-CGAAGTACAAAACTTTGTATTTTGAAAACATA-GG-TA
127 TTATGGAA-TAGAAAACCCTATAATTTG-AAA-ATAGGGAAA
* * ** * * * * *
4389239 TTTAAAGGAAAAAAAT-TCAAAACTCATGCAAACAAATGAATTTTTGAAAA-TTAATTTCATATG
1 TTTCAA-GAAAAAAATATTAAAACTCATAAAAATAAATGAATTTTTAAAAACTGAA-TTAATAAG
* * * * *
4389302 AAATAAATATATATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTAAAACATT
64 AATTAAATATA-ATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCAAAAAAACT
* * *
4389367 TATGGAATAGAAAACTCTATATTTTGATAATAGGGAAA
128 TATGGAATAGAAAACCCTATAATTTGAAAATAGGGAAA
* ** * *
4389405 TTTTAAGAAAAAAATATTAAAACTCATGCAAATAAATGAATTTTTAAAAACTGATTTAAT-AGTG
1 TTTCAAGAAAAAAATATTAAAACTCATAAAAATAAATGAATTTTTAAAAACTGAATTAATAAG-A
* *
4389469 ATTAAATAATAATATTTGATGAATTTTAAAATTTATAAACCAAGAAAAATCCCCTCAAAAAAACT
65 ATTAAAT-ATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCC-CAAAAAAACT
* *
4389534 TATGGAGA-AGAAAACCCTGTAATTTGAAAATAGGAGGAA
128 TATGGA-ATAGAAAACCCTATAATTTGAAAATAGG-GAAA
* * *
4389573 -TTCCA-AAAGAAA-ATTAATAACTCA-AAAAATAAATGAAAATTTTT-AAAACTGAATTGATAA
1 TTTCAAGAAAAAAATATTAA-AACTCATAAAAATAAATG--AATTTTTAAAAACTGAATTAATAA
*
4389633 GAATTAAATGATAATATTTGAAGAATTTT
63 GAATTAAAT-ATAATATTTGATGAATTTT
4389662 TATTTTTGAA
Statistics
Matches: 357, Mismatches: 48, Indels: 35
0.81 0.11 0.08
Matches are distributed among these distances:
164 3 0.01
165 34 0.10
166 228 0.64
167 88 0.25
168 4 0.01
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (165 bp):
TTTCAAGAAAAAAATATTAAAACTCATAAAAATAAATGAATTTTTAAAAACTGAATTAATAAGAA
TTAAATATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCAAAAAAACTTAT
GGAATAGAAAACCCTATAATTTGAAAATAGGGAAA
Found at i:4389652 original size:332 final size:330
Alignment explanation
Indices: 4388972--4389661 Score: 720
Period size: 332 Copynumber: 2.1 Consensus size: 330
4388962 TTAATGGGAG
* * ** * *
4388972 TTAAATAACAATATTAGATAAATTTTAAAAATTTTAAATCAAGAAAAATCCCCTTGAAAACATTT
1 TTAAAT-ATAATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTGAAAACATTT
* * * * * *
4389037 ACGGAGTAGAAAACTCTGTTTTTTGAAAACAATGGCTTTTCAAGGAAAAAATTAAAAACTCATGA
65 ACGGAATAGAAAACTCTATATTTTGAAAACAAGGGATTTTCAAGAAAAAAATTAAAAACTCATGA
* *
4389102 AAACAAATGCATTTTTGAAAACTAATTTAATATGAAAAAATTAAATATATTTGATGAATTTAAAA
130 AAACAAATGAATTTTTAAAAACTAATTTAATATGAAAAAATTAAATATATTTGATGAATTTAAAA
* * * ** *
4389167 ATTGAAAACCAAGAAAAATCCCCCTAAAAACATTTACGAAGTACAAAACTTTGTATTTTGAAAAC
195 ATTGAAAACCAAGAAAAATCCCCCTAAAAAAACTTACGAAGAACAAAACCCTGTAATTTGAAAAC
* * * ** *
4389232 ATAGGTATTTAAAGGAAAAAAATTCAAAACTCATGCAAACAAATGAATTTTTGAAAATTAATTTC
260 AGAGGAATTCAAA-GAAAAAAATTCAAAACTCATAAAAACAAATGAATTTTTGAAAATGAATTTC
*
4389297 ATATGAA
324 ATAAGAA
*
4389304 ATAAATATATATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCT-AAAACATTT
1 TTAAATATA-ATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTGAAAACATTT
* * * *
4389368 ATGGAATAGAAAACTCTATATTTTGATAA-TAGGGAAATTTT-AAGAAAAAAATATTAAAACTCA
65 ACGGAATAGAAAACTCTATATTTTGAAAACAAGGG--ATTTTCAAGAAAAAAAT-TAAAAACTCA
* * * **
4389431 TGCAAATAAATGAATTTTTAAAAACTGATTTAATAGTGATTAAA-T-AATAATATTTGATGAATT
127 TGAAAACAAATGAATTTTTAAAAACTAATTTAATA-TGAAAAAATTAAAT-ATATTTGATGAATT
* * * * *
4389494 TTAAAATTTATAAACCAAGAAAAAT-CCCCTCAAAAAAACTTATGGAGAAGAAAACCCTGTAATT
190 TAAAAATTGA-AAACCAAGAAAAATCCCCCT-AAAAAAACTTACGAAGAACAAAACCCTGTAATT
* * * *
4389558 TGAAAATAGGAGGAATTCCAA-AAGAAAATT-AATAACTCA-AAAAATAAATGAAAATTTTT-AA
253 TGAAAACA-GAGGAATTCAAAGAAAAAAATTCAA-AACTCATAAAAACAAATG--AATTTTTGAA
*
4389619 AACTGAA-TTGATAAGAA
314 AA-TGAATTTCATAAGAA
4389636 TTAAATGATAATATTTGA-AGAATTTT
1 TTAAAT-ATAATATTTGATA-AATTTT
4389662 TATTTTTGAA
Statistics
Matches: 295, Mismatches: 48, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
330 3 0.01
331 59 0.20
332 161 0.55
333 64 0.22
334 8 0.03
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (330 bp):
TTAAATATAATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTGAAAACATTTA
CGGAATAGAAAACTCTATATTTTGAAAACAAGGGATTTTCAAGAAAAAAATTAAAAACTCATGAA
AACAAATGAATTTTTAAAAACTAATTTAATATGAAAAAATTAAATATATTTGATGAATTTAAAAA
TTGAAAACCAAGAAAAATCCCCCTAAAAAAACTTACGAAGAACAAAACCCTGTAATTTGAAAACA
GAGGAATTCAAAGAAAAAAATTCAAAACTCATAAAAACAAATGAATTTTTGAAAATGAATTTCAT
AAGAA
Found at i:4390915 original size:84 final size:84
Alignment explanation
Indices: 4390781--4391082 Score: 306
Period size: 84 Copynumber: 3.6 Consensus size: 84
4390771 GTAAACTAAT
* * * *
4390781 AGGTCACCATAGGTA-AAGGAGGTTTAC-CGAGGACTGAACCGACAGGTAAACAAAAGAATGAAG
1 AGGTCACCA-AGGGATAAGGA-GTTTACTAG-GGACTGAGCCAACAGGTAAACAAAAGAATGAAG
* ** *
4390844 GTTTACCAAAGATTGAGCTGAT
63 GTTGACCGGAGATTGAGCTGAC
* * * *
4390866 AGGTCATCAAGGGATAAGGAGTTTATTGGGGACTGAGCCAACAGGTAAACAAAGGAATGAAGGTT
1 AGGTCACCAAGGGATAAGGAGTTTACTAGGGACTGAGCCAACAGGTAAACAAAAGAATGAAGGTT
* * *
4390931 GACGGGAGACTAAGCT-AGC
66 GACCGGAGATTGAGCTGA-C
* * * * ** *
4390950 AGGTCCCCAAGGGATAAGGGGTTTACCAAGGACTGAGCTGACAGGTAAACAAAAGGATGAAGGTT
1 AGGTCACCAAGGGATAAGGAGTTTACTAGGGACTGAGCCAACAGGTAAACAAAAGAATGAAGGTT
* *
4391015 GATCGGAGATTGAGTTGAC
66 GACCGGAGATTGAGCTGAC
*
4391034 AGGTCACCAAGGGATAA-GAGGTTTACTAGGGACTGAGTCAACAGGTAAA
1 AGGTCACCAAGGGATAAGGA-GTTTACTAGGGACTGAGCCAACAGGTAAA
4391083 TGAGGAATTA
Statistics
Matches: 175, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
83 2 0.01
84 158 0.90
85 15 0.09
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (84 bp):
AGGTCACCAAGGGATAAGGAGTTTACTAGGGACTGAGCCAACAGGTAAACAAAAGAATGAAGGTT
GACCGGAGATTGAGCTGAC
Found at i:4391071 original size:42 final size:42
Alignment explanation
Indices: 4390949--4391071 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
4390939 ACTAAGCTAG
* * * * *
4390949 CAGGTCCCCAAGGGATAAGGGGTTTACCAAGGACTGAGCTGA
1 CAGGTCACCAAGGGATAAGAGGTTTACTAGGGACTGAGTTGA
* * * * * * *
4390991 CAGGTAAACAAAAGGATGA-AGGTTGA-TCGGAGATTGAGTTGA
1 CAGGT-CACCAAGGGATAAGAGGTTTACTAGG-GACTGAGTTGA
4391033 CAGGTCACCAAGGGATAAGAGGTTTACTAGGGACTGAGT
1 CAGGTCACCAAGGGATAAGAGGTTTACTAGGGACTGAGT
4391072 CAACAGGTAA
Statistics
Matches: 58, Mismatches: 19, Indels: 8
0.68 0.22 0.09
Matches are distributed among these distances:
41 10 0.17
42 37 0.64
43 11 0.19
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.20
Consensus pattern (42 bp):
CAGGTCACCAAGGGATAAGAGGTTTACTAGGGACTGAGTTGA
Found at i:4391215 original size:44 final size:43
Alignment explanation
Indices: 4391167--4391764 Score: 322
Period size: 44 Copynumber: 13.6 Consensus size: 43
4391157 ATGCAAATCG
* * *
4391167 TTTGACCAGGGTGGTAACCATATGTCAAATAGGAAGGAGGCAGA
1 TTTGACCAGGGTGGTAACCATACGTCAAATA-GAATGAGGAAGA
* * *
4391211 TTTGACCAGGGTGATAACCATAAGTCAAATTAGAATGA-AAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAA-TAGAATGAGGAAG-A
* * * * ** * *
4391255 TCTAACCAAGGTGGTAACCATACATCAGGCCTA-AAT-AAGTAGAA
1 TTTGACCAGGGTGGTAACCATACGTCA--AATAGAATGAGGAAG-A
* * *
4391299 TTTGACCTGGGTGGTAACCACACGTCAAATAGAAAAGAGGCAA-A
1 TTTGACCAGGGTGGTAACCATACGTCAAATAG-AATGAGG-AAGA
* * ** *
4391343 TTTAACCAGGGTGGTAACCATACGTCAAATCAAAATGAAAAATA
1 TTTGACCAGGGTGGTAACCATACGTCAAAT-AGAATGAGGAAGA
* * ** * * * * *
4391387 TCTAACCAATGTGGTAACCATACATCAGACCTA-AATAAGAAAAA
1 TTTGACCAGGGTGGTAACCATACGTCA-A-ATAGAATGAGGAAGA
* * * * **
4391431 ATTGACCTGAGTGGTAACCATACTTCAAATAGAAAAAAGGCAA-A
1 TTTGACCAGGGTGGTAACCATACGTCAAATAG-AATGAGG-AAGA
* *
4391475 TTTAACCAGGGTGGTAACCATACGTCAAATCAGAATGA-AAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAAAT-AGAATGAGGAAG-A
*
4391519 TTTGACCAGGGTGGTAACCATACGTCAAACCTAAAATGA-G-AGA
1 TTTGACCAGGGTGGTAACCATACGTCAAA--TAGAATGAGGAAGA
* * * * * *
4391562 TTTTAACCAGGGTGGTAACCACATGTCAAACAGGAAGGAGGCAGA
1 -TTTGACCAGGGTGGTAACCATACGTCAAATA-GAATGAGGAAGA
* *
4391607 TTTGACCAGTGTGGTAACCATACGTCAAATTAGAATGA-AAAGCA
1 TTTGACCAGGGTGGTAACCATACGTCAAA-TAGAATGAGGAAG-A
* * * * * *
4391651 TCTGACTAAGGTGGTAACCATACGTTAGACA-AGAAGGAGGTAGA
1 TTTGACCAGGGTGGTAACCATACGTCA-A-ATAGAATGAGGAAGA
* *** * *
4391695 TTTGACCAAGGTGGTAACCATGTATAAAATCAGAATGA-AAAGTA
1 TTTGACCAGGGTGGTAACCATACGTCAAAT-AGAATGAGGAAG-A
* *
4391739 TCTGACCA-AGTGGTAACCATACGTCA
1 TTTGACCAGGGTGGTAACCATACGTCA
4391765 GACTGAAATT
Statistics
Matches: 422, Mismatches: 99, Indels: 67
0.72 0.17 0.11
Matches are distributed among these distances:
42 8 0.02
43 29 0.07
44 355 0.84
45 26 0.06
46 4 0.01
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (43 bp):
TTTGACCAGGGTGGTAACCATACGTCAAATAGAATGAGGAAGA
Found at i:4391675 original size:132 final size:132
Alignment explanation
Indices: 4391167--4391673 Score: 624
Period size: 132 Copynumber: 3.8 Consensus size: 132
4391157 ATGCAAATCG
* * * * * *
4391167 TTTGACCAGGGTGGTAACCATATGTCAAATAGGAAGGAGGCAGATTTGACCAGGGTGATAACCAT
1 TTTGACCAGGGTGGTAACCACATGTCAAATAGAAAAGAGGCAAATTTAACCAGGGTGGTAACCAT
* * * *
4391232 AAGTCAAATTAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAGGCCTAAATAAGTAG
66 ACGTCAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAGACCTAAATAAGAAG
4391297 AA
131 AA
* *
4391299 TTTGACCTGGGTGGTAACCACACGTCAAATAGAAAAGAGGCAAATTTAACCAGGGTGGTAACCAT
1 TTTGACCAGGGTGGTAACCACATGTCAAATAGAAAAGAGGCAAATTTAACCAGGGTGGTAACCAT
* *
4391364 ACGTCAAATCAAAATGAAAA-ATATCTAACCAATGTGGTAACCATACATCAGACCTAAATAAGAA
66 ACGTCAAATCAGAATGAAAAGA-ATCTAACCAAGGTGGTAACCATACATCAGACCTAAATAAGAA
*
4391428 AAA
130 GAA
* * * * *
4391431 ATTGACCTGAGTGGTAACCATACT-TCAAATAGAAAAAAGGCAAATTTAACCAGGGTGGTAACCA
1 TTTGACCAGGGTGGTAACCACA-TGTCAAATAGAAAAGAGGCAAATTTAACCAGGGTGGTAACCA
* * * * * *
4391495 TACGTCAAATCAGAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCAAACCTAAA-ATGAG
65 TACGTCAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAGACCTAAATAAGA-
*
4391559 AGAT
129 AGAA
* * * * * * *
4391563 TTTAACCAGGGTGGTAACCACATGTCAAACAGGAAGGAGGCAGATTTGACCAGTGTGGTAACCAT
1 TTTGACCAGGGTGGTAACCACATGTCAAATAGAAAAGAGGCAAATTTAACCAGGGTGGTAACCAT
* * * *
4391628 ACGTCAAATTAGAATGAAAAGCATCTGACTAAGGTGGTAACCATAC
66 ACGTCAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATAC
4391674 GTTAGACAAG
Statistics
Matches: 323, Mismatches: 47, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
131 5 0.02
132 317 0.98
133 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (132 bp):
TTTGACCAGGGTGGTAACCACATGTCAAATAGAAAAGAGGCAAATTTAACCAGGGTGGTAACCAT
ACGTCAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAGACCTAAATAAGAAG
AA
Found at i:4391845 original size:48 final size:48
Alignment explanation
Indices: 4391777--4392105 Score: 288
Period size: 48 Copynumber: 6.8 Consensus size: 48
4391767 CTGAAATTTG
* * * * *
4391777 AAGAGTTTAACTAGGTCCTAACACTAATACAATGAAACAAGGGATGAA
1 AAGAGTTTGACCAGGCCCTAACACCAATACAATCAAACAAGGGATGAA
* *
4391825 AAGAGTTTGACCAAGCCCTAACACCAATACAATCAAACGAA-GGATTAA
1 AAGAGTTTGACCAGGCCCTAACACCAATACAATCAAAC-AAGGGATGAA
* * * * *
4391873 AAGAGTTTAACTAGGCCCTAACACCAATTCAGTCAAATAA-GGAT-ACA
1 AAGAGTTTGACCAGGCCCTAACACCAATACAATCAAACAAGGGATGA-A
** * ** **
4391920 AAGAGTTTGATTAGGCCCTAACACCAATACAGTCAAACTATAAATGAAAAA
1 AAGAGTTTGACCAGGCCCTAACACCAATACAATCAAAC---AAGGGATGAA
* * * * *
4391971 AAAATGTTTGACCAAGCCCTAACACCAAAACAATCAAACGAGGGAAGAA
1 AAGA-GTTTGACCAGGCCCTAACACCAATACAATCAAACAAGGGATGAA
* ** * *
4392020 AAGAGTTTTATTAGGCCCTAACACCAATACAGTTAAACAAGGGATGAA
1 AAGAGTTTGACCAGGCCCTAACACCAATACAATCAAACAAGGGATGAA
* *
4392068 AAGAGTTT-ATCCAGGCCCTAACACCAATATAGTCAAAC
1 AAGAGTTTGA-CCAGGCCCTAACACCAATACAATCAAAC
4392106 GATGATCGAA
Statistics
Matches: 229, Mismatches: 43, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
46 1 0.00
47 42 0.18
48 137 0.60
49 11 0.05
50 2 0.01
51 6 0.03
52 30 0.13
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (48 bp):
AAGAGTTTGACCAGGCCCTAACACCAATACAATCAAACAAGGGATGAA
Found at i:4392040 original size:147 final size:148
Alignment explanation
Indices: 4391829--4392105 Score: 416
Period size: 147 Copynumber: 1.9 Consensus size: 148
4391819 GATGAAAAGA
* **
4391829 GTTTGACCAAGCCCTAACACCAATACAATCAAACGAAGGATTAAAAGAGTTTAACTAGGCCCTAA
1 GTTTGACCAAGCCCTAACACCAAAACAATCAAACGAAGGAAGAAAAGAGTTTAACTAGGCCCTAA
* * *
4391894 CACCAATTCAGTCAAATAA-GGAT-ACAAAGAGTTTGAT-TAGGCCCTAACACCAATACAGTCAA
66 CACCAATACAGTCAAACAAGGGATGA-AAAGAGTTT-ATCCAGGCCCTAACACCAATACAGTCAA
4391956 ACTATAAATGAAAAAAAAAT
129 ACTATAAATGAAAAAAAAAT
* * *
4391976 GTTTGACCAAGCCCTAACACCAAAACAATCAAACGAGGGAAGAAAAGAGTTTTATTAGGCCCTAA
1 GTTTGACCAAGCCCTAACACCAAAACAATCAAACGAAGGAAGAAAAGAGTTTAACTAGGCCCTAA
* *
4392041 CACCAATACAGTTAAACAAGGGATGAAAAGAGTTTATCCAGGCCCTAACACCAATATAGTCAAAC
66 CACCAATACAGTCAAACAAGGGATGAAAAGAGTTTATCCAGGCCCTAACACCAATACAGTCAAAC
4392106 GATGATCGAA
Statistics
Matches: 116, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
147 77 0.66
148 38 0.33
149 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19
Consensus pattern (148 bp):
GTTTGACCAAGCCCTAACACCAAAACAATCAAACGAAGGAAGAAAAGAGTTTAACTAGGCCCTAA
CACCAATACAGTCAAACAAGGGATGAAAAGAGTTTATCCAGGCCCTAACACCAATACAGTCAAAC
TATAAATGAAAAAAAAAT
Found at i:4392223 original size:35 final size:34
Alignment explanation
Indices: 4392100--4392223 Score: 95
Period size: 35 Copynumber: 3.5 Consensus size: 34
4392090 ACCAATATAG
* * *
4392100 TCAAACGATGATCGAAAGAGTTTGGCCAGATACAA
1 TCAAACGATG-TGGAAAGAGTTTGACCAGATACGA
* * * * *
4392135 CCAAACGATGATGGAAAAAAGTTTTACCAGATATGG
1 TCAAACGATG-TGG-AAAGAGTTTGACCAGATACGA
* * *
4392171 TGAAATGATGGTTGAAAGAGTTTGACCAGATACGA
1 TCAAACGAT-GTGGAAAGAGTTTGACCAGATACGA
*
4392206 TCAAACAATAGTGGAAAG
1 TCAAACGAT-GTGGAAAG
4392224 TAGTCAGATG
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
35 42 0.64
36 23 0.35
37 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (34 bp):
TCAAACGATGTGGAAAGAGTTTGACCAGATACGA
Found at i:4393026 original size:17 final size:16
Alignment explanation
Indices: 4393006--4393040 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4392996 ATTTTTTTTC
*
4393006 TCTTTTTTTATTTCTTT
1 TCTTTTTTT-TTTCATT
4393023 TCTTTTTTTTTTCATT
1 TCTTTTTTTTTTCATT
4393039 TC
1 TC
4393041 AACATGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTTTTTTTCATT
Found at i:4393033 original size:19 final size:19
Alignment explanation
Indices: 4392996--4393032 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4392986 CACTCTTTCC
*
4392996 ATTTTTTTTCTCTTTTTTT
1 ATTTCTTTTCTCTTTTTTT
4393015 ATTTCTTTTCT-TTTTTTT
1 ATTTCTTTTCTCTTTTTTT
4393033 TTCATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
ATTTCTTTTCTCTTTTTTT
Found at i:4393380 original size:12 final size:11
Alignment explanation
Indices: 4393356--4393407 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
4393346 TCTTTTCCCA
*
4393356 TTTTTTTGTTT
1 TTTTTTTCTTT
4393367 TTTTTTTCTCTT
1 TTTTTTTCT-TT
*
4393379 TTTATTTCATTT
1 TTTTTTTC-TTT
4393391 TTTATTTTACTTT
1 TTT-TTTT-CTTT
4393404 TTTT
1 TTTT
4393408 ATTTTGAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 8 0.24
12 15 0.44
13 10 0.29
14 1 0.03
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:4394951 original size:104 final size:106
Alignment explanation
Indices: 4394740--4394978 Score: 286
Period size: 104 Copynumber: 2.3 Consensus size: 106
4394730 CTACAGGGAG
* * ** * ** * *
4394740 GAAATTGACAAGTCAATAATGAGTGACTAGGATGAAATTTAAGTCAGAAATGGGGTTGACTAGGG
1 GAAATCGATAAGTCAATAAAAAGTGACTAGGATGAAACTTAAGTCAGAAAAAGGGTTGAATAGGA
* * * *
4394805 CGAAACCAATAAGTAAATAAGTTTAAGAGGTTGATAGAGAT
66 CGAAACCAATAAGTAAACAAATTAAAGAGGTTGACAGAGAT
4394846 GAAATCGATAAGTCAATAAAAAGTGACTAGGATGAAACTTAAGT-A-AAAAAGGGTTGAATAGGA
1 GAAATCGATAAGTCAATAAAAAGTGACTAGGATGAAACTTAAGTCAGAAAAAGGGTTGAATAGGA
*
4394909 CGAAACCAATAAGTCAACAAATTAAAGAGGTTGACCA-AGAT
66 CGAAACCAATAAGTAAACAAATTAAAGAGGTTGA-CAGAGAT
* * * *
4394950 GAAACCGATATGTCAAGAAAAATTGACTA
1 GAAATCGATAAGTCAATAAAAAGTGACTA
4394979 AAACCTAAGT
Statistics
Matches: 114, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
104 73 0.64
105 2 0.02
106 39 0.34
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22
Consensus pattern (106 bp):
GAAATCGATAAGTCAATAAAAAGTGACTAGGATGAAACTTAAGTCAGAAAAAGGGTTGAATAGGA
CGAAACCAATAAGTAAACAAATTAAAGAGGTTGACAGAGAT
Found at i:4395062 original size:31 final size:32
Alignment explanation
Indices: 4395001--4395063 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
4394991 GAAAGGTTTG
*
4395001 ACCAAGGCAAAACTAATAAGTCAACTAAGGGTA
1 ACCAAGGCAAAACT-ATAAGTCAACAAAGGGTA
*
4395034 ACCAGGGCAAAACT-TAAGTCGAA-AAAGGGT
1 ACCAAGGCAAAACTATAAGTC-AACAAAGGGT
4395064 TAACTACGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 12 0.44
32 2 0.07
33 13 0.48
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (32 bp):
ACCAAGGCAAAACTATAAGTCAACAAAGGGTA
Found at i:4395206 original size:67 final size:66
Alignment explanation
Indices: 4395096--4395301 Score: 216
Period size: 67 Copynumber: 3.1 Consensus size: 66
4395086 GACTAGGATG
* * * * * *
4395096 AAACCTAAGTCAAAAAGGGTGTTGACCAAGATGAAACAAATAAAGTTAACTAAAGGAAACCATGG
1 AAACCTAAGTCAAAAAAGGTGTTGACCAGGGTGAAACAGATAAAGTCAACTAAAGGAGACCA-GG
*
4395161 CG
65 CA
* * * * * * *
4395163 AAACCTAAGTCAAAAAAGATCTTGACTAGGGTGAAACTGATAAAGTCAACTAAAAGTGACTAGGA
1 AAACCTAAGTCAAAAAAGGTGTTGACCAGGGTGAAACAGATAAAGTCAACTAAAGGAGACCAGG-
4395228 CA
65 CA
** *
4395230 AAACCTAAGT-AACAAAAGGTGTTGACCAGGGCAAAACCGATAAAGTCAACTAAAGGAGACCAAG
1 AAACCTAAGTCAA-AAAAGGTGTTGACCAGGGTGAAACAGATAAAGTCAACTAAAGGAGACC-AG
4395294 GCA
64 GCA
4395297 AAACC
1 AAACC
4395302 AATAAATTCA
Statistics
Matches: 113, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
66 4 0.04
67 106 0.94
68 3 0.03
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (66 bp):
AAACCTAAGTCAAAAAAGGTGTTGACCAGGGTGAAACAGATAAAGTCAACTAAAGGAGACCAGGC
A
Found at i:4395297 original size:34 final size:34
Alignment explanation
Indices: 4395253--4395317 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
4395243 AAAAGGTGTT
* *
4395253 GACCAGGGCAAAACCGATAAAGTCAACTAAAGGA
1 GACCAAGGCAAAACCAATAAAGTCAACTAAAGGA
*
4395287 GACCAAGGCAAAACCAATAAATTCAACTAAA
1 GACCAAGGCAAAACCAATAAAGTCAACTAAA
4395318 TAAGGCCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.51, C:0.22, G:0.17, T:0.11
Consensus pattern (34 bp):
GACCAAGGCAAAACCAATAAAGTCAACTAAAGGA
Found at i:4395327 original size:34 final size:34
Alignment explanation
Indices: 4395253--4395334 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
4395243 AAAAGGTGTT
* * *
4395253 GACCAGGGCAAAACCGATAAAGTCAACTAAAGGA
1 GACCAAGGCAAAACCAATAAAGTCAACTAAAGAA
* *
4395287 GACCAAGGCAAAACCAATAAATTCAACTAAATAA
1 GACCAAGGCAAAACCAATAAAGTCAACTAAAGAA
* *
4395321 GGCCAAGGAAAAAC
1 GACCAAGGCAAAAC
4395335 TTGAGTCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.10
Consensus pattern (34 bp):
GACCAAGGCAAAACCAATAAAGTCAACTAAAGAA
Found at i:4395409 original size:67 final size:66
Alignment explanation
Indices: 4395338--4395572 Score: 235
Period size: 67 Copynumber: 3.5 Consensus size: 66
4395328 GAAAAACTTG
* * *
4395338 AGTCGAAAAGGTTATTGACTAGAGCAAAACTGATAAAGTTAACTAAAAGTGACTAGGGCAAAACC
1 AGTCGAAAAGGGT-TTGACTAGAGCAAAACCGATAAAGTCAACTAAAAGTGACTAGGGCAAAACC
4395403 TA
65 TA
* * * *
4395405 AGTCGAAATAGGGTGT-ACTA-AGGTC-AAACCAATAAAGTCAAGTAAAAGAGACTAGGGCAAAA
1 AGTCGAAA-AGGGTTTGACTAGA-G-CAAAACCGATAAAGTCAACTAAAAGTGACTAGGGCAAAA
4395467 CCTA
63 CCTA
* ** * * *
4395471 AGT-GAAAAAAGGTTTTGACCCGAACAAAACCGATAAAGTCAACTAAAAGTGACTAAGACAAAAC
1 AGTCG--AAAAGGGTTTGACTAGAGCAAAACCGATAAAGTCAACTAAAAGTGACTAGGGCAAAAC
4395535 CTA
64 CTA
* * *
4395538 AGTCAAAAAGGGTATTGACTAGAGAAAAATCGATA
1 AGTCGAAAAGGGT-TTGACTAGAGCAAAACCGATA
4395573 GGGCAAAACC
Statistics
Matches: 134, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
65 2 0.01
66 57 0.43
67 70 0.52
68 5 0.04
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.18
Consensus pattern (66 bp):
AGTCGAAAAGGGTTTGACTAGAGCAAAACCGATAAAGTCAACTAAAAGTGACTAGGGCAAAACCT
A
Found at i:4395821 original size:133 final size:134
Alignment explanation
Indices: 4395575--4395919 Score: 327
Period size: 133 Copynumber: 2.6 Consensus size: 134
4395565 AATCGATAGG
** * * * * *
4395575 GCAAAACCTAAGTCAAAAAAGACGTTAACCAGGGCAAAA-TCGATAAACCCAACTAAAAGTGACT
1 GCAAAACCTAAGTCAAAAAAGGTGTTAACCAAGGCAAAACT-AATAAAGCCAACTAAAAGTAACA
** * *** *
4395639 AGGATGAAACCTAAGTCAAAAAAGGTGTTAACCAAGGTGAAATTGATAAAATCAACAAAAAGAGA
65 AGGACAAAACCTAAGTCAAAAAAGGTGTTAACCAAGGTAAAACCAATAAAATCAACAAAAAGAAA
4395704 CTA-A
130 CTAGA
* * * *
4395708 GCGAAACCTAAGTCAAAAAGGGTGTTAACCAAGGTAAAACTAATTAAGCCAACTAAAAGTAACAA
1 GCAAAACCTAAGTCAAAAAAGGTGTTAACCAAGGCAAAACTAATAAAGCCAACTAAAAGTAACAA
* * * * * *
4395773 GGACAAAACCTTAGTC-ATAAAGTGTGTTAACGAAGGTAAAACCAATAAAGTCAACTAAAGGAAA
66 GGACAAAACCTAAGTCAAAAAAG-GTGTTAACCAAGGTAAAACCAATAAAATCAACAAAAAGAAA
*
4395837 CTAGG
130 CTAGA
* * * * * ** * *
4395842 GCAAAACCTAACTAAAAAAAGGTATTGACCAAGGCAAAACCAATAAAGTTAACTAAAAGTGACTA
1 GCAAAACCTAAGTCAAAAAAGGTGTTAACCAAGGCAAAACTAATAAAGCCAACTAAAAGTAACAA
**
4395907 GGATGAAACCTAA
66 GGACAAAACCTAA
4395920 ATTGAAAAGA
Statistics
Matches: 168, Mismatches: 41, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
132 5 0.03
133 100 0.60
134 63 0.38
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.17
Consensus pattern (134 bp):
GCAAAACCTAAGTCAAAAAAGGTGTTAACCAAGGCAAAACTAATAAAGCCAACTAAAAGTAACAA
GGACAAAACCTAAGTCAAAAAAGGTGTTAACCAAGGTAAAACCAATAAAATCAACAAAAAGAAAC
TAGA
Found at i:4395828 original size:67 final size:66
Alignment explanation
Indices: 4395576--4395919 Score: 253
Period size: 67 Copynumber: 5.2 Consensus size: 66
4395566 ATCGATAGGG
** * * * * ** * *
4395576 CAAAACCTAAGTCAAAAAAGACGTTAACCAGGGCAAAATCGATAAACCCAACTAAAAGTGACTAG
1 CAAAACCTAAGTC-AAAAAGGTGTTAACCAAGGTAAAACCAATAAAGTCAACTAAAAGTAACAAG
4395641 GA
65 GA
** * *** * *
4395643 TGAAACCTAAGTCAAAAAAGGTGTTAACCAAGGTGAAATTGATAAAATCAACAAAAAG-AGACTA
1 CAAAACCTAAGTC-AAAAAGGTGTTAACCAAGGTAAAACCAATAAAGTCAACTAAAAGTA-AC-A
4395707 A-G-
63 AGGA
* * * *
4395709 CGAAACCTAAGTCAAAAAGGGTGTTAACCAAGGTAAAACTAATTAAGCCAACTAAAAGTAACAAG
1 CAAAACCTAAGTCAAAAA-GGTGTTAACCAAGGTAAAACCAATAAAGTCAACTAAAAGTAACAAG
4395774 GA
65 GA
* * * * * *
4395776 CAAAACCTTAGTCATAAAGTGTGTTAACGAAGGTAAAACCAATAAAGTCAACTAAAGGAAACTAG
1 CAAAACCTAAGTCAAAAAG-GTGTTAACCAAGGTAAAACCAATAAAGTCAACTAAAAGTAACAAG
*
4395841 GG
65 GA
* * * * * * * *
4395843 CAAAACCTAACTAAAAAAAGGTATTGACCAAGGCAAAACCAATAAAGTTAACTAAAAGTGACTAG
1 CAAAACCTAAGT-CAAAAAGGTGTTAACCAAGGTAAAACCAATAAAGTCAACTAAAAGTAACAAG
4395908 GA
65 GA
**
4395910 TGAAACCTAA
1 CAAAACCTAA
4395920 ATTGAAAAGA
Statistics
Matches: 222, Mismatches: 47, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
65 7 0.03
66 48 0.22
67 161 0.73
68 6 0.03
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.17
Consensus pattern (66 bp):
CAAAACCTAAGTCAAAAAGGTGTTAACCAAGGTAAAACCAATAAAGTCAACTAAAAGTAACAAGG
A
Found at i:4399210 original size:22 final size:21
Alignment explanation
Indices: 4399178--4399219 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
4399168 CCATCATCTC
4399178 TTTTTTTCTTTT-TTTGTTTTG
1 TTTTTTTCTTTTATTT-TTTTG
4399199 TTTTTTTCCTTTTATTTTTTT
1 TTTTTTT-CTTTTATTTTTTT
4399220 CATGCCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (21 bp):
TTTTTTTCTTTTATTTTTTTG
Found at i:4399949 original size:147 final size:146
Alignment explanation
Indices: 4399572--4399973 Score: 392
Period size: 147 Copynumber: 2.7 Consensus size: 146
4399562 GATATATACC
*
4399572 AAAAAATTC-AAAACTCATAAAATAAATTGAATTTTTCAAAACTGATTTAATATAAATTAAACAA
1 AAAAAATTCTAAAACTCATAAAATAAATTGAATTTTT-AAAACTAATTTAATATAAATT-AA-AA
* * * *
4399636 TAATATTTGATAAATTTTAAAAATTTTAACTAAGTAAAATTCGATCGCAAAAATTTACGAAGTAG
63 TAATATTT-ATAAAATTT-AAAATTATAACTAAGAAAAATTCGATCGCAAAAATATACGAAGTAG
* *
4399701 AAAACTCCGTATTTTTTAAACA
126 AAAACT-CGTATATTTCAAACA
*
4399723 AAAAAATTCTAAAACTCATAAAATAAATTAAATTTTTAAAGACTAATTTAATATTAAA-T--AAT
1 AAAAAATTCTAAAACTCATAAAATAAATTGAATTTTTAAA-ACTAATTTAATA-TAAATTAAAAT
* * ** *
4399785 AAGATTTGAAAAAAATTT-AAATTATAAGC-ATAGAAAAATTTTA-C-CAAAAAATATACGAGGT
64 AATATTT--ATAAAATTTAAAATTATAA-CTA-AGAAAAATTCGATCGC-AAAAATATACGAAGT
*
4399846 AGAAAACT-TTATATTTCATAACA
124 AGAAAACTCGTATATTTCA-AACA
* *
4399869 AGAAAAATTCTAAAACTTATAATATAAATTGAATTTTTGAAAACTAATTTAATATAAATTAAAAT
1 A-AAAAATTCTAAAACTCATAAAATAAATTGAATTTTT-AAAACTAATTTAATATAAATTAAAAT
* *
4399934 AATATTT-TAAGAATTTTAAAAATCATAAACTTAGAAAAAT
64 AATATTTATAA-AA-TTT-AAAATTAT-AACTAAGAAAAAT
4399974 ATTACTAGAG
Statistics
Matches: 210, Mismatches: 22, Indels: 39
0.77 0.08 0.14
Matches are distributed among these distances:
145 7 0.03
146 12 0.06
147 79 0.38
148 25 0.12
149 16 0.08
150 15 0.07
151 14 0.07
152 38 0.18
153 4 0.02
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (146 bp):
AAAAAATTCTAAAACTCATAAAATAAATTGAATTTTTAAAACTAATTTAATATAAATTAAAATAA
TATTTATAAAATTTAAAATTATAACTAAGAAAAATTCGATCGCAAAAATATACGAAGTAGAAAAC
TCGTATATTTCAAACA
Found at i:4401201 original size:42 final size:42
Alignment explanation
Indices: 4401113--4401253 Score: 121
Period size: 42 Copynumber: 3.4 Consensus size: 42
4401103 CCGACAGATA
* * * **
4401113 AACAAAGGATACAAAA-ATTGACCGAGATTGAA-TCGATAAGTT
1 AACAAAGGATA-AAAACATTGACCAAGAATGAACT-GACAAGGC
* * *
4401155 AACAAAGGATAAAAAGATTTACCTAAGACT-AAGCT-AC-AGGC
1 AACAAAGGATAAAAACATTGACC-AAGAATGAA-CTGACAAGGC
*
4401196 AAACAAAGGATAAAAACATTGACCAAGAATGAACTGACAAGTC
1 -AACAAAGGATAAAAACATTGACCAAGAATGAACTGACAAGGC
4401239 AACAAAGGATAAAAA
1 AACAAAGGATAAAAA
4401254 TGATACTTGA
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
41 13 0.16
42 60 0.74
43 7 0.09
44 1 0.01
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.16
Consensus pattern (42 bp):
AACAAAGGATAAAAACATTGACCAAGAATGAACTGACAAGGC
Found at i:4401243 original size:84 final size:85
Alignment explanation
Indices: 4401067--4401253 Score: 220
Period size: 84 Copynumber: 2.2 Consensus size: 85
4401057 AAGCAGTTAG
* * * *
4401067 GTCAACAAATGATGAAAAGGGTTACCTGAAACTAAGCCGACAGATAAACAAAGGATACAAAAATT
1 GTCAACAAAGGATAAAAAGAGTTACCTGAAACTAAGCCGACAGACAAACAAAGGATACAAAAATT
* * *
4401132 GACCGAGATTGAATCGATAA
66 GACCAAGAATGAATCGACAA
* * * *
4401152 GTTAACAAAGGATAAAAAGATTTACCT-AAGACTAAG-CTACAGGCAAACAAAGGATA-AAAACA
1 GTCAACAAAGGATAAAAAGAGTTACCTGAA-ACTAAGCCGACAGACAAACAAAGGATACAAAA-A
4401214 TTGACCAAGAATGAA-CTGACAA
64 TTGACCAAGAATGAATC-GACAA
4401236 GTCAACAAAGGATAAAAA
1 GTCAACAAAGGATAAAAA
4401254 TGATACTTGA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
83 5 0.06
84 54 0.62
85 28 0.32
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (85 bp):
GTCAACAAAGGATAAAAAGAGTTACCTGAAACTAAGCCGACAGACAAACAAAGGATACAAAAATT
GACCAAGAATGAATCGACAA
Found at i:4401374 original size:44 final size:43
Alignment explanation
Indices: 4401296--4401672 Score: 240
Period size: 44 Copynumber: 8.8 Consensus size: 43
4401286 AACTAGGGCT
* ** ** *
4401296 GAACCATCACGTCGAATGAAAGTGAACGGAGTTTGACCAGGGTA
1 GAACCATCACATC-AAACAAAGTGAAAAGAGTTTGACCAAGGTA
* * * *
4401340 GAACCATCACATCAAACAATAATGAAAGGGGTTTGACCATGGTA
1 GAACCATCACATCAAACAA-AGTGAAAAGAGTTTGACCAAGGTA
* * * *
4401384 GAACCATCA-AGTTAAATGAAAGTGAAAGGAGTTTGACCATGGTA
1 GAACCATCACA-TCAAA-CAAAGTGAAAAGAGTTTGACCAAGGTA
* * * * *
4401428 AAATCATCACATTAAACGAAAGTG-AAAGGGTTTGACCAAGGCA
1 GAACCATCACATCAAAC-AAAGTGAAAAGAGTTTGACCAAGGTA
* * * *
4401471 GAACTATCACATCAAATGAAAGTGAAAAGAGTTTGACTAAGGCA
1 GAACCATCACATCAAA-CAAAGTGAAAAGAGTTTGACCAAGGTA
* ** * * *
4401515 GAACCATCACGTCAAATGAGGATGAAAAGAGTTTGACTAGGGCTA
1 GAACCATCACATCAAACAAAG-TGAAAAGAGTTTGACCAAGG-TA
* *
4401560 -AACCATTACAT----CAAA-TG----GAGTTTGACCAAGGCA
1 GAACCATCACATCAAACAAAGTGAAAAGAGTTTGACCAAGGTA
* * * *
4401593 GAACCATCACGTCAAATAATAGTGAAAGGAGTTTGACCATGGTA
1 GAACCATCACATCAAACAA-AGTGAAAAGAGTTTGACCAAGGTA
* *
4401637 GAACCATCACGTCAAACAGAA-TGAAAAGAGCTTGAC
1 GAACCATCACATCAAACA-AAGTGAAAAGAGTTTGAC
4401673 TAGGTATAGT
Statistics
Matches: 264, Mismatches: 48, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
33 1 0.00
34 21 0.08
38 4 0.02
39 1 0.00
40 3 0.01
43 53 0.20
44 176 0.67
45 5 0.02
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (43 bp):
GAACCATCACATCAAACAAAGTGAAAAGAGTTTGACCAAGGTA
Found at i:4401497 original size:87 final size:88
Alignment explanation
Indices: 4401296--4401530 Score: 269
Period size: 87 Copynumber: 2.7 Consensus size: 88
4401286 AACTAGGGCT
* * * *
4401296 GAACCATCACGTCGAATGAAAGTGAACGGAGTTTGACCAGGGTAGAACCATCACATCAAACAATA
1 GAACCATCACATCAAATGAAAGTGAAAGGAGTTTGACCAGGGTAAAACCATCACATCAAACAATA
* *
4401361 ATGAAAGGGGTTTGACCATGGTA
66 ATGAAAGGGGTTTGACCAAGGCA
* * * *
4401384 GAACCATCA-AGTTAAATGAAAGTGAAAGGAGTTTGACCATGGTAAAATCATCACATTAAACGAA
1 GAACCATCACA-TCAAATGAAAGTGAAAGGAGTTTGACCAGGGTAAAACCATCACATCAAAC-AA
*
4401448 -AGTGAAA-GGGTTTGACCAAGGCA
64 TAATGAAAGGGGTTTGACCAAGGCA
* * * * * * *
4401471 GAACTATCACATCAAATGAAAGTGAAAAGAGTTTGACTAAGGCAGAACCATCACGTCAAA
1 GAACCATCACATCAAATGAAAGTGAAAGGAGTTTGACCAGGGTAAAACCATCACATCAAA
4401531 TGAGGATGAA
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
87 62 0.50
88 59 0.48
89 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (88 bp):
GAACCATCACATCAAATGAAAGTGAAAGGAGTTTGACCAGGGTAAAACCATCACATCAAACAATA
ATGAAAGGGGTTTGACCAAGGCA
Found at i:4401598 original size:34 final size:34
Alignment explanation
Indices: 4401543--4401609 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
4401533 AGGATGAAAA
* * *
4401543 GAGTTTGACTAGGGCTAAACCATTACATCAAATG
1 GAGTTTGACCAAGGCTAAACCATCACATCAAATG
*
4401577 GAGTTTGACCAAGGC-AGAACCATCACGTCAAAT
1 GAGTTTGACCAAGGCTA-AACCATCACATCAAAT
4401610 AATAGTGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 1 0.04
34 27 0.96
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (34 bp):
GAGTTTGACCAAGGCTAAACCATCACATCAAATG
Found at i:4401642 original size:78 final size:78
Alignment explanation
Indices: 4401499--4401652 Score: 204
Period size: 78 Copynumber: 2.0 Consensus size: 78
4401489 AAAGTGAAAA
* * * *
4401499 GAGTTTGACTAAGGCAGAACCATCACGTCAAATGAGGATGAAAAGAGTTTGACTAGGGCTAAACC
1 GAGTTTGACCAAGGCAGAACCATCACGTCAAATAAAGATGAAAAGAGTTTGACCAGGGCTAAACC
*
4401564 ATTACATCAAATG
66 ATCACATCAAATG
* *
4401577 GAGTTTGACCAAGGCAGAACCATCACGTCAAATAATAG-TGAAAGGAGTTTGACCATGG-TAGAA
1 GAGTTTGACCAAGGCAGAACCATCACGTCAAATAA-AGATGAAAAGAGTTTGACCAGGGCTA-AA
*
4401640 CCATCACGTCAAA
64 CCATCACATCAAA
4401653 CAGAATGAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 2 0.03
78 63 0.95
79 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (78 bp):
GAGTTTGACCAAGGCAGAACCATCACGTCAAATAAAGATGAAAAGAGTTTGACCAGGGCTAAACC
ATCACATCAAATG
Found at i:4401767 original size:35 final size:35
Alignment explanation
Indices: 4401728--4401826 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
4401718 AACCATCATG
* * * *
4401728 TCAAATAGTAATGAAAAGAGTTTAACCAAGTGCAC
1 TCAAATAGGAATGAAAAGAGTTTCACCAAGTACAA
** **
4401763 TCAAACGGGAATGAAAAGAGTTTCACCGGGTACAA
1 TCAAATAGGAATGAAAAGAGTTTCACCAAGTACAA
4401798 TCAAATAGGAATGAAAAGATGTTTCACCA
1 TCAAATAGGAATGAAAAGA-GTTTCACCA
4401827 GGGCGAGAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 44 0.85
36 8 0.15
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.21
Consensus pattern (35 bp):
TCAAATAGGAATGAAAAGAGTTTCACCAAGTACAA
Found at i:4402182 original size:46 final size:46
Alignment explanation
Indices: 4402123--4402245 Score: 167
Period size: 45 Copynumber: 2.7 Consensus size: 46
4402113 ACCATGTATA
* * * *
4402123 GTCAAATAATAATGAATAGATGTTTGACCAGGGCGAGAACCATCAT
1 GTCAAATAGTAATGAAAAGATGTTTGACCAGGGCAAGAACCATCAC
* *
4402169 GTCAAATAGTAATGAAAAGA-GTTTGACCAAGGTAAGAACCATCAC
1 GTCAAATAGTAATGAAAAGATGTTTGACCAGGGCAAGAACCATCAC
* *
4402214 GTCAAACAGGAATGAAAAGATGTTTGACCAGG
1 GTCAAATAGTAATGAAAAGATGTTTGACCAGG
4402246 TACAATCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 39 0.58
46 28 0.42
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
GTCAAATAGTAATGAAAAGATGTTTGACCAGGGCAAGAACCATCAC
Found at i:4402196 original size:81 final size:81
Alignment explanation
Indices: 4401772--4402202 Score: 364
Period size: 81 Copynumber: 5.3 Consensus size: 81
4401762 CTCAAACGGG
* * * * * *
4401772 AATGAAAAGAGTTTCACCGGGTACAATCAAATAGGAATGAAAAGATGTTTCACCAGGGCGAGAA-
1 AATGAAAAGAGTTTGACCAGGTACAATCAAACAAGAACGAAAAGATGTTTGACCAGGGCGAGAAC
* * **
4401836 CATCATGTTAAACCGT
66 CATCACGTCAAATAGT
** ** * * * * * *
4401852 AACAAAAAGAGTTTGACTTGGTACAATCAAACAAAAACAAAAAGATGTTGGACCAAGGCGAAAAG
1 AATGAAAAGAGTTTGACCAGGTACAATCAAACAAGAACGAAAAGATGTTTGACCAGGGCGAGAAC
* *
4401917 CATCACATCAAATGGT
66 CATCACGTCAAATAGT
* * * * * *
4401933 AATTAAAAAAGTTTGACTAGGTACAGTCAAACGAGAACGAAAAGATGTTTGACTAGGGCGAGAAC
1 AATGAAAAGAGTTTGACCAGGTACAATCAAACAAGAACGAAAAGATGTTTGACCAGGGCGAGAAC
*
4401998 CATCACGTCAAATGGT
66 CATCACGTCAAATAGT
* * * * * *
4402014 AATGAAAAAAGTTTAACCAGGTACTATCAAACGGAAATGAA-AAAAAAATGTTTGACCAAGGCGA
1 AATGAAAAGAGTTTGACCAGGTACAATCAAAC---AA-GAACGAAAAGATGTTTGACCAGGGCGA
* ** *
4402078 AAACCATTGCGTCAAACAAG-
62 GAACCATCACGTCAAA-TAGT
* * * * * * *
4402098 AATGAAAAGAGTTTGACCATGTATAGTCAAATAATAATGAATAGATGTTTGACCAGGGCGAGAAC
1 AATGAAAAGAGTTTGACCAGGTACAATCAAACAAGAACGAAAAGATGTTTGACCAGGGCGAGAAC
*
4402163 CATCATGTCAAATAGT
66 CATCACGTCAAATAGT
4402179 AATGAAAAGAGTTTGACCAAGGTA
1 AATGAAAAGAGTTTGACC-AGGTA
4402203 AGAACCATCA
Statistics
Matches: 276, Mismatches: 66, Indels: 16
0.77 0.18 0.04
Matches are distributed among these distances:
80 54 0.20
81 156 0.57
82 4 0.01
84 58 0.21
85 4 0.01
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (81 bp):
AATGAAAAGAGTTTGACCAGGTACAATCAAACAAGAACGAAAAGATGTTTGACCAGGGCGAGAAC
CATCACGTCAAATAGT
Found at i:4402316 original size:128 final size:125
Alignment explanation
Indices: 4402063--4402329 Score: 313
Period size: 128 Copynumber: 2.1 Consensus size: 125
4402053 AAAAAAAAAT
* ** * * *
4402063 GTTTGACCAAGGCGAAAACCATTGCGTCAAACAAGAATGAAAAGAGTTTGACCATGTATAGTCAA
1 GTTTGACCAAGG-TAAAACCATCACGTCAAACAAGAATGAAAAGAGTTTGACCAGGTACAATCAA
* * ** * * * * **
4402128 ATAATAATGAATAGATGTTTGACCAGGGCGAGAACCATCATGTCAAATAGTAATGAAAAGA
65 ACAAGAAAAAAAAAATGTTTGACCAGGGCAAAAACCATCACATCAAATAGTAATGAAAAGA
*
4402189 GTTTGACCAAGGTAAGAACCATCACGTCAAACAGGAATGAAAAGATGTTTGACCAGGTACAATCA
1 GTTTGACCAAGGTAA-AACCATCACGTCAAACAAGAATGAAAAGA-GTTTGACCAGGTACAATCA
*
4402254 AACAAGAACAAAAAAAATGTTTGACCAGAGG-AAAAACCATCACATCAAATGGTAATGAAAAGA
64 AACAAGAA-AAAAAAAATGTTTGACCAG-GGCAAAAACCATCACATCAAATAGTAATGAAAAGA
4402317 GTTTGACC-AGGTA
1 GTTTGACCAAGGTA
4402330 TAGTCAAACG
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
125 2 0.02
126 38 0.32
127 27 0.23
128 50 0.42
129 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (125 bp):
GTTTGACCAAGGTAAAACCATCACGTCAAACAAGAATGAAAAGAGTTTGACCAGGTACAATCAAA
CAAGAAAAAAAAAATGTTTGACCAGGGCAAAAACCATCACATCAAATAGTAATGAAAAGA
Found at i:4403303 original size:21 final size:21
Alignment explanation
Indices: 4403265--4403317 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
4403255 GAACATCCTA
*
4403265 CATTATTTATTTCGTTTTTCTT
1 CATT-TTTTTTTCGTTTTTCTT
*
4403287 CCTTTCTTTTTTC-TTTTTCTT
1 CATTT-TTTTTTCGTTTTTCTT
4403308 CATTTTTTTT
1 CATTTTTTTT
4403318 GGTTTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 13 0.48
22 9 0.33
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.74
Consensus pattern (21 bp):
CATTTTTTTTTCGTTTTTCTT
Found at i:4403314 original size:31 final size:31
Alignment explanation
Indices: 4403279--4403345 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
4403269 ATTTATTTCG
*
4403279 TTTTTCTTCCTTTCTTTTTTCTTTTTCTTCA
1 TTTTTCTTCCTTTCTTTTTGCTTTTTCTTCA
* ** * *
4403310 TTTTTTTTGGTTTCTTTTTGGTTTTTCTTCT
1 TTTTTCTTCCTTTCTTTTTGCTTTTTCTTCA
4403341 TTTTT
1 TTTTT
4403346 TTTGTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (31 bp):
TTTTTCTTCCTTTCTTTTTGCTTTTTCTTCA
Found at i:4403346 original size:31 final size:30
Alignment explanation
Indices: 4403289--4403364 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
4403279 TTTTTCTTCC
**
4403289 TTTCTTTTTTCTTTTTCTTCATTTTTTTTGG
1 TTTCTTTTTGGTTTTTCTTCATTTTTTTT-G
*
4403320 TTTCTTTTTGGTTTTTCTTCTTTTTTTTTG
1 TTTCTTTTTGGTTTTTCTTCATTTTTTTTG
4403350 -TT-TTTTTGGCTTTTT
1 TTTCTTTTTGG-TTTTT
4403365 ATGTTGTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 7 0.17
29 7 0.17
30 1 0.02
31 26 0.63
ACGTcount: A:0.01, C:0.11, G:0.09, T:0.79
Consensus pattern (30 bp):
TTTCTTTTTGGTTTTTCTTCATTTTTTTTG
Found at i:4403353 original size:18 final size:17
Alignment explanation
Indices: 4403289--4403390 Score: 50
Period size: 16 Copynumber: 5.9 Consensus size: 17
4403279 TTTTTCTTCC
*
4403289 TTTCTTTTTTCTT-TTT
1 TTTCTTTTTTTTTGTTT
* * *
4403305 CTTCATTTTTTTTG--G
1 TTTCTTTTTTTTTGTTT
**
4403320 TTTCTTTTTGGTT-TTT
1 TTTCTTTTTTTTTGTTT
*
4403336 CTTCTTTTTTTTTGTTTT
1 TTTCTTTTTTTTTG-TTT
*
4403354 TTTGGCTTTTTATGTTGTTT
1 TTT--CTTTTT-TTTTGTTT
*
4403374 TTCTATTTTTTTTTGTT
1 TT-TCTTTTTTTTTGTT
4403391 CATTATCCTA
Statistics
Matches: 61, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
15 9 0.15
16 20 0.33
18 11 0.18
19 5 0.08
20 11 0.18
21 5 0.08
ACGTcount: A:0.03, C:0.09, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTTTTTGTTT
Found at i:4403362 original size:20 final size:20
Alignment explanation
Indices: 4403311--4403375 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
4403301 TTTTCTTCAT
*
4403311 TTTTTTTGG-TTTCTTTTTGG
1 TTTTTTTGGCTTT-TTTTTTG
4403331 TTTTTCTT--CTTTTTTTTTG
1 TTTTT-TTGGCTTTTTTTTTG
*
4403350 TTTTTTTGGCTTTTTATGTTG
1 TTTTTTTGGCTTTTT-TTTTG
4403371 TTTTT
1 TTTTT
4403376 CTATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 2 0.05
19 11 0.29
20 14 0.37
21 11 0.29
ACGTcount: A:0.02, C:0.06, G:0.14, T:0.78
Consensus pattern (20 bp):
TTTTTTTGGCTTTTTTTTTG
Found at i:4403364 original size:11 final size:10
Alignment explanation
Indices: 4403310--4403356 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
4403300 TTTTTCTTCA
4403310 TTTTTTTTGG
1 TTTTTTTTGG
4403320 TTTCTTTTTGG
1 TTT-TTTTTGG
* *
4403331 TTTTTCTT-C
1 TTTTTTTTGG
*
4403340 TTTTTTTTTG
1 TTTTTTTTGG
4403350 TTTTTTT
1 TTTTTTT
4403357 GGCTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 7 0.23
10 14 0.45
11 10 0.32
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (10 bp):
TTTTTTTTGG
Found at i:4403364 original size:21 final size:21
Alignment explanation
Indices: 4403311--4403375 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
4403301 TTTTCTTCAT
* *
4403311 TTTTTTTGG-TTTCTTTTTGG
1 TTTTTTTGGCTTTTTTTTTTG
4403331 TTTTTCTT--C-TTTTTTTTTG
1 TTTTT-TTGGCTTTTTTTTTTG
* *
4403350 TTTTTTTGGCTTTTTATGTTG
1 TTTTTTTGGCTTTTTTTTTTG
4403371 TTTTT
1 TTTTT
4403376 CTATTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
18 2 0.06
19 13 0.36
20 6 0.17
21 15 0.42
ACGTcount: A:0.02, C:0.06, G:0.14, T:0.78
Consensus pattern (21 bp):
TTTTTTTGGCTTTTTTTTTTG
Found at i:4403713 original size:9 final size:9
Alignment explanation
Indices: 4403699--4403724 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4403689 CTTGTTTCTA
4403699 TTTTCATTC
1 TTTTCATTC
4403708 TTTTCATTC
1 TTTTCATTC
4403717 TTTTCATT
1 TTTTCATT
4403725 TTTCTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTCATTC
Found at i:4403742 original size:14 final size:14
Alignment explanation
Indices: 4403723--4403753 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4403713 ATTCTTTTCA
4403723 TTTTTCTTTTTCTC
1 TTTTTCTTTTTCTC
*
4403737 TTTTTCTTTTTTTC
1 TTTTTCTTTTTCTC
4403751 TTT
1 TTT
4403754 CCTGTCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTCTC
Found at i:4406018 original size:15 final size:15
Alignment explanation
Indices: 4405980--4406024 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
4405970 ATTTTCATGT
4405980 CCTATATTTACCAA-G
1 CCTATATTTA-CAAGG
*
4405995 CCTTCTATTTACAAGG
1 CC-TATATTTACAAGG
4406011 CCTATATTTACAAG
1 CCTATATTTACAAG
4406025 TCTTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (15 bp):
CCTATATTTACAAGG
Found at i:4412669 original size:52 final size:52
Alignment explanation
Indices: 4412605--4412720 Score: 178
Period size: 52 Copynumber: 2.2 Consensus size: 52
4412595 GCCTGCATGT
* * *
4412605 ATCGATATATTTGGGTCAAAAACCCAGAATGTATCGATACAATGAATAATGC
1 ATCGATACATTTGGGTCAAAAACCCAGAATGTATCAATACAATAAATAATGC
* * *
4412657 ATCGATACATTTGGGTCAAAAACCTAGAATGTATCAATATAATAAATAATGT
1 ATCGATACATTTGGGTCAAAAACCCAGAATGTATCAATACAATAAATAATGC
4412709 ATCGATACATTT
1 ATCGATACATTT
4412721 TCTTTCTAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (52 bp):
ATCGATACATTTGGGTCAAAAACCCAGAATGTATCAATACAATAAATAATGC
Found at i:4412817 original size:21 final size:20
Alignment explanation
Indices: 4412750--4412823 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
4412740 TATATAGCCT
***
4412750 TGTATCGATACATTTCAAGCA
1 TGTATCGATACA-TTCACTTA
4412771 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
4412791 TGTATCGATGCATT-ACCTTA
1 TGTATCGATACATTCA-CTTA
4412811 TTGTATCGATACA
1 -TGTATCGATACA
4412824 AATTCTTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 22 0.48
21 23 0.50
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:4414845 original size:13 final size:13
Alignment explanation
Indices: 4414827--4414853 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4414817 CAATTTTTTG
4414827 TGTATCGATACAT
1 TGTATCGATACAT
4414840 TGTATCGATACAT
1 TGTATCGATACAT
4414853 T
1 T
4414854 CTTTGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4414864 original size:32 final size:33
Alignment explanation
Indices: 4414807--4414868 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
4414797 TACAAGCCAA
*
4414807 TGTATCAATACAATTTTTTGTGTATCGATACAT
1 TGTATCAATACAATTCTTTGTGTATCGATACAT
*
4414840 TGTATCGATAC-ATTCTTTGTGTATCGATA
1 TGTATCAATACAATTCTTTGTGTATCGATA
4414869 TAAGTTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCAATACAATTCTTTGTGTATCGATACAT
Found at i:4417415 original size:13 final size:13
Alignment explanation
Indices: 4417397--4417432 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
4417387 ATAATCCCCC
4417397 TGTATCGATACAG
1 TGTATCGATACAG
*
4417410 TGTATCGATACAT
1 TGTATCGATACAG
4417423 TGTATCGATA
1 TGTATCGATA
4417433 TAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:4419526 original size:15 final size:15
Alignment explanation
Indices: 4419506--4419536 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4419496 ATTTCGTTTG
*
4419506 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4419521 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4419536 G
1 G
4419537 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4423632 original size:13 final size:13
Alignment explanation
Indices: 4423614--4423640 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4423604 CAATTTTTTG
4423614 TGTATCGATACAT
1 TGTATCGATACAT
4423627 TGTATCGATACAT
1 TGTATCGATACAT
4423640 T
1 T
4423641 CTTTGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Done.