Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold424
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: 897778
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 3 of 6
Found at i:329169 original size:19 final size:18
Alignment explanation
Indices: 329145--329214 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
329135 AATTCAACAA
329145 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAA-T
329164 TTTGTATCGATAC--AA-
1 TTTGTATCGATACATAAT
329179 --TGTATCGATACATAAAT
1 TTTGTATCGATACAT-AAT
*
329196 ATTGTATCGATACATAAT
1 TTTGTATCGATACATAAT
329214 T
1 T
329215 AGCTACTACT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.25
16 2 0.05
17 2 0.05
18 3 0.07
19 26 0.59
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAT
Found at i:329184 original size:13 final size:13
Alignment explanation
Indices: 329166--329190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329156 ACATAAGTTT
329166 TGTATCGATACAA
1 TGTATCGATACAA
329179 TGTATCGATACA
1 TGTATCGATACA
329191 TAAATATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:329188 original size:32 final size:32
Alignment explanation
Indices: 329147--329209 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
329137 TTCAACAATT
* *
329147 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAATATTGTATCGATACAA
329179 TGTATCGATACATAAATATTGTATCGATACA
1 TGTATCGATACATAAATATTGTATCGATACA
329210 TAATTAGCTA
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:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATACAA
Found at i:329270 original size:13 final size:13
Alignment explanation
Indices: 329252--329277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329242 CATTTTTCTG
329252 TGTATCGATACAT
1 TGTATCGATACAT
329265 TGTATCGATACAT
1 TGTATCGATACAT
329278 GGATCTTTGT
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:329274 original size:33 final size:33
Alignment explanation
Indices: 329232--329298 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
329222 ACTAAGGAAA
***
329232 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
329265 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
329298 T
1 T
329299 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:331706 original size:51 final size:53
Alignment explanation
Indices: 331629--331749 Score: 156
Period size: 51 Copynumber: 2.3 Consensus size: 53
331619 CAATTCTCCG
* * * * * *
331629 TAATCGGGGATATTCCATCTCTGATTTTATTT-TTAAAACACTAATTTTCT-A
1 TAATCGAGGATACTCCAGCTCCGATTTTATTTCTAAAAACACCAATTTTCTCA
*
331680 TAATCGAGGATACTCCAGCTCCGATTTTATTTCTAAAAACACCAATTTTTTCA
1 TAATCGAGGATACTCCAGCTCCGATTTTATTTCTAAAAACACCAATTTTCTCA
*
331733 CAATCGAGGATACTCCA
1 TAATCGAGGATACTCCA
331750 ACCCCGTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 28 0.47
52 15 0.25
53 17 0.28
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (53 bp):
TAATCGAGGATACTCCAGCTCCGATTTTATTTCTAAAAACACCAATTTTCTCA
Found at i:331800 original size:28 final size:28
Alignment explanation
Indices: 331740--331809 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
331730 TCACAATCGA
** **
331740 GGATACTCCAACCCCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACCTCAGAGG
* *
331768 AGATACTCCAACCCCGTTACCTCCGAGG
1 GGATACTCCAACCCCGTTACCTCAGAGG
331796 GGATACTCCAACCC
1 GGATACTCCAACCC
331810 TGGCTTTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.21
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCAGAGG
Found at i:334211 original size:44 final size:44
Alignment explanation
Indices: 334073--334215 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 44
334063 GACAACATTA
* * * * * *
334073 GCATTTGTATTATCTCATGTGCATTTGCCTTTTTATTCATGCTT
1 GCATTTGTATCATTTCATATGCATTTCCCATTTTATTGATGCTT
* * * * *
334117 GCATTTGCATCATTTC--ATGTATATCTGCATTTTA--GATGAAATT
1 GCATTTGTATCATTTCATATGCATTTC-CCATTTTATTGATG--CTT
*
334160 GGTATTTGTATCATTTCATATGCATTTCCCATTTTATTGATGCTT
1 -GCATTTGTATCATTTCATATGCATTTCCCATTTTATTGATGCTT
334205 GCATTTGTATC
1 GCATTTGTATC
334216 GTTTATGCAT
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
41 3 0.04
42 5 0.07
43 8 0.11
44 37 0.51
45 9 0.12
46 7 0.10
47 4 0.05
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (44 bp):
GCATTTGTATCATTTCATATGCATTTCCCATTTTATTGATGCTT
Found at i:335574 original size:79 final size:79
Alignment explanation
Indices: 335191--335574 Score: 432
Period size: 79 Copynumber: 4.9 Consensus size: 79
335181 TGGGGATAAC
* * *
335191 AACGGGGTTGAAGTATCCCCGATTATGAAAAATT-AGTGTTTTGAAAATAAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTGGAAATAAAACCGGGGTTGGAG
* *
335255 TATTCCCTTGAAAAT
65 TATCCCCTCGAAAAT
* * * ** *
335270 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAGT
*
335335 ATCACCTCGAAAAT
66 ATCCCCTCGAAAAT
** * ** * * * * *
335349 AACGGGGTTGGAGTATCCCCGATTGCGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTAGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAGT
*
335414 ATCCCCTCGGAAAT
66 ATCCCCTCGAAAAT
* * * * * *
335428 AACGGGATTGGAGTATCCCCGATTAT-AGAAAATTGGTATTTTGAAAATAAAATCAGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAG
335492 TATCCCCTC-AGAAAT
65 TATCCCCTCGA-AAAT
** *
335507 AATAGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAGT
335572 ATC
66 ATC
335575 TCCGAGATAA
Statistics
Matches: 253, Mismatches: 48, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
78 1 0.00
79 250 0.99
80 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTGGAGT
ATCCCCTCGAAAAT
Found at i:337920 original size:32 final size:30
Alignment explanation
Indices: 337884--337942 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
337874 GAAAACAAAT
337884 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
337916 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
337943 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:338241 original size:13 final size:13
Alignment explanation
Indices: 338223--338248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
338213 CAATTTTTTG
338223 TGTATCGATACAT
1 TGTATCGATACAT
338236 TGTATCGATACAT
1 TGTATCGATACAT
338249 ACTTGGTGTA
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:338263 original size:32 final size:33
Alignment explanation
Indices: 338203--338266 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
338193 TACAAGCCAA
** *
338203 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
338236 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
338267 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:340829 original size:13 final size:13
Alignment explanation
Indices: 340793--340830 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
340783 ATAATCCCCC
*
340793 TGTATCGATAAAG
1 TGTATCGATACAG
*
340806 TGTATCGATACAT
1 TGTATCGATACAG
340819 TGTATCGATACA
1 TGTATCGATACA
340831 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:342929 original size:15 final size:15
Alignment explanation
Indices: 342909--342939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
342899 ATTTCGTTTG
*
342909 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
342924 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
342939 G
1 G
342940 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:344771 original size:21 final size:21
Alignment explanation
Indices: 344742--344786 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
344732 AAGTTTTTAT
*
344742 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
344762 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
344784 TTT
1 TTT
344787 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:346709 original size:31 final size:31
Alignment explanation
Indices: 346668--346726 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
346658 GAAAACAAAT
346668 ACAAAGAGC-TTAGAAAAATAATAACAATATGA
1 ACAAAGAGCTTTAGAAAAAT-ATAA-AATATGA
*
346700 ACAAA-AGCTTTTGAAAAATATAAAATA
1 ACAAAGAGCTTTAGAAAAATATAAAATA
346727 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 7 0.28
32 14 0.56
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.22
Consensus pattern (31 bp):
ACAAAGAGCTTTAGAAAAATATAAAATATGA
Found at i:347882 original size:69 final size:69
Alignment explanation
Indices: 347764--347967 Score: 311
Period size: 69 Copynumber: 3.0 Consensus size: 69
347754 AAAATGCCTG
* * *
347764 AATGTATCGATACATTGTAAAATGTATCGATACATCTGGGTAAATCCAGAATGTATCGATACAAT
1 AATGTATCGATACAATGCAAAATGTATCGATACATCTGGGTAAACCCAGAATGTATCGATACAAT
347829 GAGC
66 GAGC
** * *
347833 AATGTATCGGCACAATGCAAAATGTATCGATACATCTGGGTAGACCCAGAGTGTATCGATACAAT
1 AATGTATCGATACAATGCAAAATGTATCGATACATCTGGGTAAACCCAGAATGTATCGATACAAT
347898 GAGC
66 GAGC
* *
347902 AATATATCGATACAATGCAAAATGTATCGATACATCTGGGTAAACCTA-AAGTGTATCGATACAA
1 AATGTATCGATACAATGCAAAATGTATCGATACATCTGGGTAAACCCAGAA-TGTATCGATACAA
347966 TG
65 TG
347968 TATCGATACA
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
68 1 0.01
69 120 0.99
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (69 bp):
AATGTATCGATACAATGCAAAATGTATCGATACATCTGGGTAAACCCAGAATGTATCGATACAAT
GAGC
Found at i:347929 original size:20 final size:20
Alignment explanation
Indices: 347813--347935 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
347803 GTAAATCCAG
*
347813 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
**
347833 AATGTATCGGCACAATGCA-A
1 AATGTATCGATACAATG-AGA
*
347853 AATGTATCGATACATCTGGGTAGA
1 AATGTATCGATACA-AT--G-AGA
*
347877 CCCAGAGTGTATCGATACAATGAGC
1 ---A-A-TGTATCGATACAATGAGA
*
347902 AATATATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
347922 AATGTATCGATACA
1 AATGTATCGATACA
347936 TCTGGGTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 54 0.68
21 4 0.05
22 1 0.01
23 2 0.03
24 1 0.01
25 2 0.03
26 1 0.01
27 1 0.01
28 2 0.03
29 12 0.15
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:347971 original size:13 final size:13
Alignment explanation
Indices: 347953--347978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
347943 AAACCTAAAG
347953 TGTATCGATACAA
1 TGTATCGATACAA
347966 TGTATCGATACAA
1 TGTATCGATACAA
347979 ATTGTGAAAA
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):
TGTATCGATACAA
Found at i:349598 original size:40 final size:40
Alignment explanation
Indices: 349517--349666 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
349507 CCCTTTAAAC
* * * * *
349517 TTGTTGACTTGTAGG-TT-GTCCTGGTTAACTCTTTTCAT
1 TTGTTGACTTGTAGGTTTCGTCATTGTCAACCCTTTTTAT
*
349555 TTGTTAACTTGTAGGTTTCGTCATTGTCAACCCTTTTTAT
1 TTGTTGACTTGTAGGTTTCGTCATTGTCAACCCTTTTTAT
* * * *
349595 TTGTTGACTTGCAAGTTTCGCCCA-AGTCAACCCTTTTTAT
1 TTGTTGACTTGTAGGTTTCG-TCATTGTCAACCCTTTTTAT
*
349635 TTGTTGACTTATAGGTTTCGTC-TTAGTCAACC
1 TTGTTGACTTGTAGGTTTCGTCATT-GTCAACC
349667 TCTTAAACTT
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 14 0.15
39 3 0.03
40 72 0.79
41 2 0.02
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.46
Consensus pattern (40 bp):
TTGTTGACTTGTAGGTTTCGTCATTGTCAACCCTTTTTAT
Found at i:349891 original size:65 final size:65
Alignment explanation
Indices: 349787--349912 Score: 191
Period size: 65 Copynumber: 1.9 Consensus size: 65
349777 TTGGTCAATC
** *
349787 CCTTTAGTTGACTATATCGATTTCGTCTAAGTCAACTCTTTTTTATTCAGGTTTTGTCTTAGTCA
1 CCTTTAGTTGACTATATCGATTTCCCCTAAGTCAACTCTTTTTTATTCAAGTTTTGTCTTAGTCA
* *
349852 CCTTTAGTTGACTATATTGGTTTCACCCT-AGTCAACTCTTTTTTATTCAAGTTTTGTCTTA
1 CCTTTAGTTGACTATATCGATTTC-CCCTAAGTCAACTCTTTTTTATTCAAGTTTTGTCTTA
349913 TAGTTTTGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 53 0.96
66 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (65 bp):
CCTTTAGTTGACTATATCGATTTCCCCTAAGTCAACTCTTTTTTATTCAAGTTTTGTCTTAGTCA
Found at i:352515 original size:20 final size:20
Alignment explanation
Indices: 352490--352543 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
352480 TTCAAATGCA
352490 TGTATCGATACATTCCAAAT
1 TGTATCGATACATTCCAAAT
352510 TGTATCGATACATTCCAAAT
1 TGTATCGATACATTCCAAAT
352530 TGTATCGATACATT
1 TGTATCGATACATT
352544 GACACGGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTCCAAAT
Found at i:359571 original size:28 final size:29
Alignment explanation
Indices: 359531--359609 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 29
359521 TTTTGGAGAT
359531 AATAACGGGGTTGGAGTATCCCCTCGA-A
1 AATAACGGGGTTGGAGTATCCCCTCGATA
* * *
359559 AATAACGGGGTTGGAGAAT-CTC-CGATG
1 AATAACGGGGTTGGAGTATCCCCTCGATA
*
359586 ATTAACGGGGTTGGAGTATCCCCT
1 AATAACGGGGTTGGAGTATCCCCT
359610 ATTGTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 3 0.07
27 19 0.45
28 20 0.48
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (29 bp):
AATAACGGGGTTGGAGTATCCCCTCGATA
Found at i:359756 original size:51 final size:51
Alignment explanation
Indices: 359595--359829 Score: 301
Period size: 51 Copynumber: 4.6 Consensus size: 51
359585 GATTAACGGG
* * * *
359595 GTTGGAGTATCCCCTATTGTGAAAATTTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGAAAATAAAACCGGA
** * *
359647 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
* *
359699 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
* * *
359750 GCTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-AGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAACCGGA
* *
359801 GTTGGAGTATCCTCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTGTGAAAAATTG
359830 AGAAACTTAA
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.01
51 96 0.61
52 51 0.32
53 10 0.06
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
Found at i:359811 original size:102 final size:104
Alignment explanation
Indices: 359591--359829 Score: 349
Period size: 102 Copynumber: 2.3 Consensus size: 104
359581 CGATGATTAA
* * * * *
359591 CGGGGTTGGAGTATCCCCTATTGTGAAAATTTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGCTGGAGTA
* *
359656 TCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
66 TCCCCGATTAAAGAAAAATTAGTGTTTTGAAAATAAAAC
359695 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTCGAAAATAAAATCGGAGCTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGCTGGAGTA
**
359759 TCCCCGATT-GTGAAAAATTAGTGTTTT-AGAAATAAAAC
66 TCCCCGATTAAAGAAAAATTAGTGTTTTGA-AAATAAAAC
* *
359797 CGGGGTTGGAGTATCCTCGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTG
359830 AGAAACTTAA
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
101 1 0.01
102 54 0.44
103 34 0.28
104 34 0.28
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (104 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGCTGGAGTA
TCCCCGATTAAAGAAAAATTAGTGTTTTGAAAATAAAAC
Found at i:362201 original size:20 final size:21
Alignment explanation
Indices: 362173--362234 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
362163 TTCCTAGATG
*
362173 TATCGATACAAAG-ATCGATA
1 TATCAATACAAAGTATCGATA
*
362193 TATCAATACAATGTATCGATA
1 TATCAATACAAAGTATCGATA
*
362214 CATTC--TACAAATGTATCGATA
1 TA-TCAATACAAA-GTATCGATA
362235 CATTTCCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 16 0.46
21 17 0.49
22 2 0.06
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (21 bp):
TATCAATACAAAGTATCGATA
Found at i:362292 original size:19 final size:21
Alignment explanation
Indices: 362268--362319 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
362258 AGCGATACAC
*
362268 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
362287 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
362308 TGTATCGATACA
1 TGTATCGATACA
362320 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:362678 original size:13 final size:13
Alignment explanation
Indices: 362660--362698 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
362650 ACAACATTCT
362660 TTGTATCGATACA
1 TTGTATCGATACA
*
362673 TTGTATCAATACA
1 TTGTATCGATACA
*
362686 GTGTATCGATACA
1 TTGTATCGATACA
362699 AAGGGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:365167 original size:13 final size:13
Alignment explanation
Indices: 365149--365173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
365139 ATTTTGCTCA
365149 GTATCGATACATT
1 GTATCGATACATT
365162 GTATCGATACAT
1 GTATCGATACAT
365174 AGCATTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:366387 original size:20 final size:20
Alignment explanation
Indices: 366335--366387 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
366325 TTTTGGACTA
* * *
366335 AAATATATTGATACATAAGT
1 AAATGTATTGATACACAAGG
*
366355 AAATG-ACTCGATACACAAGG
1 AAATGTA-TTGATACACAAGG
366375 AAATGTATTGATA
1 AAATGTATTGATA
366388 TATTCATCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (20 bp):
AAATGTATTGATACACAAGG
Found at i:368939 original size:141 final size:139
Alignment explanation
Indices: 368685--369006 Score: 418
Period size: 141 Copynumber: 2.3 Consensus size: 139
368675 ATTTATCTCG
* * * * *
368685 TACCTTAATGG-AAGCCTAAAAAGATACGAAAAA-TTTTAAAGATTATTATATCCC-CA-TGGAA
1 TACCTTAATGGAAAACC-GAAAAGATAC-AAAAAGTTTTGAAGATTTTTATA-CCCTTAGT-GAA
* *
368746 AGCCATAAGAATATAGAAATCTTGAAAAATTAAGACTATAATTTTTATTTAATTTTTTAATTTCA
62 AACCATAAGAATATAGAAATCTTGAAAAATTAAGACGATAATTTTTATTTAATTTTTTAATTTC-
368811 AAAGAATTCATTTCA
126 AAA-AATTCATTTCA
** *
368826 TACCTTAATGGAAAACCGAAAAGATATGAAAGGTTTTGAAGATTTTTATACCCTTAGTGAAAACC
1 TACCTTAATGGAAAACCGAAAAGATACAAAAAGTTTTGAAGATTTTTATACCCTTAGTGAAAACC
* *
368891 ATAAGAATATAGAAATCTTGAAAAATTAAGAGGATAATTTTTATTTAATTTTTTATTTTCAAAAA
66 ATAAGAATATAGAAATCTTGAAAAATTAAGACGATAATTTTTATTTAATTTTTTAATTTCAAAAA
*
368956 TTCATTTTA
131 TTCATTTCA
* **
368965 TACCTTAATGGAGAATTGAAAAGATACAAAAAGTTTTGAAGA
1 TACCTTAATGGAAAACCGAAAAGATACAAAAAGTTTTGAAGA
369007 CTTCCATACC
Statistics
Matches: 158, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
139 46 0.29
140 9 0.06
141 98 0.62
142 5 0.03
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (139 bp):
TACCTTAATGGAAAACCGAAAAGATACAAAAAGTTTTGAAGATTTTTATACCCTTAGTGAAAACC
ATAAGAATATAGAAATCTTGAAAAATTAAGACGATAATTTTTATTTAATTTTTTAATTTCAAAAA
TTCATTTCA
Found at i:369981 original size:10 final size:11
Alignment explanation
Indices: 369956--369986 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
369946 TTTGCCTTAA
369956 TTTTTTCTCTC
1 TTTTTTCTCTC
*
369967 TTTTTTCTTTC
1 TTTTTTCTCTC
369978 TTTTTTCTC
1 TTTTTTCTC
369987 CCTTGCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCTCTC
Found at i:370565 original size:165 final size:164
Alignment explanation
Indices: 370309--370716 Score: 433
Period size: 165 Copynumber: 2.5 Consensus size: 164
370299 TGAAATAATT
* * * ** * * **
370309 TGAATTTTTCAAAACTAATTTAACGTGAATTTAATAATAATATTAGATGAATTTTAAAAATTTTA
1 TGAACTTTTGAAAACTAATTTGATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
* * * * * * * * *** * **
370374 AACTAAGGAAAATCGCCCCGAAAACATTTATGGAATAGAAAATTC-AGTTTTTTGGTAACAAGGA
66 AACAAAGAAAAATCGCCCCAAAAACATATACGGAATAAAAAACTCTA-TATTCCAGAAACAAAAA
** *
370438 AATTTCAAATAAAAAATTCAAAACTCATGAAAATAAA
130 AATTT-AAA-AAAAAATGAAAAACTAATGAAAATAAA
* * *
370475 TG-ACTTTTGAAAACTGATTTGATATGAATTAAATAATAATATTTGATAAATTTAAAAAATTAAA
1 TGAACTTTTGAAAACTAATTTGATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
* * *
370539 AACAAAAAAAAATCTCCCCAAAAACATATACGGAGTAAAAAACTCTATATTCCAGAAACAAAAAA
66 AACAAAGAAAAATCGCCCCAAAAACATATACGGAATAAAAAACTCTATATTCCAGAAACAAAAAA
* *
370604 ATTTAAAAAAAAATGAAAAATTAATGAAAATGAA
131 ATTTAAAAAAAAATGAAAAACTAATGAAAATAAA
* **
370638 TGAATTTTTGAAAACTAATTTTCTATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
1 TGAACTTTTGAAAACTAATTTGATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
*
370703 AACCAAGAAAAATC
66 AACAAAGAAAAATC
370717 CTTCCTAAAA
Statistics
Matches: 198, Mismatches: 42, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
163 24 0.12
164 71 0.36
165 100 0.51
166 3 0.02
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (164 bp):
TGAACTTTTGAAAACTAATTTGATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
AACAAAGAAAAATCGCCCCAAAAACATATACGGAATAAAAAACTCTATATTCCAGAAACAAAAAA
ATTTAAAAAAAAATGAAAAACTAATGAAAATAAA
Found at i:370667 original size:164 final size:165
Alignment explanation
Indices: 370437--370747 Score: 421
Period size: 164 Copynumber: 1.9 Consensus size: 165
370427 GGTAACAAGG
** * *
370437 AAATTTCAAATAAAAAATTCAAAACTCATGAAAATAAATGACTTTTGAAAACTGATTTGATATGA
1 AAATTTCAAATAAAAAATGAAAAACTAATGAAAATAAATGACTTTTGAAAACTAATTTGATATGA
370502 ATTAAATAATAATATTTGATAAATTTAAAAAATTAAAAACAAAAAAAAAT-CTCCCCAAAAACAT
66 ATTAAATAATAATATTTGATAAATTTAAAAAATTAAAAACAAAAAAAAATCCT-CCCAAAAACAT
*
370566 ATACGGAGTAAAAAACTCTATATTCCAGAAACAAAA
130 ATACAGAGTAAAAAACTCTATATTCCAGAAACAAAA
* * * **
370602 AAATTT-AAA-AAAAAATGAAAAATTAATGAAAATGAATGAATTTTTGAAAACTAATTTTCTATG
1 AAATTTCAAATAAAAAATGAAAAACTAATGAAAATAAATG-ACTTTTGAAAACTAATTTGATATG
* * * * * *
370665 AATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCTAAAACAT
65 AATTAAATAATAATATTTGATAAATTTAAAAAATTAAAAACAAAAAAAAATCCTCCCAAAAACAT
* *
370730 TTACAGAGTAGAAAACTC
130 ATACAGAGTAAAAAACTC
370748 CGTATTTCAA
Statistics
Matches: 126, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
163 24 0.19
164 94 0.75
165 8 0.06
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (165 bp):
AAATTTCAAATAAAAAATGAAAAACTAATGAAAATAAATGACTTTTGAAAACTAATTTGATATGA
ATTAAATAATAATATTTGATAAATTTAAAAAATTAAAAACAAAAAAAAATCCTCCCAAAAACATA
TACAGAGTAAAAAACTCTATATTCCAGAAACAAAA
Found at i:371885 original size:85 final size:84
Alignment explanation
Indices: 371796--372243 Score: 282
Period size: 85 Copynumber: 5.3 Consensus size: 84
371786 CAGTCTAGTT
* * * *
371796 AATAAAGTATGAAAGGGGTTACGC-AGGACTAAGTCG-ATAGGTAAACAAAAGATACAAAAGTTG
1 AATAAAGGATAAAAGGAGTTAC-CTAGGACTAAG-CGAACAGGTAAACAAAAGATA-AAAAGTTG
*
371859 ATCGATATTAAATTGACAAGTC
63 ATCGAGATTAAATTGACAAGTC
* * * *
371881 AATAAAGGATAAAAGGATTTACCTGGGACTAAGCGAACAGGTAAACAAAGGATAAAAAGTTGATT
1 AATAAAGGATAAAAGGAGTTACCTAGGACTAAGCGAACAGGTAAACAAAAGATAAAAAGTTGATC
*** *
371946 GAGATTAAACCAACTAGTC
66 GAGATTAAATTGACAAGTC
* * * * *
371965 AACAAAAGATAAAAGGATTTTTACCCT-GGACTAATTCG-ACAGGTAAACAAAGGATAAAAAAGT
1 AATAAAGGATAAAAGGA--GTTA-CCTAGGACTAA-GCGAACAGGTAAACAAAAGAT-AAAAAGT
* * * * *
372028 TTATCGGGATTGAACTGATAAGTC
61 TGATCGAGATTAAATTGACAAGTC
* * * * * * * *
372052 AACAAATGATGAAAGGATTTA-CTCGAGACTAAGCCAACAGGTAAACAAAGGATGAAAAGGTTGA
1 AATAAAGGATAAAAGGAGTTACCTAG-GACTAAGCGAACAGGTAAACAAAAGAT-AAAAAGTTGA
* * * * *
372116 -CCATGGTTGAACTGATAAGTC
64 TCGA-GATTAAATTGACAAGTC
* * * * * *
372137 AACAAAGGATAAAAGGATTTACC-CGAGACTAAGCCG-ACAAGTAAGCAAAGGATAAAAAGGTTG
1 AATAAAGGATAAAAGGAGTTACCTAG-GACTAAG-CGAACAGGTAAACAAAAGATAAAAA-GTTG
* * * *
372200 ACCAAGATTGAATCGACAAGTC
63 ATCGAGATTAAATTGACAAGTC
* *
372222 AAAAAAGGATAAAAGGATTTAC
1 AATAAAGGATAAAAGGAGTTAC
372244 TAAGGACCGA
Statistics
Matches: 302, Mismatches: 46, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
83 2 0.01
84 49 0.16
85 176 0.58
86 32 0.11
87 43 0.14
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (84 bp):
AATAAAGGATAAAAGGAGTTACCTAGGACTAAGCGAACAGGTAAACAAAAGATAAAAAGTTGATC
GAGATTAAATTGACAAGTC
Found at i:371932 original size:43 final size:42
Alignment explanation
Indices: 371884--372193 Score: 119
Period size: 43 Copynumber: 7.3 Consensus size: 42
371874 ACAAGTCAAT
371884 AAAGGATAAAAGGATTTACCTGGGACTAAGCGAACAGGTAAAC
1 AAAGGATAAAAGGATTTACCTGGGACTAAGCGAACA-GTAAAC
* * * * * * * *
371927 AAAGGATAAAAAG-TTGA-TTGAGATTAAACCAACTAGTCAAC
1 AAAGGATAAAAGGATTTACCTGGGACTAAGCGAAC-AGTAAAC
* *
371968 AAAAGATAAAAGGATTTTTACCCT-GGACTAATTCG-ACAGGTAAAC
1 AAAGGATAAAAGGA--TTTA-CCTGGGACTAA-GCGAACA-GTAAAC
* * * *
372013 AAAGGATAAAA-AAGTTTATC-GGGATTGAA-CTGATA-AGTCAAC
1 AAAGGATAAAAGGA-TTTACCTGGGACT-AAGC-GA-ACAGTAAAC
* * * *
372055 AAATGATGAAAGGATTTA-CTCGAGACTAAGCCAACAGGTAAAC
1 AAAGGATAAAAGGATTTACCT-GGGACTAAGCGAACA-GTAAAC
* * *
372098 AAAGGATGAAAAGG-TTGACCAT-GG-TTGAA-CTGATA-AGTCAAC
1 AAAGGAT-AAAAGGATTTACC-TGGGACT-AAGC-GA-ACAGTAAAC
* * *
372140 AAAGGATAAAAGGATTTACCCGAGACTAAGCCG-ACAAGTAAGC
1 AAAGGATAAAAGGATTTACCTGGGACTAAG-CGAAC-AGTAAAC
372183 AAAGGATAAAA
1 AAAGGATAAAA
372194 AGGTTGACCA
Statistics
Matches: 192, Mismatches: 43, Indels: 64
0.64 0.14 0.21
Matches are distributed among these distances:
41 37 0.19
42 54 0.28
43 62 0.32
44 14 0.07
45 23 0.12
46 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.20
Consensus pattern (42 bp):
AAAGGATAAAAGGATTTACCTGGGACTAAGCGAACAGTAAAC
Found at i:372218 original size:42 final size:41
Alignment explanation
Indices: 372095--372235 Score: 126
Period size: 42 Copynumber: 3.3 Consensus size: 41
372085 CCAACAGGTA
* * * *
372095 AACAAAGGATGAAAAGGTTGACCATGGTTGAACTGATAAGTC
1 AACAAAGGATAAAAAGGTTGACCAAGATTGAAC-GACAAGTC
* * *
372137 AACAAAGGAT-AAAAGGATTTACCCGAGACT-AAGCCGACAAGT-
1 AACAAAGGATAAAAAGG-TTGA-CCAAGATTGAA--CGACAAGTC
372179 AAGCAAAGGATAAAAAGGTTGACCAAGATTGAATCGACAAGTC
1 AA-CAAAGGATAAAAAGGTTGACCAAGATTGAA-CGACAAGTC
*
372222 AAAAAAGGATAAAA
1 AACAAAGGATAAAA
372236 GGATTTACTA
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
41 6 0.08
42 42 0.52
43 25 0.31
44 7 0.09
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (41 bp):
AACAAAGGATAAAAAGGTTGACCAAGATTGAACGACAAGTC
Found at i:372239 original size:170 final size:171
Alignment explanation
Indices: 371821--372244 Score: 441
Period size: 171 Copynumber: 2.5 Consensus size: 171
371811 GGGTTACGCA
* * * * * * * * * * *
371821 GGACTAAGTCGATAGGTAAACAAAAGATACAAAAGTTGATCGATATTAAATTGACAAGTCAATAA
1 GGACTAAGCCGACAAGTAAACAAAGGATAAAAAAGTTGACCAAGATTGAACTGACAAGTCAAAAA
* * *
371886 AGGATAAAAGGATTTAC-CTGGGACTAAGCGAACAGGTAAACAAAGGATAAAAAGTTGATTGAGA
66 AGGATAAAAGGATTTACTCTGAGACTAAGCCAACAGGTAAACAAAGGATAAAAAGTTGAATGAGA
371950 TTAAACCAACTAGTCAACAAAAGATAAAAGGATTTTTACCCT
131 TTAAACCAACTAGTCAACAAAAGATAAAAGGA-TTTTACCCT
** * * * ** * *
371992 GGACTAATTCGACAGGTAAACAAAGGATAAAAAAGTTTATCGGGATTGAACTGATAAGTCAACAA
1 GGACTAAGCCGACAAGTAAACAAAGGATAAAAAAGTTGACCAAGATTGAACTGACAAGTCAAAAA
* * *
372057 ATGATGAAAGGATTTACTC-GAGACTAAGCCAACAGGTAAACAAAGGATGAAAAGGTTGACCATG
66 AGGATAAAAGGATTTACTCTGAGACTAAGCCAACAGGTAAACAAAGGAT-AAAAAGTTGA--ATG
* ** *
372121 -G-TTGAACTGA-TAAGTCAACAAAGGATAAAAGGA-TTTACCC-
128 AGATTAAACCAACT-AGTCAACAAAAGATAAAAGGATTTTACCCT
* *
372161 GAGACTAAGCCGACAAGTAAGCAAAGGATAAAAAGGTTGACCAAGATTGAA-TCGACAAGTCAAA
1 G-GACTAAGCCGACAAGTAAACAAAGGATAAAAAAGTTGACCAAGATTGAACT-GACAAGTCAAA
372225 AAAGGATAAAAGGATTTACT
64 AAAGGATAAAAGGATTTACT
372245 AAGGACCGAG
Statistics
Matches: 212, Mismatches: 34, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
169 2 0.01
170 74 0.35
171 97 0.46
172 36 0.17
173 1 0.00
174 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (171 bp):
GGACTAAGCCGACAAGTAAACAAAGGATAAAAAAGTTGACCAAGATTGAACTGACAAGTCAAAAA
AGGATAAAAGGATTTACTCTGAGACTAAGCCAACAGGTAAACAAAGGATAAAAAGTTGAATGAGA
TTAAACCAACTAGTCAACAAAAGATAAAAGGATTTTACCCT
Found at i:372541 original size:44 final size:43
Alignment explanation
Indices: 372493--372631 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 43
372483 TTTGATCAGA
*
372493 GTGGTAATCATATGTTAAACGGAAATGAAAAGAGCTTGACTAGG
1 GTGGTAATCATAAGTTAAACGGAAATGAAAAGAG-TTGACTAGG
* * * * * *
372537 GTGGTAACCACACA-TCAAGCAGG-AATGAAATGAGTCTAACTAGG
1 GTGGTAATCATA-AGTTAAAC-GGAAATGAAAAGAGT-TGACTAGG
* **
372581 GTGGT-ATCCATAAGTTAAACTGACTTGAAAAGAGTTTGACTAGG
1 GTGGTAAT-CATAAGTTAAACGGAAATGAAAAGAG-TTGACTAGG
372625 GTGGTAA
1 GTGGTAA
372632 CCGTATATCA
Statistics
Matches: 71, Mismatches: 16, Indels: 15
0.70 0.16 0.15
Matches are distributed among these distances:
43 4 0.06
44 63 0.89
45 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (43 bp):
GTGGTAATCATAAGTTAAACGGAAATGAAAAGAGTTGACTAGG
Found at i:372804 original size:44 final size:44
Alignment explanation
Indices: 372661--372817 Score: 149
Period size: 44 Copynumber: 3.6 Consensus size: 44
372651 GTGGCAAATT
* * * * *
372661 TGACCATGGTGGTAACCATGCGTCAAATTAGGATGAAAAAAAATC
1 TGACCAGGGTGGTAACCATACGTCAAATCAGAATG-AAAAGAATC
* * * *
372706 TGACCAGGGTGGTAATCATACGTCAAA-CTGAAAT-AAGAAGAGTT
1 TGACCAGGGTGGTAACCATACGTCAAATCAG-AATGAA-AAGAATC
** *
372750 TGACTGGGGTGGTAACCATACATCAAATCAGAATGAAAAGAATC
1 TGACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATC
*
372794 TAACCAGGGTGGTAACC-TACGTCA
1 TGACCAGGGTGGTAACCATACGTCA
372818 GACCAAAAAA
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
43 8 0.09
44 50 0.57
45 30 0.34
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (44 bp):
TGACCAGGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATC
Found at i:376324 original size:167 final size:166
Alignment explanation
Indices: 375942--376529 Score: 668
Period size: 165 Copynumber: 3.5 Consensus size: 166
375932 GAAATATATA
** * * * * * * *
375942 GAAAAAATTCAAAATTTATG-AAATAAATTGAATTTTTCATAATTGATTTAATAGGAGTTAAATG
1 GAAAAAATGAAAAATTAATGAAAATGAA-TGAATTTTTAAAAATTGATTTAATATGAATTAAATA
* * * ** * * * * * ** *
376006 ACAATATTAGATGAATTTTAAAAGTTTTAGATCGAGAAAAATCCCCTCAAAAATATCAATGGAAT
65 ATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTAAAAACATTTATGGAGT
* * * *
376071 AGAAAACTCAGTATTTTGAAAATAAAAGATTTTTAAG
130 AGAAAACTCTGTATTTTGAAAATAAGAGAATTTCAAG
* * *
376108 G-AAAAATGAAAAATTCATGAAAAT-ACGTGAATTTTTTAAAATTGATTTAATATGAATTAAATA
1 GAAAAAATGAAAAATTAATGAAAATGA-ATGAATTTTTAAAAATTGATTTAATATGAATTAAATA
* * * *
376171 ATAACATTTGATGAATTTTAAAAATTAAAAACCTAGAAAAATCCCCTTAAAAACATTTACGGAGC
65 ATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTAAAAACATTTATGGAGT
*
376236 A-AAAACTCTGTATTTCGAAAATAAGAGAATTTCAAG
130 AGAAAACTCTGTATTTTGAAAATAAGAGAATTTCAAG
* *
376272 GAAAAAAACTGAAAAATTAATGAAAATGAATGCATTTTTGAAAATTGATTTAATATGAATTAAAT
1 G-AAAAAA-TGAAAAATTAATGAAAATGAATGAATTTTTAAAAATTGATTTAATATGAATTAAAT
* * *
376337 TATAATATTTGATAAATTTTAAAAATTAAAAACCAAG-AAAATCCCCTTAAAAACATTTATGAAG
64 AATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTAAAAACATTTATGGAG
* *
376401 TAGAAAACTCTGTATTTTAAAAAT-TGAAGAATTTCAA-
129 TAGAAAACTCTGTATTTTGAAAATAAG-AGAATTTCAAG
* * *
376438 GAAAAAATGAAAAATGAATGAAAATGAATGAATTTTTAAAAACTGATTTAATATAAATTAAATAA
1 GAAAAAATGAAAAATTAATGAAAATGAATGAATTTTTAAAAATTGATTTAATATGAATTAAATAA
*
376503 TAATATTTGATGAATTTTTTAAAATTA
66 TAATATTTGATGAA-TTTTAAAAATTA
376530 GAAATCGAAA
Statistics
Matches: 361, Mismatches: 52, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
164 96 0.27
165 114 0.32
166 38 0.11
167 112 0.31
168 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (166 bp):
GAAAAAATGAAAAATTAATGAAAATGAATGAATTTTTAAAAATTGATTTAATATGAATTAAATAA
TAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTAAAAACATTTATGGAGTA
GAAAACTCTGTATTTTGAAAATAAGAGAATTTCAAG
Found at i:376649 original size:167 final size:163
Alignment explanation
Indices: 376070--376687 Score: 527
Period size: 167 Copynumber: 3.7 Consensus size: 163
376060 ATCAATGGAA
* * * * * * * ** *
376070 TAGAAAACTCAGTATTTTGAAAATAAAAGATTTTTAAGGAAAAATGAAAAATTCATGAAAAT-AC
1 TAGAAAACTCTGTATTTTAAAAATAGAAGAATTTCAAGAAAAAATCAAAAATGAATGAAAATAAA
* * *
376134 GTGAATTTTTTAAAATTGATTTAATATGAATTAAATAATAACATTTGATGAA-TTTTAAAAATTA
66 G-GAATTTTTAAAAACTGATTTAATAT-AATTAAATAATAATATTTGATGAATTTTTAAAAATTA
* **
376198 AAAACCTAGAAAAATCCCCTTAAAAACATTTACGGAG
129 AAAACC-AAAAAAATCCCC-TAAAAACATTTACAAAG
* ** * *
376235 CA-AAAACTCTGTATTTCGAAAATA-AGAGAATTTCAAGGAAAAAAACTGAAAAATTAATGAAAA
1 TAGAAAACTCTGTATTTTAAAAATAGA-AGAATTTCAA-G-AAAAAA-TCAAAAATGAATGAAAA
* * * * * * *
376298 TGAATGCATTTTTGAAAATTGATTTAATATGAATTAAATTATAATATTTGAT-AAATTTTAAAAA
62 TAAAGGAATTTTTAAAAACTGATTTAATAT-AATTAAATAATAATATTTGATGAATTTTTAAAAA
* **
376362 TTAAAAACCAAGAAAATCCCCTTAAAAACATTTATGAAG
126 TTAAAAACCAAAAAAATCCCC-TAAAAACATTTACAAAG
* * *
376401 TAGAAAACTCTGTATTTTAAAAATTGAAGAATTTCAAGAAAAAATGAAAAATGAATGAAAATGAA
1 TAGAAAACTCTGTATTTTAAAAATAGAAGAATTTCAAGAAAAAATCAAAAATGAATGAAAATAAA
* *
376466 TGAATTTTTAAAAACTGATTTAATATAAATTAAATAATAATATTTGATGAATTTTTTAAAATTAG
66 GGAATTTTTAAAAACTGATTTAATAT-AATTAAATAATAATATTTGATGAATTTTTAAAAATTA-
* * * *
376531 AAATCGAAAAAAATCTCTCC-GAAAATATTTACAAAG
129 AAAACCAAAAAAATC-C-CCTAAAAACATTTACAAAG
* * * * *
376567 TAGAAAACGTC-GTATTTTTAAAATAGAAAGAATTTTAA-AAGAATATCAATAACT-CAT-AAAA
1 TAGAAAAC-TCTGTATTTTAAAAATAG-AAGAATTTCAAGAA-AAAATCAA-AAATGAATGAAAA
* * * * * *
376628 TAAAAGGAATTTTTCAAAACTGATTTTATGATGATTAAATGATAATATTTAAGGAATTTT
62 T-AAAGGAATTTTTAAAAACTGATTTAAT-ATAATTAAATAATAATATTTGATGAATTTT
376688 GGAATTAAAA
Statistics
Matches: 384, Mismatches: 51, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
163 1 0.00
164 91 0.24
165 21 0.05
166 87 0.23
167 175 0.46
168 9 0.02
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (163 bp):
TAGAAAACTCTGTATTTTAAAAATAGAAGAATTTCAAGAAAAAATCAAAAATGAATGAAAATAAA
GGAATTTTTAAAAACTGATTTAATATAATTAAATAATAATATTTGATGAATTTTTAAAAATTAAA
AACCAAAAAAATCCCCTAAAAACATTTACAAAG
Found at i:376667 original size:331 final size:329
Alignment explanation
Indices: 375962--376677 Score: 719
Period size: 331 Copynumber: 2.2 Consensus size: 329
375952 AAAATTTATG
* * * * * * * *
375962 AAATAAATTGAATTTTTCATAATTGATTTAATAGGAGTTAAATGACAATATTAGATGAATTTTAA
1 AAATAAA-GGAATTTTTCAAAACTGATTTAATATGAATTAAATGATAATATTTGATAAATTTTAA
* ** * * * * *
376027 AAGTTTTAGATCGAGAAAAATCCCCTCAAAAATATCAATGGAATAGAAAACTCAGTATTTTGAAA
65 AAATTAAAAACCAAG-AAAATCCCCTCAAAAACATCAATGGAATAGAAAACTCAGTATTTTAAAA
* * * ** * * *
376092 ATAAAAGATTTTTAAGGAAAAATGAAAAATTCATGAAAATACGTGAATTTTTTAAAATTGATTTA
129 ATAAAAGAATTTCAAGAAAAAATGAAAAATGAATGAAAATACATGAATTTTTAAAAACTGATTTA
* * *
376157 ATATGAATTAAATAATAACATTTGATGAATTTTAAAAATTAAAAACCTAGAAAAATCCCCTTAAA
194 ATATAAATTAAATAATAACATTTGATGAATTTTAAAAATTAAAAACCGAAAAAAATCCCC-TAAA
** * *
376222 AACATTTACGGAGCAAAAACTCTGTATTTCGAAAATAAGAGAATTTCAAGGAAAAAAACTGAAAA
258 AACATTTACAAAGCAAAAACTCTGTATTTCGAAAATAAAAGAATTTCAA-GAAAAAAACTCAAAA
*
376287 ATTAATGA
322 ACTAATGA
* * * * * *
376295 AAATGAATGCATTTTTGAAAATTGATTTAATATGAATTAAATTATAATATTTGATAAATTTTAAA
1 AAATAAAGGAATTTTTCAAAACTGATTTAATATGAATTAAATGATAATATTTGATAAATTTTAAA
* ** *
376360 AATTAAAAACCAAGAAAATCCCCTTAAAAACATTTAT-GAAGTAGAAAACTCTGTATTTTAAAAA
66 AATTAAAAACCAAGAAAATCCCCTCAAAAACATCAATGGAA-TAGAAAACTCAGTATTTTAAAAA
**
376424 TTGAAGAATTTCAAGAAAAAATGAAAAATGAATGAAAATGA-ATGAATTTTTAAAAACTGATTTA
130 TAAAAGAATTTCAAGAAAAAATGAAAAATGAATGAAAAT-ACATGAATTTTTAAAAACTGATTTA
* * * * *
376488 ATATAAATTAAATAATAATATTTGATGAATTTTTTAAAATTAGAAATCGAAAAAAATCTCTCC-G
194 ATATAAATTAAATAATAACATTTGATGAA-TTTTAAAAATTAAAAACCGAAAAAAATC-C-CCTA
* * ** * * *
376552 AAAATATTTACAAAGTAGAAAACGTC-GTATTTTTAAAATAGAAAGAATTTTAA-AAGAATA-TC
256 AAAACATTTACAAAGCA-AAAAC-TCTGTATTTCGAAAATA-AAAGAATTTCAAGAAAAAAACTC
* *
376614 AATAACTCAT-A
318 AAAAACTAATGA
*
376625 AAATAAAAGGAATTTTTCAAAACTGATTTTATGATG-ATTAAATGATAATATTT
1 AAAT-AAAGGAATTTTTCAAAACTGATTTAAT-ATGAATTAAATGATAATATTT
376678 AAGGAATTTT
Statistics
Matches: 312, Mismatches: 61, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
330 8 0.03
331 164 0.53
332 102 0.33
333 24 0.08
334 14 0.04
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (329 bp):
AAATAAAGGAATTTTTCAAAACTGATTTAATATGAATTAAATGATAATATTTGATAAATTTTAAA
AATTAAAAACCAAGAAAATCCCCTCAAAAACATCAATGGAATAGAAAACTCAGTATTTTAAAAAT
AAAAGAATTTCAAGAAAAAATGAAAAATGAATGAAAATACATGAATTTTTAAAAACTGATTTAAT
ATAAATTAAATAATAACATTTGATGAATTTTAAAAATTAAAAACCGAAAAAAATCCCCTAAAAAC
ATTTACAAAGCAAAAACTCTGTATTTCGAAAATAAAAGAATTTCAAGAAAAAAACTCAAAAACTA
ATGA
Found at i:378657 original size:13 final size:13
Alignment explanation
Indices: 378639--378663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378629 GAATATCCTC
378639 TCTAATCTACCAT
1 TCTAATCTACCAT
378652 TCTAATCTACCA
1 TCTAATCTACCA
378664 CAACTTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (13 bp):
TCTAATCTACCAT
Found at i:384925 original size:13 final size:13
Alignment explanation
Indices: 384907--384933 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
384897 TGCAATGAAC
384907 ATGTATCGATACA
1 ATGTATCGATACA
384920 ATGTATCGATACA
1 ATGTATCGATACA
384933 A
1 A
384934 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:388068 original size:32 final size:33
Alignment explanation
Indices: 388025--388089 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
388015 TAGCCAAACT
*
388025 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCAATACACAAAAATATGTATCGATACAA
*
388057 TGTATCAATACACAAAAAATTTGTATCGATACA
1 TGTATCAATACAC-AAAAATATGTATCGATACA
388090 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
34 17 0.59
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (33 bp):
TGTATCAATACACAAAAATATGTATCGATACAA
Found at i:394266 original size:13 final size:13
Alignment explanation
Indices: 394248--394285 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
394238 CATTTTTCTT
394248 TGTATCGATACAA
1 TGTATCGATACAA
*
394261 TGTATCGATACAC
1 TGTATCGATACAA
394274 TGTATCGATACA
1 TGTATCGATACA
394286 GGGGGATTAT
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:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:394440 original size:20 final size:20
Alignment explanation
Indices: 394397--394442 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
394387 AAATCTTTTG
394397 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
394418 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
394438 CAAAA
1 CAAAA
394443 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:396476 original size:13 final size:13
Alignment explanation
Indices: 396458--396483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
396448 TACACAAAAT
396458 ATGTATCGATACA
1 ATGTATCGATACA
396471 ATGTATCGATACA
1 ATGTATCGATACA
396484 CAAAAAATTT
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:402579 original size:20 final size:19
Alignment explanation
Indices: 402554--402626 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
402544 CTGCCAGTTT
**
402554 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
402574 CATGTATCGATAGAATGAA
1 CATGTATCGATACAATGAA
*
402593 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
402614 -ATGTATCGATACA
1 CATGTATCGATACA
402627 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:402598 original size:19 final size:20
Alignment explanation
Indices: 402554--402607 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
402544 CTGCCAGTTT
**
402554 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
402574 CATGTATCGATAGAA-TGAA
1 CATGTATCGATACAATTGAA
402593 CATGTATCGATACAA
1 CATGTATCGATACAA
402608 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:412604 original size:23 final size:23
Alignment explanation
Indices: 412574--412625 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
412564 CAATGAATTT
412574 AAAT-TTAATTATAAAATATA-TA
1 AAATATTAA-TATAAAATATATTA
*
412596 AAATATTAATATAAAATATATTT
1 AAATATTAATATAAAATATATTA
412619 AAATATT
1 AAATATT
412626 TAAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATTAATATAAAATATATTA
Found at i:415561 original size:111 final size:109
Alignment explanation
Indices: 415344--415761 Score: 295
Period size: 111 Copynumber: 3.9 Consensus size: 109
415334 TGAAAAATGC
* * * * ** * *
415344 ATTATCTTATATAAAGGGCTTTCGTAC-ACAGTCTTATGACTCTAGACGATGACCTGTTTTGGTG
1 ATTATCCTATATAAAGGGCATTCGTACGCCACT-TTATGACTCTAGACGATGATTTATTTCGG-G
* *** * * *
415408 GGCTAATATTTTGGTGCCCGAATTTACGTAATTAATACAAAAAATGA
64 GTC-AATCCCTTGGTACCCGAATGTACGTAATTAATACAAAAAAAGA
* * * * * * *
415455 ATTATCTTATGTAAAGGTCATTTGTACGCTACTTTATGACTTTATACGATGATTTATTTCGGGGT
1 ATTATCCTATATAAAGGGCATTCGTACGCCACTTTATGACTCTAGACGATGATTTATTTCGGGGT
*
415520 CAATCCCTTGGTACCCGAATAGTACGTAATTAATGCAAAAAAAAGA
66 CAATCCCTTGGTACCCGAAT-GTACGTAATTAATAC-AAAAAAAGA
* * ***
415566 ATTATCCTATATAAAGGGCGTTCGTACGCCGCTTTATGACTCTAGACGATGACCAATTTCGGGG-
1 ATTATCCTATATAAAGGGCATTCGTACGCCACTTTATGACTCTAGACGATGATTTATTTCGGGGT
* * ** *
415630 ------C-T-G--CTCGAATTTACGTAATTAATGTAAAAAATGA
66 CAATCCCTTGGTACCCGAATGTACGTAATTAATACAAAAAAAGA
* * * * * * *
415664 ATTATCCTATATAAAGGGCGTTCGTACGTCGCTTTACGACTCTAGACAACGATCTATTTCGGGG-
1 ATTATCCTATATAAAGGGCATTCGTACGCCACTTTATGACTCTAGACGATGATTTATTTCGGGGT
** * *
415728 CTAATCTTTTGGTGCCCGAATCTACGTAATTAAT
66 C-AATCCCTTGGTACCCGAATGTACGTAATTAAT
415762 GTAATTAAAT
Statistics
Matches: 247, Mismatches: 46, Indels: 30
0.76 0.14 0.09
Matches are distributed among these distances:
98 66 0.27
99 13 0.05
100 6 0.02
102 1 0.00
103 1 0.00
104 1 0.00
106 1 0.00
107 1 0.00
109 33 0.13
110 16 0.06
111 106 0.43
112 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
ATTATCCTATATAAAGGGCATTCGTACGCCACTTTATGACTCTAGACGATGATTTATTTCGGGGT
CAATCCCTTGGTACCCGAATGTACGTAATTAATACAAAAAAAGA
Found at i:415674 original size:98 final size:99
Alignment explanation
Indices: 415542--415729 Score: 297
Period size: 98 Copynumber: 1.9 Consensus size: 99
415532 ACCCGAATAG
*
415542 TACGTAATTAATGCAAAAAAAAGAATTATCCTATATAAAGGGCGTTCGTACGCCGCTTTATGACT
1 TACGTAATTAATGCAAAAAAAAGAATTATCCTATATAAAGGGCGTTCGTACGCCGCTTTACGACT
* *
415607 CTAGACGATGACCAATTTCGGGGCTGCTCGAATT
66 CTAGACAACGACCAATTTCGGGGCTGCTCGAATT
* * *
415641 TACGTAATTAATG-TAAAAAATGAATTATCCTATATAAAGGGCGTTCGTACGTCGCTTTACGACT
1 TACGTAATTAATGCAAAAAAAAGAATTATCCTATATAAAGGGCGTTCGTACGCCGCTTTACGACT
* *
415705 CTAGACAACGATCTATTTCGGGGCT
66 CTAGACAACGACCAATTTCGGGGCT
415730 AATCTTTTGG
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 68 0.84
99 13 0.16
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (99 bp):
TACGTAATTAATGCAAAAAAAAGAATTATCCTATATAAAGGGCGTTCGTACGCCGCTTTACGACT
CTAGACAACGACCAATTTCGGGGCTGCTCGAATT
Found at i:416154 original size:15 final size:15
Alignment explanation
Indices: 416134--416168 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
416124 ATGTGCACCA
416134 ATATATATACACTAT
1 ATATATATACACTAT
416149 ATATATATACACTAT
1 ATATATATACACTAT
416164 ATATA
1 ATATA
416169 CACAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATATACACTAT
Found at i:417509 original size:22 final size:22
Alignment explanation
Indices: 417469--417520 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
417459 TTTTCATTTG
*
417469 ATTTTTTTTTTTTGCTTTTGTT
1 ATTTTTTTTTTTTGCTTTTGGT
* *
417491 CTTTTTTTCTTTTT-TTTTTGGT
1 ATTTTTTT-TTTTTGCTTTTGGT
417513 ATTTTTTT
1 ATTTTTTT
417521 AAGAACTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.04, C:0.06, G:0.08, T:0.83
Consensus pattern (22 bp):
ATTTTTTTTTTTTGCTTTTGGT
Found at i:419845 original size:21 final size:20
Alignment explanation
Indices: 419816--419872 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
419806 AGTATCAATT
* *
419816 AATTATATCGATACATACTTG
1 AATTGTATCGATACATA-GTG
*
419837 AATTGTATCAATACATAGTG
1 AATTGTATCGATACATAGTG
*
419857 CATTGTATCGATACAT
1 AATTGTATCGATACAT
419873 TGAGTACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (20 bp):
AATTGTATCGATACATAGTG
Found at i:421100 original size:20 final size:19
Alignment explanation
Indices: 421046--421101 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
421036 AAAACCCTTA
*
421046 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
421066 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
421086 AATGTATCGATACATG
1 AAAGTATCGATACATG
421102 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:421189 original size:13 final size:13
Alignment explanation
Indices: 421171--421196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
421161 TACACAAAAT
421171 ATGTATCGATACA
1 ATGTATCGATACA
421184 ATGTATCGATACA
1 ATGTATCGATACA
421197 CAAAAAAATT
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:421216 original size:34 final size:32
Alignment explanation
Indices: 421153--421217 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
421143 TAGCCAAACT
*
421153 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
*
421185 TGTATCGATACACAAAAAAATTGTATTGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
421218 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 5 0.17
34 11 0.38
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:424573 original size:15 final size:15
Alignment explanation
Indices: 424553--424583 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
424543 TAAAAATGTC
*
424553 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
424568 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
424583 C
1 C
424584 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:426685 original size:13 final size:13
Alignment explanation
Indices: 426667--426704 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
426657 CATTTTTCTT
426667 TGTATCGATACAA
1 TGTATCGATACAA
*
426680 TGTATCGATACAC
1 TGTATCGATACAA
426693 TGTATCGATACA
1 TGTATCGATACA
426705 GGGGGATTAT
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:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:426840 original size:21 final size:22
Alignment explanation
Indices: 426816--426856 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
426806 AAATCTTTTG
426816 CAAAATACTT-GTTTTTCATTT
1 CAAAATACTTCGTTTTTCATTT
*
426837 CAAATTACTTCGTTTTTCAT
1 CAAAATACTTCGTTTTTCAT
426857 CAAAACCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (22 bp):
CAAAATACTTCGTTTTTCATTT
Found at i:426859 original size:20 final size:20
Alignment explanation
Indices: 426816--426861 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
426806 AAATCTTTTG
426816 CAAAATACTTGTTTTTCATTT
1 CAAAATACTTGTTTTTCA-TT
*
426837 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCATT
426857 CAAAA
1 CAAAA
426862 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCATT
Found at i:427321 original size:310 final size:310
Alignment explanation
Indices: 426759--427357 Score: 1119
Period size: 310 Copynumber: 1.9 Consensus size: 310
426749 GATACTTTCA
426759 TACCCAAAATTCTCTCAAACCCTATCTTCCAAACTTCAAAATTCTTCAAATCTTTTGCAAAATAC
1 TACCCAAAATTCTCTCAAACCCTATCTTCCAAACTTCAAAATTCTTCAAATCTTTTGCAAAATAC
* *
426824 TTGTTTTTCATTTCAAATTACTTCGTTTTTCATCAAAACCAGCATCAAAAACAAGTTTTTAATCC
66 TTGTTTTTCACTTCAAATTACTTCGTTTTTCATCAAAACCAGCATCAAAAACAAGCTTTTAATCC
*
426889 ATCAAATCACTTCTACAAAACTGTCAAAACCCACAGTTTTGTATCTTTTTAAACCCTTCGAAAAT
131 ATCAAATCACTTCTACAAAACTGTCAAAACCCACAGTTTTGTATATTTTTAAACCCTTCGAAAAT
426954 CTTATTTAGAAAGTGTTTTTGAACCAAATTTTTGCATAAATCCTTTCCAAAACACTTAATCTCTA
196 CTTATTTAGAAAGTGTTTTTGAACCAAATTTTTGCATAAATCCTTTCCAAAACACTTAATCTCTA
427019 GGTTTGTGGTCTTGGTTTGCATCAAAATCCCTAGGGAACCACCTAAAATT
261 GGTTTGTGGTCTTGGTTTGCATCAAAATCCCTAGGGAACCACCTAAAATT
*
427069 TACCCAAATTTCTCTCAAACCCTATCTTCCAAACTTCAAAATTCTTCAAATCTTTTGCAAAATAC
1 TACCCAAAATTCTCTCAAACCCTATCTTCCAAACTTCAAAATTCTTCAAATCTTTTGCAAAATAC
*
427134 TTGTTTTTCACTTCGAATTACTTCGTTTTTCATCAAAACCAGCATCAAAAACAAGCTTTTAATCC
66 TTGTTTTTCACTTCAAATTACTTCGTTTTTCATCAAAACCAGCATCAAAAACAAGCTTTTAATCC
427199 ATCAAATCA-TTCCTACAAAACTGTCAAAACCCACAGTTTTGTATATTTTTAAACCCTTCGAAAA
131 ATCAAATCACTT-CTACAAAACTGTCAAAACCCACAGTTTTGTATATTTTTAAACCCTTCGAAAA
* *
427263 TCTTATTTAGAAAGTGTTTTTGAACCTAATTTTTGCATAAATCCTTTCCCAAACACTTAATCTCT
195 TCTTATTTAGAAAGTGTTTTTGAACCAAATTTTTGCATAAATCCTTTCCAAAACACTTAATCTCT
427328 AGGTTTGTGGTCTTGGTTTGCATCAAAATC
260 AGGTTTGTGGTCTTGGTTTGCATCAAAATC
427358 GTCCCATTTT
Statistics
Matches: 281, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
309 2 0.01
310 279 0.99
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (310 bp):
TACCCAAAATTCTCTCAAACCCTATCTTCCAAACTTCAAAATTCTTCAAATCTTTTGCAAAATAC
TTGTTTTTCACTTCAAATTACTTCGTTTTTCATCAAAACCAGCATCAAAAACAAGCTTTTAATCC
ATCAAATCACTTCTACAAAACTGTCAAAACCCACAGTTTTGTATATTTTTAAACCCTTCGAAAAT
CTTATTTAGAAAGTGTTTTTGAACCAAATTTTTGCATAAATCCTTTCCAAAACACTTAATCTCTA
GGTTTGTGGTCTTGGTTTGCATCAAAATCCCTAGGGAACCACCTAAAATT
Found at i:429490 original size:20 final size:19
Alignment explanation
Indices: 429436--429491 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
429426 AAAACCCTTA
*
429436 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
*
429456 AAAGTATCAATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
429476 AATGTATCGATACATG
1 AAAGTATCGATACATG
429492 AAAAAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:429503 original size:21 final size:21
Alignment explanation
Indices: 429477--429533 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
429467 ACATGTTGCA
429477 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
429498 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
429519 ATGTATCGATACATG
1 ATGTATCGATACATG
429534 TCATTGGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:429600 original size:13 final size:13
Alignment explanation
Indices: 429582--429607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429572 TACACAAAAT
429582 ATGTATCGATACA
1 ATGTATCGATACA
429595 ATGTATCGATACA
1 ATGTATCGATACA
429608 CAAAAAAATT
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:429605 original size:32 final size:34
Alignment explanation
Indices: 429564--429628 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
429554 TAGCCAAACT
*
429564 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
429596 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
429629 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:440467 original size:20 final size:20
Alignment explanation
Indices: 440442--440506 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
440432 TACAAGCCAA
440442 TGTATCGATACATTTTATGG
1 TGTATCGATACATTTTATGG
440462 TGTATCGATACA----A---
1 TGTATCGATACATTTTATGG
440475 TGTATCGATACATTTTATGG
1 TGTATCGATACATTTTATGG
440495 TGTATCGATACA
1 TGTATCGATACA
440507 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
16 1 0.03
17 1 0.03
20 24 0.63
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTTATGG
Found at i:440476 original size:33 final size:33
Alignment explanation
Indices: 440439--440540 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
440429 CGTTACAAGC
440439 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATTTTATGGTGTATCGATA
440472 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATTTTATGGTGTATCGATA
* **
440505 CAATGTATCGATACATATGGT-GTGTATCGATA
1 CAATGTATCGATACATTTTATGGTGTATCGATA
440537 CAAT
1 CAAT
440541 TTTGGCTACT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 15 0.23
33 51 0.77
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATTTTATGGTGTATCGATA
Found at i:440480 original size:13 final size:13
Alignment explanation
Indices: 440462--440519 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
440452 CATTTTATGG
440462 TGTATCGATACAA
1 TGTATCGATACAA
440475 TGTATCGATACATTTTA
1 TGTATCGATACA----A
440492 TGGTGTATCGATACAA
1 ---TGTATCGATACAA
440508 TGTATCGATACA
1 TGTATCGATACA
440520 TATGGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
16 1 0.03
17 1 0.03
20 12 0.32
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:440618 original size:20 final size:21
Alignment explanation
Indices: 440571--440623 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
440561 TCTAATGACC
**
440571 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
440592 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
440612 TGTATCGATACA
1 TGTATCGATACA
440624 ATGCAATCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:440635 original size:20 final size:20
Alignment explanation
Indices: 440612--440662 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
440602 CATTTGGTCA
*
440612 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
440632 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
440652 TGTATCGATAC
1 TGTATCGATAC
440663 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:449202 original size:20 final size:20
Alignment explanation
Indices: 449177--449229 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
449167 GTTGGGCATA
*
449177 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGT-TCC
449197 ATGTATCGATACAATGTTCC
1 ATGTATCGATACAATGTTCC
449217 ATGTATCGATACA
1 ATGTATCGATACA
449230 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTTCC
Found at i:449333 original size:20 final size:20
Alignment explanation
Indices: 449308--449363 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
449298 ATGTATCGAT
449308 ATAATGTATCGATACT-AGG
1 ATAATGTATCGATACTCAGG
* *
449327 CATAATGTAGCGATACATCTGG
1 -ATAATGTATCGATAC-TCAGG
449349 AT-ATGTATCGATACT
1 ATAATGTATCGATACT
449364 TTCTAGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 25 0.81
21 3 0.10
22 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (20 bp):
ATAATGTATCGATACTCAGG
Found at i:449715 original size:48 final size:50
Alignment explanation
Indices: 449632--449728 Score: 162
Period size: 48 Copynumber: 2.0 Consensus size: 50
449622 GATTCTAACA
*
449632 ATCTTGTTAAGGGGGAGCAAAATTTATTGAGGGGGAGTACTAAATTGAAT
1 ATCTTGTTAAGGGGGAGCAAAATTTATTAAGGGGGAGTACTAAATTGAAT
*
449682 ATCTTGTTAAGGGGG-G-AAAATTTATTAATGGGGAGTACTAAATTGAA
1 ATCTTGTTAAGGGGGAGCAAAATTTATTAAGGGGGAGTACTAAATTGAA
449729 AATTTGCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 29 0.64
49 1 0.02
50 15 0.33
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (50 bp):
ATCTTGTTAAGGGGGAGCAAAATTTATTAAGGGGGAGTACTAAATTGAAT
Found at i:456564 original size:20 final size:20
Alignment explanation
Indices: 456539--456618 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
456529 TCAAAAACCC
*
456539 ATAATGTATCGATACAATGA
1 ATAATGTATCGATACAATCA
* *
456559 ATAATGTATTGATACAATTTA
1 ATAATGTATCGATACAA-TCA
* *
456580 AGCAATGTATCGATACATTCA
1 A-TAATGTATCGATACAATCA
* *
456601 CTTATGTATCGATACAAT
1 ATAATGTATCGATACAAT
456619 TTTTTTCCAG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
20 30 0.62
21 5 0.10
22 13 0.27
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
ATAATGTATCGATACAATCA
Found at i:456608 original size:42 final size:42
Alignment explanation
Indices: 456541--456620 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
456531 AAAAACCCAT
* *
456541 AATGTATCGATACAATGAATAATGTATTGATACAATTTAAGC
1 AATGTATCGATACAATCAATAATGTATCGATACAATTTAAGC
* * *
456583 AATGTATCGATACATTCACTTATGTATCGATACAATTT
1 AATGTATCGATACAATCAATAATGTATCGATACAATTT
456621 TTTTCCAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (42 bp):
AATGTATCGATACAATCAATAATGTATCGATACAATTTAAGC
Found at i:456760 original size:20 final size:20
Alignment explanation
Indices: 456735--456772 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
456725 GTTGGGACCT
456735 TGTATCGATACATTTACTTA
1 TGTATCGATACATTTACTTA
456755 TGTATCGATACATTTACT
1 TGTATCGATACATTTACT
456773 ATTTATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTACTTA
Found at i:456778 original size:90 final size:90
Alignment explanation
Indices: 456643--456838 Score: 284
Period size: 90 Copynumber: 2.2 Consensus size: 90
456633 CAGAGTGATT
*** * *
456643 TTGTATCAATACATTTCAGGCATGTATCGATATATTTACTGTTTATATCGATACAAATTGTAAAA
1 TTGTATCAATACATTT-ACTTATGTATCGATACATTTACTATTTATATCGATACAAATTGTAAAA
**
456708 ATTTAAAATTTTTGGTTGTTGGGACC
65 ATTTAAAATTTTTGACTGTTGGGACC
* *
456734 TTGTATCGATACATTTACTTATGTATCGATACATTTACTATTTATATGGATACAAATTGTAAAAA
1 TTGTATCAATACATTTACTTATGTATCGATACATTTACTATTTATATCGATACAAATTGTAAAAA
* *
456799 TTTGAAGTTTTTGACTGTTGGGACC
66 TTTAAAATTTTTGACTGTTGGGACC
456824 TTGTATCAATACATT
1 TTGTATCAATACATT
456839 CAAGAAATGT
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 78 0.84
91 15 0.16
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (90 bp):
TTGTATCAATACATTTACTTATGTATCGATACATTTACTATTTATATCGATACAAATTGTAAAAA
TTTAAAATTTTTGACTGTTGGGACC
Found at i:457395 original size:87 final size:87
Alignment explanation
Indices: 457295--457464 Score: 236
Period size: 87 Copynumber: 2.0 Consensus size: 87
457285 TTTGGTATTT
* * *
457295 TAAGGCTTGACCTCCTT-AAACAGGTGCCAACTAATA-TGGATTTGACTTAAACTTAGGTGCCAC
1 TAAGGCTTGACCT-CTTCAAACAGATGCCAACTAA-AGTGGACTTGACTCAAACTTAGGTGCCAC
* *
457358 CAGCTTTTGTGGGCTTTGACATTC
64 CAGCTTGTGTAGGCTTTGACATTC
* * *
457382 TAAGGCTTGACCTCTTCAGATAGATGCCAACTAAAGTGGACTTGACTCAGACTTAGGTGCCACCA
1 TAAGGCTTGACCTCTTCAAACAGATGCCAACTAAAGTGGACTTGACTCAAACTTAGGTGCCACCA
457447 GCTTGTGTAGGCTTTGAC
66 GCTTGTGTAGGCTTTGAC
457465 TTGGGTGCCG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 4 0.05
87 69 0.95
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (87 bp):
TAAGGCTTGACCTCTTCAAACAGATGCCAACTAAAGTGGACTTGACTCAAACTTAGGTGCCACCA
GCTTGTGTAGGCTTTGACATTC
Found at i:457579 original size:37 final size:35
Alignment explanation
Indices: 457535--457794 Score: 186
Period size: 37 Copynumber: 7.4 Consensus size: 35
457525 CGCCAGCTTG
457535 TGTGGGCTTTGACTCAGACTTAGGTGCCACTAGCTT
1 TGTGGGCTTTGACTCAGACTTAGGTGCCACTAGC-T
* * *
457571 TGGTGGGCTTTAACTCAGACTTAGGTGCCCCCAGCT
1 T-GTGGGCTTTGACTCAGACTTAGGTGCCACTAGCT
* *
457607 TGTGTGCGCTTTGACT----C--AGGTGCCGCCAGCT
1 TGTG-G-GCTTTGACTCAGACTTAGGTGCCACTAGCT
* * * *
457638 TGTACGAGCTTTGACTTAGACGTAGGTGCCACTAACTT
1 TGT--GGGCTTTGACTCAGACTTAGGTGCCACTAGC-T
*
457676 ATGTGGGCTTTGACTC-G----A-GTGCCGCTAGCT
1 -TGTGGGCTTTGACTCAGACTTAGGTGCCACTAGCT
*
457706 TGTGCGAGCTTTGACTCAAACTTAGGTGCCA-TCAGCTT
1 TGTG-G-GCTTTGACTCAGACTTAGGTGCCACT-AGC-T
*
457744 GTGTGGGCTTTGACTCATACTTAGGTGCCACTAGCT
1 -TGTGGGCTTTGACTCAGACTTAGGTGCCACTAGCT
457780 CATGTGGGCTTTGAC
1 --TGTGGGCTTTGAC
457795 ATCCTTAGAT
Statistics
Matches: 181, Mismatches: 17, Indels: 51
0.73 0.07 0.20
Matches are distributed among these distances:
29 4 0.02
30 2 0.01
31 44 0.24
32 1 0.01
33 2 0.01
35 4 0.02
36 8 0.04
37 105 0.58
38 4 0.02
39 7 0.04
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (35 bp):
TGTGGGCTTTGACTCAGACTTAGGTGCCACTAGCT
Found at i:457649 original size:68 final size:69
Alignment explanation
Indices: 457577--457760 Score: 246
Period size: 68 Copynumber: 2.7 Consensus size: 69
457567 GCTTTGGTGG
* * *
457577 GCTTTAACTCAGACTTAGGTGCCCCCAGCTTGTGTGCGCTTTGACTCAG-GTGCCGCCAGCTTGT
1 GCTTTGACTCAGACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTCAGAGTGCCGCCAGCTTGT
457641 ACGA
66 ACGA
* * * * * *
457645 GCTTTGACTTAGACGTAGGTGCCACTAACTTATGTGGGCTTTGACTC-GAGTGCCGCTAGCTTGT
1 GCTTTGACTCAGACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTCAGAGTGCCGCCAGCTTGT
*
457709 GCGA
66 ACGA
* *
457713 GCTTTGACTCAAACTTAGGTGCCATCAGCTTGTGTGGGCTTTGACTCA
1 GCTTTGACTCAGACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTCA
457761 TACTTAGGTG
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
67 1 0.01
68 96 0.99
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (69 bp):
GCTTTGACTCAGACTTAGGTGCCACCAGCTTGTGTGGGCTTTGACTCAGAGTGCCGCCAGCTTGT
ACGA
Found at i:457717 original size:31 final size:32
Alignment explanation
Indices: 457593--457722 Score: 102
Period size: 31 Copynumber: 4.0 Consensus size: 32
457583 ACTCAGACTT
* * * *
457593 AGGTGCCCCCAGCTTGTGTGCGCTTTGACTC-
1 AGGTGCCGCTAGCTTGTGCGAGCTTTGACTCG
* *
457624 AGGTGCCGCCAGCTTGTACGAGCTTTGACTTAGACG
1 AGGTGCCGCTAGCTTGTGCGAGCTTTGAC-T---CG
* * * * *
457660 TAGGTGCCACTAACTTATGTGGGCTTTGACTCG
1 -AGGTGCCGCTAGCTTGTGCGAGCTTTGACTCG
457693 A-GTGCCGCTAGCTTGTGCGAGCTTTGACTC
1 AGGTGCCGCTAGCTTGTGCGAGCTTTGACTC
457723 AAACTTAGGT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
31 49 0.64
32 2 0.03
33 2 0.03
35 1 0.01
36 1 0.01
37 22 0.29
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (32 bp):
AGGTGCCGCTAGCTTGTGCGAGCTTTGACTCG
Found at i:457951 original size:36 final size:36
Alignment explanation
Indices: 457877--457945 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
457867 AAGAGGAAGG
*
457877 AAAAGGAGTGGACATCCTGCTCTTTGAAGACAAAGA
1 AAAAGGAGTGGACATCCTACTCTTTGAAGACAAAGA
* *
457913 AAAAGGAGT-G-CATCTTACTCTTTGAGGACAAAG
1 AAAAGGAGTGGACATCCTACTCTTTGAAGACAAAG
457946 GGAAAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 20 0.67
35 1 0.03
36 9 0.30
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.22
Consensus pattern (36 bp):
AAAAGGAGTGGACATCCTACTCTTTGAAGACAAAGA
Found at i:458131 original size:44 final size:42
Alignment explanation
Indices: 457919--458160 Score: 146
Period size: 44 Copynumber: 5.9 Consensus size: 42
457909 AAGAAAAAGG
* * * * *
457919 AGTGCATCTTACTCTTTGAGGACAAAGGGAAAAGAAGAATGA
1 AGTGCATCCTACTCCTTGAGGACAAAGGAAAAAAAAAAATGA
* * * * * *
457961 AATAG-GTCCTACTCCTCGAGGAGAAAGGAAACAGGAAAAAAGGA
1 AGT-GCATCCTACTCCTTGAGGACAAAGGAAA-A-AAAAAAATGA
* * * *
458005 A-AGCATCC-AGCTCTTTGAGGACAAAGG---GAAAAAGAT--
1 AGTGCATCCTA-CTCCTTGAGGACAAAGGAAAAAAAAAAATGA
* * **
458041 A-TACATCCTACTCCTCGAGGACAAAGG-AAAAAGGAAATGA
1 AGTGCATCCTACTCCTTGAGGACAAAGGAAAAAAAAAAATGA
* *
458081 AGTGCATCTTGCTCCTTGAGGACAAAGGAAAAAATTAAAAATGGA
1 AGTGCATCCTACTCCTTGAGGACAAAGGAAAAAA--AAAAAT-GA
*
458126 A-TGCATCCTACTCCTTGAGGACAAAGGGAAAAAAA
1 AGTGCATCCTACTCCTTGAGGACAAAGGAAAAAAAA
458161 GTGTGCCCTA
Statistics
Matches: 148, Mismatches: 37, Indels: 30
0.69 0.17 0.14
Matches are distributed among these distances:
36 21 0.14
37 1 0.01
38 10 0.07
40 1 0.01
41 22 0.15
42 31 0.21
43 19 0.13
44 40 0.27
45 3 0.02
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (42 bp):
AGTGCATCCTACTCCTTGAGGACAAAGGAAAAAAAAAAATGA
Found at i:464940 original size:20 final size:20
Alignment explanation
Indices: 464915--464952 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
464905 TGAGCCTTAA
*
464915 TATCGATACATTCACTTAGG
1 TATCGATACATTAACTTAGG
*
464935 TATCGATATATTAACTTA
1 TATCGATACATTAACTTA
464953 TTATATTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
TATCGATACATTAACTTAGG
Found at i:466187 original size:52 final size:51
Alignment explanation
Indices: 466123--466259 Score: 150
Period size: 50 Copynumber: 2.7 Consensus size: 51
466113 AGAGTTTGAT
* * * * * *
466123 CCAAATGCATCGATACATTTTTTATTGTATCGATATTTTTTGGGTTTTTAAC
1 CCAAATGTATCGATACATTATTTATTGTATCGATATATTCT-AGATTTTAAC
* * *
466175 CCAAATGTATCGATACATTATATATTGTAT-AATATATTCTAGATTTTGAC
1 CCAAATGTATCGATACATTATTTATTGTATCGATATATTCTAGATTTTAAC
* * *
466225 CCAAATGTATCGATACATTCTTCAATGTATCGATA
1 CCAAATGTATCGATACATTATTTATTGTATCGATA
466260 CATCCAGTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
50 33 0.47
51 10 0.14
52 27 0.39
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (51 bp):
CCAAATGTATCGATACATTATTTATTGTATCGATATATTCTAGATTTTAAC
Found at i:466241 original size:50 final size:52
Alignment explanation
Indices: 466117--466243 Score: 150
Period size: 52 Copynumber: 2.5 Consensus size: 52
466107 GATATAAGAG
* * * * * * * * *
466117 TTTGATCCAAATGCATCGATACATTTTTTATTGTATCGATATTTTTTGGGTT
1 TTTGACCCAAATGTATCGATACATTATATATTGTATCAATATATTCTGAGAT
*
466169 TTTAACCCAAATGTATCGATACATTATATATTGTAT-AATATATTCT-AGAT
1 TTTGACCCAAATGTATCGATACATTATATATTGTATCAATATATTCTGAGAT
466219 TTTGACCCAAATGTATCGATACATT
1 TTTGACCCAAATGTATCGATACATT
466244 CTTCAATGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 26 0.41
51 7 0.11
52 31 0.48
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (52 bp):
TTTGACCCAAATGTATCGATACATTATATATTGTATCAATATATTCTGAGAT
Found at i:470025 original size:79 final size:79
Alignment explanation
Indices: 469942--470099 Score: 246
Period size: 79 Copynumber: 2.0 Consensus size: 79
469932 ATTCATGTTT
* *
469942 TTATTTCCGAGGGGATACTCCAACCTCGGTTTTAT-TCCCAAAACACCAATTTTTCATAATCGGT
1 TTATTTCCGAGGGGATACTCCAACCTCGGTTTTATAT-CCAAAACACCAATTTTTCACAATCGGG
470006 GATACTCCAACCCTG
65 GATACTCCAACCCTG
* * *
470021 TTATTTCTGAGGGGATACTCCTACCTTGGTTTTATATCCAAAACACCAATTTTTCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAACCTCGGTTTTATATCCAAAACACCAATTTTTCACAATCGGGG
*
470086 ATACTCCAATCCTG
66 ATACTCCAACCCTG
470100 GTTTTATTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
79 71 0.99
80 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (79 bp):
TTATTTCCGAGGGGATACTCCAACCTCGGTTTTATATCCAAAACACCAATTTTTCACAATCGGGG
ATACTCCAACCCTG
Found at i:470091 original size:51 final size:51
Alignment explanation
Indices: 470031--470148 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
470021 TTATTTCTGA
* *
470031 GGGGATACTCCTA-CCTTGGTTTTATATCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAATCC-TGGTTTTATATCCAAAACACCAATTTTCCACAATC
* * *
470082 GGGGATACTCCAATCCTGGTTTTATTTCCACAACACCAATTTTCCATAATC
1 GGGGATACTCCAATCCTGGTTTTATATCCAAAACACCAATTTTCCACAATC
470133 GGGGATACTCCAATCC
1 GGGGATACTCCAATCC
470149 CGATATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 59 0.97
52 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAATCCTGGTTTTATATCCAAAACACCAATTTTCCACAATC
Found at i:470167 original size:28 final size:28
Alignment explanation
Indices: 470134--470203 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
470124 TCCATAATCG
*
470134 GGGATACTCCAATCCCGA-TATTTTTGAA
1 GGGATACTCCAA-CCCGATTATTTTCGAA
* *
470162 TGGATACTCCAACCCTATTATTTTCGAA
1 GGGATACTCCAACCCGATTATTTTCGAA
470190 GGGATACTCCAACC
1 GGGATACTCCAACC
470204 TCAGTGTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (28 bp):
GGGATACTCCAACCCGATTATTTTCGAA
Found at i:470279 original size:28 final size:28
Alignment explanation
Indices: 470239--470312 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
470229 TTTCATAATC
470239 GGGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
*
470267 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
470295 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
470313 ATTTTATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:470390 original size:107 final size:107
Alignment explanation
Indices: 470082--470393 Score: 360
Period size: 106 Copynumber: 2.9 Consensus size: 107
470072 TTTCACAATC
* * * * * *
470082 GGGGATACTCCAATCCTGGTTTTATTTCCACAACACCAATTTTCCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAAC
* ** **
470147 CCCGATATTTTTGAATGGATACTCCAACCCTATTATTTTCGA
66 CCCGTTATTTTTGAGGGGATACTCCAACCCCGTTATTTTCGA
* * * * *
470189 AGGGATACTCCAACCTC-AGTGTTATTTCCAAATAC-T-GATTTTTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGA-TTTTATTTCCAAA-ACATCAATTTTCCATAATCGGGGATACTCCA
* *
470251 ACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTTATTTTTGA
64 ACCCCGTTATTTTTGAGGGGATACTCCAACCCCGTTATTTTCGA
** ** *
470295 GGGGATACTCCAACCCCGATTTTATTTTTAAAACATCAATTTTCCACCATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAAC
* *
470360 CCCGTTATTTTTGAGGGGGTACTCCGACCCCGTT
66 CCCGTTATTTTTGAGGGGATACTCCAACCCCGTT
470394 TTTATCTCTA
Statistics
Matches: 169, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
105 2 0.01
106 86 0.51
107 79 0.47
108 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAAC
CCCGTTATTTTTGAGGGGATACTCCAACCCCGTTATTTTCGA
Found at i:472427 original size:4 final size:4
Alignment explanation
Indices: 472418--472456 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
472408 TTTTGAGGTG
*
472418 TTTA TTTA TTTA TTTA TTCT- TTCA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTT
472457 TGTTTTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 30 0.97
5 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:478791 original size:17 final size:17
Alignment explanation
Indices: 478769--478804 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
478759 GGACTAAAAA
*
478769 TGGTGCCTTTTAGGATT
1 TGGTGCCCTTTAGGATT
478786 TGGTGCCCTTTAGGATT
1 TGGTGCCCTTTAGGATT
478803 TG
1 TG
478805 TTCCGAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.14, G:0.31, T:0.44
Consensus pattern (17 bp):
TGGTGCCCTTTAGGATT
Found at i:482567 original size:1 final size:1
Alignment explanation
Indices: 482563--482633 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
482553 CCTTTTTCTC
* * * * * * * *
482563 AAAAAACAAAACAAAACAAAAAAAACAATAAAAAAGAAAAAAAGAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
482628 AGAAAA
1 AAAAAA
482634 GAACCTACTT
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.01
Consensus pattern (1 bp):
A
Found at i:482580 original size:10 final size:9
Alignment explanation
Indices: 482563--482625 Score: 72
Period size: 10 Copynumber: 6.7 Consensus size: 9
482553 CCTTTTTCTC
482563 AAAAAACAA
1 AAAAAACAA
482572 AACAAAACAA
1 AA-AAAACAA
482582 AAAAAACAA
1 AAAAAACAA
*
482591 TAAAAAAGAA
1 -AAAAAACAA
*
482601 AAAAAGAAAA
1 AAAAA-ACAA
*
482611 AAAAAAGAA
1 AAAAAACAA
482620 AAAAAA
1 AAAAAA
482626 AAAGAAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
9 23 0.48
10 25 0.52
ACGTcount: A:0.87, C:0.06, G:0.05, T:0.02
Consensus pattern (9 bp):
AAAAAACAA
Found at i:482587 original size:19 final size:18
Alignment explanation
Indices: 482563--482636 Score: 87
Period size: 19 Copynumber: 4.0 Consensus size: 18
482553 CCTTTTTCTC
*
482563 AAAAAACAAAACAAAACAA
1 AAAAAACAAAA-AAAAGAA
482582 AAAAAACAATAAAAAAGAA
1 AAAAAACAA-AAAAAAGAA
*
482601 AAAAAGAAAAAAAAAAGAA
1 AAAAA-ACAAAAAAAAGAA
*
482620 AAAAAA-AAAGAAAAGAA
1 AAAAAACAAAAAAAAGAA
482637 CCTACTTAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
17 10 0.20
18 1 0.02
19 34 0.68
20 5 0.10
ACGTcount: A:0.86, C:0.05, G:0.07, T:0.01
Consensus pattern (18 bp):
AAAAAACAAAAAAAAGAA
Found at i:484028 original size:62 final size:62
Alignment explanation
Indices: 483572--484040 Score: 576
Period size: 62 Copynumber: 7.6 Consensus size: 62
483562 AACCTTTTAT
* *
483572 CCTTTCAGTCCTCAAAGAGCAGGAC-AC--TTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-
1 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
483631 TCTTCTAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-
1 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
483692 CTTTTCAGTCCACAAAGAGCAGGACACCTTTTCCTTTTCAAATCCCACATAAGTTGGTGGCAC
1 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
483755 CCTTCAGTCCTCAAAAAGCAGGAC-ACTTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCAC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTCAAAGCCCACACAAGTTGGTGGCAC
** * * **
483817 CCTTTAGTCCTCAAAGAGCAGGACATCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGTGC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* **
483879 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCAC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
483941 CCTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAA-TTGGTGGCAC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACAC-AAGTTGGTGGCAC
** * *
484003 ATTTTAGTCCTCAAAGAGCAGGATGCCTTTTTGTTTTC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTC
484041 TTCTTTGTCC
Statistics
Matches: 359, Mismatches: 41, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
59 21 0.06
60 3 0.01
61 59 0.16
62 266 0.74
63 10 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (62 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:486872 original size:79 final size:79
Alignment explanation
Indices: 486768--487004 Score: 332
Period size: 79 Copynumber: 3.0 Consensus size: 79
486758 ATTCATGTTT
* * * * *
486768 TTATTTTCGAGGGAATACTCTAACCCCGGTTTTATTCCCAAAACACTAGTTTTTCACAATTGGGA
1 TTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCACAATTGGGA
486833 ATACTCCAACCTCG
66 ATACTCCAACCTCG
* * * * * * * *
486847 TTATTTTTGAGGGGATATTTCAACCCCGATTTTATTTCTTAAACACTAATTTTTCATAATCGAGA
1 TTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCACAATTGGGA
486912 ATACTCCAACC-CTG
66 ATACTCCAACCTC-G
*
486926 TTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACTAATTTTTCACAATTGGGA
1 TTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCACAATTGGGA
486991 ATACTCCAACCTCG
66 ATACTCCAACCTCG
487005 GTTTTATTTT
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
78 1 0.01
79 132 0.99
80 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
TTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCACAATTGGGA
ATACTCCAACCTCG
Found at i:487053 original size:51 final size:51
Alignment explanation
Indices: 486936--487054 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
486926 TTATTTTCGA
* * * *
486936 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACACTAATTTTTCACAATT
1 GGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCACAATT
* * *
486987 GGGAATACTCCAACCTCGGTTTTATTTTCACAACACCAATTTTCCGCAATT
1 GGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCACAATT
487038 GGGGATACTCCAACCTC
1 GGGGATACTCCAACCTC
487055 ATTATTTTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCACAATT
Found at i:487070 original size:28 final size:28
Alignment explanation
Indices: 487038--487109 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
487028 TTCCGCAATT
* *
487038 GGGGATACTCCAACCTCATTATTTTTGA
1 GGGGATACTCCAACCCCATTATTTTCGA
487066 GGGGATACTCCAACCCCATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
**
487094 AAGGATACTCCAACCC
1 GGGGATACTCCAACCC
487110 TGGTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:487136 original size:107 final size:107
Alignment explanation
Indices: 486991--487189 Score: 258
Period size: 107 Copynumber: 1.9 Consensus size: 107
486981 ACAATTGGGA
* * * ** *
486991 ATACTCCAACCTCGGTTTTATTTTCACAACACCAATTTTCCGCAATTGGGGATACTCCAACCTCA
1 ATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCACAATCGAAGATACTCCAACCCCA
*
487056 TTATTTTTGAGGGGATACTCCAACCCCATTATTTTCGAAAGG
66 TTATTTTAGAGGGGATACTCCAACCCCATTATTTTCGAAAGG
* * *
487098 ATACTCCAACC-CTGGTTTTA-TTTCTAAAATACTAATTTTTCACAATCGAAGATACTCCAACCC
1 ATACTCCAACCTC-GGTTTTATTTTC-AAAACACCAATTTTCCACAATCGAAGATACTCCAACCC
* *
487161 CGTTATTTTAGAGGGGATACTCCAGCCCC
64 CATTATTTTAGAGGGGATACTCCAACCCC
487190 GATTTTATTT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 5 0.06
107 73 0.94
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (107 bp):
ATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCACAATCGAAGATACTCCAACCCCA
TTATTTTAGAGGGGATACTCCAACCCCATTATTTTCGAAAGG
Found at i:487152 original size:79 final size:79
Alignment explanation
Indices: 487069--487248 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 79
487059 TTTTTGAGGG
* * * *
487069 GATACTCCAACCCCATTATTTTCGAAAGGATACTCCAACCCTGGTTTTATTTCTAAAATACTAAT
1 GATACTCCAACCCCGTTATTTTAGAAAGGATACTCCAACCCCGATTTTATTTCTAAAATACTAAT
*
487134 TTTTCACAATCGAA
66 TTTCCACAATCGAA
** * * *
487148 GATACTCCAACCCCGTTATTTTAGAGGGGATACTCCAGCCCCGATTTTATTTCTAAAATATTGAT
1 GATACTCCAACCCCGTTATTTTAGAAAGGATACTCCAACCCCGATTTTATTTCTAAAATACTAAT
* * **
487213 TTTCCACCATTGGG
66 TTTCCACAATCGAA
*
487227 GATACTCAAACCCCGTTATTTT
1 GATACTCCAACCCCGTTATTTT
487249 TGAAGGGGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 86 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCCGTTATTTTAGAAAGGATACTCCAACCCCGATTTTATTTCTAAAATACTAAT
TTTCCACAATCGAA
Found at i:487275 original size:79 final size:79
Alignment explanation
Indices: 487066--487295 Score: 210
Period size: 79 Copynumber: 2.9 Consensus size: 79
487056 TTATTTTTGA
* * * * * * * *
487066 GGGGATACTCCAACCCCATTATTTTCGAAAGGATACTCCAACCCTGGTTTTATTTCTAAAATACT
1 GGGGATACTCCAACCCCGTTATTTTAGAAGGGGTATTCTAACCCTGATTTTATTTCTAAAATATT
*
487131 AATTTTTCACAATC
66 AATTTTCCACAATC
** * * * *
487145 GAAGATACTCCAACCCCGTTATTTTAG-AGGGGATACTCCAGCCCCGATTTTATTTCTAAAATAT
1 GGGGATACTCCAACCCCGTTATTTTAGAAGGGG-TATTCTAACCCTGATTTTATTTCTAAAATAT
* * *
487209 TGATTTTCCACCATT
65 TAATTTTCCACAATC
* * * * * * *
487224 GGGGATACTCAAACCCCGTTATTTTTGAAGGGGTATTCTGACCTTGTTTTTATCTCCAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTAGAAGGGGTATTCTAACCCTGATTTTATTTCTAAAATATT
487289 AAATTTT
66 -AATTTT
487296 TCATCAGGAG
Statistics
Matches: 120, Mismatches: 28, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
78 3 0.03
79 107 0.89
80 10 0.08
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTTAGAAGGGGTATTCTAACCCTGATTTTATTTCTAAAATATT
AATTTTCCACAATC
Found at i:491340 original size:37 final size:37
Alignment explanation
Indices: 491274--491345 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
491264 GTTTAACTGA
*
491274 GACTAGGTTGCCACTAGCTTAGGTAGGCTTTGACTCG
1 GACTAGGTTGCCACGAGCTTAGGTAGGCTTTGACTCG
* *
491311 GACTAGGTTGCCACCGA-CTTATGTGGGCTTTGACT
1 GACTAGGTTGCCA-CGAGCTTAGGTAGGCTTTGACT
491346 TAAGTGCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 29 0.94
38 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (37 bp):
GACTAGGTTGCCACGAGCTTAGGTAGGCTTTGACTCG
Found at i:491543 original size:29 final size:29
Alignment explanation
Indices: 491504--491577 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
491494 TAGGAGAGGA
*
491504 TGCCATTAACTTGTGGACTTTTGAAAGGG
1 TGCCACTAACTTGTGGACTTTTGAAAGGG
* *
491533 TGTCACTAACTTATGGACTTTTGAAAGGG
1 TGCCACTAACTTGTGGACTTTTGAAAGGG
491562 TGCCACTAACTTGTGG
1 TGCCACTAACTTGTGG
491578 GCTTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (29 bp):
TGCCACTAACTTGTGGACTTTTGAAAGGG
Found at i:491719 original size:31 final size:30
Alignment explanation
Indices: 491650--491832 Score: 147
Period size: 31 Copynumber: 5.8 Consensus size: 30
491640 GGATAGGTTT
* * * *
491650 GGTGCTACCGACTTGTGTGGGCTTTGAA-TGG
1 GGTGCCACCAACTTGTGTGGACTTT-AACT-A
* *
491681 GGTGCCACCAACTTTTGTAGACTTTAACTA
1 GGTGCCACCAACTTGTGTGGACTTTAACTA
** *
491711 TGGTGCCACCAACTCATGTGGACTTTGAA-AA
1 -GGTGCCACCAACTTGTGTGGACTTT-AACTA
*
491742 GGTTGCCACCAACTTGTGTGGACTTTGACTGA
1 GG-TGCCACCAACTTGTGTGGACTTTAACT-A
*
491774 GGTGCCACCAACTTGTGTGGACTTTGAA-AA
1 GGTGCCACCAACTTGTGTGGACTTT-AACTA
491804 GGATTATGCCACCAACTTGTGTGGACTTT
1 GG----TGCCACCAACTTGTGTGGACTTT
491833 GAAAAAAGTT
Statistics
Matches: 125, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
30 8 0.06
31 88 0.70
32 6 0.05
34 23 0.18
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (30 bp):
GGTGCCACCAACTTGTGTGGACTTTAACTA
Found at i:491749 original size:62 final size:62
Alignment explanation
Indices: 491665--491832 Score: 212
Period size: 62 Copynumber: 2.7 Consensus size: 62
491655 TACCGACTTG
* ** * * *
491665 TGTGGGCTTTGAATGGGGTGCCACCAACTTTTGTAGACTTTAACT-ATGGTGCCACCAACTCA
1 TGTGGACTTTGAAAAGGTTGCCACCAACTTGTGTGGACTTTAACTGA-GGTGCCACCAACTCA
* **
491727 TGTGGACTTTGAAAAGGTTGCCACCAACTTGTGTGGACTTTGACTGAGGTGCCACCAACTTG
1 TGTGGACTTTGAAAAGGTTGCCACCAACTTGTGTGGACTTTAACTGAGGTGCCACCAACTCA
491789 TGTGGACTTTGAAAAGGATTATGCCACCAACTTGTGTGGACTTT
1 TGTGGACTTTGAAAAGG--T-TGCCACCAACTTGTGTGGACTTT
491833 GAAAAAAGTT
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
62 68 0.73
63 1 0.01
64 1 0.01
65 23 0.25
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (62 bp):
TGTGGACTTTGAAAAGGTTGCCACCAACTTGTGTGGACTTTAACTGAGGTGCCACCAACTCA
Found at i:491919 original size:74 final size:72
Alignment explanation
Indices: 491714--491953 Score: 236
Period size: 74 Copynumber: 3.5 Consensus size: 72
491704 TTAACTATGG
**
491714 TGCCACCAACTCATGTGGACTTTG-AAAAGG--T-TGCCACCAACTTGTGTGGACTTTG-----A
1 TGCCACCAACTTGTGTGGACTTTGAAAAAGGATTATGCCACCAACTTGTGTGGACTTTGAAAAAA
* **
491770 CTGAGG-
66 GTTTGGT
491776 TGCCACCAACTTGTGTGGACTTTG-AAAAGGATTATGCCACCAACTTGTGTGGACTTTGAAAAAA
1 TGCCACCAACTTGTGTGGACTTTGAAAAAGGATTATGCCACCAACTTGTGTGGACTTTGAAAAAA
491840 GTTTGGT
66 GTTTGGT
* * * * * **
491847 TGCCATCAACTCGTGTGGAGTTTGAAAAAGGTTTGGTTGCCACGGACTTGTGTGGACTTT-AAAA
1 TGCCACCAACTTGTGTGGACTTTGAAAAAGGATT--ATGCCACCAACTTGTGTGGACTTTGAAAA
*
491911 ATGATTTGGT
64 AAG-TTTGGT
*
491921 TGCCACCAACTTGTGTGGACTTT-AAAAATGATT
1 TGCCACCAACTTGTGTGGACTTTGAAAAAGGATT
491954 TAGTTTGTGT
Statistics
Matches: 147, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
62 28 0.19
64 1 0.01
65 24 0.16
70 4 0.03
71 21 0.14
72 8 0.05
73 14 0.10
74 47 0.32
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (72 bp):
TGCCACCAACTTGTGTGGACTTTGAAAAAGGATTATGCCACCAACTTGTGTGGACTTTGAAAAAA
GTTTGGT
Found at i:491949 original size:37 final size:37
Alignment explanation
Indices: 491742--491954 Score: 223
Period size: 37 Copynumber: 6.0 Consensus size: 37
491732 ACTTTGAAAA
* *
491742 GGTTGCCACCAACTTGTGTGGACTTT--GACTGA---
1 GGTTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
* *
491774 GG-TGCCACCAACTTGTGTGGACTTTGAAAAGGA-TT
1 GGTTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
* *
491809 --ATGCCACCAACTTGTGTGGACTTTGAAAAAAG-TTT
1 GGTTGCCACCAACTTGTGTGGACTTT-AAAAATGATTT
* * * *
491844 GGTTGCCATCAACTCGTGTGGAGTTTGAAAAA-GGTTT
1 GGTTGCCACCAACTTGTGTGGACTTT-AAAAATGATTT
**
491881 GGTTGCCACGGACTTGTGTGGACTTTAAAAATGATTT
1 GGTTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
491918 GGTTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
1 GGTTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
491955 AGTTTGTGTA
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
31 23 0.15
32 2 0.01
33 3 0.02
34 23 0.15
35 7 0.05
36 6 0.04
37 89 0.58
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (37 bp):
GGTTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
Found at i:492081 original size:200 final size:200
Alignment explanation
Indices: 491859--492235 Score: 574
Period size: 200 Copynumber: 1.9 Consensus size: 200
491849 CCATCAACTC
** *
491859 GTGTGGAGTTTGAAAAAGGTTTGGTTGCCACGGACTTGTGTGGACTTTAAAAATGATTTGGTTGC
1 GTGTGGACCTTGAAAAAGGTTTGGTTGCCACGAACTTGTGTGGACTTTAAAAATGATTTGGTTGC
* * * * *
491924 CACCAACTTGTGTGGACTTTAAAAATGATTTAGTTTGTGTATACTTTAAGTGTGGCCAACTTATG
66 CACCAACTTGGGTGGACTTTAAAAATGATTTAGTTTATGTAGACTTTAAGTGTCGCCAACTCATG
* * * *
491989 CAAGCTTTAAAAGGATTTGTGTTAACAAGAATTTCTTGGCAAATGCCGCTTGACAGTGGTAGGTA
131 CAAGCTTAAAAAAGATTTGTGTTAACAAAAATTTCTTGACAAATGCCGCTTGACAGTGGTAGGTA
492054 CTACT
196 CTACT
*
492059 GTGTGGACCTTGAAAAAGGTTTGGTTGCCACTAACTTGTGTGGACTTTAAAAATGATTTGGTTGC
1 GTGTGGACCTTGAAAAAGGTTTGGTTGCCACGAACTTGTGTGGACTTTAAAAATGATTTGGTTGC
** * *
492124 CACTGACTTGGGTGGACTTTAAAAATGATTTAGTTTATGTAGACTTTAAGTGTCGTCAGCTCATG
66 CACCAACTTGGGTGGACTTTAAAAATGATTTAGTTTATGTAGACTTTAAGTGTCGCCAACTCATG
* * *
492189 CAGGCTTAAAAAATATTTGTGTTGACAAAAATTTCTTGACAAATGCC
131 CAAGCTTAAAAAAGATTTGTGTTAACAAAAATTTCTTGACAAATGCC
492236 TCATGACAAT
Statistics
Matches: 157, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
200 157 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (200 bp):
GTGTGGACCTTGAAAAAGGTTTGGTTGCCACGAACTTGTGTGGACTTTAAAAATGATTTGGTTGC
CACCAACTTGGGTGGACTTTAAAAATGATTTAGTTTATGTAGACTTTAAGTGTCGCCAACTCATG
CAAGCTTAAAAAAGATTTGTGTTAACAAAAATTTCTTGACAAATGCCGCTTGACAGTGGTAGGTA
CTACT
Found at i:492119 original size:37 final size:37
Alignment explanation
Indices: 492058--492154 Score: 142
Period size: 37 Copynumber: 2.6 Consensus size: 37
492048 TAGGTACTAC
* *
492058 TGTGTGGACCTTGAAAAA-GGTTTGGTTGCCACTAACT
1 TGTGTGGA-CTTTAAAAATGATTTGGTTGCCACTAACT
*
492095 TGTGTGGACTTTAAAAATGATTTGGTTGCCACTGACT
1 TGTGTGGACTTTAAAAATGATTTGGTTGCCACTAACT
*
492132 TGGGTGGACTTTAAAAATGATTT
1 TGTGTGGACTTTAAAAATGATTT
492155 AGTTTATGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 8 0.15
37 47 0.85
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (37 bp):
TGTGTGGACTTTAAAAATGATTTGGTTGCCACTAACT
Found at i:497404 original size:61 final size:61
Alignment explanation
Indices: 497319--497442 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
497309 ATGAGAAGGG
*
497319 TGATAAAGGTGCCAATATGCTGATTCACGGCCAGCGATATTAGGCTTAAAGATGAGAAAAA
1 TGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGAGAAAAA
* * * *
497380 TGATAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAAAGATGCGAAGAA
1 TGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGAGAAAAA
497441 TG
1 TG
497443 TCAATACGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (61 bp):
TGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAGATGAGAAAAA
Found at i:497522 original size:52 final size:52
Alignment explanation
Indices: 497389--497641 Score: 226
Period size: 52 Copynumber: 4.9 Consensus size: 52
497379 ATGATAAAGG
* * * * *
497389 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAAAGATGCGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
* * * * * * *
497441 TGTCAATACGTTGATTTATGGCTAGCGACATTAGACTTGAAGATGAGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
* * * * * *
497493 TGCCAATATGTTGATTCAAGGCCAACGACATTTGGCTT-GAGA-AAGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
* * * *
497543 GGTGCCAATGTGCTGATTTAAGGCCAGCGACATTAGACTTAAAGATGATAA-AGG
1 --TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGA-A
* * *
497597 TGCCAATATGCTGATTCAAGG-CAGTGACATTGGTCTTAAAGATGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGA
497642 AGGTGCTAAT
Statistics
Matches: 159, Mismatches: 37, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
50 7 0.04
51 24 0.15
52 121 0.76
53 4 0.03
54 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
Found at i:497662 original size:48 final size:48
Alignment explanation
Indices: 497385--497841 Score: 218
Period size: 52 Copynumber: 9.5 Consensus size: 48
497375 AAAAATGATA
* * * *
497385 AAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAAAGATGCG
1 AAGGTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTTAAAGAT--G
* * * * * * *
497436 AAGAATGTCAATACGTTGATTTATGGCTAGCGACATTAGACTTGAAGATGAG
1 AAG-GTGCCAATATGCTGATTCAAGGC-AGCGACATTAGACTTAAAGAT--G
* * * * * *
497488 AAGAATGCCAATATGTTGATTCAAGGCCAACGACATTTGGCTTGAGAAAGAAG
1 AAG-GTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTT---AAAGATG
* *
497541 AAGGTGCCAATGTGCTGATTTAAGGCCAGCGACATTAGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTTAAAGATG
* * *
497590 ATAAAGGTGCCAATATGCTGATTCAAGGCAGTGACATTGGTCTTAAAGATG
1 ---AAGGTGCCAATATGCTGATTCAAGGCAGCGACATTAGACTTAAAGATG
* * * * * **
497641 AAGGTGCTAATATGTTAATTCAAGGCCAACGATATT-GGGTT-----T-
1 AAGGTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTTAAAGATG
* * * * * *
497683 ---GTGCCAA-GTGTTGATTCAAGGCCAGCGACCTTGGTCTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTTAAAGATG
* *
497728 AAGGTGCCAATATGTTGATTCAAGGCCAGCGACATTAGGC-T-----T-
1 AAGGTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTTAAAGATG
* * *
497770 -A--TGCCAATATGCTGATTCAAGGCCAACGACATTGGCCTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGG-CAGCGACATTAGACTTAAAGATG
*
497816 AAGGTGCCAATATGTTGATTCAAGGC
1 AAGGTGCCAATATGCTGATTCAAGGC
497842 CAGCAATATT
Statistics
Matches: 316, Mismatches: 59, Indels: 65
0.72 0.13 0.15
Matches are distributed among these distances:
38 20 0.06
39 41 0.13
40 1 0.00
41 1 0.00
43 2 0.01
44 1 0.00
45 1 0.00
47 1 0.00
48 34 0.11
49 58 0.18
51 24 0.08
52 123 0.39
53 5 0.02
55 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (48 bp):
AAGGTGCCAATATGCTGATTCAAGGCAGCGACATTAGACTTAAAGATG
Found at i:497754 original size:49 final size:47
Alignment explanation
Indices: 497683--497845 Score: 175
Period size: 49 Copynumber: 3.6 Consensus size: 47
497673 TATTGGGTTT
* *
497683 GTGCCAA-GTGTTGATTCAAGGCCAGCGACCTTGGTCTTAAAGATAAAG
1 GTGCCAATATGTTGATTCAAGGCCAGCGACATTGG-CTTAAAGAT-AAG
497731 GTGCCAATATGTTGATTCAAGGCCAGCGACATTAGGC-T-----T-A-
1 GTGCCAATATGTTGATTCAAGGCCAGCGACATT-GGCTTAAAGATAAG
* *
497771 -TGCCAATATGCTGATTCAAGGCCAACGACATTGGCCTTAAAGATGAAG
1 GTGCCAATATGTTGATTCAAGGCCAGCGACATTGG-CTTAAAGAT-AAG
497819 GTGCCAATATGTTGATTCAAGGCCAGC
1 GTGCCAATATGTTGATTCAAGGCCAGC
497846 AATATTGGGC
Statistics
Matches: 96, Mismatches: 6, Indels: 25
0.76 0.05 0.20
Matches are distributed among these distances:
38 2 0.02
39 31 0.32
40 1 0.01
41 1 0.01
43 1 0.01
45 1 0.01
47 1 0.01
48 8 0.08
49 48 0.50
50 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (47 bp):
GTGCCAATATGTTGATTCAAGGCCAGCGACATTGGCTTAAAGATAAG
Found at i:497821 original size:88 final size:88
Alignment explanation
Indices: 497596--498118 Score: 604
Period size: 88 Copynumber: 6.0 Consensus size: 88
497586 GATGATAAAG
* * * * *
497596 GTGCCAATATGCTGATTCAAGG-CAGTGACATTGGTCTTAAAGATGAAGGTGCTAATATGTTAAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
*
497660 TCAAGGCCAACGATATTGGGTTT
66 TCAAGGCCAACGATATTGGGCTT
* * * *
497683 GTGCCAA-GTGTTGATTCAAGGCCAGCGACCTTGGTCTTAAAGATAAAGGTGCCAATATGTTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
* * *
497747 TCAAGGCCAGCGACATTAGGCTT
66 TCAAGGCCAACGATATTGGGCTT
* * * * *
497770 ATGCCAATATGCTGATTCAAGGCCAACGACATTGGCCTTAAAGATGAAGGTGCCAATATGTTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
* *
497835 TCAAGGCCAGCAATATTGGGCTT
66 TCAAGGCCAACGATATTGGGCTT
* * * * * *
497858 GTGCTAATGTGTTGATTCAAAGCCAACAACATTGGTCTTAAAGATGAAGGTGCC-A-ATGCTAAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
* * * *
497921 TCAACGCTAGCAATATTGGGCTT
66 TCAAGGCCAACGATATTGGGCTT
* * *
497944 GTGCCAATGTGATTATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAGTGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
* *
498009 TCAAGGCCAACGATTTTAGGCTT
66 TCAAGGCCAACGATATTGGGCTT
* * * * * * *
498032 GTGCCAATTTGCTGATTCAAGACTAGCGACATTAGACTTAAAGATGAAAAGAATGCCAATGTGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG--AAG-GTGCCAATATGCT
*
498097 GATTCAAGGCCAACGACATTGG
63 GATTCAAGGCCAACGATATTGG
498119 ACTTAAAGGT
Statistics
Matches: 370, Mismatches: 59, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
86 86 0.23
87 71 0.19
88 181 0.49
90 2 0.01
91 30 0.08
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (88 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
TCAAGGCCAACGATATTGGGCTT
Done.