Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008100.1 Hibiscus syriacus cultivar Beakdansim tig00110630_pilon, whole genome shotgun sequence
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: 1372717
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 7
Found at i:399285 original size:3 final size:3
Alignment explanation
Indices: 399265--399354 Score: 96
Period size: 3 Copynumber: 30.7 Consensus size: 3
399255 TTTTTCATTT
*
399265 TTA TT- TTA TT- TATA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
399309 TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA ATA TTA ATA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
399355 TAATATTACA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 5 0.07
3 66 0.92
4 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:399842 original size:15 final size:15
Alignment explanation
Indices: 399822--399863 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
399812 ACAACTCAGC
399822 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
399837 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
399852 AAAGAAGAGAAA
1 AAAGAAAAGAAA
399864 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:399847 original size:20 final size:20
Alignment explanation
Indices: 399822--399863 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
399812 ACAACTCAGC
*
399822 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
399842 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
399862 AA
1 AA
399864 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:402208 original size:30 final size:30
Alignment explanation
Indices: 402172--402243 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
402162 CCCGCAGGAC
*
402172 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
402202 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
402232 CTGTCCATAGGT
1 CTATCCAGAGGT
402244 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:402268 original size:31 final size:30
Alignment explanation
Indices: 402230--402354 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 30
402220 GATCCTCGGC
* *
402230 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
**
402260 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTCCGAAGAACATAGGT
402291 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
402322 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
402354 A
1 A
402355 CCCTCGACTC
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
30 5 0.06
31 49 0.61
32 23 0.29
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:403129 original size:20 final size:21
Alignment explanation
Indices: 403104--403146 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
403094 ATTTTATTCG
* *
403104 CTTGAA-GGGTATCGGTTCCC
1 CTTGAATGGGTACCGATTCCC
403124 CTTGAATGGGTACCGATTCCC
1 CTTGAATGGGTACCGATTCCC
403145 CT
1 CT
403147 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.16, C:0.28, G:0.26, T:0.30
Consensus pattern (21 bp):
CTTGAATGGGTACCGATTCCC
Found at i:409524 original size:235 final size:229
Alignment explanation
Indices: 409108--409571 Score: 833
Period size: 235 Copynumber: 2.0 Consensus size: 229
409098 ATAAACAAGA
*
409108 TGTGGGCATGCTTATAGCATCTCATGACATAATGACATCCATTTAGACATCCAATATTGCTTAAA
1 TGTGGGCATGCTTATAGCATCTCATGACATAATGACATACATTTAGACATCCAATATTGCTTAAA
409173 CATTAAAAATGCATGTTTTAACAAATCACTAGGAACTTAATCTATCAACTCTCCCGTCCACACAA
66 CATTAAAAATGCATGTTTTAACAAATCACTAGGAACTTAATCTATCAACTCTCCCGTCCACACAA
409238 AACATGAGTTAGGCTAAAAAACATTTTCTTCCCCCCTCTCTCTTGAAAGAACC-TATTTACTAAG
131 AACATGAGTTAGGCTAAAAAACATTTTCTTCCCCCCTCTCTCTTGAAAGAACCTTATTTACTAAG
409302 TCATAGAAGTTCTTTGAACGATGAAAA-ACACAAT
196 TCATAGAAGTTC-TTGAACGATGAAAACACACAAT
409336 TGTGGGCATGCTTTATAGCATCTCATGACATAATGACATACATTTAGACATCCCAATATTTGCTT
1 TGTGGGCATGC-TTATAGCATCTCATGACATAATGACATACATTTAGACAT-CCAATA-TTGCTT
409401 AAACATTAAAAAATGCATGTTTTAACAATAATCACTAGGAAACTTAATCTATCAACTCTCCCGTC
63 AAACATT-AAAAATGCATGTTTTAAC-A-AATCACTAGG-AACTTAATCTATCAACTCTCCCGTC
409466 CACACAAAACATGAGTTAGGCTAAAAAACATTTTCTTCCCCCCTCTCTCTTGAAAGAACCTTATT
124 CACACAAAACATGAGTTAGGCTAAAAAACATTTTCTTCCCCCCTCTCTCTTGAAAGAACCTTATT
409531 TACTAAGTCATAGAAGTTCTTGAACGATGAAAACACACAAT
189 TACTAAGTCATAGAAGTTCTTGAACGATGAAAACACACAAT
409572 AACCAAAAAA
Statistics
Matches: 226, Mismatches: 1, Indels: 10
0.95 0.00 0.04
Matches are distributed among these distances:
228 11 0.05
229 38 0.17
230 6 0.03
231 13 0.06
232 18 0.08
233 1 0.00
234 10 0.04
235 99 0.44
236 30 0.13
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (229 bp):
TGTGGGCATGCTTATAGCATCTCATGACATAATGACATACATTTAGACATCCAATATTGCTTAAA
CATTAAAAATGCATGTTTTAACAAATCACTAGGAACTTAATCTATCAACTCTCCCGTCCACACAA
AACATGAGTTAGGCTAAAAAACATTTTCTTCCCCCCTCTCTCTTGAAAGAACCTTATTTACTAAG
TCATAGAAGTTCTTGAACGATGAAAACACACAAT
Found at i:410533 original size:14 final size:14
Alignment explanation
Indices: 410509--410559 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
410499 GTTATGTAAA
410509 ATTTA-TTTTATAT
1 ATTTATTTTTATAT
*
410522 ATTTATTTTTATTT
1 ATTTATTTTTATAT
* *
410536 ATTTAATTTTA-AA
1 ATTTATTTTTATAT
410549 ATTTATTTTTA
1 ATTTATTTTTA
410560 ATTAATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 15 0.47
14 17 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTATTTTTATAT
Found at i:410539 original size:27 final size:27
Alignment explanation
Indices: 410508--410568 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
410498 TGTTATGTAA
*
410508 AATTTATTTTATATATTTATTTTT-ATT
1 AATTTATTTTA-AAATTTATTTTTAATT
*
410535 TATTTAATTTTAAAATTTATTTTTAATT
1 AATTT-ATTTTAAAATTTATTTTTAATT
410563 AATTTA
1 AATTTA
410569 AAGTAATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
AATTTATTTTAAAATTTATTTTTAATT
Found at i:410558 original size:13 final size:13
Alignment explanation
Indices: 410505--410560 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
410495 TGATGTTATG
410505 TAAAATTTA-TTT
1 TAAAATTTATTTT
*
410517 TATATATTTATTTT
1 TA-AAATTTATTTT
** *
410531 TATTTATTTAATTT
1 TA-AAATTTATTTT
410545 TAAAATTTATTTT
1 TAAAATTTATTTT
410558 TAA
1 TAA
410561 TTAATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 2 0.06
13 17 0.47
14 17 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAAAATTTATTTT
Found at i:420812 original size:2 final size:2
Alignment explanation
Indices: 420805--420840 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
420795 AACTTTATGA
420805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
420841 TACGGTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424194 original size:19 final size:20
Alignment explanation
Indices: 424170--424215 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
424160 TGACCCTTTA
*
424170 GTATCGATATT-GAGGTTTG
1 GTATCGATATTGGAGGCTTG
*
424189 GTATCGATATTGGATGCTTG
1 GTATCGATATTGGAGGCTTG
424209 GTATCGA
1 GTATCGA
424216 GGTTGGCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.22, C:0.09, G:0.30, T:0.39
Consensus pattern (20 bp):
GTATCGATATTGGAGGCTTG
Found at i:424221 original size:20 final size:20
Alignment explanation
Indices: 424186--424237 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
424176 ATATTGAGGT
*
424186 TTGGTATCGATATTGGATGC
1 TTGGTATCGAGATTGGATGC
* *
424206 TTGGTATCGAGGTTGGCTGC
1 TTGGTATCGAGATTGGATGC
* *
424226 TCGGTCTCGAGA
1 TTGGTATCGAGA
424238 GTGATTAGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (20 bp):
TTGGTATCGAGATTGGATGC
Found at i:424268 original size:20 final size:20
Alignment explanation
Indices: 424243--424366 Score: 176
Period size: 20 Copynumber: 6.2 Consensus size: 20
424233 CGAGAGTGAT
424243 TAGTCTTCATACTGAAGGAC
1 TAGTCTTCATACTGAAGGAC
*
424263 TAGTCTTCATACTGAAGTAC
1 TAGTCTTCATACTGAAGGAC
424283 TAGTCTTCATACTGAAGGAC
1 TAGTCTTCATACTGAAGGAC
424303 TAGTCTTCATACTGAAGGAC
1 TAGTCTTCATACTGAAGGAC
* ** * *
424323 TAGTCTCCATACCAAAGAAT
1 TAGTCTTCATACTGAAGGAC
* *
424343 TAGTCTCCATACCGAAGGAC
1 TAGTCTTCATACTGAAGGAC
424363 TAGT
1 TAGT
424367 ATCCATACCA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
TAGTCTTCATACTGAAGGAC
Found at i:424372 original size:40 final size:39
Alignment explanation
Indices: 424303--424417 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 39
424293 ACTGAAGGAC
* * *
424303 TAGTCTTCATACTGAAGGACTAGTCTCCATACCAAAGAAT
1 TAGTCTCCATACCGAAGGACTAGTATCCATACCAAAG-AT
*
424343 TAGTCTCCATACCGAAGGACTAGTATCCATACCAGAGAT
1 TAGTCTCCATACCGAAGGACTAGTATCCATACCAAAGAT
** * *
424382 TAAGAATCCATACCGAAGG-CTTGATATCAATACCAA
1 T-AGTCTCCATACCGAAGGACTAG-TATCCATACCAA
424418 TTGGTTGATT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 6 0.09
40 58 0.91
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (39 bp):
TAGTCTCCATACCGAAGGACTAGTATCCATACCAAAGAT
Found at i:428154 original size:29 final size:31
Alignment explanation
Indices: 428105--428180 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
428095 ATTTTAGTTA
* ** *
428105 GTGATTAAAATATAAGTTTTG-AAAG-TTTG
1 GTGACTAAAATATAAACTTTGAAAAGATTAG
428134 GTGACTAAAATATAAACTTTGTAAAAGATTAG
1 GTGACTAAAATATAAACTTTG-AAAAGATTAG
428166 G-GACTAAAATTATAA
1 GTGACTAAAA-TATAA
428181 TATTAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 18 0.46
31 12 0.31
32 9 0.23
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (31 bp):
GTGACTAAAATATAAACTTTGAAAAGATTAG
Found at i:444361 original size:20 final size:20
Alignment explanation
Indices: 444336--444384 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
444326 GGAGTATATG
444336 GATGCACTACATGGTGCATC
1 GATGCACTACATGGTGCATC
444356 GATGCACTACATGGTGCATC
1 GATGCACTACATGGTGCATC
444376 GATGCACTA
1 GATGCACTA
444385 GTGGCAGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
GATGCACTACATGGTGCATC
Found at i:444541 original size:30 final size:31
Alignment explanation
Indices: 444507--444567 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
444497 AAACTTTGAA
444507 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
444537 TAAATTCTATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
444568 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:447776 original size:20 final size:20
Alignment explanation
Indices: 447751--447845 Score: 163
Period size: 20 Copynumber: 4.8 Consensus size: 20
447741 TTGCAGCCTT
447751 GATGCATGGATGCACAGCAG
1 GATGCATGGATGCACAGCAG
447771 GATGCATGGATGCACAGCAG
1 GATGCATGGATGCACAGCAG
*
447791 GATGCATCGATGCACAGCAG
1 GATGCATGGATGCACAGCAG
*
447811 GATGCATGGATGCACAGCAA
1 GATGCATGGATGCACAGCAG
*
447831 GATGCATCGATGCAC
1 GATGCATGGATGCAC
447846 TAAGTTCATT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.31, C:0.22, G:0.32, T:0.16
Consensus pattern (20 bp):
GATGCATGGATGCACAGCAG
Found at i:447890 original size:20 final size:20
Alignment explanation
Indices: 447865--447966 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 20
447855 TCGAAATGGA
447865 GTGCATGGATGCACTA-CATG
1 GTGCATGGATGCACTAGCA-G
*
447885 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTA---GCAG
*
447908 GTGCATGGATGCACTAGTGGCAA
1 GTGCATGGATGCACTA---GCAG
447931 GTGCATGGATGCACT-GCAGGG
1 GTGCATGGATGCACTAGCA--G
*
447952 GTGCATAGATGCACT
1 GTGCATGGATGCACT
447967 TTGGCACCCT
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
19 3 0.04
20 15 0.21
21 14 0.20
23 37 0.52
24 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTAGCAG
Found at i:447918 original size:23 final size:23
Alignment explanation
Indices: 447865--447945 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
447855 TCGAAATGGA
447865 GTGCATGGATGCACTA----CATG
1 GTGCATGGATGCACTAGTGGCA-G
*
447885 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGGCAG
*
447908 GTGCATGGATGCACTAGTGGCAA
1 GTGCATGGATGCACTAGTGGCAG
447931 GTGCATGGATGCACT
1 GTGCATGGATGCACT
447946 GCAGGGGTGC
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
20 15 0.28
23 37 0.69
24 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (23 bp):
GTGCATGGATGCACTAGTGGCAG
Found at i:448080 original size:30 final size:31
Alignment explanation
Indices: 448046--448106 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
448036 AAACTTTGAA
448046 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
448076 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
448107 CCTTAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:449143 original size:20 final size:20
Alignment explanation
Indices: 449120--449173 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
449110 TTTGTTTTGC
* **
449120 AAAGGATCGATCCCTTTTCA
1 AAAGGATCGATCCCTGTGAA
* *
449140 AAAGAATAGATCCCCTGTGAA
1 AAAGGATCGAT-CCCTGTGAA
449161 AAAGGATCGATCC
1 AAAGGATCGATCC
449174 ATTCATTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAGGATCGATCCCTGTGAA
Found at i:459713 original size:63 final size:63
Alignment explanation
Indices: 459614--459739 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
459604 TCCAGAGTAT
*
459614 AATTAGTCTGAACTGAAATAAAGTGAGTAGACTTGGTGAGACGATCAACGATAACCTATACTA
1 AATTAGTCTGAACCGAAATAAAGTGAGTAGACTTGGTGAGACGATCAACGATAACCTATACTA
459677 AATTAGTCTGAACCGAAATAAAGTGAGTAGACTTGGTGAGACGATCAACGATAACCTATACTA
1 AATTAGTCTGAACCGAAATAAAGTGAGTAGACTTGGTGAGACGATCAACGATAACCTATACTA
459740 TATTCTTCTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (63 bp):
AATTAGTCTGAACCGAAATAAAGTGAGTAGACTTGGTGAGACGATCAACGATAACCTATACTA
Found at i:464089 original size:12 final size:11
Alignment explanation
Indices: 464039--464086 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
464029 CACCAAAAGA
*
464039 AAAACTTAAAG
1 AAAACTTAATG
* *
464050 AAAACCTAGTG
1 AAAACTTAATG
464061 AAAACTTAATG
1 AAAACTTAATG
*
464072 AAAACTTTATG
1 AAAACTTAATG
464083 AAAA
1 AAAA
464087 ACTGATGCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (11 bp):
AAAACTTAATG
Found at i:465210 original size:12 final size:11
Alignment explanation
Indices: 465175--465212 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
465165 ATTTGCACGA
465175 TTTTTTCCTTT
1 TTTTTTCCTTT
465186 TTCTTTTCC-TT
1 TT-TTTTCCTTT
465197 TTTTTTCTCTTT
1 TTTTTTC-CTTT
465209 TTTT
1 TTTT
465213 AGGTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.21
11 7 0.29
12 12 0.50
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCCTTT
Found at i:467785 original size:102 final size:102
Alignment explanation
Indices: 467676--467886 Score: 327
Period size: 102 Copynumber: 2.1 Consensus size: 102
467666 CTCAAGAATT
* *
467676 TCTTTCTCTTCT-TCTTCTTT-TCTGGACTTAGCAAATCTAGAGGGAAAAGGAGGTTCTATGACA
1 TCTTTCTCTTCTGT-TTGTTTCT-TGGACTTAGCAAATCTAGAGGGAAAAGGAGGATCTATGACA
467739 AATTCATTCGATTTTTCGCTTTTGAGTCCTTTAGGTTGG
64 AATTCATTCGATTTTTCGCTTTTGAGTCCTTTAGGTTGG
* * *
467778 TCTTTCTCTTCTGTTTGTTTCTTGTACTTAGCGAATCTAGTGGGAAAAGGAGGATCTATGACAAA
1 TCTTTCTCTTCTGTTTGTTTCTTGGACTTAGCAAATCTAGAGGGAAAAGGAGGATCTATGACAAA
* *
467843 TTCCTTCGGTTTTTCGCTTTTGAGTCCTTTAGGTTGG
66 TTCATTCGATTTTTCGCTTTTGAGTCCTTTAGGTTGG
467880 TCTTTCT
1 TCTTTCT
467887 GAGTCTGAGG
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
102 98 0.98
103 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (102 bp):
TCTTTCTCTTCTGTTTGTTTCTTGGACTTAGCAAATCTAGAGGGAAAAGGAGGATCTATGACAAA
TTCATTCGATTTTTCGCTTTTGAGTCCTTTAGGTTGG
Found at i:471707 original size:25 final size:26
Alignment explanation
Indices: 471670--471722 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
471660 GATATAATCC
*
471670 TATATAGAATAAAA-AAATACATCAA
1 TATACAGAATAAAAGAAATACATCAA
* * *
471695 TATACAGATTAAAAGTAATGCATCAA
1 TATACAGAATAAAAGAAATACATCAA
471721 TA
1 TA
471723 ATCAGAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.26
Consensus pattern (26 bp):
TATACAGAATAAAAGAAATACATCAA
Found at i:473898 original size:138 final size:138
Alignment explanation
Indices: 473709--473987 Score: 486
Period size: 138 Copynumber: 2.0 Consensus size: 138
473699 TCAAAAAAAA
473709 AATACAATCAACTCAACATACTCTAAATTCTAAATTAATAGAAAAATAATATCAACTAAATTAAA
1 AATACAATCAACTCAACATACTCTAAATTCTAAATTAATAGAAAAATAATATCAACTAAATTAAA
* * *
473774 AATTGATCGGTATAGTTTGAATTAATTAGATACTTACAAAATTTGTTTGTTAAAAGATTTGACCC
66 AATTGATCGATATAGTTTGAATTAATTAGATAATTACAAAATTTGTTTGTTAAAAGACTTGACCC
473839 TTATGAAC
131 TTATGAAC
* * *
473847 AATACAATCAACTCAACATACTCTAAATTCTAAATTATTATAATAATAATATCAACTAAATTAAA
1 AATACAATCAACTCAACATACTCTAAATTCTAAATTAATAGAAAAATAATATCAACTAAATTAAA
* *
473912 ATTTGATCGATATAGTTTGAATTAATTAGATAATTACAAAATTTGTTTGTTACAAGACTTGACCC
66 AATTGATCGATATAGTTTGAATTAATTAGATAATTACAAAATTTGTTTGTTAAAAGACTTGACCC
473977 TTATGAAC
131 TTATGAAC
473985 AAT
1 AAT
473988 TTTTTATATC
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 133 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (138 bp):
AATACAATCAACTCAACATACTCTAAATTCTAAATTAATAGAAAAATAATATCAACTAAATTAAA
AATTGATCGATATAGTTTGAATTAATTAGATAATTACAAAATTTGTTTGTTAAAAGACTTGACCC
TTATGAAC
Found at i:488502 original size:25 final size:25
Alignment explanation
Indices: 488474--488538 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
488464 ATAAGTAAAG
488474 CTTTACTTGCAAGAAAGCCTAAAAA
1 CTTTACTTGCAAGAAAGCCTAAAAA
488499 CTTTACTTGCAAGAAAGCCTAAAAA
1 CTTTACTTGCAAGAAAGCCTAAAAA
488524 CTTTACTTGCAAGAA
1 CTTTACTTGCAAGAA
488539 GAAAGCCTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (25 bp):
CTTTACTTGCAAGAAAGCCTAAAAA
Found at i:494769 original size:19 final size:19
Alignment explanation
Indices: 494745--494782 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
494735 CTATGAACTA
494745 CTCCTTCCAAGCTTAAATT
1 CTCCTTCCAAGCTTAAATT
* *
494764 CTCCTTCTAAGCTTCAATT
1 CTCCTTCCAAGCTTAAATT
494783 TAAGCCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.39
Consensus pattern (19 bp):
CTCCTTCCAAGCTTAAATT
Found at i:495788 original size:41 final size:41
Alignment explanation
Indices: 495727--496217 Score: 524
Period size: 41 Copynumber: 12.0 Consensus size: 41
495717 TTATAGCGGC
* * *
495727 GGCGTTTTTAGAACAAACGCCGCTAAATACTTGTACTTTAGT
1 GGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTACTTTAGT
*
495769 GGCGTTTTTTTACAAACGCCGCTAAAGACT-GT-CTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * * * * *
495808 GGCATATTTAGAACAAACGCCGCTAAATAC-CATACTTTAAT
1 GGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTACTTTAGT
* *
495849 GGCGTTTTTAATACAAACACCGATAAAGAC-CGTACTTTAGT
1 GGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTACTTTAGT
* *
495890 GACGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * *
495931 GGTGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * * *
495972 GGCGTTTTTATACAAACGCCGCTAAATAGTCATACTTTATT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * * *
496013 GGCGTTTTTATATAAATGTCGCTAAAGACTCATACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * * *
496054 GGCGTTTTAATACAAACGCCGCTATAGACTAGTCCTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* *
496095 GGCGTTTTTATATAAACGCCGCTATAGACTC-TAACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGT-ACTTTAGT
* * * * * * * *
496136 GGCATTTTTTTACAAACACCGCTATACACTCATGCTTTACT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
* * * *
496177 GGTGTTTTTATACAAACGCCGTTATAGACTCGTGCTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
496218 TGGAGCCCCT
Statistics
Matches: 377, Mismatches: 65, Indels: 15
0.82 0.14 0.03
Matches are distributed among these distances:
39 14 0.04
40 38 0.10
41 314 0.83
42 11 0.03
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGT
Found at i:498581 original size:2 final size:2
Alignment explanation
Indices: 498574--498623 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
498564 TATTACGATA
498574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
498616 AT AT AT AT
1 AT AT AT AT
498624 GTAGAGAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:500019 original size:43 final size:43
Alignment explanation
Indices: 499948--500193 Score: 248
Period size: 42 Copynumber: 5.9 Consensus size: 43
499938 AAGGTAATTA
* *
499948 GCGGCGTTT-T-T-CAATAACGCCGCTATAGATCT-ACTCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTGAC-CTTTT
* * *
499988 ACGGCGTTTGTATCCAAAAACGCCACAATAGATCTGTCC-TTT
1 GCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTGACCTTTT
* * * *
500030 GCGGTGTTT-AATCCAAAAA---CACACTAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTGACCTTTT
*
500069 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCAATAGATCT-GACCTTTT
* *
500113 GCGGCGTTTGT-TCC-AAAACGCCGCGATAGATATTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCAATAGAT-CTGACCTTTT
*
500155 GCGGCGTTTGT-T-CAAAAACGCCGCGATAGATCTTGACCT
1 GCGGCGTTTGTATCCAAAAACGCCGCAATAGATC-TGACCT
500194 ATGGCGTTTT
Statistics
Matches: 175, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
38 14 0.08
39 11 0.06
40 17 0.10
41 11 0.06
42 70 0.40
43 32 0.18
44 20 0.11
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTGACCTTTT
Found at i:500074 original size:81 final size:84
Alignment explanation
Indices: 499972--500193 Score: 251
Period size: 81 Copynumber: 2.7 Consensus size: 84
499962 TAACGCCGCT
* * *
499972 ATAGATCT-ACTCTTTTACGGCGTTTGTATCCAAAAACGCCACAATAGATCT-GTCC-TTTGCGG
1 ATAGATCTGAC-CTTTTGCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTCGACCTTTTGCGG
*
500034 TGTTTAATCCAAAA--ACAC
65 CGTTTAATCCAAAACGACAC
*
500052 ACTAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
1 A-TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTCGACCTTTTGCGG
** * *
500117 CGTTTGTTCCAAAACGCCGC
65 CGTTTAATCCAAAACGACAC
* * *
500137 GATAGATATTGACCTTTTGCGGCGTTTGT-T-CAAAAACGCCGCGATAGATCTTGACCT
1 -ATAGAT-CTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTCGACCT
500194 ATGGCGTTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
80 1 0.01
81 44 0.36
82 5 0.04
83 18 0.15
84 25 0.20
85 8 0.07
86 21 0.17
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (84 bp):
ATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCAATAGATCTCGACCTTTTGCGGC
GTTTAATCCAAAACGACAC
Found at i:500207 original size:84 final size:86
Alignment explanation
Indices: 500060--500220 Score: 229
Period size: 84 Copynumber: 1.9 Consensus size: 86
500050 ACACTAGATC
* * *
500060 TGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTT
1 TGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCGATAGATCTCGACCTATGGCGGCGTTTGTT
500125 C-CAAAACGCCGCGATAGATAT
66 CTC-AAACGCCGCGATAGATAT
* ***
500146 TGACCTTTTGCGGCGTTTGT-T-CAAAAACGCCGCGATAGATCTTGACCTATGGCGTTTTTTGTT
1 TGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCGATAGATCTCGACCTATGGCGGCGTTTGTT
500209 CTCAAACGCCGC
66 CTCAAACGCCGC
500221 TAACTTTAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 45 0.67
85 2 0.03
86 20 0.30
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (86 bp):
TGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCGATAGATCTCGACCTATGGCGGCGTTTGTT
CTCAAACGCCGCGATAGATAT
Found at i:501382 original size:26 final size:26
Alignment explanation
Indices: 501343--501393 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
501333 AGAGGCTCAA
501343 CTCTACATCATATCCTTAAGACCACG
1 CTCTACATCATATCCTTAAGACCACG
*
501369 CTCTACATCCTATCCTTAAGACCAC
1 CTCTACATCATATCCTTAAGACCAC
501394 ACTCGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.27
Consensus pattern (26 bp):
CTCTACATCATATCCTTAAGACCACG
Found at i:513186 original size:21 final size:22
Alignment explanation
Indices: 513157--513197 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
513147 GAGAAGATCT
* *
513157 ATAAGAAAGGAGTA-AAAATCA
1 ATAACAAAGGAATATAAAATCA
513178 ATAACAAAGGAATATAAAAT
1 ATAACAAAGGAATATAAAAT
513198 GAAGAAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17
Consensus pattern (22 bp):
ATAACAAAGGAATATAAAATCA
Found at i:538700 original size:22 final size:22
Alignment explanation
Indices: 538672--538725 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
538662 GCAAGAAGAC
538672 CCATGTGCATTCATGTAGGCTG
1 CCATGTGCATTCATGTAGGCTG
*
538694 CCATGTGCATTTATGTAGGCTG
1 CCATGTGCATTCATGTAGGCTG
538716 CCATGTGCAT
1 CCATGTGCAT
538726 CATTCAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (22 bp):
CCATGTGCATTCATGTAGGCTG
Found at i:540785 original size:21 final size:21
Alignment explanation
Indices: 540761--540803 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
540751 AACTAAAACT
*
540761 AAATTCCCAATTAATTGGATG
1 AAATTCCCAATTAATGGGATG
540782 AAATTCCCAATTAATGGGATG
1 AAATTCCCAATTAATGGGATG
540803 A
1 A
540804 TTGATAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (21 bp):
AAATTCCCAATTAATGGGATG
Found at i:551392 original size:17 final size:16
Alignment explanation
Indices: 551363--551395 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
551353 TCTCATTCTG
551363 AAATAAAAAATGAATT
1 AAATAAAAAATGAATT
551379 AAATAAACAAATGAATT
1 AAATAAA-AAATGAATT
551396 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (16 bp):
AAATAAAAAATGAATT
Found at i:551416 original size:31 final size:31
Alignment explanation
Indices: 551381--551444 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
551371 AATGAATTAA
551381 ATAAACAAATGAATTTTTATTTTATGTTCAC
1 ATAAACAAATGAATTTTTATTTTATGTTCAC
* *
551412 ATAAACGAATGAATTTTTATTTTATTTTCAC
1 ATAAACAAATGAATTTTTATTTTATGTTCAC
551443 AT
1 AT
551445 TAGAAATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (31 bp):
ATAAACAAATGAATTTTTATTTTATGTTCAC
Found at i:555534 original size:32 final size:32
Alignment explanation
Indices: 555487--555585 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
555477 CCTAAGGTGG
* * *
555487 CCTTGGGTAGGCTCTAAGTCCCCAAGGCATTT
1 CCTTGGGTAAGCTCTAAGGCCCCAAGGCACTT
* *
555519 CCTTGGGTAATCTCTAAGGCCCCAAGGTACTT
1 CCTTGGGTAAGCTCTAAGGCCCCAAGGCACTT
* * * * *
555551 CCTTGGATAGGCTCTTAGGCCCTAAGGTAC-T
1 CCTTGGGTAAGCTCTAAGGCCCCAAGGCACTT
555582 CCTT
1 CCTT
555586 TGGGGCTCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 5 0.09
32 52 0.91
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.29
Consensus pattern (32 bp):
CCTTGGGTAAGCTCTAAGGCCCCAAGGCACTT
Found at i:556212 original size:19 final size:20
Alignment explanation
Indices: 556185--556222 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
556175 AATGATTTTC
556185 TAAACTTGTATT-TTATTTA
1 TAAACTTGTATTATTATTTA
* *
556204 TAAATTTGTTTTATTATTT
1 TAAACTTGTATTATTATTT
556223 TACACGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TAAACTTGTATTATTATTTA
Found at i:561905 original size:24 final size:24
Alignment explanation
Indices: 561862--561916 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
561852 TATTATATTC
561862 TATTATTAGAAATATTAATAAAT-A
1 TATT-TTAGAAATATTAATAAATAA
*
561886 TATTTTA-AAATATTTGAATAATTAA
1 TATTTTAGAAATA-TT-AATAAATAA
561911 TATTTT
1 TATTTT
561917 GATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
23 5 0.19
24 10 0.37
25 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTTAGAAATATTAATAAATAA
Found at i:561934 original size:25 final size:24
Alignment explanation
Indices: 561902--561950 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
561892 AAAATATTTG
*
561902 AATAATT-AATATTTTGATTAAAAT
1 AATAATTAAATATTAT-ATTAAAAT
561926 AATATATTAAATATTATATTAAAAT
1 AATA-ATTAAATATTATATTAAAAT
561951 TAAATACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 11 0.50
26 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATAATTAAATATTATATTAAAAT
Found at i:563120 original size:17 final size:17
Alignment explanation
Indices: 563080--563121 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
563070 AGGTAAAGAG
*
563080 CTTCTCCTGAAATGAGT
1 CTTCTCTTGAAATGAGT
563097 CTTCTCTTGAAATGAGT
1 CTTCTCTTGAAATGAGT
563114 CTTCTCTT
1 CTTCTCTT
563122 TATGTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (17 bp):
CTTCTCTTGAAATGAGT
Found at i:575440 original size:49 final size:47
Alignment explanation
Indices: 575343--575468 Score: 110
Period size: 49 Copynumber: 2.6 Consensus size: 47
575333 AGATAATTAC
* * ** * *
575343 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGAAAT
1 AATATATATATAATAATAATA-AAATATAAGTAAAAAAATAAAGAAAT
575391 ATATATATATATAATAATAATAAAATAT-AGTAAAAAAATAAATGAAAAT
1 A-ATATATATATAATAATAATAAAATATAAGTAAAAAAATAAA-G-AAAT
* *
575440 AATTTAATATATATATAATACATATAATA
1 AATAT-ATATATA-ATAATA-ATAAAATA
575469 ATAACATGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
47 12 0.19
48 9 0.14
49 30 0.47
50 6 0.09
51 7 0.11
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (47 bp):
AATATATATATAATAATAATAAAATATAAGTAAAAAAATAAAGAAAT
Found at i:575496 original size:17 final size:18
Alignment explanation
Indices: 575463--575498 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
575453 TATAATACAT
*
575463 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
575481 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
575498 A
1 A
575499 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:575910 original size:37 final size:37
Alignment explanation
Indices: 575860--575960 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
575850 GTGCTTGTGG
* * * * * *
575860 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
575897 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
575934 ATCCTATTTTTAGGAGTTTGAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCCTA
575961 ATAGGACGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:576811 original size:105 final size:105
Alignment explanation
Indices: 576507--577137 Score: 864
Period size: 105 Copynumber: 6.0 Consensus size: 105
576497 GAATTGTTCC
* * ** *
576507 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
576571 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
576613 GAGTTCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * * *
576673 CAGTGGTCCCTTTGTCGTGGATTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
576713 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
576778 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
576818 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
576883 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
576923 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
576988 GAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
577028 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTA-ATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AGATTGGGAAGTTG-TTGTTGACA
* * * *
577092 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
577134 GAGT
1 GAGT
577138 GTCACGATCT
Statistics
Matches: 473, Mismatches: 43, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
100 77 0.16
101 1 0.00
102 7 0.01
104 5 0.01
105 300 0.63
106 82 0.17
107 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:577150 original size:15 final size:15
Alignment explanation
Indices: 577130--577160 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
577120 ACTTGTGTTG
577130 TCTCGAGTGTCACGA
1 TCTCGAGTGTCACGA
577145 TCTCGAGTGTCACGA
1 TCTCGAGTGTCACGA
577160 T
1 T
577161 ATCCTCCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (15 bp):
TCTCGAGTGTCACGA
Found at i:577399 original size:36 final size:36
Alignment explanation
Indices: 577352--577424 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
577342 TGTTTGGAGA
* ** *
577352 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGAAAGACAAAATTCATTTCAAGG
*
577388 GAAACTATCTCAAGAAAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGAAAGACAAAATTCATTTCAAGG
577424 G
1 G
577425 CAATGTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (36 bp):
GAAACTATCTCAAGAAAGACAAAATTCATTTCAAGG
Found at i:577537 original size:104 final size:104
Alignment explanation
Indices: 577329--577619 Score: 462
Period size: 104 Copynumber: 2.8 Consensus size: 104
577319 CATTAAATTA
* ** *
577329 TTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
* * *
577391 ACTATCTCAAGAAAGATAAAATTCATTTCAAGGGCAATG
66 ACTATCTCAAGAAAGAAAAAAATCATTTCAAGGGAAATG
577430 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
*
577495 ACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAATG
66 ACTATCTCAAGAAAGAAAAAAATCATTTCAAGGGAAATG
*
577534 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTTCTGTTTCGAGGGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
* *
577599 ACTATCTCAAGCAAGATAAAA
66 ACTATCTCAAGAAAGAAAAAA
577620 TCTTCTTAAA
Statistics
Matches: 175, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 44 0.25
103 3 0.02
104 128 0.73
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (104 bp):
TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAA
ACTATCTCAAGAAAGAAAAAAATCATTTCAAGGGAAATG
Found at i:577730 original size:36 final size:36
Alignment explanation
Indices: 577685--577798 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
577675 GGTCTAAAGC
*
577685 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * ** * **
577721 GAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* *
577757 GAGACAAAGT-ATGTTTTAAG-AAAACAAAT-TTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
577792 GAGATAA
1 GAGATAA
577799 TCATCTGCAT
Statistics
Matches: 58, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
35 15 0.26
36 42 0.72
37 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:577791 original size:71 final size:74
Alignment explanation
Indices: 577625--577798 Score: 198
Period size: 72 Copynumber: 2.4 Consensus size: 74
577615 TAAAATCTTC
** * *
577625 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTAAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTAAAGCGAGA
*
577689 CAAATCTTGTT
64 CAAATCATGTT
* *
577700 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTAAAGCGAGACA
577763 AAGT-ATGTT
66 AA-TCATGTT
*
577772 TTAAG-AAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
577799 TCATCTGCAT
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
71 17 0.19
72 32 0.36
73 12 0.14
75 8 0.09
76 19 0.22
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTAAAGCGAGACA
AATCATGTT
Found at i:579260 original size:183 final size:183
Alignment explanation
Indices: 578939--579475 Score: 968
Period size: 183 Copynumber: 2.9 Consensus size: 183
578929 ATCAGGTTTA
* *
578939 ACTGAAAGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** *
579004 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTACTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
579068 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
579122 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
579187 GCAAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
579252 TCCTCTATAACCAATTGCCTTAGTGGAATAGATCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
579305 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACTGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
579370 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
579435 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
579476 CGGATTTAAT
Statistics
Matches: 340, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
183 339 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:584380 original size:46 final size:46
Alignment explanation
Indices: 584328--584419 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
584318 TATTAAAGAA
* *
584328 ATATATATAATAATA-ATAATAATAGTAAAAAAATAAATGAAAATAATT
1 ATATATAT-AT-ATACAT-ATAATAATAAAAAAATAAATAAAAATAATT
* *
584376 ATATATATATATACATATAATAATAATAACATAAATAAAAATAA
1 ATATATATATATACATATAATAATAAAAAAATAAATAAAAATAA
584420 ATGAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 27 0.69
47 4 0.10
48 8 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (46 bp):
ATATATATATATACATATAATAATAAAAAAATAAATAAAAATAATT
Found at i:584439 original size:55 final size:54
Alignment explanation
Indices: 584328--584447 Score: 133
Period size: 55 Copynumber: 2.2 Consensus size: 54
584318 TATTAAAGAA
* * *
584328 ATATATATAATAATAATAATAATAGTAAAAAAATAAATGAAAATAATTATATAT
1 ATATATACAATAATAATAATAACAGTAAAAAAATAAATGAAAATAATTATACAT
*
584382 ATATATACATATAATAATAATAACA-TAAATAAAAATAAATGAATAA-AA-TATCCAT
1 ATATATACA-ATAATAATAATAACAGT-AA-AAAAATAAATGAA-AATAATTATACAT
584437 ATA-ATA-AATAA
1 ATATATACAATAA
584448 AGGGACTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
52 4 0.07
53 1 0.02
54 12 0.21
55 24 0.41
56 15 0.26
57 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (54 bp):
ATATATACAATAATAATAATAACAGTAAAAAAATAAATGAAAATAATTATACAT
Found at i:585188 original size:19 final size:18
Alignment explanation
Indices: 585151--585201 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
585141 TATTTTCACT
* *
585151 ATTTTATTTTTGAATATA
1 ATTTTATTTTTTAAAATA
585169 AGTTTTATTTTTTAAAATA
1 A-TTTTATTTTTTAAAATA
*
585188 ATTATATTCTTTTA
1 ATTTTATT-TTTTA
585202 GAACCAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
ATTTTATTTTTTAAAATA
Found at i:587270 original size:54 final size:53
Alignment explanation
Indices: 587215--587489 Score: 318
Period size: 54 Copynumber: 5.3 Consensus size: 53
587205 CAACTACAAT
*
587215 AATAAATCAATCCATA-TTT-AAATAAATAAATTCATACTAATAAATTATTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTAA
* *
587266 AATAAATCAATCCATATTTTAAAATAAATCAGTCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-TTAA
* *** * * * *
587320 AATAAATCAATTCATACAACTACAAT-AAT-AAATCA-ATTCAT--ATT-TTAA
1 AATAAATCAATCCATA-TTTTAAAATAAATCAATTCATACTAATAAATTATTAA
* *
587368 AATAAATCAATTCATATTTTAAAATAAATCAA-TCTATACTAATAAACTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACTAATAAATTA-TTAA
*
587422 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAA-TATTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTAA
587474 AATAAATCAATCCATA
1 AATAAATCAATCCATA
587490 CTAATAAATA
Statistics
Matches: 189, Mismatches: 22, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
47 5 0.03
48 25 0.13
49 3 0.02
50 7 0.04
51 16 0.08
52 29 0.15
53 30 0.16
54 68 0.36
55 6 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTAA
Found at i:587287 original size:22 final size:22
Alignment explanation
Indices: 587262--587303 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
587252 TAATAAATTA
587262 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
*
587284 TTAAAATAAATCAGTCCATA
1 TTAAAATAAATCAATCCATA
587304 CTAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAATAAATCAATCCATATT
Found at i:587312 original size:22 final size:22
Alignment explanation
Indices: 587263--587311 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
587253 AATAAATTAT
**
587263 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
587285 TAAAATAAATCAGTCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
587308 TAAA
1 TAAA
587312 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:587374 original size:22 final size:22
Alignment explanation
Indices: 587346--587400 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
587336 CAACTACAAT
587346 AATAAATCAATTCATATTTTAA
1 AATAAATCAATTCATATTTTAA
587368 AATAAATCAATTCATATTTTAA
1 AATAAATCAATTCATATTTTAA
587390 AATAAATCAAT
1 AATAAATCAAT
587401 CTATACTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATCAATTCATATTTTAA
Found at i:587441 original size:76 final size:79
Alignment explanation
Indices: 587158--587520 Score: 318
Period size: 76 Copynumber: 4.6 Consensus size: 79
587148 AATAAATTAT
* * **
587158 TTAAAA-AAATCAATCCATACTAATAATTA-TT-AAATAAATC-ATCCATACAACTACAATAATA
1 TTAAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCAATCCAT---ATTTTAA-AATA
587219 AATCAATC--C-AT-AT-
62 AATCAATCTACAATAATA
* *
587232 TT-AAATAAATAAATTCATACTAATAAAT-TATTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TTAAAATAAATCAATCCATACTAATAAATAT-TTAAAATAAATCAATCCATATTTTAAAATAAAT
*
587295 CAGTCCATACTAATAAATTA
65 CAAT-C-TAC-AAT-AA-TA
* * *
587315 TTTAAAATAAATCAATTCATAC-AACTACA-A--T--AATAAATCAATTCATATTTTAAAATAAA
1 -TTAAAATAAATCAATCCATACTAA-TAAATATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
587374 TCAAT-T-C-AT-ATT
64 TCAATCTACAATAATA
*
587386 TTAAAATAAATCAATCTATACTAATAAACTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TTAAAATAAATCAATCCATACTAATAAA-TATTTAAAATAAATCAATCCATATTTTAAAATAAAT
587451 CAATCCATACTAATAAATA
65 CAAT-C-TAC-AAT-AATA
587470 TTAAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCAATCCATA
1 TTAAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCAATCCATA
587521 CTAATAATTA
Statistics
Matches: 237, Mismatches: 18, Indels: 59
0.75 0.06 0.19
Matches are distributed among these distances:
70 22 0.09
71 3 0.01
72 2 0.01
73 13 0.05
74 29 0.12
75 2 0.01
76 42 0.18
77 8 0.03
79 3 0.01
80 32 0.14
81 1 0.00
82 4 0.02
83 23 0.10
84 33 0.14
85 20 0.08
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (79 bp):
TTAAAATAAATCAATCCATACTAATAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATC
AATCTACAATAATA
Found at i:587443 original size:22 final size:22
Alignment explanation
Indices: 587417--587459 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
587407 TAATAAACTA
587417 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
587439 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
587460 CTAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:587469 original size:22 final size:22
Alignment explanation
Indices: 587419--587467 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
587409 ATAAACTATT
**
587419 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
587441 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
587464 TAAA
1 TAAA
587468 TATTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:587498 original size:102 final size:102
Alignment explanation
Indices: 587215--587489 Score: 317
Period size: 102 Copynumber: 2.6 Consensus size: 102
587205 CAACTACAAT
587215 AATAAATCAATCCATATTT-AAATAAATAAATTCATACTAATAAATTATTAAAATAAATCAATCC
1 AATAAATCAATCCATATTTAAAATAAATAAA-TCATACTAATAAA-TATTAAAATAAATCAATCC
* *
587279 ATATTTTAAAATAAATCAGTCCATACTAATAAATTATTTAA
64 ATA-TTT-AAATAAATCAATCCATACTAATAAACTATTTAA
* ** * * * * *
587320 AATAAATCAATTCATACAACTACAAT-AATAAATCA-ATTCAT--ATTTTAAAATAAATCAATTC
1 AATAAATCAATCCAT--ATTTAAAATAAATAAATCATACTAATAAATATTAAAATAAATCAATCC
*
587381 ATATTTTAAAATAAATCAATCTATACTAATAAACTATTTAA
64 ATA-TTT-AAATAAATCAATCCATACTAATAAACTATTTAA
*
587422 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATATTAAAATAAATCAATCC
1 AATAAATCAATCCATA-TTTAAAATAAATAAAT-CATACTAATAAATATTAAAATAAATCAATCC
587487 ATA
64 ATA
587490 CTAATAAATA
Statistics
Matches: 141, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
100 1 0.01
101 5 0.04
102 75 0.53
103 3 0.02
104 4 0.03
105 18 0.13
106 24 0.17
107 8 0.06
108 3 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (102 bp):
AATAAATCAATCCATATTTAAAATAAATAAATCATACTAATAAATATTAAAATAAATCAATCCAT
ATTTAAATAAATCAATCCATACTAATAAACTATTTAA
Found at i:587508 original size:31 final size:31
Alignment explanation
Indices: 587439--587541 Score: 183
Period size: 30 Copynumber: 3.4 Consensus size: 31
587429 CAATCCATAT
587439 TTTAAAATAAATCAATCCATACTAATAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATA
587470 -TTAAAATAAATCAATCCATACTAATAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
587500 TTTAAAATAAATCAATCCATACTAATAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATA
587531 TTT-AAATAAAT
1 TTTAAAATAAAT
587542 ATTTAAAATT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
30 38 0.54
31 32 0.46
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:587567 original size:14 final size:14
Alignment explanation
Indices: 587548--587605 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
587538 AAATATTTAA
587548 AATTATTTTAAAAT
1 AATTATTTTAAAAT
*
587562 AATTATTTTAATA-
1 AATTATTTTAAAAT
587575 AATTATTTTAAAATT
1 AATTATTTTAAAA-T
* *
587590 AAATATTTAAAAAT
1 AATTATTTTAAAAT
587604 AA
1 AA
587606 ATAACCTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.32
14 15 0.39
15 11 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATTTTAAAAT
Found at i:587580 original size:13 final size:13
Alignment explanation
Indices: 587522--587585 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
587512 CAATCCATAC
587522 TAAT-AATTATTT
1 TAATAAATTATTT
*
587534 AAATAAA-TA-TT
1 TAATAAATTATTT
587545 T-A-AAATTATTT
1 TAATAAATTATTT
*
587556 TAAAATAATTATTT
1 TAATA-AATTATTT
587570 TAATAAATTATTT
1 TAATAAATTATTT
587583 TAA
1 TAA
587586 AATTAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
9 3 0.07
10 3 0.07
11 5 0.12
12 6 0.14
13 14 0.33
14 12 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAAATTATTT
Found at i:587598 original size:27 final size:25
Alignment explanation
Indices: 587526--587603 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 25
587516 CCATACTAAT
587526 AATTA-TTT-AAATAAATATTT-AA
1 AATTATTTTAAAATAAATATTTAAA
*
587548 AATTATTTTAAAATAATTATTTTAATA
1 AATTATTTTAAAATAAATA-TTTAA-A
587575 AATTATTTTAAAATTAAATATTTAAA
1 AATTATTTTAAAA-TAAATATTTAAA
587601 AAT
1 AAT
587604 AAATAACCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.10
23 3 0.06
24 8 0.17
25 3 0.06
26 5 0.10
27 19 0.40
28 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTATTTTAAAATAAATATTTAAA
Found at i:587602 original size:15 final size:14
Alignment explanation
Indices: 587534--587608 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
587524 ATAATTATTT
587534 AAATAAATATTT-A
1 AAATAAATATTTAA
*
587547 AAAT---TATTTTA
1 AAATAAATATTTAA
*
587558 AAATAATTATTT--
1 AAATAAATATTTAA
*
587570 TAATAAATTATTTTAA
1 AAATAAA-TA-TTTAA
*
587586 AATTAAATATTTAA
1 AAATAAATATTTAA
587600 AAATAAATA
1 AAATAAATA
587609 ACCTTATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
10 5 0.10
11 5 0.10
12 5 0.10
13 6 0.12
14 21 0.43
15 2 0.04
16 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATAAATATTTAA
Found at i:587606 original size:14 final size:13
Alignment explanation
Indices: 587523--587608 Score: 72
Period size: 12 Copynumber: 6.6 Consensus size: 13
587513 AATCCATACT
*
587523 AATAATTATTT-A
1 AATAAATATTTAA
587535 AATAAATATTTAA
1 AATAAATATTTAA
*
587548 AAT-TAT-TTTAA
1 AATAAATATTTAA
* *
587559 AATAATTATTT-T
1 AATAAATATTTAA
587571 AATAAATTATTTTAA
1 AATAAA-TA-TTTAA
587586 AATTAAATATTTAAA
1 AA-TAAATATTT-AA
587601 AATAAATA
1 AATAAATA
587609 ACCTTATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 8 0.14
12 18 0.31
13 9 0.15
14 12 0.20
15 8 0.14
16 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:589398 original size:18 final size:18
Alignment explanation
Indices: 589367--589414 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
589357 GAGTTTGAAT
*
589367 ATATCTAT-TTTTTTGTA
1 ATATCTATATATTTTGTA
589384 ATATCTATATATTTTGTA
1 ATATCTATATATTTTGTA
589402 ATA--TATATATTTT
1 ATATCTATATATTTT
589415 AATATTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 10 0.34
17 8 0.28
18 11 0.38
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
ATATCTATATATTTTGTA
Found at i:589410 original size:16 final size:17
Alignment explanation
Indices: 589377--589414 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
589367 ATATCTATTT
589377 TTTTGTAATATCTATATA
1 TTTTGTAATA-CTATATA
589395 TTTTGTAATA-TATATA
1 TTTTGTAATACTATATA
589411 TTTT
1 TTTT
589415 AATATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTGTAATACTATATA
Found at i:593806 original size:3 final size:3
Alignment explanation
Indices: 593798--593866 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
593788 TTATATATTT
* *
593798 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA AGA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
593846 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
593867 TGGATAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:594918 original size:15 final size:15
Alignment explanation
Indices: 594900--594928 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
594890 TCTTTTTTTT
594900 TTCTCTGTGTCTCTG
1 TTCTCTGTGTCTCTG
594915 TTCTCTGTGTCTCT
1 TTCTCTGTGTCTCT
594929 TTCAGGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.28, G:0.17, T:0.55
Consensus pattern (15 bp):
TTCTCTGTGTCTCTG
Found at i:595391 original size:3 final size:3
Alignment explanation
Indices: 595373--595452 Score: 110
Period size: 3 Copynumber: 26.7 Consensus size: 3
595363 TATATATGTT
*
595373 TAA TATA TAT TAA TAA TAA T-A TAA TAA T-A TAA GTAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
595418 TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
595453 TGGATAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 59 0.86
4 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:596024 original size:112 final size:113
Alignment explanation
Indices: 595770--596405 Score: 843
Period size: 112 Copynumber: 5.7 Consensus size: 113
595760 GAATTATGCG
* * *
595770 AAAAG-TTGAACAAGTT-TTCTTATTATGAAC-TCTTCTT--TTTTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * **
595830 TATGAACTTCT-CC-AGAAATGTTGATCCATCAATTGATGAATTCTTGC
66 TATGAAC-TCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAGC
595877 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
595942 TATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAGC
66 TATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAGC
*
595990 AAAAGATTGAACAAGTTC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *** * * **
596054 TATGAACT-TTCTCTGGAAAAAATAATCCATCAAGTGAT-AGATTTGAGC
66 TATGAACTCTAC-CTGGAAATGTTGATCCATCAAATGATGA-ATTCAAGC
*
596102 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
596167 TATGAA--CTACCTGGCAATGTTGATCCATCAGATGATGAATTCAAGC
66 TATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAGC
* *
596213 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTC-TCTCAT
1 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *** * * **
596277 TATGAACT-TTCTCTGGAAAAAATAATCCATCAAGTGAT-AGATTTGAGC
66 TATGAACTCTAC-CTGGAAATGTTGATCCATCAAATGATGA-ATTCAAGC
*
596325 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
596390 TATGAACTCTACCTGG
66 TATGAACTCTACCTGG
596406 CAAAAAAAAT
Statistics
Matches: 464, Mismatches: 47, Indels: 30
0.86 0.09 0.06
Matches are distributed among these distances:
107 5 0.01
108 10 0.02
109 13 0.03
110 19 0.04
111 89 0.19
112 210 0.45
113 116 0.25
114 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGAAATGTTGATCCATCAAATGATGAATTCAAGC
Found at i:596219 original size:336 final size:333
Alignment explanation
Indices: 595770--596438 Score: 974
Period size: 336 Copynumber: 2.0 Consensus size: 333
595760 GAATTATGCG
* * *
595770 AAAAGTTGAACAAGTTTTCTTATTATGAACTCTTCTTTTTTTCAGATGAGTTCTTCTCATTATGA
1 AAAAGTTGAACAAATTTTCTCATTATGAACTCTTCTTTTCTTCAGATGAGTTCTTCTCATTATGA
* **
595835 ACTTCTCCAGAAATGTTGATCCATCAATTGATGAATTCTTGCAAAAGATTGAACAAATTCTTCTC
66 ACTACTCCAGAAATGTTGATCCATCAATTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTC
* ***
595900 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGT
131 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TCTCATTATGAACT-TACTCTGGAAAAAA
* *
595964 TGATCCATCAAATGAT-GAATTCAAGCAAAAGATTGAACAAGTTC-TCTCATTATGAACTTCTTC
194 TAATCCATCAAATGATAG-ATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTC
*
596027 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGG-AAAAAATAATCCATCAAGTG
258 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAAAATAATCCATCAAGTG
596090 ATAGATTTGAGC
322 ATAGATTTGAGC
596102 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATT-TTCTCATTATGAAC-TCTTCTT--TTCTTCAGATGAGTTCTTCTCAT
** * *
596167 TATGAACTAC-CTGGCAATGTTGATCCATCAGA-TGATGAATTCAAGCAAAAGATTGAACAAGTT
61 TATGAACTACTCCAGAAATGTTGATCCATCA-ATTGATGAATTCAAGCAAAAGATTGAACAAATT
* *
596230 CTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTCTCATTATGAACTTTCTCTGGAA
125 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCTCATTATGAACTTACTCTGGAA
* ** *
596295 AAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
190 AAAATAATCCATCAAATGATAGATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTC
596360 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAAAAAAAATAATCCATCA
255 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG--AAAAAAATAATCCATCA
596425 AGTGATAGATTTGA
318 AGTGATAGATTTGA
596439 ATCTTTGCTA
Statistics
Matches: 301, Mismatches: 23, Indels: 19
0.88 0.07 0.06
Matches are distributed among these distances:
332 4 0.01
333 11 0.04
334 15 0.05
335 63 0.21
336 144 0.48
337 34 0.11
339 30 0.10
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (333 bp):
AAAAGTTGAACAAATTTTCTCATTATGAACTCTTCTTTTCTTCAGATGAGTTCTTCTCATTATGA
ACTACTCCAGAAATGTTGATCCATCAATTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCTCATTATGAACTTACTCTGGAAAAAATA
ATCCATCAAATGATAGATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAAAATAATCCATCAAGTGATAG
ATTTGAGC
Found at i:596295 original size:223 final size:225
Alignment explanation
Indices: 595770--596408 Score: 1057
Period size: 223 Copynumber: 2.9 Consensus size: 225
595760 GAATTATGCG
*
595770 AAAAG-TTGAACAAGTT-TTCTTATTATGAAC-TCTTCTTT-TT-TTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
** *** * * * *
595830 TATGAAC-TTCTCCAGAAATGTTGATCCATCAATTGAT-GAATTCT-TGCAAAAGATTGAACAAA
66 TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATAG-ATT-TGAGCAAAAGGTTGAACAAA
595892 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
129 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CTACCTG
595957 GCAATGTTGATCCATCAAATGATGAATTCAAGC
193 GCAATGTTGATCCATCAAATGATGAATTCAAGC
*
595990 AAAAGATTGAACAAGTTC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
596054 TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
596119 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTACCTGGCA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACCTGGCA
*
596183 ATGTTGATCCATCAGATGATGAATTCAAGC
196 ATGTTGATCCATCAAATGATGAATTCAAGC
596213 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTC-TCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
596277 TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
596342 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGC
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CTACCTGGC
596407 AA
195 AA
596409 AAAAAATAAT
Statistics
Matches: 395, Mismatches: 13, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
220 5 0.01
221 23 0.06
222 7 0.02
223 184 0.47
224 66 0.17
225 109 0.28
226 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (225 bp):
AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACCTGGCA
ATGTTGATCCATCAAATGATGAATTCAAGC
Found at i:597178 original size:83 final size:83
Alignment explanation
Indices: 597085--597707 Score: 1107
Period size: 83 Copynumber: 7.6 Consensus size: 83
597075 GTAGTTCTCA
*
597085 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
597150 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
597168 CCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
597233 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
597251 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
597316 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
597334 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC-AATTCATCTTC--
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
597395 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
597414 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCATCTTCTA
597479 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
597498 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA-TCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
597562 ATTC-ATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
597579 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
597643 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * * *
597662 TCTAACCAGATCAGATAACTCAAAGAATACTTCCAAAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
597708 GAGTCTCTTT
Statistics
Matches: 522, Mismatches: 8, Indels: 20
0.95 0.01 0.04
Matches are distributed among these distances:
79 2 0.00
80 63 0.12
81 66 0.13
82 55 0.11
83 268 0.51
84 68 0.13
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:597532 original size:164 final size:164
Alignment explanation
Indices: 597085--597707 Score: 1092
Period size: 164 Copynumber: 3.8 Consensus size: 164
597075 GTAGTTCTCA
*
597085 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
*
597150 ATTCAATGATTGGTTCTGCCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
*
597215 GACAAATTCATCTTCTAAATTCAATGATTGGTTCTG
131 GGC-AATTCATCTTC-AAATTCAATGATTGGTTCTG
597251 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
597316 ATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
66 ATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
597380 TGGCAATTCATCTTC-AATTCAATGATTGGTTCTG
130 TGGCAATTCATCTTCAAATTCAATGATTGGTTCTG
597414 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCATCTTCTA
597479 AATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
65 AATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
597544 TGGCAAATCATCTTCTAAATTC-ATGATTGGTTCTG
130 TGGCAATTCATCTTC-AAATTCAATGATTGGTTCTG
597579 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
* * * *
597643 AATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAATACTTCCAAAAGATGCTAT
65 AATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
597708 GAGTCTCTTT
Statistics
Matches: 443, Mismatches: 8, Indels: 14
0.95 0.02 0.03
Matches are distributed among these distances:
163 68 0.15
164 171 0.39
165 68 0.15
166 134 0.30
167 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (164 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
GGCAATTCATCTTCAAATTCAATGATTGGTTCTG
Found at i:610168 original size:20 final size:21
Alignment explanation
Indices: 610145--610185 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
610135 TATTATATGT
**
610145 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
610165 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
610186 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:611129 original size:8 final size:8
Alignment explanation
Indices: 611116--611152 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
611106 CTTTTTTTTT
611116 TCTCTGTG
1 TCTCTGTG
611124 TCTCTGTG
1 TCTCTGTG
611132 TCTCTGTG
1 TCTCTGTG
611140 TCTCTGTG
1 TCTCTGTG
611148 TCTCT
1 TCTCT
611153 TTCAGGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.27, G:0.22, T:0.51
Consensus pattern (8 bp):
TCTCTGTG
Found at i:611626 original size:3 final size:3
Alignment explanation
Indices: 611618--611703 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
611608 AATATATATT
*
611618 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
611666 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
611704 TGGATAAAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:612249 original size:24 final size:24
Alignment explanation
Indices: 612205--612255 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
612195 GAAAATGAAA
*
612205 TTTTTTGAAATAATATGAAATACAT
1 TTTTTTGAAATAAAATGAAATA-AT
612230 TTTTTTG-AATAAAAAT-AAATAAT
1 TTTTTTGAAAT-AAAATGAAATAAT
612253 TTT
1 TTT
612256 AAAATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 8 0.33
25 11 0.46
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTTTTGAAATAAAATGAAATAAT
Found at i:614840 original size:38 final size:37
Alignment explanation
Indices: 614789--614864 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 37
614779 TTGATATTAC
*
614789 ATATTTTTACCAATATGTGCATTATCAATTGTTAAGAA
1 ATATTTTTACCAATATGTGCATTAACAATTGTT-AGAA
614827 ATATTTTTACCAATATGTGCATTAACAATTGTTAGAA
1 ATATTTTTACCAATATGTGCATTAACAATTGTTAGAA
614864 A
1 A
614865 AAGTTGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (37 bp):
ATATTTTTACCAATATGTGCATTAACAATTGTTAGAA
Found at i:623294 original size:37 final size:37
Alignment explanation
Indices: 623218--623294 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
623208 TTTTAATATT
*
623218 TTTAATTTTGTAAAAAATATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
* *
623255 TTTAATTTTTTAAAGAAA-A-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAATATTATATAAATATTAT-CAA
623292 TTT
1 TTT
623295 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 19 0.54
38 3 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
Found at i:623390 original size:29 final size:31
Alignment explanation
Indices: 623348--623436 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 31
623338 TACATTCCAA
**
623348 TAATCTTTTATTCCT-T-CAACCAAACACGG
1 TAATCTTACATTCCTCTACAACCAAACACGG
623377 TAATCTTACATTCCTGCTAAACCAACCAAACACGG
1 TAATCTTACATTCCT-CT--A-CAACCAAACACGG
623412 TAATCTTACATTCCTGCTA-AACCAA
1 TAATCTTACATTCCT-CTACAACCAA
623437 CCAAACACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
29 13 0.25
31 7 0.13
33 1 0.02
35 31 0.60
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.29
Consensus pattern (31 bp):
TAATCTTACATTCCTCTACAACCAAACACGG
Found at i:623407 original size:35 final size:35
Alignment explanation
Indices: 623364--623444 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
623354 TTTATTCCTT
623364 CAACCAAACACGGTAATCTTACATTCCTGCTAAAC
1 CAACCAAACACGGTAATCTTACATTCCTGCTAAAC
623399 CAACCAAACACGGTAATCTTACATTCCTGCTAAAC
1 CAACCAAACACGGTAATCTTACATTCCTGCTAAAC
623434 CAACCAAACAC
1 CAACCAAACAC
623445 AAAATACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (35 bp):
CAACCAAACACGGTAATCTTACATTCCTGCTAAAC
Found at i:623511 original size:20 final size:20
Alignment explanation
Indices: 623475--623512 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
623465 ATCCTATTCC
**
623475 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
623495 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
623513 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:626904 original size:13 final size:13
Alignment explanation
Indices: 626841--626904 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
626831 ATGTGAAAGT
*
626841 ATGAATTATGAAA
1 ATGAAATATGAAA
*
626854 ATGAAATGTGAAA
1 ATGAAATATGAAA
*
626867 GTG-AATATGAAA
1 ATGAAATATGAAA
* *
626879 GA-GAAAGACGAAA
1 -ATGAAATATGAAA
*
626892 ATGAGATATGAAA
1 ATGAAATATGAAA
626905 GTTTTTTATT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
12 10 0.26
13 28 0.74
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.20
Consensus pattern (13 bp):
ATGAAATATGAAA
Found at i:626997 original size:39 final size:39
Alignment explanation
Indices: 626938--627018 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
626928 AAAGAATATA
*
626938 ATATAACTATTATGTATGATATTGTTTATCATGACTTTG
1 ATATAACTATTATATATGATATTGTTTATCATGACTTTG
* * **
626977 ATATGACTATTATATGTGATATTGTTTATCATGGTTTTG
1 ATATAACTATTATATATGATATTGTTTATCATGACTTTG
627016 ATA
1 ATA
627019 AAATCATGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (39 bp):
ATATAACTATTATATATGATATTGTTTATCATGACTTTG
Found at i:628058 original size:2 final size:2
Alignment explanation
Indices: 628051--628080 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
628041 TTTAATAAAT
628051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
628081 AACTCGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:630115 original size:134 final size:134
Alignment explanation
Indices: 629875--630316 Score: 499
Period size: 134 Copynumber: 3.3 Consensus size: 134
629865 TATGGGGTTG
* *
629875 TTGATTCTTTCCACTGTTCCTCAGGGAAGATTGAATTGAGGCAGACTTGTTCCACTATTACTCAA
1 TTGATTCTTTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAA
** * * * * * *
629940 AAAATATCAAATATTGGAAGAGATAGATTTGTTTCGCTTCTTCTTGAGGGAAAACCATATTTG-G
66 GGAATATCAAATCTTGAAAGAGATAGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGAG
*
630004 AAATA
131 -AACA
*** * * *
630009 TTGATTCTTTCTGTTGTTCCTCAGGGAATATTGAATGGAGGCAGACTTGTTCCACTGTTACTCAG
1 TTGATTCTTTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAA
* * *
630074 GGAATATCAAATCTTAAAAGAGATAGATATGTTCCGCTTCTTGTTGAGGGAAAATCAGATCTGAG
66 GGAATATCAAATCTTGAAAGAGATAGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGAG
* *
630139 GACG
131 AACA
* ** * * * * *
630143 TCGATTCAGTCCACTGTTACTCAGGGAAGATTGAATCGAGGAAAACTTGTTCCACTGTTACTTAT
1 TTGATTCTTTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAA
* * * * * *
630208 GGAATATCAAATCTTGAATGAGATGGATCTGTTCGGCTTCTTCTTGAGGGAAAATCATATATGGG
66 GGAATATCAAATCTTGAAAGAGATAGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGAG
**
630273 TTCA
131 AACA
* * *
630277 TTGATTCATTCCACTGTTACTCAAGGAAGATTGAATCGAG
1 TTGATTCTTTCCACTGTTCCTCAGGGAAGATTGAATCGAG
630317 TTCGATTTGT
Statistics
Matches: 258, Mismatches: 49, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
134 257 1.00
135 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (134 bp):
TTGATTCTTTCCACTGTTCCTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAA
GGAATATCAAATCTTGAAAGAGATAGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGAG
AACA
Found at i:631577 original size:6 final size:6
Alignment explanation
Indices: 631560--631630 Score: 83
Period size: 6 Copynumber: 11.8 Consensus size: 6
631550 ATTTTATTTA
* * *
631560 TTCTTT TT-TTT TTCTTTT TTCATT TTCATTT TCCTTT TTCTTT TTCTAT
1 TTCTTT TTCTTT TTC-TTT TTCTTT TTC-TTT TTCTTT TTCTTT TTCTTT
631609 TT-TTT TTCTTT TTCTTT TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTT
631631 ATTTTTCTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
5 9 0.16
6 36 0.65
7 10 0.18
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:631622 original size:17 final size:16
Alignment explanation
Indices: 631564--631627 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 16
631554 TATTTATTCT
*
631564 TTTTTTTTTCTTTTTTC
1 TTTTTCTTT-TTTTTTC
*
631581 ATTTTCATTTTCCTTTTTC
1 TTTTTC-TTTT--TTTTTC
631600 TTTTTCTATTTTTTTTC
1 TTTTTCT-TTTTTTTTC
631617 TTTTTCTTTTT
1 TTTTTCTTTTT
631628 CTTATTTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 4 0.10
17 18 0.45
18 4 0.10
19 14 0.35
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:631626 original size:15 final size:15
Alignment explanation
Indices: 631594--631639 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
631584 TTCATTTTCC
631594 TTTTTCTTTTTCTATTT
1 TTTTTCTTTTTC--TTT
631611 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
* *
631626 TTCTTATTTTTCTT
1 TTTTTCTTTTTCTT
631640 CAGGTGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 15 0.56
17 12 0.44
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:638851 original size:32 final size:33
Alignment explanation
Indices: 638806--638869 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
638796 TCGATGCTGC
* * *
638806 CTTTTTAATTTCAA-CTCTTTTATGCTTCGTCT
1 CTTTTTAAGTTCAAGCTCCTCTATGCTTCGTCT
* *
638838 CTTTTTAGGTTCAAGCTCCTCTATTCTTCGTC
1 CTTTTTAAGTTCAAGCTCCTCTATGCTTCGTC
638870 CTCTAATCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.14, C:0.25, G:0.09, T:0.52
Consensus pattern (33 bp):
CTTTTTAAGTTCAAGCTCCTCTATGCTTCGTCT
Found at i:641847 original size:15 final size:15
Alignment explanation
Indices: 641818--641886 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
641808 ATGTATAAAT
*
641818 AAATAAATTTGGAGAA
1 AAAT-AATTTTGAGAA
641834 AAATAATTTTGAGAA
1 AAATAATTTTGAGAA
641849 AAATAATTTT-A-AA
1 AAATAATTTTGAGAA
*
641862 AGATAATTTTGAGAA
1 AAATAATTTTGAGAA
641877 AAATAATTTT
1 AAATAATTTT
641887 AAAAGATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
13 11 0.23
14 2 0.04
15 31 0.65
16 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
AAATAATTTTGAGAA
Found at i:641871 original size:28 final size:28
Alignment explanation
Indices: 641832--641895 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
641822 AAATTTGGAG
641832 AAAA-ATAATTTTGAGAAAAATAATTTT
1 AAAAGATAATTTTGAGAAAAATAATTTT
641859 AAAAGATAATTTTGAGAAAAATAATTTT
1 AAAAGATAATTTTGAGAAAAATAATTTT
641887 AAAAGATAA
1 AAAAGATAA
641896 AAAAATGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (28 bp):
AAAAGATAATTTTGAGAAAAATAATTTT
Found at i:643329 original size:18 final size:18
Alignment explanation
Indices: 643306--643341 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
643296 TTTTTGCGTG
643306 TTGATTTGTGATAGATGT
1 TTGATTTGTGATAGATGT
643324 TTGATTTGTGATAGATGT
1 TTGATTTGTGATAGATGT
643342 GGTGGTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (18 bp):
TTGATTTGTGATAGATGT
Found at i:643785 original size:3 final size:3
Alignment explanation
Indices: 643777--643834 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
643767 TATTTTATTT
* *
643777 ATA ATA ATA ATA AGTA ATA ATAA ATA ATA ATA TTA ATA ATA A-A TATG
1 ATA ATA ATA ATA A-TA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA
643824 ATA ATA ATA AT
1 ATA ATA ATA AT
643835 TATTAAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 1 0.02
3 40 0.85
4 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:644141 original size:16 final size:17
Alignment explanation
Indices: 644120--644160 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
644110 GTAAAAATTG
644120 ATATTTAAATTTA-AAA
1 ATATTTAAATTTATAAA
*
644136 ATATTTAAATTTATTAA
1 ATATTTAAATTTATAAA
644153 ATATTTAA
1 ATATTTAA
644161 TCAAGTAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTTAAATTTATAAA
Found at i:653705 original size:21 final size:21
Alignment explanation
Indices: 653659--653708 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
653649 TGAAGGAAAT
653659 AGTAT-GA-ACTGGATGAACA
1 AGTATCGATACTGGATGAACA
* *
653678 A-TATCGATACTGGTTGAAGA
1 AGTATCGATACTGGATGAACA
653698 AGTATCGATAC
1 AGTATCGATAC
653709 GAATGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 11 0.42
21 9 0.35
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (21 bp):
AGTATCGATACTGGATGAACA
Found at i:658747 original size:6 final size:6
Alignment explanation
Indices: 658736--658776 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
658726 TAACACCTTG
658736 TGCATT TGCATT TGCATT TGCATT TGCATTT TGCA-T TGCAT
1 TGCATT TGCATT TGCATT TGCATT TGCA-TT TGCATT TGCAT
658777 GTATTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TGCATT
Found at i:661101 original size:6 final size:6
Alignment explanation
Indices: 661086--661196 Score: 54
Period size: 6 Copynumber: 18.0 Consensus size: 6
661076 AGAGAAATAT
* * *
661086 AGAAAG AGAAAA AG-AAA AGATAAA A-AAAA TG-AAA TGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
661132 TA-AAAA AGGAAA AGAAAG AGAAAA ATTGAAAA TGAGAAAA ATG-AAA
1 -AGAAAA AGAAAA AGAAAA AGAAAA A--GAAAA --AGAAAA A-GAAAA
661178 A-AAAA AGAATGAA AGAAAA
1 AGAAAA AGAA--AA AGAAAA
661197 TCGATCAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 30
0.69 0.06 0.25
Matches are distributed among these distances:
5 18 0.22
6 42 0.51
7 6 0.07
8 16 0.19
10 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:661110 original size:12 final size:11
Alignment explanation
Indices: 661065--661156 Score: 53
Period size: 12 Copynumber: 7.8 Consensus size: 11
661055 TTGACATCAT
*
661065 AAAGAGAAAGA
1 AAAGAAAAAGA
*
661076 AGAGAAATATAGA
1 AAAGAAA-A-AGA
661089 AAGAGAAAAAGA
1 AA-AGAAAAAGA
661101 AAAGATAAAA-A
1 AAAGA-AAAAGA
*
661112 AAATG-AAATGAA
1 AAA-GAAAAAG-A
*
661124 AAAGAAAATAAA
1 AAAGAAAA-AGA
*
661136 AAAGGAAAAGA
1 AAAGAAAAAGA
661147 AAGAGAAAAA
1 AA-AGAAAAA
661157 TTGAAAATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.05
11 17 0.27
12 32 0.52
13 5 0.08
14 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:661143 original size:24 final size:23
Alignment explanation
Indices: 661095--661156 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
661085 TAGAAAGAGA
* *
661095 AAAAG-AAAAGATAAAAAAAATG
1 AAAAGAAAAAGAAAAAAAAAAGG
*
661117 AAATGAAAAAGAAAATAAAAAAGG
1 AAAAGAAAAAGAAAA-AAAAAAGG
*
661141 AAAAGAAAGAGAAAAA
1 AAAAGAAAAAGAAAAA
661157 TTGAAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 4 0.12
23 9 0.27
24 20 0.61
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAAAAAAAGG
Found at i:661179 original size:16 final size:16
Alignment explanation
Indices: 661149--661178 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
661139 GGAAAAGAAA
661149 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
661165 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
661179 AAAAAGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:661186 original size:17 final size:17
Alignment explanation
Indices: 661094--661186 Score: 52
Period size: 17 Copynumber: 5.5 Consensus size: 17
661084 ATAGAAAGAG
661094 AAAAAGAAAAGAT-AAAA
1 AAAAAGAAAA-ATGAAAA
*
661111 AAAATG--AAATGAAAA
1 AAAAAGAAAAATGAAAA
* *
661126 AGAAAATAAAAAAGGAAAA
1 A-AAAA-GAAAAATGAAAA
*
661145 GAAAGAGAAAAATTG--AA
1 -AAAAAGAAAAA-TGAAAA
**
661162 AATGAGAAAAATGAAAA
1 AAAAAGAAAAATGAAAA
661179 AAAAAGAA
1 AAAAAGAA
661187 TGAAAGAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
14 2 0.04
15 9 0.16
16 13 0.23
17 15 0.26
18 5 0.09
19 12 0.21
20 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAATGAAAA
Found at i:663395 original size:36 final size:36
Alignment explanation
Indices: 663348--663502 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
663338 AGTCAATCCT
663348 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
663384 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
663420 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * * *
663456 AAGTCTTCACCAGAGAGTAGTAAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
663492 AAGTCTTCACC
1 AAGCCTTCACC
663503 AAAAAGTAGT
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
35 1 0.01
36 107 0.98
37 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:663983 original size:51 final size:51
Alignment explanation
Indices: 663918--664519 Score: 735
Period size: 51 Copynumber: 11.7 Consensus size: 51
663908 AAGATTATTT
* * * *
663918 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * *
663969 TAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
664020 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* *
664071 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCATTTGAAGA-GATGTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-TC
* * * * *
664123 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGC
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
664175 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
664226 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* * *
664277 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC--ATGAAGAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * *
664328 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
664379 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCAAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
664430 GAGTTCTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * * *
664483 GAGTTCTATACTCTCTAGAGAAATAGGGAGCGAACCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCC
664520 ATCATTGAAG
Statistics
Matches: 485, Mismatches: 55, Indels: 20
0.87 0.10 0.04
Matches are distributed among these distances:
49 2 0.00
50 2 0.00
51 392 0.81
52 6 0.01
53 83 0.17
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
Found at i:664602 original size:55 final size:55
Alignment explanation
Indices: 664469--665430 Score: 1250
Period size: 55 Copynumber: 17.7 Consensus size: 55
664459 GCGAACCCGT
* * * *
664469 TTGAAGAGATGTTCGAGT-TCTATACTCTCT-AGAGAAATAGGGAGC-GAAC-CCATCA
1 TTGAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCAG-ACGCAATCG
* * *
664524 TTGAAGATTG-T-GGGTCTTATACTCCCTGAAGAAATAGGGGGCAGACGCGATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* *
664577 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * * *
664632 ATGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * *
664685 TTGAAGATCGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* *
664740 ATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* *
664793 TTGAAGATTGTTCG-GATCTTATACTCTCTGAAGAAATAAGGGGCAGACGCAATAG
1 TTGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* *
664848 TTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
*
664903 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * * * *
664958 ATGAAGATT-AT-GGGTCTTATACTCTTTGAAGAAATAGGGGGCAGACACAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * *
665011 TTGAAGATTGTTCGAGTTTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * *
665066 ATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGTAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* *
665119 TTGAAGATTGTTCG-GATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
*
665174 ATGAAGATTGTT-G-GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * * *
665227 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGATGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * *
665282 ATGAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * *
665335 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGTGGGCATA--CAAGTTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA--TCG
*
665390 TTGAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGG
1 TTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
665431 AGCAAACCCA
Statistics
Matches: 800, Mismatches: 83, Indels: 48
0.86 0.09 0.05
Matches are distributed among these distances:
52 26 0.03
53 299 0.37
54 20 0.03
55 454 0.57
56 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
Found at i:664654 original size:108 final size:108
Alignment explanation
Indices: 664525--665430 Score: 1476
Period size: 108 Copynumber: 8.4 Consensus size: 108
664515 AACCCATCAT
* *
664525 TGAAGATTGTGGGTCTTATACTCCCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
664590 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * *
664633 TGAAGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGTTGAAGATCGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
664698 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
664741 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
* * * *
664806 G-GATCTTATACTCTCTGAAGAAATAAGGGGCAGACGCAATAGT
66 GAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
664849 TGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCAATCGTTGAAGATTGT
1 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGT
*
664914 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGA
64 TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
* * *
664959 TGAAGATTATGGGTCTTATACTCTTTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
*
665024 GAGTTTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
665067 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGTAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
665132 G-GATCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
66 GAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
665175 TGAAGATTGTTGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
* *
665240 GAGTCTTATACTCTCTGAAGAAATAGGGGGTAGATGCGATTGA
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
*
665283 TGAAGATTATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
1 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
* * ** * *
665348 GAGTCTTATACTCTCTGAAGAAATAGTGGGCATACAAGTTTGT
66 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
**
665391 TGAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGG
1 TGAAGATTG--T-GGGTCTTATACTCTCTGAAGAAATAGGG
665431 AGCAAACCCA
Statistics
Matches: 745, Mismatches: 44, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
107 3 0.00
108 611 0.82
109 4 0.01
110 126 0.17
111 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (108 bp):
TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTC
GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA
Found at i:669948 original size:23 final size:23
Alignment explanation
Indices: 669918--669992 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
669908 GTCGAGGGTT
669918 CTATGTGGTCTTTCGGGACAAAA
1 CTATGTGGTCTTTCGGGACAAAA
*
669941 CTATGTGGTACTTT-GGGACAAAC
1 CTATGTGGT-CTTTCGGGACAAAA
* *
669964 CTATCTGGTCCTTCGGGAC-AAA
1 CTATGTGGTCTTTCGGGACAAAA
669986 -TATGTGG
1 CTATGTGG
669993 CACTTCGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.13
22 5 0.11
23 30 0.67
24 4 0.09
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCTTTCGGGACAAAA
Found at i:670000 original size:21 final size:22
Alignment explanation
Indices: 669929--670013 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 22
669919 TATGTGGTCT
*
669929 TTCGGGACAAAACTATGTGGTAC
1 TTCGGGAC-AAACTATGTGGCAC
* *
669952 TTTGGGACAAACCTATCTGGTC-C
1 TTCGGGACAAA-CTATGTGG-CAC
669975 TTCGGGACAAA-TATGTGGCAC
1 TTCGGGACAAACTATGTGGCAC
*
669996 TTCGGTG-CAAATTATGTG
1 TTCGG-GACAAACTATGTG
670014 AGTTGTGGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 1 0.02
21 16 0.31
22 10 0.19
23 25 0.48
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (22 bp):
TTCGGGACAAACTATGTGGCAC
Found at i:670187 original size:14 final size:14
Alignment explanation
Indices: 670168--670205 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
670158 AATTATTTGA
670168 GAAATGTTTTATAT
1 GAAATGTTTTATAT
*
670182 GAAATG-TTTAAAT
1 GAAATGTTTTATAT
670195 -AAATGTTTTAT
1 GAAATGTTTTAT
670206 GATTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 5 0.24
13 10 0.48
14 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
GAAATGTTTTATAT
Done.