Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008052.1 Hibiscus syriacus cultivar Beakdansim tig00110547_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: 532719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:260288 original size:22 final size:22
Alignment explanation
Indices: 260263--260307 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
260253 TGATTCCTGA
260263 TGATTTGTAATAAATTGGACAC
1 TGATTTGTAATAAATTGGACAC
260285 TGATTTGTAATAAATTGGACAC
1 TGATTTGTAATAAATTGGACAC
260307 T
1 T
260308 CCTCGTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGATTTGTAATAAATTGGACAC
Found at i:265775 original size:2 final size:2
Alignment explanation
Indices: 265768--265803 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
265758 TTTCACTCCA
*
265768 AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC A- AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
265804 GCAGCAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:266262 original size:7 final size:7
Alignment explanation
Indices: 266250--266275 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
266240 TATAATTAAA
266250 TATTTTT
1 TATTTTT
266257 TATTTTT
1 TATTTTT
266264 TATTTTT
1 TATTTTT
266271 TATTT
1 TATTT
266276 ATGTGTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:266546 original size:9 final size:10
Alignment explanation
Indices: 266520--266545 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
266510 TAGATTTAAA
266520 AAAAAAATTT
1 AAAAAAATTT
266530 AAAAAAATTT
1 AAAAAAATTT
266540 AAAAAA
1 AAAAAA
266546 TATACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:267020 original size:25 final size:25
Alignment explanation
Indices: 266988--267045 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
266978 TTTGATTACA
* * *
266988 TTTTAAAATTGTTATAAAAACTAAT
1 TTTTAAAAGTATTATAAAAACAAAT
*
267013 TTTTAAAAGTATTGTAAAAACAAAT
1 TTTTAAAAGTATTATAAAAACAAAT
267038 TATTTAAA
1 T-TTTAAA
267046 GATATTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (25 bp):
TTTTAAAAGTATTATAAAAACAAAT
Found at i:267046 original size:25 final size:25
Alignment explanation
Indices: 267002--267059 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
266992 AAAATTGTTA
*
267002 TAAAAACTAATTTTTAAAAG-TATT
1 TAAAAACAAATTTTTAAAAGATATT
267026 GTAAAAACAAATTATTT-AAAGATATT
1 -TAAAAACAAATT-TTTAAAAGATATT
*
267052 TCAAAACA
1 TAAAAACA
267060 TAGTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (25 bp):
TAAAAACAAATTTTTAAAAGATATT
Found at i:267051 original size:26 final size:24
Alignment explanation
Indices: 266988--267059 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
266978 TTTGATTACA
* * *
266988 TTTTAAAATTGTTATAAAAACTAAT
1 TTTTAAAAGTATT-TAAAAACAAAT
267013 TTTTAAAAGTATTGTAAAAACAAAT
1 TTTTAAAAGTATT-TAAAAACAAAT
*
267038 TATTT-AAAGATATTTCAAAACA
1 T-TTTAAAAG-TATTTAAAAACA
267060 TAGTTAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 33 0.82
26 7 0.17
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (24 bp):
TTTTAAAAGTATTTAAAAACAAAT
Found at i:267815 original size:2 final size:2
Alignment explanation
Indices: 267808--267844 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
267798 CTGCGGTTCA
267808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
267845 ATCATAAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:270192 original size:27 final size:27
Alignment explanation
Indices: 270152--270221 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
270142 GTAGGAGTAA
* *
270152 CAGGGTATGGTTCGAGCAACTTGATAG
1 CAGGGCATGATTCGAGCAACTTGATAG
*
270179 CAGGGCATGATTCGAGCAATTTGATAG
1 CAGGGCATGATTCGAGCAACTTGATAG
*
270206 CAGGACATGATTCGAG
1 CAGGGCATGATTCGAG
270222 AAATTTTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (27 bp):
CAGGGCATGATTCGAGCAACTTGATAG
Found at i:270226 original size:27 final size:27
Alignment explanation
Indices: 270162--270227 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
270152 CAGGGTATGG
* *
270162 TTCGAGCAACTTGATAGCAGGGCATGA
1 TTCGAGCAATTTGATAGCAGGACATGA
270189 TTCGAGCAATTTGATAGCAGGACATGA
1 TTCGAGCAATTTGATAGCAGGACATGA
*
270216 TTCGAGAAATTT
1 TTCGAGCAATTT
270228 TATCAAGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (27 bp):
TTCGAGCAATTTGATAGCAGGACATGA
Found at i:278749 original size:21 final size:21
Alignment explanation
Indices: 278711--278750 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
278701 GATAAACACT
* *
278711 ATCGCACTCCACCCAAGAATG
1 ATCGCACTCCAACAAAGAATG
*
278732 ATCGTACTCCAACAAAGAA
1 ATCGCACTCCAACAAAGAA
278751 GGAACATCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.33, G:0.12, T:0.15
Consensus pattern (21 bp):
ATCGCACTCCAACAAAGAATG
Found at i:279255 original size:22 final size:23
Alignment explanation
Indices: 279223--279289 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
279213 AATACTCAAA
*
279223 ATAAT-TT-TATTTTATGA-ATT
1 ATAATATTATATTTTATAATATT
279243 -TAATATTA-ATATTTATAATATT
1 ATAATATTATAT-TTTATAATATT
279265 ATAATATTATA-TTTATAATATT
1 ATAATATTATATTTTATAATATT
279287 ATA
1 ATA
279290 TAAAATAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 6 0.15
22 17 0.43
23 8 0.20
24 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
ATAATATTATATTTTATAATATT
Found at i:279268 original size:8 final size:8
Alignment explanation
Indices: 279249--279289 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
279239 AATTTAATAT
279249 TAATATTTA
1 TAATA-TTA
279258 TAATATTA
1 TAATATTA
279266 TAATATTA
1 TAATATTA
279274 T-AT-TTA
1 TAATATTA
279280 TAATATTA
1 TAATATTA
279288 TA
1 TA
279290 TAAAATAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 4 0.13
7 4 0.13
8 17 0.57
9 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TAATATTA
Found at i:279282 original size:14 final size:15
Alignment explanation
Indices: 279249--279319 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
279239 AATTTAATAT
279249 TAATATTTATAATATTA
1 TAATA-TTAT-ATATTA
279266 TAATATTATAT-TTA
1 TAATATTATATATTA
**
279280 TAATATTATATAAAA
1 TAATATTATATATTA
*
279295 TAATCAAT-TATATTA
1 TAAT-ATTATATATTA
*
279310 TAATAATATA
1 TAATATTATA
279320 AGATATTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 17 0.37
15 18 0.39
16 6 0.13
17 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATTATATATTA
Found at i:279342 original size:29 final size:28
Alignment explanation
Indices: 279277--279364 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
279267 AATATTATAT
* * * *
279277 TTATAATATTATATAAAATAATCAATTATA
1 TTATAATAATATATAATA-AAT-ATTTTTA
*
279307 TTATAATAATATA-AGATATTATATTTTTA
1 TTATAATAATATATA-ATA-AATATTTTTA
*
279336 TTTTAATAATATATAATAAATATTTTTA
1 TTATAATAATATATAATAAATATTTTTA
279364 T
1 T
279365 ATATTTAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
28 10 0.20
29 21 0.43
30 18 0.37
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
TTATAATAATATATAATAAATATTTTTA
Found at i:279368 original size:21 final size:22
Alignment explanation
Indices: 279334--279375 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
279324 ATTATATTTT
279334 TATTTTAATAATATATAATAAA
1 TATTTTAATAATATATAATAAA
* *
279356 TATTTTTAT-ATATTTAATAA
1 TATTTTAATAATATATAATAA
279376 TGAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTTAATAATATATAATAAA
Found at i:279381 original size:24 final size:27
Alignment explanation
Indices: 279348--279406 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
279338 TTAATAATAT
279348 ATAAT-AAATATT-TTTATATATTT-A
1 ATAATAAAATATTATTTATATATTTAA
279372 ATAATGAATAATATTATTTATATATTTAA
1 ATAAT-AA-AATATTATTTATATATTTAA
279401 ATAATA
1 ATAATA
279407 TTTTAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.17
26 1 0.03
27 6 0.20
28 12 0.40
29 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAATAAAATATTATTTATATATTTAA
Found at i:279385 original size:19 final size:19
Alignment explanation
Indices: 279363--279415 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
279353 AAATATTTTT
*
279363 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
279382 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
279404 ATAT-TTTAATAA
1 ATATATTTAATAA
279416 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:279582 original size:48 final size:47
Alignment explanation
Indices: 279526--279635 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 47
279516 ATACAAAAAT
*
279526 TATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TATTATTTTTATT-ATAAAATAATAAAAATAAT-TTTAATAATAAATAA
* * * * *
279575 -ATTATTTTAATATTTTAAAATAATAATATTAATTTTTATGATAAATAA
1 TATTATTTT--TATTATAAAATAATAAAAATAATTTTAATAATAAATAA
279623 TATTATTTATTAT
1 TATTATTT-TTAT
279636 ATTTAATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
48 24 0.47
49 22 0.43
50 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (47 bp):
TATTATTTTTATTATAAAATAATAAAAATAATTTTAATAATAAATAA
Found at i:279606 original size:22 final size:22
Alignment explanation
Indices: 279569--279627 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
279559 ATTTAATAAT
* *
279569 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAAT-TTTTA
279592 AAAT-AATAATATTAATTTTTA
1 AAATAAATAATATTAATTTTTA
**
279613 TGATAAATAATATTA
1 AAATAAATAATATTA
279628 TTTATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAAATAATATTAATTTTTA
Found at i:279643 original size:22 final size:22
Alignment explanation
Indices: 279595--279643 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
279585 TATTTTAAAA
279595 TAATAATATTAATTTTTATGAT
1 TAATAATATTAATTTTTATGAT
*
279617 AAATAATATT-ATTTATTAT-ATT
1 TAATAATATTAATTT-TTATGA-T
279639 TAATA
1 TAATA
279644 TTTGTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATAATATTAATTTTTATGAT
Found at i:279842 original size:15 final size:15
Alignment explanation
Indices: 279797--279842 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
279787 TTTTATAAAT
279797 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
279812 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
279826 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
279841 GT
1 GT
279843 TCCAGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:279860 original size:21 final size:21
Alignment explanation
Indices: 279821--279861 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
279811 AGAATTCAAA
**
279821 TTCCAGTAATTCATTTTTCAG
1 TTCCAGTAATTCAAATTTCAG
279842 TTCCAGTAATTCAAATTTCA
1 TTCCAGTAATTCAAATTTCA
279862 ATAATTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTTCAG
Found at i:282419 original size:34 final size:34
Alignment explanation
Indices: 282381--282446 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
282371 TAAAAAATAA
282381 TAAAATAGTCACACACATATATATATATATATTT
1 TAAAATAGTCACACACATATATATATATATATTT
282415 TAAAATAGTCACACACATATATATATATATAT
1 TAAAATAGTCACACACATATATATATATATAT
282447 ATATATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (34 bp):
TAAAATAGTCACACACATATATATATATATATTT
Found at i:286560 original size:90 final size:89
Alignment explanation
Indices: 286386--286557 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 89
286376 TCCTGAATAT
* * *
286386 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCACTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCACTAATATGACTAG
286451 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
* *
286475 TTAAATTCTAATTAATTAAATGTAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCACTAATATGACTA
*
286539 GGGTAACTTGGTTATAAAA
65 GGGTAACTTGGATATAAAA
286558 AGGTGTGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
89 36 0.47
90 40 0.53
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCACTAATATGACTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:287714 original size:20 final size:22
Alignment explanation
Indices: 287675--287714 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
287665 AAAAAATAAC
287675 ATATTTGATGTTAATTTAATGA
1 ATATTTGATGTTAATTTAATGA
*
287697 ATATTT-AT-TTATTTTAAT
1 ATATTTGATGTTAATTTAAT
287715 TAATTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
ATATTTGATGTTAATTTAATGA
Found at i:288575 original size:30 final size:30
Alignment explanation
Indices: 288539--288597 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
288529 TTAATTTCAA
288539 ATTAACTCGTGAACTAACTCATAATAGTGC
1 ATTAACTCGTGAACTAACTCATAATAGTGC
* *
288569 ATTAACTTGTGAACTAATTCATAATAGTG
1 ATTAACTCGTGAACTAACTCATAATAGTG
288598 TATTTCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (30 bp):
ATTAACTCGTGAACTAACTCATAATAGTGC
Found at i:289919 original size:21 final size:21
Alignment explanation
Indices: 289867--289919 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
289857 ATAAAATTAT
* **
289867 TAAAAAGATAAAGATGAAAGA
1 TAAAAAAATAAAGAAAAAAGA
*
289888 TAAGAAAATAAAGAAAAAAGA
1 TAAAAAAATAAAGAAAAAAGA
289909 -AAAAAATATAA
1 TAAAAAA-ATAA
289920 TCTGTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (21 bp):
TAAAAAAATAAAGAAAAAAGA
Found at i:290038 original size:17 final size:18
Alignment explanation
Indices: 290006--290040 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
289996 ACCATAAACT
*
290006 TTTACATTTTATTTTAAA
1 TTTACATTTCATTTTAAA
290024 TTTAC-TTTCATTTTAAA
1 TTTACATTTCATTTTAAA
290041 AATGTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTACATTTCATTTTAAA
Found at i:292778 original size:16 final size:16
Alignment explanation
Indices: 292757--292790 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
292747 ATTAAAGAAT
292757 TCGAACTC-ATATAGTA
1 TCGAACTCAAT-TAGTA
292773 TCGAACTCAATTAGTA
1 TCGAACTCAATTAGTA
292789 TC
1 TC
292791 AACCTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (16 bp):
TCGAACTCAATTAGTA
Found at i:294238 original size:12 final size:12
Alignment explanation
Indices: 294218--294267 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
294208 TTGCTTTGAG
*
294218 TTAATTTAATTA
1 TTAAATTAATTA
294230 TTAAATTAA-TA
1 TTAAATTAATTA
*
294241 TTTAATTAATTA
1 TTAAATTAATTA
*
294253 -TAATTATAATTA
1 TTAAAT-TAATTA
294265 TTA
1 TTA
294268 TGTTAGGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 13 0.42
12 16 0.52
13 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAATTAATTA
Found at i:303937 original size:20 final size:20
Alignment explanation
Indices: 303912--304002 Score: 92
Period size: 20 Copynumber: 4.3 Consensus size: 20
303902 TTGATTTTTA
* *
303912 ATGTTTGAAATTTAAGATTT
1 ATGTTTTAAATTTAAAATTT
*
303932 ATGTTTAAAATTTAAAATTAT
1 ATGTTTTAAATTTAAAATT-T
* *
303953 ATATTTTAATATTTAAGAATTA
1 ATGTTTTAA-ATTTAA-AATTT
*
303975 AAGTTTTAAATTTAAAATTT
1 ATGTTTTAAATTTAAAATTT
303995 ATAGTTTT
1 AT-GTTTT
304003 TTTTATTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
20 22 0.38
21 19 0.33
22 13 0.22
23 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATGTTTTAAATTTAAAATTT
Found at i:303945 original size:7 final size:7
Alignment explanation
Indices: 303935--303995 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
303925 AAGATTTATG
303935 TTTAAAA
1 TTTAAAA
303942 TTTAAAA
1 TTTAAAA
* *
303949 TTATATAT
1 TT-TAAAA
*
303957 TTTAATA
1 TTTAAAA
303964 TTTAAGAA
1 TTTAA-AA
*
303972 -TTAAAG
1 TTTAAAA
*
303978 TTTTAAA
1 TTTAAAA
303985 TTTAAAA
1 TTTAAAA
303992 TTTA
1 TTTA
303996 TAGTTTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
6 1 0.02
7 34 0.83
8 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (7 bp):
TTTAAAA
Found at i:303989 original size:43 final size:42
Alignment explanation
Indices: 303921--304002 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
303911 AATGTTTGAA
* *
303921 ATTTAAGATTTATGTTTAAAATTTAAAATTATATA-TTTTAAT
1 ATTTAAGATTAAAGTTTAAAATTTAAAATT-TATAGTTTTAAT
*
303963 ATTTAAGAATTAAAGTTTTAAATTTAAAATTTATAGTTTT
1 ATTTAAG-ATTAAAGTTTAAAATTTAAAATTTATAGTTTT
304003 TTTTATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 11 0.31
43 24 0.69
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (42 bp):
ATTTAAGATTAAAGTTTAAAATTTAAAATTTATAGTTTTAAT
Found at i:304000 original size:21 final size:21
Alignment explanation
Indices: 303914--304002 Score: 94
Period size: 21 Copynumber: 4.2 Consensus size: 21
303904 GATTTTTAAT
* *
303914 GTTTGAAATTTAAGATTTAT-
1 GTTTTAAATTTAAAATTTATA
*
303934 GTTTAAAATTTAAAATTATATA
1 GTTTTAAATTTAAAATT-TATA
*
303956 -TTTTAATATTTAAGAA-TTAAA
1 GTTTTAA-ATTTAA-AATTTATA
303977 GTTTTAAATTTAAAATTTATA
1 GTTTTAAATTTAAAATTTATA
303998 GTTTT
1 GTTTT
304003 TTTTATTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
20 17 0.29
21 26 0.45
22 13 0.22
23 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
GTTTTAAATTTAAAATTTATA
Found at i:311202 original size:41 final size:41
Alignment explanation
Indices: 311157--311238 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
311147 TATGACAGGT
311157 GCTTGTTTAGAAATATCAAAACATAAGCGTATGTAGTCAGA
1 GCTTGTTTAGAAATATCAAAACATAAGCGTATGTAGTCAGA
*
311198 GCTTGTTTAGAAATATCAAAACATAAGCGTATGTATTCAGA
1 GCTTGTTTAGAAATATCAAAACATAAGCGTATGTAGTCAGA
311239 TTACTAGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (41 bp):
GCTTGTTTAGAAATATCAAAACATAAGCGTATGTAGTCAGA
Found at i:317025 original size:2 final size:2
Alignment explanation
Indices: 317018--317048 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
317008 ATTGAAATCA
317018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
317049 ATTATTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:318683 original size:37 final size:37
Alignment explanation
Indices: 318610--318684 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
318600 GTTGAAAAAT
*
318610 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
318647 ATTTATATAATTTT-TTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
318684 A
1 A
318685 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:324383 original size:14 final size:14
Alignment explanation
Indices: 324364--324390 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
324354 AAGCGTTTTG
324364 TAATTGCCTTTAAC
1 TAATTGCCTTTAAC
324378 TAATTGCCTTTAA
1 TAATTGCCTTTAA
324391 AATGCAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATTGCCTTTAAC
Found at i:333086 original size:16 final size:16
Alignment explanation
Indices: 333065--333095 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
333055 TACGTTCGTG
333065 TGGGAAATAACCCGAT
1 TGGGAAATAACCCGAT
333081 TGGGAAATAACCCGA
1 TGGGAAATAACCCGA
333096 ATTCCCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (16 bp):
TGGGAAATAACCCGAT
Found at i:339787 original size:208 final size:208
Alignment explanation
Indices: 339429--339845 Score: 834
Period size: 208 Copynumber: 2.0 Consensus size: 208
339419 GCGACCATCG
339429 ATTGTCTTAAAGCTGTTCATTATCAACTCCTGCTTCAACTTGATTACCATGTCGCTCTTGAACAC
1 ATTGTCTTAAAGCTGTTCATTATCAACTCCTGCTTCAACTTGATTACCATGTCGCTCTTGAACAC
339494 GATCCAAAGAGGGTAGTCCTGGATCACAGCATGACGCAAGGTCCCGGGTTTGGGGTTAACAGGGT
66 GATCCAAAGAGGGTAGTCCTGGATCACAGCATGACGCAAGGTCCCGGGTTTGGGGTTAACAGGGT
339559 CGTCATCGGTGTGGTCGGTGACGACGTAGAAGCGTCCGTCACGCCCACCGATTGCATTCCTCCCG
131 CGTCATCGGTGTGGTCGGTGACGACGTAGAAGCGTCCGTCACGCCCACCGATTGCATTCCTCCCG
339624 AAACCAATGCCGC
196 AAACCAATGCCGC
339637 ATTGTCTTAAAGCTGTTCATTATCAACTCCTGCTTCAACTTGATTACCATGTCGCTCTTGAACAC
1 ATTGTCTTAAAGCTGTTCATTATCAACTCCTGCTTCAACTTGATTACCATGTCGCTCTTGAACAC
339702 GATCCAAAGAGGGTAGTCCTGGATCACAGCATGACGCAAGGTCCCGGGTTTGGGGTTAACAGGGT
66 GATCCAAAGAGGGTAGTCCTGGATCACAGCATGACGCAAGGTCCCGGGTTTGGGGTTAACAGGGT
339767 CGTCATCGGTGTGGTCGGTGACGACGTAGAAGCGTCCGTCACGCCCACCGATTGCATTCCTCCCG
131 CGTCATCGGTGTGGTCGGTGACGACGTAGAAGCGTCCGTCACGCCCACCGATTGCATTCCTCCCG
339832 AAACCAATGCCGC
196 AAACCAATGCCGC
339845 A
1 A
339846 CTCGGCTAGT
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 209 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (208 bp):
ATTGTCTTAAAGCTGTTCATTATCAACTCCTGCTTCAACTTGATTACCATGTCGCTCTTGAACAC
GATCCAAAGAGGGTAGTCCTGGATCACAGCATGACGCAAGGTCCCGGGTTTGGGGTTAACAGGGT
CGTCATCGGTGTGGTCGGTGACGACGTAGAAGCGTCCGTCACGCCCACCGATTGCATTCCTCCCG
AAACCAATGCCGC
Found at i:341031 original size:59 final size:59
Alignment explanation
Indices: 340909--341040 Score: 133
Period size: 59 Copynumber: 2.2 Consensus size: 59
340899 TAGTCGGTGA
* * * ** *
340909 CATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAAATAGCGATAATCGGGGAT
1 CATTTTGTAACTTTTAATAGTCAATGAACTCAACAAAACAAATAGCGATAATCCAGGAC
* * * * *
340968 CATTTTGTTATTTTTAATAGTCAATGAACTCAACAAAACAATATA-CTATAGTCCATGAC
1 CATTTTGTAACTTTTAATAGTCAATGAACTCAACAAAACAA-ATAGCGATAATCCAGGAC
341027 CA-TTTGTATACTTT
1 CATTTTGTA-ACTTT
341041 ACCCATAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
58 5 0.09
59 50 0.86
60 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTCAATGAACTCAACAAAACAAATAGCGATAATCCAGGAC
Found at i:344670 original size:26 final size:26
Alignment explanation
Indices: 344630--344769 Score: 122
Period size: 26 Copynumber: 5.3 Consensus size: 26
344620 TTTTTTCTTT
344630 AACATTAATCGAACCGAAATTATTTG
1 AACATTAATCGAACCGAAATTATTTG
* * *
344656 ACCGTTAATCAAACCGAAAATTATTTG
1 AACATTAATCGAACCG-AAATTATTTG
* * * * *
344683 AAAATT-AT-TAACCGAATTTTTTTCTTT
1 AACATTAATCGAACCGAA--ATTAT-TTG
344710 AACATTAATCGAACCGAAATTATTTG
1 AACATTAATCGAACCGAAATTATTTG
* *
344736 ACCGTTAATCGAACCGAAATTTATTTG
1 AACATTAATCGAACCGAAA-TTATTTG
*
344763 AAAATTA
1 AACATTA
344770 TGTGAAAGTT
Statistics
Matches: 87, Mismatches: 20, Indels: 13
0.73 0.17 0.11
Matches are distributed among these distances:
24 2 0.02
25 5 0.06
26 37 0.43
27 34 0.39
28 2 0.02
29 7 0.08
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (26 bp):
AACATTAATCGAACCGAAATTATTTG
Found at i:344742 original size:80 final size:80
Alignment explanation
Indices: 344609--344770 Score: 306
Period size: 80 Copynumber: 2.0 Consensus size: 80
344599 ACCGAACCAA
344609 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAA
344674 AATTATTTGAAAATT
66 AATTATTTGAAAATT
*
344689 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAA
*
344754 ATTTATTTGAAAATT
66 AATTATTTGAAAATT
344769 AT
1 AT
344771 GTGAAAGTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (80 bp):
ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAA
AATTATTTGAAAATT
Found at i:347745 original size:2 final size:2
Alignment explanation
Indices: 347738--347777 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
347728 ACGATGTAGC
347738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
347778 AGAGTTTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351373 original size:88 final size:88
Alignment explanation
Indices: 351224--351399 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
351214 AAGCAACTCA
351224 TTGCGTATAAAGGTAGAGCTTGAAGGACCGACTTAATAAAAATCTCCTTACCCCTTGAGATAGAA
1 TTGCGTATAAAGGTAGAGCTTGAAGGACCGACTTAATAAAAATCTCCTTACCCCTTGAGATAGAA
351289 CTCGCACATTCCAGCTTCGAATT
66 CTCGCACATTCCAGCTTCGAATT
351312 TTGCGTATAAAGGTAGAGCTTGAAGGACCGACTTAATAAAAATCTCCTTACCCCTTGAGATAGAA
1 TTGCGTATAAAGGTAGAGCTTGAAGGACCGACTTAATAAAAATCTCCTTACCCCTTGAGATAGAA
351377 CTCGCACATTCCAGCTTCGAATT
66 CTCGCACATTCCAGCTTCGAATT
351400 CTACACTTAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (88 bp):
TTGCGTATAAAGGTAGAGCTTGAAGGACCGACTTAATAAAAATCTCCTTACCCCTTGAGATAGAA
CTCGCACATTCCAGCTTCGAATT
Found at i:359601 original size:100 final size:100
Alignment explanation
Indices: 359428--359631 Score: 408
Period size: 100 Copynumber: 2.0 Consensus size: 100
359418 TGTTAAATTT
359428 GATTATCAATTTATTATAACATAGTTGATCAATGATTCAATATAGCAATGTCTACGATGTGATCT
1 GATTATCAATTTATTATAACATAGTTGATCAATGATTCAATATAGCAATGTCTACGATGTGATCT
359493 ACAAATTCTTAAATGTAAACCGTCTCTACTCAAAA
66 ACAAATTCTTAAATGTAAACCGTCTCTACTCAAAA
359528 GATTATCAATTTATTATAACATAGTTGATCAATGATTCAATATAGCAATGTCTACGATGTGATCT
1 GATTATCAATTTATTATAACATAGTTGATCAATGATTCAATATAGCAATGTCTACGATGTGATCT
359593 ACAAATTCTTAAATGTAAACCGTCTCTACTCAAAA
66 ACAAATTCTTAAATGTAAACCGTCTCTACTCAAAA
359628 GATT
1 GATT
359632 TGCAGAATAT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 104 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (100 bp):
GATTATCAATTTATTATAACATAGTTGATCAATGATTCAATATAGCAATGTCTACGATGTGATCT
ACAAATTCTTAAATGTAAACCGTCTCTACTCAAAA
Found at i:369930 original size:2 final size:2
Alignment explanation
Indices: 369925--369964 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
369915 ATACACACAC
369925 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
369965 TTTCATAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:370235 original size:2 final size:2
Alignment explanation
Indices: 370228--370254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
370218 TAAACCTTCT
370228 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
370255 TAATTTAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:371029 original size:20 final size:20
Alignment explanation
Indices: 371001--371044 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
370991 TATATAAGAC
* *
371001 ATTTTATTATAAACCAAATT
1 ATTTAATTAAAAACCAAATT
**
371021 ATTTAATTAAAAATTAAATT
1 ATTTAATTAAAAACCAAATT
371041 ATTT
1 ATTT
371045 TAACTTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAATTAAAAACCAAATT
Found at i:371118 original size:23 final size:24
Alignment explanation
Indices: 371059--371125 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
371049 TTTATTTTGG
* *
371059 AATAAAAAATAAATATATTTTAAAA
1 AATAAATATTAAA-ATATTTTAAAA
* *
371084 AATCAATATTAAACTATTTTAAAA
1 AATAAATATTAAAATATTTTAAAA
**
371108 TTTAAAT-TTAAAATATTT
1 AATAAATATTAAAATATTT
371126 ATTTATAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 10 0.29
24 14 0.41
25 10 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAAATATTAAAATATTTTAAAA
Found at i:377416 original size:21 final size:20
Alignment explanation
Indices: 377330--377487 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
377320 AAATGACCAA
**
377330 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
377349 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
377369 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
377389 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
377410 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
377431 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
377451 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
377472 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
377488 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:377516 original size:20 final size:20
Alignment explanation
Indices: 377454--377647 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
377444 CGATTTTCCA
* ** *
377454 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
377474 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
377494 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
377514 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
377534 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
377554 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
377574 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
377594 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
377614 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
377635 AAATCGCAACGCG
1 AAATCGCAACGCG
377648 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:377538 original size:60 final size:60
Alignment explanation
Indices: 377454--377647 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
377444 CGATTTTCCA
* ** * *
377454 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
377514 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
377574 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
377635 AAATCGCAACGCG
1 AAATCGCAACGCG
377648 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:378079 original size:19 final size:19
Alignment explanation
Indices: 378055--378102 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
378045 ACGATTCTGT
*
378055 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTGTCATTTCG
378074 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTGTCATTTCG
378093 CGTTGCGATT
1 CGTTGCGATT
378103 CTCTCGTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTGTCATTTCG
Found at i:378244 original size:20 final size:20
Alignment explanation
Indices: 378200--378309 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
378190 TGCAGAAGAG
*
378200 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
378221 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
378241 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
378262 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
378276 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
378295 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
378310 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:378257 original size:41 final size:38
Alignment explanation
Indices: 378193--378309 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
378183 TTCAATTTGC
* *
378193 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
378231 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
378272 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
378305 AGAAT
1 AGAAT
378310 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:378279 original size:14 final size:14
Alignment explanation
Indices: 378260--378316 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
378250 GAGAAATGAA
378260 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
378274 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
378293 AATCGCAACGAGAG
1 AATCGCAACGAGAG
378307 AATCGCAACG
1 AATCGCAACG
378317 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:378292 original size:33 final size:33
Alignment explanation
Indices: 378252--378332 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
378242 CGCAACGAGA
378252 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
378285 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
378318 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
378333 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:378350 original size:19 final size:18
Alignment explanation
Indices: 378328--378447 Score: 84
Period size: 19 Copynumber: 7.1 Consensus size: 18
378318 GAAACCAAAA
378328 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
378347 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
378363 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
378380 TCGCATTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
*
378396 TCG-TTGCGATTGTCATT
1 TCGCTTGCGATTTTCATT
*
378413 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
378429 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
378446 TC
1 TC
378448 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
14 18 0.23
16 20 0.25
17 19 0.24
19 22 0.28
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:378369 original size:14 final size:14
Alignment explanation
Indices: 378350--378439 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
378340 TTTCATTTCG
378350 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
378364 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
378381 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
378397 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
378416 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
378430 CGTTGCGATT
1 CGTTGCGATT
378440 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 26 0.42
15 1 0.02
16 9 0.15
17 9 0.15
18 1 0.02
19 16 0.26
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:378375 original size:33 final size:33
Alignment explanation
Indices: 378333--378447 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
378323 CAAAATCGCA
378333 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
378366 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
378399 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
378432 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
378448 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:380303 original size:93 final size:93
Alignment explanation
Indices: 380144--380426 Score: 532
Period size: 93 Copynumber: 3.1 Consensus size: 93
380134 TAGATTGCTT
*
380144 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
380209 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
380237 AGTAAATTTGTTCGATTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
380302 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
380330 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
380395 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
380422 AGTAA
1 AGTAA
380427 TGCAATCCAT
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
92 6 0.03
93 179 0.97
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:380575 original size:19 final size:19
Alignment explanation
Indices: 380474--380569 Score: 112
Period size: 19 Copynumber: 5.3 Consensus size: 19
380464 TAGTTTACTT
* *
380474 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
*
380494 TCTCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
380513 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
380532 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
380546 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
380565 TCGCA
1 TCGCA
380570 TTGCGATTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 37 0.57
20 12 0.18
ACGTcount: A:0.46, C:0.30, G:0.15, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:380600 original size:19 final size:19
Alignment explanation
Indices: 380565--380684 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
380555 GAAACCAAAA
*
380565 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
380583 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
380602 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
380618 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
380635 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
380654 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
380674 TCGTGTTGCGA
1 TCGCGTTGCGA
380685 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
18 10 0.12
19 46 0.54
20 12 0.14
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:382762 original size:19 final size:19
Alignment explanation
Indices: 382746--382843 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
382736 AAAAATGACT
382746 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
382765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
382784 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
382798 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
382817 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
382837 ATCGCAA
1 ATCGCAA
382844 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:382875 original size:53 final size:53
Alignment explanation
Indices: 382746--382861 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
382736 AAAAATGACT
382746 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
382798 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
382851 ATCGCAATGCG
1 ATCGCAATGCG
382862 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:382905 original size:33 final size:33
Alignment explanation
Indices: 382868--383020 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
382858 TGCGTTTATA
382868 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
382901 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
382941 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
382972 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
383005 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
383021 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:382914 original size:19 final size:19
Alignment explanation
Indices: 382890--383106 Score: 249
Period size: 19 Copynumber: 12.4 Consensus size: 19
382880 GATTCTCTCG
382890 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
382909 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
382928 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
382942 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
382961 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
382980 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
382994 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
383013 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
383032 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
383046 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
383066 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
383080 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
383099 TTGCGATT
1 TTGCGATT
383107 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:382925 original size:52 final size:52
Alignment explanation
Indices: 382868--383078 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
382858 TGCGTTTATA
382868 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
382920 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
382972 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
383024 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
383077 AT
1 AT
383079 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:383128 original size:33 final size:33
Alignment explanation
Indices: 382909--383120 Score: 234
Period size: 33 Copynumber: 6.2 Consensus size: 33
382899 TCATTTCGCA
382909 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
382942 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
382978 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
383013 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
383046 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
383080 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
383113 TTGCGATT
1 TTGCGATT
383121 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 16, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 73 0.49
34 29 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:385420 original size:12 final size:12
Alignment explanation
Indices: 385403--385427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
385393 TCTTCGGGGA
385403 CTTTTTCTTCTT
1 CTTTTTCTTCTT
385415 CTTTTTCTTCTT
1 CTTTTTCTTCTT
385427 C
1 C
385428 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:385633 original size:24 final size:24
Alignment explanation
Indices: 385599--385645 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
385589 CTGAAACATC
385599 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
385623 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
385646 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:386354 original size:20 final size:20
Alignment explanation
Indices: 386326--386535 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
386316 AAATTTCAGT
* * * *
386326 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
386346 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
386366 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
386386 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
386406 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
386426 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
386446 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
386466 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
386486 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
386506 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
386526 GTTGCGATTT
1 GTTGCGATTT
386536 TCATATTCGC
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:386544 original size:20 final size:19
Alignment explanation
Indices: 386503--386556 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
386493 TTTACGGATA
* *
386503 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATATT
386523 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATATT
*
386543 CGCGTTTCGATTTT
1 CGCGTTGCGATTTT
386557 GGAAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
CGCGTTGCGATTTTATATT
Found at i:396257 original size:131 final size:132
Alignment explanation
Indices: 396022--396286 Score: 482
Period size: 132 Copynumber: 2.0 Consensus size: 132
396012 AATCAACATG
396022 AGATCTAAATAAAATGAAGAAAAAAAAATAATACAGTCACCAAGAATAATATTAATATAGTTTCA
1 AGATCTAAATAAAATGAAGAAAAAAAAAT-ATACAGTCACCAAGAATAATATTAATATAGTTTCA
396087 ACATATTTAATTTACCTCTTAATCCAATTTTTTATTATTAT-AAAAATTAGTCACAAAAATTAAT
65 ACATATTTAATTTACCTCTTAATCCAATTTTTTATTATTATAAAAAATTAGTCACAAAAATTAAT
396151 CTC
130 CTC
396154 AGATCTAAATAAAATGAAGAAAAAAATAAT-TACAGTCACCAAGAATAATATTTAATATAGTTTC
1 AGATCTAAATAAAATGAAGAAAAAAA-AATATACAGTCACCAAGAATAATA-TTAATATAGTTTC
396218 AACATATTTAA-TTACCTCTTAATCCAATTTTTTATTATTATAAAAAATTAGTCACAAAAATTAA
64 AACATATTTAATTTACCTCTTAATCCAATTTTTTATTATTATAAAAAATTAGTCACAAAAATTAA
396282 TCTC
129 TCTC
396286 A
1 A
396287 TTCATTGCCT
Statistics
Matches: 130, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
131 50 0.38
132 77 0.59
133 3 0.02
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (132 bp):
AGATCTAAATAAAATGAAGAAAAAAAAATATACAGTCACCAAGAATAATATTAATATAGTTTCAA
CATATTTAATTTACCTCTTAATCCAATTTTTTATTATTATAAAAAATTAGTCACAAAAATTAATC
TC
Found at i:403418 original size:6 final size:6
Alignment explanation
Indices: 403409--403444 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
403399 AATCGCCTCA
403409 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
403445 CGAGACGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:404123 original size:5 final size:5
Alignment explanation
Indices: 404115--404193 Score: 95
Period size: 6 Copynumber: 14.4 Consensus size: 5
404105 CCGTCTCGTC
404115 TCGGG TCGGG TCGGGG TCGGG TCGGG TCGGGG TCGGG TCGGG TCGGG TCGTGG
1 TCGGG TCGGG TC-GGG TCGGG TCGGG TC-GGG TCGGG TCGGG TCGGG TCG-GG
404168 TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCG-GG TCG-GG TCG-GG TCG-GG TC
404194 ATACGTGTCT
Statistics
Matches: 71, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
5 33 0.46
6 38 0.54
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:404136 original size:16 final size:16
Alignment explanation
Indices: 404115--404193 Score: 106
Period size: 16 Copynumber: 4.8 Consensus size: 16
404105 CCGTCTCGTC
404115 TCGGGTCGGGTCGGGG
1 TCGGGTCGGGTCGGGG
404131 TCGGGTCGGGTCGGGG
1 TCGGGTCGGGTCGGGG
404147 TCGGGTCGGGTC-GGG
1 TCGGGTCGGGTCGGGG
*
404162 TCGTGGTCGTGGTCGTGG
1 TCG-GGTCG-GGTCGGGG
404180 TCGTGGTCGTGGTC
1 TCG-GGTCG-GGTC
404194 ATACGTGTCT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
15 6 0.10
16 33 0.56
17 4 0.07
18 16 0.27
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (16 bp):
TCGGGTCGGGTCGGGG
Found at i:404323 original size:20 final size:20
Alignment explanation
Indices: 404300--404494 Score: 117
Period size: 20 Copynumber: 9.6 Consensus size: 20
404290 TCCTTTTTAA
404300 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
404320 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
404340 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
404360 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
404383 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* * *
404404 CGTTGCGCTTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
404422 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
404444 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
404464 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
404483 CGTTGCGATTTT
1 CGTTGCGATTTT
404495 ATTGGTCATT
Statistics
Matches: 137, Mismatches: 30, Indels: 17
0.74 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.12
20 88 0.64
21 12 0.09
22 4 0.03
23 14 0.10
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:404484 original size:19 final size:20
Alignment explanation
Indices: 404444--404494 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
404434 TTCTTTTTAA
*
404444 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
404464 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
404483 CGTTGCGATTTT
1 CGTTGCGATTTT
404495 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:405661 original size:36 final size:36
Alignment explanation
Indices: 405583--405736 Score: 179
Period size: 36 Copynumber: 4.2 Consensus size: 36
405573 TGAAAATACG
* *
405583 TATATAATATAT-ATGGTTTTTAAAACACTTTTAAAAA
1 TATATAATATATAAT--TTTTAAAAACATTTTTAAAAA
* *
405620 CTATATATTATAT-ATATTTTCAAAACATTTTTAAAAA
1 -TATATAATATATAAT-TTTTAAAAACATTTTTAAAAA
405657 TATATAATATATAATTTTTGAAAAACA-TTTTAAAAA
1 TATATAATATATAATTTTT-AAAAACATTTTTAAAAA
* *
405693 TATATAAAATATAATTTTTGAAAACATTTTTAAAAA
1 TATATAATATATAATTTTTAAAAACATTTTTAAAAA
*
405729 AATATAAT
1 TATATAAT
405737 TTTAAAAGAA
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
35 6 0.06
36 57 0.55
37 27 0.26
38 13 0.13
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATAATATATAATTTTTAAAAACATTTTTAAAAA
Found at i:405696 original size:29 final size:28
Alignment explanation
Indices: 405662--405780 Score: 80
Period size: 29 Copynumber: 3.9 Consensus size: 28
405652 AAAAATATAT
405662 AATATATAATTTTTGAAAAACATTTTAAAAA
1 AATATATAATTTTTG-AAAACATTTT--AAA
405693 TATATAAAATATAATTTTTGAAAACATTTTTAAA
1 -A-AT---ATATAATTTTTGAAAACA-TTTTAAA
* **
405727 AAAATATAATTTTAAAAGAAC-TTTTAAA
1 AATATATAATTTTTGAA-AACATTTTAAA
*
405755 AAT-TATTAGTTTTTTGAAAACATTTT
1 AATATA-TA-ATTTTTGAAAACATTTT
405781 TGAAAATTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
27 2 0.03
28 14 0.20
29 22 0.31
30 3 0.04
32 2 0.03
33 3 0.04
34 3 0.04
35 6 0.08
36 16 0.23
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (28 bp):
AATATATAATTTTTGAAAACATTTTAAA
Found at i:405751 original size:28 final size:29
Alignment explanation
Indices: 405698--405756 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
405688 AAAAATATAT
* *
405698 AAAATATAATTTTTGAAAACATTTTTAAA
1 AAAATATAATTTTTGAAAAAACTTTTAAA
405727 AAAATATAA-TTTT-AAAAGAACTTTTAAA
1 AAAATATAATTTTTGAAAA-AACTTTTAAA
405755 AA
1 AA
405757 TTATTAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 14 0.52
29 9 0.33
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATATAATTTTTGAAAAAACTTTTAAA
Found at i:407910 original size:19 final size:19
Alignment explanation
Indices: 407866--407911 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
407856 ATCTATTTTT
*
407866 CATAGTTAAATTAAAAAAA
1 CATAATTAAATTAAAAAAA
407885 CATTAATTAAA-TAAATAAAA
1 CA-TAATTAAATTAAA-AAAA
407905 CATAATT
1 CATAATT
407912 TCGAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
CATAATTAAATTAAAAAAA
Found at i:411303 original size:16 final size:16
Alignment explanation
Indices: 411279--411333 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
411269 CGTTTAATAA
* *
411279 ATAACCGAATACGAAC
1 ATAAACGAACACGAAC
411295 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
411311 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
411327 ATAAACG
1 ATAAACG
411334 TTGGAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.55, C:0.22, G:0.13, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:412289 original size:24 final size:24
Alignment explanation
Indices: 412259--412308 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
412249 AATGAAAAAA
412259 AAACGAACATAACCGAACAAACAT
1 AAACGAACATAACCGAACAAACAT
*
412283 AAACGAACATAACCGAACGAACAT
1 AAACGAACATAACCGAACAAACAT
412307 AA
1 AA
412309 CTGAATGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.24, G:0.10, T:0.08
Consensus pattern (24 bp):
AAACGAACATAACCGAACAAACAT
Found at i:412301 original size:14 final size:14
Alignment explanation
Indices: 412260--412309 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
412250 ATGAAAAAAA
412260 AACGAACATAACCG
1 AACGAACATAACCG
*
412274 AACAAACAT-A---
1 AACGAACATAACCG
412284 AACGAACATAACCG
1 AACGAACATAACCG
412298 AACGAACATAAC
1 AACGAACATAAC
412310 TGAATGTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
13 1 0.03
14 20 0.67
ACGTcount: A:0.56, C:0.26, G:0.10, T:0.08
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:412649 original size:19 final size:20
Alignment explanation
Indices: 412627--412664 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
412617 AAAATTTATT
412627 AATTAA-ATTAAATAAAAAA
1 AATTAACATTAAATAAAAAA
412646 AATTAACATTAAATAAAAA
1 AATTAACATTAAATAAAAA
412665 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AATTAACATTAAATAAAAAA
Found at i:417202 original size:31 final size:31
Alignment explanation
Indices: 417160--417229 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
417150 TTTTACATAA
* * *
417160 ATGTAAAATTGTTAATGA-AGATGCTTGTATG
1 ATGTAATATTGTTAATGAGA-ATGCGTGGATG
417191 ATGTAATATTGTTAATGAGAATGCGTGGATG
1 ATGTAATATTGTTAATGAGAATGCGTGGATG
417222 ATGTAATA
1 ATGTAATA
417230 CAGGACCACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (31 bp):
ATGTAATATTGTTAATGAGAATGCGTGGATG
Found at i:417443 original size:14 final size:15
Alignment explanation
Indices: 417410--417449 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
417400 TTAGTTTTAG
*
417410 TTTCATTTTAGTACAT
1 TTTCATTTTAG-AAAT
417426 TTTCATTTTA-AAAT
1 TTTCATTTTAGAAAT
417440 TTTCATTTTA
1 TTTCATTTTA
417450 TTTCATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTCATTTTAGAAAT
Found at i:417593 original size:21 final size:21
Alignment explanation
Indices: 417567--417621 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
417557 CGGTGCTAAA
417567 GTGACGATCTATAGTACTGAT
1 GTGACGATCTATAGTACTGAT
*
417588 GTGACGATCCATAGTACTGAT
1 GTGACGATCTATAGTACTGAT
*
417609 GTGACAATCTATA
1 GTGACGATCTATA
417622 ATGGTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (21 bp):
GTGACGATCTATAGTACTGAT
Found at i:421849 original size:16 final size:16
Alignment explanation
Indices: 421828--421866 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
421818 AACATAAAAA
*
421828 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
421844 AAACATATCCATTAAG
1 AAACATATCCATTAAG
421860 AAACATA
1 AAACATA
421867 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:423458 original size:19 final size:19
Alignment explanation
Indices: 423434--423471 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
423424 AACTAGTTCA
423434 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
423453 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
423472 CGATTCCAAT
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:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:430648 original size:15 final size:15
Alignment explanation
Indices: 430607--430662 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
430597 CTGGGTGGGC
* *
430607 GGATGTGGGGCAGGT
1 GGATGCGGGGCGGGT
430622 GGATGCGGGGCGGGT
1 GGATGCGGGGCGGGT
* *
430637 GGATGCGGGGCGAGC
1 GGATGCGGGGCGGGT
*
430652 GGATGCAGGGC
1 GGATGCGGGGC
430663 AGATGCGGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.12, C:0.14, G:0.61, T:0.12
Consensus pattern (15 bp):
GGATGCGGGGCGGGT
Found at i:438815 original size:6 final size:6
Alignment explanation
Indices: 438799--438840 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
438789 AAGATCAAAC
438799 ACATG- ACATGA ACATGA ACATGA ACATGA ACATGA ACATGA A
1 ACATGA ACATGA ACATGA ACATGA ACATGA ACATGA ACATGA A
438841 TCTGTCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ACATGA
Found at i:442334 original size:6 final size:6
Alignment explanation
Indices: 442313--442346 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
442303 TCTCGTCTCG
442313 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
442347 ATACCAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:443773 original size:21 final size:21
Alignment explanation
Indices: 443744--443793 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
443734 GGGTTGAATT
*
443744 CATTACGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
443765 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
443786 CGTTGCGA
1 CATTGCGA
443794 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:447772 original size:59 final size:59
Alignment explanation
Indices: 447691--447824 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 59
447681 ATTATTTACC
447691 ATTT-TTATGTTCATTTTATATTTTAAAAAATCT-ATCACGATACTTCAATCAATAGAATA
1 ATTTGTTA-GTTCATTTTATATTTT-AAAAATCTCATCACGATACTTCAATCAATAGAATA
* * * * * *
447750 ATTTGTTAGTTCATTTTGTATTTTAAAATTTTCATCATGATATTTCAGTCAATAGAATA
1 ATTTGTTAGTTCATTTTATATTTTAAAAATCTCATCACGATACTTCAATCAATAGAATA
* *
447809 TTTTGTTAGTCCATTT
1 ATTTGTTAGTTCATTT
447825 ACTTAAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
58 6 0.09
59 56 0.86
60 3 0.05
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (59 bp):
ATTTGTTAGTTCATTTTATATTTTAAAAATCTCATCACGATACTTCAATCAATAGAATA
Found at i:447856 original size:23 final size:24
Alignment explanation
Indices: 447830--447878 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
447820 CATTTACTTA
*
447830 AATTTTGCCT-CAATT-CATTTTAT
1 AATTTTG-CTACAATTGAATTTTAT
447853 AA-TTTGCTACAATTGAATTTTAT
1 AATTTTGCTACAATTGAATTTTAT
447876 AAT
1 AAT
447879 AAACTCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 2 0.09
22 9 0.41
23 11 0.50
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (24 bp):
AATTTTGCTACAATTGAATTTTAT
Found at i:463772 original size:16 final size:17
Alignment explanation
Indices: 463738--463779 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
463728 CTTTCAAAAG
*
463738 TTAATT-TTATTTTTCA
1 TTAATTATTATTATTCA
463754 TTAATTATTATTATT-A
1 TTAATTATTATTATTCA
*
463770 TTATTTATTA
1 TTAATTATTA
463780 ACTATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATTATTATTATTCA
Found at i:465902 original size:18 final size:19
Alignment explanation
Indices: 465861--465905 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
465851 TTTGGTTCAC
* *
465861 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-A
465881 GGAATAAAAGATTACCA-A
1 GGAATAAAAGATTACCAGA
465899 GGAATAA
1 GGAATAA
465906 GATTATTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGA
Found at i:466077 original size:15 final size:15
Alignment explanation
Indices: 466059--466089 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
466049 AAATTTTAAA
466059 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
466074 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
466089 T
1 T
466090 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:467215 original size:12 final size:12
Alignment explanation
Indices: 467198--467225 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
467188 TTATTCAAAG
467198 GCATGCACCGAT
1 GCATGCACCGAT
467210 GCATGCACCGAT
1 GCATGCACCGAT
467222 GCAT
1 GCAT
467226 CAGTCCATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (12 bp):
GCATGCACCGAT
Found at i:467298 original size:19 final size:19
Alignment explanation
Indices: 467274--467312 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
467264 TCGAATGCAT
467274 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
467293 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
467312 T
1 T
467313 GAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:467329 original size:65 final size:62
Alignment explanation
Indices: 467211--467439 Score: 205
Period size: 64 Copynumber: 3.5 Consensus size: 62
467201 TGCACCGATG
** *
467211 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGATATAATTGAACATCGAATGCATT
1 CATGCACCGATGCATC--TCCATGCATCGATGCACTCGA--ATATTTTTAAACATCGAATGCATT
*
467275 C
62 T
467276 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTTAAAACATCGAATGCATTT
1 CATGCACCGATGCA-TCTCCATGCATCGATGCACTC-GAATATTTTT-AAACATCGAATGCATTT
* * * **
467341 GATGCATCGATGCA-CAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATT
1 CATGCACCGATGCATC--TCCATGCATCGATGCACTC-GAATATTTTT-AAACATCGAATGCATT
467404 T
62 T
* * *
467405 TATGCATCGATGCATC-CTTAGTGCATCGATGCACT
1 CATGCACCGATGCATCTC-CA-TGCATCGATGCACT
467440 AAGTGTCCCA
Statistics
Matches: 141, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.01
64 74 0.52
65 60 0.43
66 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (62 bp):
CATGCACCGATGCATCTCCATGCATCGATGCACTCGAATATTTTTAAACATCGAATGCATTT
Found at i:467410 original size:64 final size:65
Alignment explanation
Indices: 467260--467418 Score: 212
Period size: 65 Copynumber: 2.5 Consensus size: 65
467250 GATATAATTG
* * *** *
467260 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTTAA
* ** *
467325 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTTAA
*
467389 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
467419 TCCTTAGTGC
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 39 0.47
65 44 0.53
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTTAA
Found at i:473989 original size:31 final size:31
Alignment explanation
Indices: 473918--473997 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
473908 ATTTAACAAA
* * **
473918 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
473949 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
473980 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
473998 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:474405 original size:19 final size:19
Alignment explanation
Indices: 474381--474419 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
474371 TCGAATGCAT
474381 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
474400 TCCATGCATCGATGTACTC
1 TCCATGCACCGATGCACTC
474419 T
1 T
474420 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:474518 original size:64 final size:65
Alignment explanation
Indices: 474367--474525 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 65
474357 GATATAATTG
* * *** * *
474367 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGTACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
474432 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
474495 A
65 A
*
474496 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
474526 TCCTTAGTGC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
64 34 0.41
65 48 0.59
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:482510 original size:20 final size:19
Alignment explanation
Indices: 482468--482514 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
482458 ATGATTTTCT
* * *
482468 TTTGAAAACAAAATTAGAT
1 TTTGAAAACAAAATGAAAA
482487 TTTGAAAGACAAAATGAAAA
1 TTTGAAA-ACAAAATGAAAA
482507 TTTGAAAA
1 TTTGAAAA
482515 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (19 bp):
TTTGAAAACAAAATGAAAA
Found at i:484222 original size:21 final size:21
Alignment explanation
Indices: 484185--484229 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
484175 GATTTCTGGG
*
484185 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
484206 CAAGGGGAA-CAGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
484227 CAA
1 CAA
484230 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:484281 original size:20 final size:20
Alignment explanation
Indices: 484256--484293 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
484246 GAATGTTAGA
*
484256 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
484276 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
484294 TAATGAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:485078 original size:31 final size:30
Alignment explanation
Indices: 485008--485135 Score: 107
Period size: 31 Copynumber: 4.1 Consensus size: 30
484998 GTCGAAGGTT
** *
485008 TACCTATGTTCTTCGGGACATATGGACAGAA
1 TACCTATGTTC-TAAGGACATATGGACAGTA
*
485039 TTACCTATG-TCTTTAGAGACATATGGACAGTA
1 -TACCTATGTTC-TAAG-GACATATGGACAGTA
*
485071 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGG-ACATATGGACAGTA
* ** *
485102 TACCTAGGTTCTTCGGAACCTATGGACAGT-
1 TACCTATGTTCTAAGG-ACATATGGACAGTA
485132 TACC
1 TACC
485136 GAGGATCTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
30 5 0.06
31 55 0.65
32 24 0.29
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (30 bp):
TACCTATGTTCTAAGGACATATGGACAGTA
Found at i:492017 original size:2 final size:2
Alignment explanation
Indices: 492012--492043 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
492002 ATGAAAAAAA
492012 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
492044 CTTATATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:492909 original size:8 final size:8
Alignment explanation
Indices: 492898--492929 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
492888 TTTTTAATCA
*
492898 TTTAATAT
1 TTTAAAAT
492906 TTTAAAAT
1 TTTAAAAT
492914 TTTAAAAT
1 TTTAAAAT
492922 TTTAAAAT
1 TTTAAAAT
492930 AAATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:493687 original size:19 final size:19
Alignment explanation
Indices: 493660--493714 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
493650 TGAATTTCAT
*
493660 AATTTATTTTAAAATTATA
1 AATTAATTTTAAAATTATA
*
493679 AATTCATTTTAAAATTA-A
1 AATTAATTTTAAAATTATA
**
493697 AATTAAAATTAAAATTAT
1 AATTAATTTTAAAATTAT
493715 TAAACAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTAATTTTAAAATTATA
Found at i:493698 original size:6 final size:6
Alignment explanation
Indices: 493668--493713 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
493658 ATAATTTATT
* **
493668 TTAAAA TTATAAA TTCATT TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTA-AAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTA
493714 TTAAACAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAA
Found at i:501021 original size:57 final size:57
Alignment explanation
Indices: 500933--501056 Score: 167
Period size: 57 Copynumber: 2.2 Consensus size: 57
500923 TGCTTGACAA
* * *
500933 GATGTACAACGGTCGAATTGTGCCGATGTCTTAGGTGTGCCATGCATCTAAGCCTGG
1 GATGTACAACAGTAGAATTGTGCCGATGTCTTAGGCGTGCCATGCATCTAAGCCTGG
* * * * * *
500990 GATGTACAACATTAGAATTTTGCCGATGTCTTAGGCGTGTCATGCCTTTAGGCCTGG
1 GATGTACAACAGTAGAATTGTGCCGATGTCTTAGGCGTGCCATGCATCTAAGCCTGG
501047 GATGTACAAC
1 GATGTACAAC
501057 GGTCCGGGTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (57 bp):
GATGTACAACAGTAGAATTGTGCCGATGTCTTAGGCGTGCCATGCATCTAAGCCTGG
Found at i:513225 original size:29 final size:29
Alignment explanation
Indices: 513182--513254 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
513172 CCAAGCATAG
* *
513182 GTCGTCATGCCCTCCTGGCGATCC-TGTAA
1 GTCGCCATGCACTCCTGGCGA-CCTTGTAA
*
513211 GTCGCCATGCACTCCTGGCGACCTTGTAG
1 GTCGCCATGCACTCCTGGCGACCTTGTAA
513240 GTCGCCATGCACTCC
1 GTCGCCATGCACTCC
513255 CTCCTGCTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.05
29 38 0.95
ACGTcount: A:0.14, C:0.37, G:0.25, T:0.25
Consensus pattern (29 bp):
GTCGCCATGCACTCCTGGCGACCTTGTAA
Done.