Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold416
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: 497255
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.30
Warning! 57273 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:312324 original size:29 final size:30
Alignment explanation
Indices: 312287--312345 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
312277 TATGGTTTAA
*
312287 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
* *
312316 TGTGCAATTTTGTACATGAAATTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
312346 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (30 bp):
TGTGCAATTTTATACATGAAACTTTGATTT
Found at i:312354 original size:30 final size:29
Alignment explanation
Indices: 312292--312360 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
312282 TTTAATGTGT
* *
312292 AATTTTATACATGAACTTTGATTTTGTGC
1 AATTTTGTACATGAACTTTGATTTTGTCC
*
312321 AATTTTGTACATGAAATTTTGA-TTTGATCC
1 AATTTTGTACATG-AACTTTGATTTTG-TCC
312351 AATTCTTGTA
1 AATT-TTGTA
312361 AAATATTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.47
30 13 0.38
31 5 0.15
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (29 bp):
AATTTTGTACATGAACTTTGATTTTGTCC
Found at i:312955 original size:27 final size:27
Alignment explanation
Indices: 312917--313014 Score: 108
Period size: 27 Copynumber: 3.6 Consensus size: 27
312907 GAGGAGGGTA
*
312917 TCCCATGGGCGGCACCAAATGTGCCTT
1 TCCCATAGGCGGCACCAAATGTGCCTT
* *
312944 TCCCATAGGCGGCACC-GATAGTGTCTT
1 TCCCATAGGCGGCACCAAAT-GTGCCTT
* * *
312971 TCCCATAGGCGGCACCCAAGGTGCTTT
1 TCCCATAGGCGGCACCAAATGTGCCTT
**
312998 TATCATAGGCGGCACCA
1 TCCCATAGGCGGCACCA
313015 CTTGTGTTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.03
27 56 0.95
28 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.22
Consensus pattern (27 bp):
TCCCATAGGCGGCACCAAATGTGCCTT
Found at i:313111 original size:10 final size:10
Alignment explanation
Indices: 313096--313132 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
313086 GATGGTGCCG
313096 GAAAAAGAGA
1 GAAAAAGAGA
313106 GAAAAAGAGA
1 GAAAAAGAGA
*
313116 GAAAGAAAAGA
1 GAAA-AAGAGA
313127 GAAAAA
1 GAAAAA
313133 AAAGTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:313405 original size:35 final size:36
Alignment explanation
Indices: 313337--313406 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
313327 TATGGTTAGT
* *
313337 TATTATTTTTAGTAAAACCCTAATTATTATTGTTAA
1 TATTATTTTGAGTAAAACACTAATTATTATTGTTAA
313373 TATTATTTTGAGTATAAA-ACT-ATTATTATTGTTA
1 TATTATTTTGAGTA-AAACACTAATTATTATTGTTA
313407 TTGTATTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 13 0.42
36 15 0.48
37 3 0.10
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (36 bp):
TATTATTTTGAGTAAAACACTAATTATTATTGTTAA
Found at i:320928 original size:14 final size:14
Alignment explanation
Indices: 320909--320935 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
320899 CGCCCAAGAC
320909 TGCAGCAATGTGAT
1 TGCAGCAATGTGAT
320923 TGCAGCAATGTGA
1 TGCAGCAATGTGA
320936 GGCATCCGCC
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:0.15, G:0.30, T:0.26
Consensus pattern (14 bp):
TGCAGCAATGTGAT
Found at i:322154 original size:148 final size:145
Alignment explanation
Indices: 322002--322466 Score: 426
Period size: 148 Copynumber: 3.1 Consensus size: 145
321992 GTATTTTATT
322002 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTTAAAA
1 ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCT-AATTTTTAAAA
* *
322067 AATTTAGTAAAACACTCTTACTTCGGCCATTTATTCGTATTTTTTCTCTGTATTTTATTATTTTA
65 AATTTAGTAAAACACTCTTACTTCAGCCATTT-TTCGTATTTTTTCTCTGAATTTTATTATTTTA
322132 AAAATATCATAATTTCTA
129 AAAA-ATCATAATTTCTA
* * * * *
322150 ATTTTACT-TTATCTCAGTGCATTATGTTTG-AA-A-TT-TATTAATTTAGTGTGT--TTTTTAA
1 ATTTTA-TATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAA-TTA-TTTCTAATTTTTAA
* * * * * *
322208 ATTAATTTAGTGTAAAAAAAACCCTTA-TTCCTGCCCTTTCTCGTATTATTTTCTC-GAATTTTA
63 A-AAATTTA--GT--AAAACACTCTTACTT-CAGCCATTTTTCGTATT-TTTTCTCTGAATTTTA
* *
322271 TTACTTTGAATGAAAATGCATTATTTTCGTATTTTA
121 TTA-TTTTAA--AAAAT-CA-TAATTTC------TA
322307 TTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAA
1 --ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCT-AATTTTTAA
* *
322372 AAAATTTAGTAAAACACTCTTACTTCAGTCATTTGTTCGTAATTTTTTCTCTGCATTTTATTATT
63 AAAATTTAGTAAAACACTCTTACTTCAGCCATTT-TTCGT-ATTTTTTCTCTGAATTTTATTATT
*
322437 TTAAAAAACATCATAATTTTTA
126 TT-AAAAA-ATCATAATTTCTA
322459 ATTTTATA
1 ATTTTATA
322467 ATTTTACATT
Statistics
Matches: 250, Mismatches: 30, Indels: 72
0.71 0.09 0.20
Matches are distributed among these distances:
143 8 0.03
144 12 0.05
145 5 0.02
146 6 0.02
147 21 0.08
148 54 0.22
149 3 0.01
150 13 0.05
151 6 0.02
152 2 0.01
157 2 0.01
158 6 0.02
159 46 0.18
160 20 0.08
161 21 0.08
162 5 0.02
163 12 0.05
164 8 0.03
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (145 bp):
ATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAATTTTTAAAAA
ATTTAGTAAAACACTCTTACTTCAGCCATTTTTCGTATTTTTTCTCTGAATTTTATTATTTTAAA
AAATCATAATTTCTA
Found at i:322317 original size:307 final size:305
Alignment explanation
Indices: 321748--322507 Score: 1072
Period size: 307 Copynumber: 2.4 Consensus size: 305
321738 GCAAGTTGAA
* *
321748 AAAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCTGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTA-TTTTTTCTCTGCATTTTATTA
* * *
321813 CTTTACAAAATATTATAATTTTTAATTTTATAATTTTACATTATTTCAGTGAATTATGTTTGAAA
65 -TTT-TAAAA-A-TATCA----TAA-TTTATAATTTTACATTATCTCAGTGAATTATGTTTGAAA
* *
321878 TTTATTAATTTAGTGTTTTTTTAAATTAATTTAGTGTAAAAAATCCTTATTCTTGCCCTTTGCTC
121 TTTATTAATTTAGTGTTTTTTTAAATTAATTTAGTGTAAAAAACCCTTATTCCTGCCCTTTGCTC
* * *
321943 ATATTACTTTCCCGAATTTTTTTACTTTTAATAAAAATATATTATTTTCGTATTTTATTATTTTA
186 ATATTACTTTCCCGAATTTTATTACTTTGAATAAAAATACATTATTTTCGTATTTTATTATTTTA
322008 TATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTT
251 TATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTT
* *
322063 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTATTCGTATTTTTTCTCTGTATTTTATTAT
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTCTCTGCATTTTATTAT
* * *
322128 TTTAAAAATATCATAATTTCTAATTTTACTTTATCTCAGTGCATTATGTTTGAAATTTATTAATT
66 TTTAAAAATATCATAATTTATAATTTTACATTATCTCAGTGAATTATGTTTGAAATTTATTAATT
* *
322193 TAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCCTTATTCCTGCCCTTT-CTCGTATTAT
131 TAGTGT-TTTTTTAAATTAATTTAGTGT--AAAAAACCCTTATTCCTGCCCTTTGCTCATATTAC
* * *
322257 TTTCTCGAATTTTATTACTTTGAATGAAAATGCATTATTTTCGTATTTTATTATTTTATATTATT
193 TTTCCCGAATTTTATTACTTTGAATAAAAATACATTATTTTCGTATTTTATTATTTTATATTATT
*
322322 TCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
258 TCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTT
* *
322370 AAAAAATTTAGTAAAACACTCTTACTTCAGTCATTTGTTCGTAATTTTTTCTCTGCATTTTATTA
1 AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGT-ATTTTTTCTCTGCATTTTATTA
* * *
322435 TTTTAAAAAACATCATAATTTTTAATTTTATAATTTTACATTATTTCAGTGTATTATGTTTGAAA
65 TTTT--AAAA-AT-ATCA----TAA-TTTATAATTTTACATTATCTCAGTGAATTATGTTTGAAA
322500 TTTATTAA
121 TTTATTAA
322508 ATATATCATT
Statistics
Matches: 402, Mismatches: 30, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
305 51 0.13
306 24 0.06
307 153 0.38
308 47 0.12
310 8 0.02
311 3 0.01
312 7 0.02
313 3 0.01
314 20 0.05
315 40 0.10
316 3 0.01
317 43 0.11
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (305 bp):
AAAAAATTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTCTCTGCATTTTATTAT
TTTAAAAATATCATAATTTATAATTTTACATTATCTCAGTGAATTATGTTTGAAATTTATTAATT
TAGTGTTTTTTTAAATTAATTTAGTGTAAAAAACCCTTATTCCTGCCCTTTGCTCATATTACTTT
CCCGAATTTTATTACTTTGAATAAAAATACATTATTTTCGTATTTTATTATTTTATATTATTTCA
GTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTT
Found at i:322791 original size:18 final size:18
Alignment explanation
Indices: 322756--322805 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
322746 GAAAAAAAAG
322756 AAAAAAAAG--GAA-AGA
1 AAAAAAAAGAAGAAGAGA
** *
322771 AAAGGAAAGGAGAAGAGA
1 AAAAAAAAGAAGAAGAGA
322789 AAAAAAAAGAAGAAGAG
1 AAAAAAAAGAAGAAGAG
322806 GGAAGGAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 7 0.26
17 3 0.11
18 17 0.63
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAGAAGAGA
Found at i:329053 original size:3 final size:3
Alignment explanation
Indices: 329045--329072 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
329035 TAACTAACAC
329045 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
329073 GTTTTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:329484 original size:27 final size:26
Alignment explanation
Indices: 329445--329544 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 26
329435 ATAACACAAG
*
329445 TGGTGCTGCCTATGGGAAAGGCACCT
1 TGGTGCCGCCTATGGGAAAGGCACCT
*
329471 TGGGTGCCGCCTATGGTAAAGGCACCAT
1 T-GGTGCCGCCTATGGGAAAGGCACC-T
* *
329499 TGGTGCTGCCTATGGGAAAGGCACTAT
1 TGGTGCCGCCTATGGGAAAGGCAC-CT
*
329526 TGGTGCCGCCAATGGGAAA
1 TGGTGCCGCCTATGGGAAA
329545 CCCTCCTCCA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.02
27 61 0.95
28 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
TGGTGCCGCCTATGGGAAAGGCACCT
Found at i:329936 original size:10 final size:11
Alignment explanation
Indices: 329909--329941 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
329899 CAAGTATGAG
329909 TCAAAAAATAT
1 TCAAAAAATAT
329920 TCAAAAAATAT
1 TCAAAAAATAT
329931 TCAAAAAATAT
1 TCAAAAAATAT
329942 AATTAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (11 bp):
TCAAAAAATAT
Found at i:330156 original size:216 final size:212
Alignment explanation
Indices: 329722--330176 Score: 544
Period size: 216 Copynumber: 2.1 Consensus size: 212
329712 AATTTTTTTT
* *
329722 AAAATATAATTAATATCACATGATAGATTCTTGATTTTTTAACTCATACCTACAAGTAAGGGTTT
1 AAAATATAATTAATATCACATGATAGATTCTTGATTTTTTAACACATACATACAAGTAAGGGTTT
* * * *
329787 TTTATACTCTTATTGTTAGTGTTTTTTTTTTCAATCATCATTAATTTATTATTGGAAAAAATAAT
66 TTTATACTCTCATAGTTAGTGTTTTTTTTTTCAACCATCATTAATTTATTATTAGAAAAAATAAT
* * * * * * * *
329852 TTATTATATATTAATTTATTTTTAACAAATAGCTATTTATTTAGCTGCAAGTATGAGTCAAAAAA
131 TCATTACATATTAATTTAATTTTAACAAAAAACTAATTATTTAGCTGCAAGGATAAGTCAAAAAA
* *
329917 TATTCAAAAAATATTCAA
196 CATT-AAAAAATAGTCAA
* *
329935 AAAATATAATTAATATCACATGATAGATT-TTTATTTTTTAACACATACATGCAAGTAAGGG-TT
1 AAAATATAATTAATATCACATGATAGATTCTTGATTTTTTAACACATACATACAAGTAAGGGTTT
* * *
329998 TTTATACTCTCATAGTTAGTGTCTTTTTGTTGGTTCAACCATCGTTAGTTTATTATTAGAAAAGA
66 TTTATACTCTCATAGTTAGTGT-TTTTT-TT--TTCAACCATCATTAATTTATTATTAGAAAAAA
330063 TAAATTCATTACATATTAATTTAATTTTAACAAAAAAAAAACTAATTATTTA-CTTGCAAGGATA
127 T-AATTCATTACATATTAATTTAATTTTAAC----AAAAAACTAATTATTTAGC-TGCAAGGATA
* * *
330127 AGTTAAAAAACATT-TAAGA-AGT-AA
186 AGTCAAAAAACATTAAAAAATAGTCAA
*
330151 AAAATATAATCAATATCACATGATAG
1 AAAATATAATTAATATCACATGATAG
330177 CTAGATCAAA
Statistics
Matches: 207, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
211 22 0.11
212 33 0.16
213 31 0.15
215 28 0.14
216 53 0.26
217 2 0.01
218 3 0.01
219 1 0.00
220 34 0.16
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (212 bp):
AAAATATAATTAATATCACATGATAGATTCTTGATTTTTTAACACATACATACAAGTAAGGGTTT
TTTATACTCTCATAGTTAGTGTTTTTTTTTTCAACCATCATTAATTTATTATTAGAAAAAATAAT
TCATTACATATTAATTTAATTTTAACAAAAAACTAATTATTTAGCTGCAAGGATAAGTCAAAAAA
CATTAAAAAATAGTCAA
Found at i:331793 original size:41 final size:41
Alignment explanation
Indices: 331748--331863 Score: 196
Period size: 41 Copynumber: 2.8 Consensus size: 41
331738 TATATATGGT
* *
331748 ACTTAGTGTGCAGAATTATAATAGCTTCGGCTATGTAAGGC
1 ACTTAGTGTGCGGAATTATAATAGCTTCGGCTATGTAAGAC
*
331789 ACTTAGTGTGCGGAATTATAATAGTTTCGGCTATGTAAGAC
1 ACTTAGTGTGCGGAATTATAATAGCTTCGGCTATGTAAGAC
*
331830 ACTTAGTGTGCGGAATTATAATAGCTTCGCCTAT
1 ACTTAGTGTGCGGAATTATAATAGCTTCGGCTAT
331864 ATGATTGGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (41 bp):
ACTTAGTGTGCGGAATTATAATAGCTTCGGCTATGTAAGAC
Found at i:334928 original size:40 final size:40
Alignment explanation
Indices: 334884--334966 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
334874 AGATAGAGTT
*
334884 TTAGCGGCGCT-AAACAAAAAAACGCCGCAATAAACCTGCA
1 TTAGCGGCGCTCAAA-AAAAAAACGCAGCAATAAACCTGCA
* * * *
334924 TTAGCGGCGCTCGAAAAACAAACGCATCAATAGACCTGCA
1 TTAGCGGCGCTCAAAAAAAAAACGCAGCAATAAACCTGCA
334964 TTA
1 TTA
334967 CCGGTGATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (40 bp):
TTAGCGGCGCTCAAAAAAAAAACGCAGCAATAAACCTGCA
Found at i:336828 original size:15 final size:16
Alignment explanation
Indices: 336802--336836 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
336792 ATTTATAAAT
336802 TTTAATATTGATAGTA
1 TTTAATATTGATAGTA
336818 TTTAA-ATTGATAGTA
1 TTTAATATTGATAGTA
336833 TTTA
1 TTTA
336837 TAAATTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTAATATTGATAGTA
Found at i:339574 original size:21 final size:20
Alignment explanation
Indices: 339547--339604 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
339537 TAATATAATA
*
339547 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
* *
339568 TATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
339589 CATAACTTATATATAA
1 CATAACTTATATATAA
339605 TAACATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 4 0.13
21 23 0.74
22 4 0.13
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:341128 original size:3 final size:3
Alignment explanation
Indices: 341120--341213 Score: 102
Period size: 3 Copynumber: 30.7 Consensus size: 3
341110 AAGTAATTAA
* *
341120 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT GAAT -AT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
341165 AAT AAT AGT AA- AGAT AAT AAT AAT AAT AAT AAT AAC AACT AAAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA-T -AAT AAT
341212 AA
1 AA
341214 AATTGCCAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
2 3 0.04
3 67 0.87
4 5 0.06
5 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:346230 original size:132 final size:132
Alignment explanation
Indices: 346066--346367 Score: 505
Period size: 132 Copynumber: 2.3 Consensus size: 132
346056 NNNNNNNNNN
* *
346066 TATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGT
1 TATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGG
* * *
346131 AATCTTCAACCTACTCCACTACTGCTTATGGTGATTGAACTAATGGCTTAAATCTGCATCTCCAC
66 AATCTTCAACCGACTCCACTACTGCTTAGGGTGATAGAACTAATGGCTTAAATCTGCATCTCCAC
346196 TG
131 TG
* * *
346198 TATTTGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTAGTGGTTAGGGTGACAGAATCTGG
1 TATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGG
* *
346263 AATCTTCAACCGACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
66 AATCTTCAACCGACTCCACTACTGCTTAGGGTGATAGAACTAATGGCTTAAATCTGCATCTCCAC
346328 TG
131 TG
*
346330 TATTGGGAAGATAAGATTCATCATCTTCGATCTACTCC
1 TATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCC
346368 GCTGCCAAAT
Statistics
Matches: 158, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 158 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (132 bp):
TATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGG
AATCTTCAACCGACTCCACTACTGCTTAGGGTGATAGAACTAATGGCTTAAATCTGCATCTCCAC
TG
Found at i:346419 original size:46 final size:46
Alignment explanation
Indices: 346352--346744 Score: 588
Period size: 46 Copynumber: 8.5 Consensus size: 46
346342 AAGATTCATC
** * *
346352 ATCTTCGATCTACTCCGCTGCCAAATACAGGAAAACACGATCTGCT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
346398 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGAT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
346444 ATCTTCGATCCCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * *
346490 ATATTCGATCTCCTCCGCTACCAAAATACAGGAAGACAAAATCTGCT
1 ATCTTCGATCCCCTCCGCTGCC-AAATACAGGAAGACAAGATCTGCT
*
346537 ATCTTCGATCCCCTCCGCTGCCAATTACAGGAAGACAAGATCTGCT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
346583 ATCTTCGATCCCTTCCGCTGCCAATTACAGGAAGACAAGATCTGCT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * *
346629 ATCTTCGATCCCCTCCGCTGCCAATTACAAGAAGACAATATCTACT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
346675 ATATTCGATCCCCTCCGCTGCCAAATACAAGAAGACAAGATCTGCT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
346721 ATCTTCGATCCCCTCCGCTGCCAA
1 ATCTTCGATCCCCTCCGCTGCCAA
346745 NNNNNNNNNN
Statistics
Matches: 317, Mismatches: 29, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 275 0.87
47 42 0.13
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.24
Consensus pattern (46 bp):
ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
Found at i:346665 original size:185 final size:184
Alignment explanation
Indices: 346352--346744 Score: 617
Period size: 185 Copynumber: 2.1 Consensus size: 184
346342 AAGATTCATC
** *
346352 ATCTTCGATCTACTCCGCTGCCAAATACAGGAAAACACGATCTGCTATCTTCGATCTCCTTCGCT
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAAACAAGATCTGCTATCTTCGATCTCCTTCGCT
* *
346417 GCCAAATACAGGAAGACAAGATCTGATATCTTCGATCCCCTCTGCTGCCAAATACAGGAAGACAA
66 GCCAAATACAGGAAGACAAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAAGAAGACAA
* * *
346482 GATCTGCTATATTCGATCTCCTCCGCTACCAAAATACAGGAAGACAAAATCTGCT
131 GATCTACTATATTCGATCCCCTCCGCTACC-AAATACAAGAAGACAAAATCTGCT
* *
346537 ATCTTCGATCCCCTCCGCTGCCAATTACAGGAAGACAAGATCTGCTATCTTCGATC-CCTTCCGC
1 ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAAACAAGATCTGCTATCTTCGATCTCCTT-CGC
* * *
346601 TGCCAATTACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAATTACAAGAAGACA
65 TGCCAAATACAGGAAGACAAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAAGAAGACA
* * *
346666 ATATCTACTATATTCGATCCCCTCCGCTGCCAAATACAAGAAGACAAGATCTGCT
130 AGATCTACTATATTCGATCCCCTCCGCTACCAAATACAAGAAGACAAAATCTGCT
346721 ATCTTCGATCCCCTCCGCTGCCAA
1 ATCTTCGATCCCCTCCGCTGCCAA
346745 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
184 50 0.26
185 141 0.74
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.24
Consensus pattern (184 bp):
ATCTTCGATCCCCTCCGCTGCCAAATACAGGAAAACAAGATCTGCTATCTTCGATCTCCTTCGCT
GCCAAATACAGGAAGACAAGATCTGATATCTTCGATCCCCTCCGCTGCCAAATACAAGAAGACAA
GATCTACTATATTCGATCCCCTCCGCTACCAAATACAAGAAGACAAAATCTGCT
Found at i:348562 original size:23 final size:21
Alignment explanation
Indices: 348524--348567 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
348514 TTAGCCTCTC
348524 CATTTTTACTTTTTCATTTTT
1 CATTTTTACTTTTTCATTTTT
*
348545 CATTTTTTCTTTCATTCATTTTT
1 CATTTTTACTTT--TTCATTTTT
348568 TATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
CATTTTTACTTTTTCATTTTT
Found at i:349395 original size:8 final size:8
Alignment explanation
Indices: 349382--349457 Score: 72
Period size: 9 Copynumber: 9.6 Consensus size: 8
349372 TGGCCTCTCC
349382 TTTTTCTT
1 TTTTTCTT
349390 TTTTTC--
1 TTTTTCTT
*
349396 -TTTTCTC
1 TTTTTCTT
349403 TTTTTC-T
1 TTTTTCTT
349410 TTTTTCTT
1 TTTTTCTT
349418 CTTTTTCCTT
1 -TTTTT-CTT
349428 TTTTTC-T
1 TTTTTCTT
349435 TTTTTCTTT
1 TTTTTC-TT
349444 TTTCTTCTT
1 TTT-TTCTT
349453 TTTTT
1 TTTTT
349458 TATTTTTTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 18
0.75 0.01 0.23
Matches are distributed among these distances:
5 5 0.09
7 13 0.22
8 15 0.26
9 19 0.33
10 6 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:349399 original size:7 final size:7
Alignment explanation
Indices: 349382--349458 Score: 77
Period size: 7 Copynumber: 10.6 Consensus size: 7
349372 TGGCCTCTCC
349382 TTTTTCT
1 TTTTTCT
349389 TTTTT-T
1 TTTTTCT
*
349395 CTTTTCT
1 TTTTTCT
349402 CTTTTTCT
1 -TTTTTCT
349410 TTTTTCTT
1 TTTTTC-T
349418 CTTTTTCCTT
1 -TTTTT-C-T
349428 TTTTTCT
1 TTTTTCT
349435 TTTTTCT
1 TTTTTCT
349442 TTTTTCT
1 TTTTTCT
*
349449 TCTTT-T
1 TTTTTCT
349455 TTTT
1 TTTT
349459 ATTTTTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
6 9 0.15
7 31 0.51
8 8 0.13
9 10 0.16
10 3 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:349464 original size:32 final size:32
Alignment explanation
Indices: 349388--349464 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
349378 CTCCTTTTTC
*
349388 TTTTTTTCTTTTCTCTTTTTCTTTTTTCTTCT
1 TTTTTTTTTTTTCTCTTTTTCTTTTTTCTTCT
*
349420 TTTTCCTTTTTTTCT-TTTTTCTTTTTTCTTCT
1 TTTT-TTTTTTTTCTCTTTTTCTTTTTTCTTCT
349452 TTTTTTTATTTTT
1 TTTTTTT-TTTTT
349465 TATTTCTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 2 0.05
32 30 0.75
33 8 0.20
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (32 bp):
TTTTTTTTTTTTCTCTTTTTCTTTTTTCTTCT
Found at i:352383 original size:19 final size:20
Alignment explanation
Indices: 352354--352405 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
352344 CACTTCGTGA
* *
352354 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
352373 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
352393 AAATG-AATGCAAA
1 AAATGTAATGCAAA
352406 AAGAGACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:363257 original size:64 final size:64
Alignment explanation
Indices: 363134--363282 Score: 192
Period size: 64 Copynumber: 2.3 Consensus size: 64
363124 TAAAACGGAG
* *
363134 GCAGCATCGAGAGAAGCAGAGGTTCAAAAAAGATATGAAGAACTTCAGCTAAAACTTAAAGAAGA
1 GCAGCAGCGAGAGAAGC--AGGTTCAAAAAAGATATGAAGAACTCCAGCTAAAACTTAAAGAAGA
363199 T
64 T
* ** ** *
363200 GCAGCAGCGAGAGAAGCAGGTTCAACGAAAG-TATGAAGAACTCCAGCTGTAGTTTAAAGCAGAT
1 GCAGCAGCGAGAGAAGCAGGTTCAA-AAAAGATATGAAGAACTCCAGCTAAAACTTAAAGAAGAT
363264 GCAGCAGCGAGAGAAGCAG
1 GCAGCAGCGAGAGAAGCAG
363283 AGGCTACAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 54 0.73
65 4 0.05
66 16 0.22
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.15
Consensus pattern (64 bp):
GCAGCAGCGAGAGAAGCAGGTTCAAAAAAGATATGAAGAACTCCAGCTAAAACTTAAAGAAGAT
Found at i:363280 original size:21 final size:21
Alignment explanation
Indices: 363256--363326 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
363246 CTGTAGTTTA
* *
363256 AAGCAGATGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGGG
363277 AAGCAGAGGCTA-CAGCGAGGG
1 AAGCAGAGGC-AGCAGCGAGGG
* *
363298 AAGTAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGGG
363319 AAGCAGAG
1 AAGCAGAG
363327 TAGCGTAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.42, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGGG
Found at i:363743 original size:43 final size:43
Alignment explanation
Indices: 363696--363918 Score: 170
Period size: 43 Copynumber: 5.2 Consensus size: 43
363686 TGGTCATTTG
* * *
363696 CGGCGTTTGTGGAAAAAGCACCGTTAAATATCAGGGTCTTTAC
1 CGGCGTTTGTGGAAAAAGCACCGCTAAAGATCAGAGTCTTTAC
* *
363739 CGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAGAGTCTTTAG
1 CGGCGTTTGTGGAAAAAGCACCGCTAAAGATCAGAGTCTTTAC
* ** *
363782 CGGCGTTTGTTTGG--AAAGCACCGCTAAAGGTCATTGTCTTTAG
1 CGGCGTTTG--TGGAAAAAGCACCGCTAAAGATCAGAGTCTTTAC
* * ** * *
363825 TGGCGTTTGTCGG-AGAAGTGCCGCTAAAGGTCATG-GTCTTTAG
1 CGGCGTTTGT-GGAAAAAGCACCGCTAAAGATCA-GAGTCTTTAC
** * * *
363868 CGGCGTTTG-CCAGAAAAGCATCGCTAAAGGTCATG-GTCTTTAG
1 CGGCGTTTGTGGA-AAAAGCACCGCTAAAGATCA-GAGTCTTTAC
363911 CGGCGTTT
1 CGGCGTTT
363919 ATTTCTAAAA
Statistics
Matches: 152, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 2 0.01
43 146 0.96
45 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
CGGCGTTTGTGGAAAAAGCACCGCTAAAGATCAGAGTCTTTAC
Found at i:363767 original size:86 final size:86
Alignment explanation
Indices: 363665--363918 Score: 248
Period size: 86 Copynumber: 2.9 Consensus size: 86
363655 GCATTTTTTA
* * * *
363665 AAAAAACGCCACTAAAGGTCATGGTCATTT-GCGGCGTTTG-TGGAAAAAGCACCGTTAAATATC
1 AAAAAGCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTTGG--AAAGCACCGCTAAAGATC
363728 AGGGTCTTTACCGGCGTTTGT-GG
63 AGGGTCTTTACCGGCGTTTGTCGG
* *
363751 AAAAAGCGCCGCTAAAGATCA-GAGTCTTTAGCGGCGTTTGTTTGGAAAGCACCGCTAAAGGTCA
1 AAAAAGCGCCGCTAAAGGTCATG-GTCTTTAGCGGCGTTTG-TTGGAAAGCACCGCTAAAGATCA
** **
363815 TTGTCTTTAGTGGCGTTTGTCGG
64 GGGTCTTTACCGGCGTTTGTCGG
* * ** * * * *
363838 -AGAAGTGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCCAGAAAAGCATCGCTAAAGGTCAT
1 AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTG-TTGGAAAGCACCGCTAAAGATCAG
*
363902 GGTCTTTAGCGGCGTTT
65 GGTCTTTACCGGCGTTT
363919 ATTTCTAAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
85 4 0.03
86 132 0.93
87 3 0.02
88 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (86 bp):
AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTTGGAAAGCACCGCTAAAGATCAGG
GTCTTTACCGGCGTTTGTCGG
Found at i:368421 original size:41 final size:41
Alignment explanation
Indices: 368320--368455 Score: 161
Period size: 41 Copynumber: 3.3 Consensus size: 41
368310 GAAATTCGAG
* * * *
368320 ATAGCTTCAGTTAT-TAATGGCACTTA--GTGTGCAATTTGGA
1 ATAGCTTCGGCTATGTAA-GGCACTTAGTGTGTGGAA-TTGTA
* *
368360 ATGGCTTTGGCTATGTAAGGCACTTAGTGTGTGGAATTGTA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGTGGAATTGTA
* *
368401 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGGAATTATA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGTGGAATTGTA
368442 ATAGCTTCGGCTAT
1 ATAGCTTCGGCTAT
368456 ATGATTGGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 18 0.22
41 58 0.70
42 7 0.08
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (41 bp):
ATAGCTTCGGCTATGTAAGGCACTTAGTGTGTGGAATTGTA
Found at i:369902 original size:37 final size:38
Alignment explanation
Indices: 369856--369929 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
369846 TTTTTGTTAC
*
369856 TATGTATTTTGAAATTAAAAAT-ATATTAAATATAAAAA
1 TATGTATTTTGAAA-TAAAAATCATATTAAAGATAAAAA
** *
369894 TATG-ATTTTTTAATAAAAATCATCTTAAAGATAAAA
1 TATGTATTTTGAAATAAAAATCATATTAAAGATAAAA
369930 TGTAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 7 0.23
37 20 0.65
38 4 0.13
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (38 bp):
TATGTATTTTGAAATAAAAATCATATTAAAGATAAAAA
Found at i:370588 original size:32 final size:32
Alignment explanation
Indices: 370547--370613 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
370537 ATTTTTTTAA
* * *
370547 TTTTGGAGTTAA-TCAAATTAAGTTATTCGATT
1 TTTTCGAGTTAACTCAAA-TAAGTAATTCGAGT
370579 TTTTCGAGTTAACTCAAATAAGTAATTCGAGT
1 TTTTCGAGTTAACTCAAATAAGTAATTCGAGT
370611 TTT
1 TTT
370614 GTATTCGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (32 bp):
TTTTCGAGTTAACTCAAATAAGTAATTCGAGT
Found at i:370655 original size:9 final size:9
Alignment explanation
Indices: 370641--370675 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
370631 AATTTTAAAT
370641 TCGAATAAC
1 TCGAATAAC
*
370650 TCGAATAAT
1 TCGAATAAC
370659 TCGAATAAC
1 TCGAATAAC
*
370668 TCAAATAA
1 TCGAATAA
370676 AAAATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:370661 original size:18 final size:18
Alignment explanation
Indices: 370638--370675 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
370628 TTGAATTTTA
*
370638 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCAAAT
370656 AATTCGAATAACTCAAAT
1 AATTCGAATAACTCAAAT
370674 AA
1 AA
370676 AAAATTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:380160 original size:37 final size:38
Alignment explanation
Indices: 380114--380187 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
380104 TTTTTGTTAC
*
380114 TATGTATTTTGAAATTAAAAAT-ATATTAAATATAAAAA
1 TATGTATTTTGAAA-TAAAAATCATATTAAAGATAAAAA
** *
380152 TATG-ATTTTTTAATAAAAATCATCTTAAAGATAAAA
1 TATGTATTTTGAAATAAAAATCATATTAAAGATAAAA
380188 TGTAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 7 0.23
37 20 0.65
38 4 0.13
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (38 bp):
TATGTATTTTGAAATAAAAATCATATTAAAGATAAAAA
Found at i:380846 original size:32 final size:32
Alignment explanation
Indices: 380805--380871 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
380795 ATTTTTTTAA
* * *
380805 TTTTGGAGTTAA-TCAAATTAAGTTATTCGATT
1 TTTTCGAGTTAACTCAAA-TAAGTAATTCGAGT
380837 TTTTCGAGTTAACTCAAATAAGTAATTCGAGT
1 TTTTCGAGTTAACTCAAATAAGTAATTCGAGT
380869 TTT
1 TTT
380872 GTATTCGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (32 bp):
TTTTCGAGTTAACTCAAATAAGTAATTCGAGT
Found at i:380913 original size:9 final size:9
Alignment explanation
Indices: 380899--380933 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
380889 AATTTTAAAT
380899 TCGAATAAC
1 TCGAATAAC
*
380908 TCGAATAAT
1 TCGAATAAC
380917 TCGAATAAC
1 TCGAATAAC
*
380926 TCAAATAA
1 TCGAATAA
380934 AAAATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:380919 original size:18 final size:18
Alignment explanation
Indices: 380896--380933 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
380886 TTGAATTTTA
*
380896 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCAAAT
380914 AATTCGAATAACTCAAAT
1 AATTCGAATAACTCAAAT
380932 AA
1 AA
380934 AAAATTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:396104 original size:3 final size:3
Alignment explanation
Indices: 396096--396130 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
396086 AGAAAATGAA
396096 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
396131 ATATTAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:401287 original size:45 final size:45
Alignment explanation
Indices: 401223--401311 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
401213 CATGATCACT
*
401223 GACTCTCCCAGCTGGTGAAATCAAAGGATGATGGTTTAATGGTAC
1 GACTCCCCCAGCTGGTGAAATCAAAGGATGATGGTTTAATGGTAC
*
401268 GACTCCCCCAGCTGGTGAAATGAAAGGATGATGGTTTAATGGTA
1 GACTCCCCCAGCTGGTGAAATCAAAGGATGATGGTTTAATGGTA
401312 GAATATAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (45 bp):
GACTCCCCCAGCTGGTGAAATCAAAGGATGATGGTTTAATGGTAC
Found at i:402266 original size:33 final size:33
Alignment explanation
Indices: 402027--402269 Score: 243
Period size: 33 Copynumber: 7.0 Consensus size: 33
402017 CTTTTTCAGA
* * *
402027 AGTCGTTACTTTTTCCGAAGGAGAAGTAGAAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* * *
402060 AGTCGTTTCTTTTGCCGGAGGAGAGGTGGCAGTAGCAAG
1 AGTCGTTACTTTTTCCGGAGGAGA----G--GTAGCAGG
402099 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGTAGCAGG
1 AGTCGTTACTTTTTCCGGA-G-GA-G-AG--GTAGCAGG
* * *
402138 AGTCGTTACTTTTTCCAGAGGAGAGGTAGAAGA
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* * *
402171 AGTCGTTACCTTTTCCGGAGGAAAGGTAACAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
* *
402204 AGTCGTTTCTTTTTCCGGAGGAAAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
*
402237 AGTCGTTTCTTTTTCCGGAGGAGAGGTAGCAGG
1 AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
402270 GGATGATGCC
Statistics
Matches: 178, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
33 116 0.65
35 2 0.01
36 1 0.01
37 2 0.01
38 1 0.01
39 51 0.29
40 1 0.01
41 2 0.01
42 1 0.01
43 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (33 bp):
AGTCGTTACTTTTTCCGGAGGAGAGGTAGCAGG
Found at i:402616 original size:17 final size:17
Alignment explanation
Indices: 402594--402627 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
402584 AGAAACTGTA
*
402594 ACTAATTGTAACAGAAT
1 ACTAATTGCAACAGAAT
402611 ACTAATTGCAACAGAAT
1 ACTAATTGCAACAGAAT
402628 CATAACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (17 bp):
ACTAATTGCAACAGAAT
Found at i:403058 original size:31 final size:31
Alignment explanation
Indices: 402998--403092 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 31
402988 TTTAAAAATC
402998 AAATATTATTTATCCTTTCATAAAAATTTTAA
1 AAATATTATTTATCCTTTCAT-AAAATTTTAA
403030 AAATATTATTTATCCTTTCATAAAATTTTAAA
1 AAATATTATTTATCCTTTCATAAAATTTT-AA
*
403062 AAATATTATTTATTCTTTCATAAAATTTTAA
1 AAATATTATTTATCCTTTCATAAAATTTTAA
403093 TTGCTTAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
31 10 0.16
32 51 0.84
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATATTATTTATCCTTTCATAAAATTTTAA
Found at i:403150 original size:42 final size:43
Alignment explanation
Indices: 403098--403253 Score: 167
Period size: 42 Copynumber: 3.6 Consensus size: 43
403088 TTTAATTGCT
*
403098 TAAATATTAAGGATAAATAATATTTTAAATATTTTGACTCTTA
1 TAAATATTAAGGATAAATAATATTTTAAATATTTTGACTGTTA
* * * *
403141 TAAAT-TTAAGGAT-AATATTTATCCTTTCATAAAATTTTAATTGTT-
1 TAAATATTAAGGATAAATA-ATAT--TTT-A-AATATTTTGACTGTTA
*
403186 TAAATATTAAGGATAAATAATATTTTAGATATTTTGACTGTTA
1 TAAATATTAAGGATAAATAATATTTTAAATATTTTGACTGTTA
* *
403229 TAAAT-TTAAGGATAATTATTATTTT
1 TAAATATTAAGGATAAATAATATTTT
403254 TCATAAAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
41 4 0.04
42 40 0.43
43 11 0.12
44 6 0.06
45 6 0.06
46 22 0.24
47 4 0.04
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (43 bp):
TAAATATTAAGGATAAATAATATTTTAAATATTTTGACTGTTA
Found at i:403177 original size:88 final size:87
Alignment explanation
Indices: 403068--403268 Score: 323
Period size: 88 Copynumber: 2.3 Consensus size: 87
403058 TAAAAAATAT
403068 TATTTATTCTTTCATAAAATTTTAATTGCTTAAATATTAAGGATAAATAATATTTTAAATATTTT
1 TATTTA-TCTTTCATAAAATTTTAATTGCTTAAATATTAAGGATAAATAATATTTTAAATATTTT
403133 GACTCTTATAAATTTAAGGATAA
65 GACTCTTATAAATTTAAGGATAA
* *
403156 TATTTATCCTTTCATAAAATTTTAATTGTTTAAATATTAAGGATAAATAATATTTTAGATATTTT
1 TATTTAT-CTTTCATAAAATTTTAATTGCTTAAATATTAAGGATAAATAATATTTTAAATATTTT
*
403221 GACTGTTATAAATTTAAGGATAA
65 GACTCTTATAAATTTAAGGATAA
*
403244 T-TATTATTTTTCATAAAAATTTTAA
1 TAT-TTATCTTTCAT-AAAATTTTAA
403269 AAATATTATT
Statistics
Matches: 106, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
87 8 0.08
88 98 0.92
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (87 bp):
TATTTATCTTTCATAAAATTTTAATTGCTTAAATATTAAGGATAAATAATATTTTAAATATTTTG
ACTCTTATAAATTTAAGGATAA
Found at i:404120 original size:32 final size:32
Alignment explanation
Indices: 404080--404176 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
404070 TTAAGGATAA
* * *
404080 AATATTATTTATCCATTCATAAACTTTTAAAT
1 AATATTATTTATTCTTTCATAAAATTTTAAAT
*
404112 AATATTATTTATTCTTTCATAAAATTTTTAAT
1 AATATTATTTATTCTTTCATAAAATTTTAAAT
*
404144 AATATTATTTATTCTTTCATAATATTTTTAAAT
1 AATATTATTTATTCTTTCATAA-AATTTTAAAT
404177 TTTAATTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 50 0.86
33 8 0.14
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (32 bp):
AATATTATTTATTCTTTCATAAAATTTTAAAT
Found at i:410001 original size:14 final size:14
Alignment explanation
Indices: 409982--410010 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
409972 CTACCATTTC
409982 ACTATTATGTTGTT
1 ACTATTATGTTGTT
409996 ACTATTATGTTGTT
1 ACTATTATGTTGTT
410010 A
1 A
410011 TTGCTTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (14 bp):
ACTATTATGTTGTT
Found at i:412159 original size:21 final size:21
Alignment explanation
Indices: 412133--412188 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
412123 ATGTTCCTGA
* *
412133 TGAAATGGGACTTGA-TGCATT
1 TGAAATGGGACTTCATTCCA-T
*
412154 TGAAATGGGATTTCATTCCAT
1 TGAAATGGGACTTCATTCCAT
412175 TGAAATGGGACTTC
1 TGAAATGGGACTTC
412189 TATCTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (21 bp):
TGAAATGGGACTTCATTCCAT
Found at i:412704 original size:6 final size:6
Alignment explanation
Indices: 412693--412721 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
412683 TGCACTATTT
412693 TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
412722 ACACTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCC
Found at i:427786 original size:19 final size:19
Alignment explanation
Indices: 427762--427798 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
427752 ATAATCTTCA
427762 ATGATATGCAATCCTAGAT
1 ATGATATGCAATCCTAGAT
*
427781 ATGATATGCAATCTTAGA
1 ATGATATGCAATCCTAGA
427799 AGATATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGATATGCAATCCTAGAT
Found at i:427824 original size:22 final size:22
Alignment explanation
Indices: 427762--427821 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 22
427752 ATAATCTTCA
*
427762 ATGATATGCAATCCT---AGAT
1 ATGATATGCAATCTTAGAAGAT
427781 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
427803 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
427822 GATTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.41
22 8 0.24
23 12 0.35
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:428170 original size:16 final size:15
Alignment explanation
Indices: 428149--428184 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
428139 TTAACATTTT
*
428149 TTATTTATTCATTTAA
1 TTATTTAATCA-TTAA
428165 TTATTTAATCATTAA
1 TTATTTAATCATTAA
428180 TTATT
1 TTATT
428185 CTTTTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTTAATCATTAA
Found at i:431271 original size:34 final size:34
Alignment explanation
Indices: 431228--431304 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
431218 AAACCCGCTC
**
431228 ATATTATTTTTTTATTTAAAAAAATATTTATAT-T
1 ATATTATTTTAATATTTAAAAAAAT-TTTATATAT
*
431262 ATATTATTTTAATATTTAATAAAATTTTATATAT
1 ATATTATTTTAATATTTAAAAAAATTTTATATAT
*
431296 ATTTTATTT
1 ATATTATTT
431305 ATTGAAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 7 0.18
34 31 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
ATATTATTTTAATATTTAAAAAAATTTTATATAT
Found at i:432718 original size:18 final size:18
Alignment explanation
Indices: 432695--432729 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
432685 ATGCAATGGC
*
432695 AGCATGGTGAATGGTGGT
1 AGCATGGTGAACGGTGGT
432713 AGCATGGTGAACGGTGG
1 AGCATGGTGAACGGTGG
432730 CTCTGTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.09, G:0.46, T:0.23
Consensus pattern (18 bp):
AGCATGGTGAACGGTGGT
Found at i:435768 original size:41 final size:41
Alignment explanation
Indices: 435681--435860 Score: 192
Period size: 40 Copynumber: 4.5 Consensus size: 41
435671 CGATTTCGAG
* *
435681 TCGATGAGACACTGGGTGTCAATTTACTACTT-GGATTAAT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTAAT
*
435721 TCGATGAGGCACTAGGTGCCAATTTACTACTTCGGATTAAT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTAAT
* * **
435762 TCGATGAGGCGCTGGGTGCCAA-TT--TACTTCGGTTTAGC
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTAAT
* * * *
435800 T-GATGAGACACTGGGTGTCAATTTATTACTTCGAATT-AT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTAAT
* * *
435839 CCGATAAGGCACTAGGTGCCAA
1 TCGATGAGGCACTGGGTGCCAA
435861 ACTGGTGTGT
Statistics
Matches: 115, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
37 17 0.15
38 14 0.12
40 56 0.49
41 28 0.24
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (41 bp):
TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTAAT
Found at i:439172 original size:25 final size:25
Alignment explanation
Indices: 439138--439187 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
439128 AATACGTTTG
439138 TTTTTTTGGTAAGGGGGTGTTACAA
1 TTTTTTTGGTAAGGGGGTGTTACAA
439163 TTTTTTTGGTAAGGGGGTGTTACAA
1 TTTTTTTGGTAAGGGGGTGTTACAA
439188 CCACTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.32, T:0.44
Consensus pattern (25 bp):
TTTTTTTGGTAAGGGGGTGTTACAA
Found at i:440246 original size:82 final size:81
Alignment explanation
Indices: 440154--440308 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
440144 CCCAATAAGA
*
440154 TAAAACAATCGTAATA-CCTCTGTAGTG-TAAAATGACCGAAAAACCCCTCATAAGGTAAAATGA
1 TAAAACAATCGTAATACCCT-TATAG-GATAAAATGACCGAAAAACCCCT-ATAAGGTAAAATGA
440217 CCGTAATGCCCTTGTAGGG
63 CCGTAATGCCCTTGTAGGG
* * * * * *
440236 TAAAATAATCGTAATACCCTTATAGGATTAAATGGCCGAAATACCCCTGTAAGGTAAAATGATCG
1 TAAAACAATCGTAATACCCTTATAGGATAAAATGACCGAAAAACCCCTATAAGGTAAAATGACCG
440301 TAATGCCC
66 TAATGCCC
440309 CTAGAGGGTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
81 24 0.38
82 37 0.58
83 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (81 bp):
TAAAACAATCGTAATACCCTTATAGGATAAAATGACCGAAAAACCCCTATAAGGTAAAATGACCG
TAATGCCCTTGTAGGG
Found at i:440309 original size:27 final size:27
Alignment explanation
Indices: 440072--440310 Score: 146
Period size: 27 Copynumber: 8.8 Consensus size: 27
440062 CCCAATATTT
* * *
440072 GTAAAATGATTGTAATACCCTTGTAGG
1 GTAAAATGATCGTAATACCCCTGTAAG
* *
440099 GTAAAATGATCGTAATGCCCCCGT-AG
1 GTAAAATGATCGTAATACCCCTGTAAG
** **
440125 GATAAAATGA-CTGTAATGTCCCAATAAG
1 G-TAAAATGATC-GTAATACCCCTGTAAG
* ** *
440153 ATAAAACAATCGTAATACCTCTGT-AG
1 GTAAAATGATCGTAATACCCCTGTAAG
* * * *
440179 TGTAAAATGACCGAAAAACCCCTCATAAG
1 -GTAAAATGATCGTAATACCCCT-GTAAG
* * * *
440208 GTAAAATGACCGTAATGCCCTTGTAGG
1 GTAAAATGATCGTAATACCCCTGTAAG
*
440235 GTAAAATAATCGTAATA-CCCT-TATAG
1 GTAAAATGATCGTAATACCCCTGTA-AG
* ** *
440261 GATTAAATGGCCGAAATACCCCTGTAAG
1 G-TAAAATGATCGTAATACCCCTGTAAG
*
440289 GTAAAATGATCGTAATGCCCCT
1 GTAAAATGATCGTAATACCCCT
440311 AGAGGGTAAA
Statistics
Matches: 156, Mismatches: 45, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
25 2 0.01
26 10 0.06
27 111 0.71
28 29 0.19
29 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (27 bp):
GTAAAATGATCGTAATACCCCTGTAAG
Found at i:440320 original size:136 final size:135
Alignment explanation
Indices: 440072--440324 Score: 283
Period size: 136 Copynumber: 1.9 Consensus size: 135
440062 CCCAATATTT
** * * * *
440072 GTAAAATGATTGTAATACCCTTGTAGGGTAAAATGATCGTAATGCCCCCGTAGGATAAAATGACT
1 GTAAAATGACCGTAATACCCTTGTAGGGTAAAATAATCGTAATACCCCCATAGGATAAAATGACC
* ** * *
440137 GTAATGTCCCAATAAGATAAAACAATCGTAATACCTCTGTAGTGTAAAATGACCGAAAAACCCCT
66 GAAATACCCCAATAAGATAAAACAATCGTAATACCCCTGTAGGGT-AAATGACCGAAAAACCCCT
440202 CATAAG
130 CATAAG
* ** * *
440208 GTAAAATGACCGTAATGCCCTTGTAGGGTAAAATAATCGTAATACCCTTATAGGATTAAATGGCC
1 GTAAAATGACCGTAATACCCTTGTAGGGTAAAATAATCGTAATACCCCCATAGGATAAAATGACC
** * ** *
440273 GAAATACCCCTGTAAGGTAAAATGATCGTAATGCCCCTAG-AGGGTAAATGAC
66 GAAATACCCCAATAAGATAAAACAATCGTAATACCCCT-GTAGGGTAAATGAC
440325 TATTTTACCC
Statistics
Matches: 94, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
135 7 0.07
136 86 0.91
137 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (135 bp):
GTAAAATGACCGTAATACCCTTGTAGGGTAAAATAATCGTAATACCCCCATAGGATAAAATGACC
GAAATACCCCAATAAGATAAAACAATCGTAATACCCCTGTAGGGTAAATGACCGAAAAACCCCTC
ATAAG
Found at i:440389 original size:24 final size:24
Alignment explanation
Indices: 440343--440437 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
440333 CCCTCGAGTT
* **
440343 TAAATGATTGATTTGTCCATGATG
1 TAAATGACTGATTTGTCTGTGATG
* *
440367 TAAATGACTGATTTGTTTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
*
440391 TAAATGACTAATTTGTCTGTGATTGG
1 TAAATGACTGATTTGTCTGTGA-T-G
*
440417 T--ATGATTGATTTGTCTGTGAT
1 TAAATGACTGATTTGTCTGTGAT
440438 TTGTATTACT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
23 1 0.02
24 56 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.46
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:440450 original size:24 final size:24
Alignment explanation
Indices: 440370--440451 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
440360 CATGATGTAA
* **
440370 ATGACTGATTTGTTTGTGATTTAA
1 ATGACTGATTTGTCTGTGATTTGT
* *
440394 ATGACTAATTTGTCTGTGATTGGT
1 ATGACTGATTTGTCTGTGATTTGT
*
440418 ATGATTGATTTGTCTGTGATTTGT
1 ATGACTGATTTGTCTGTGATTTGT
*
440442 ATTACTGATT
1 ATGACTGATT
440452 CTGAGCATGG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTTGT
Found at i:440600 original size:26 final size:26
Alignment explanation
Indices: 440567--440620 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
440557 TTGGCCACAT
* * *
440567 ATACTATTACTGGTAGCTTTGCTGTA
1 ATACTATTACTAGCAGCTTTGCGGTA
*
440593 ATACTATTGCTAGCAGCTTTGCGGTA
1 ATACTATTACTAGCAGCTTTGCGGTA
440619 AT
1 AT
440621 GCTACTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (26 bp):
ATACTATTACTAGCAGCTTTGCGGTA
Found at i:440746 original size:22 final size:22
Alignment explanation
Indices: 440721--440772 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
440711 ATTACTATAC
* * * *
440721 TTATGGCTTGTAGTTATTCTGT
1 TTATAGCTTATAGCTATCCTGT
440743 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCTATCCTGT
*
440765 TTACAGCT
1 TTATAGCT
440773 CTTAGTCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (22 bp):
TTATAGCTTATAGCTATCCTGT
Found at i:441014 original size:46 final size:46
Alignment explanation
Indices: 440945--441032 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
440935 ATTGTTGCAT
*
440945 TTCTATTACTGATTCTGTCACTGTATTAGGCTTA-GGCCCACATGTA
1 TTCTATTACTGATTCTGTCACTGTAATAGGC-TACGGCCCACATGTA
** *
440991 TTCTATTTTTGATTCTGAT-ACTGTAATGGGCTACGGCCCACA
1 TTCTATTACTGATTCTG-TCACTGTAATAGGCTACGGCCCACA
441033 CTACACTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 2 0.06
46 33 0.92
47 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (46 bp):
TTCTATTACTGATTCTGTCACTGTAATAGGCTACGGCCCACATGTA
Found at i:442016 original size:17 final size:19
Alignment explanation
Indices: 441986--442022 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
441976 AAGTATATAT
441986 ATAAATATATAATATAATA
1 ATAAATATATAATATAATA
442005 ATAAATA-A-AATATAATA
1 ATAAATATATAATATAATA
442022 A
1 A
442023 AACAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAATATATAATATAATA
Found at i:442054 original size:27 final size:26
Alignment explanation
Indices: 442001--442055 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
441991 TATATAATAT
*
442001 AATAATAAATAAAATATAATAAAACA
1 AATAATAAATAAAATATAAGAAAACA
*
442027 AATAAGTAAATGAAATA-AAGAAAGACA
1 AATAA-TAAATAAAATATAAGAAA-ACA
442054 AA
1 AA
442056 AGCAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (26 bp):
AATAATAAATAAAATATAAGAAAACA
Found at i:448181 original size:20 final size:21
Alignment explanation
Indices: 448153--448203 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
448143 TTATGATTAA
*
448153 ATTTGAATTTTAATAT-TTTT
1 ATTTTAATTTTAATATGTTTT
*
448173 ATTTTAA-TTTGATATGTTTT
1 ATTTTAATTTTAATATGTTTT
*
448193 -TTTTATTTTTA
1 ATTTTAATTTTA
448204 TAATATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
ATTTTAATTTTAATATGTTTT
Found at i:458929 original size:16 final size:16
Alignment explanation
Indices: 458908--458938 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
458898 AACATGTGAC
458908 AAAAATGATAAAAAAT
1 AAAAATGATAAAAAAT
*
458924 AAAAATTATAAAAAA
1 AAAAATGATAAAAAA
458939 AGTATTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATGATAAAAAAT
Found at i:458971 original size:19 final size:19
Alignment explanation
Indices: 458915--458972 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
458905 GACAAAAATG
458915 ATAAAAA-ATAAAAATTATA
1 ATAAAAATATAAAAATT-TA
* *
458934 A-AAAAAGTATTAAATTTTA
1 ATAAAAA-TATAAAAATTTA
458953 ATAAAAATATAAAAATTTA
1 ATAAAAATATAAAAATTTA
458972 A
1 A
458973 ATTTTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.16
19 15 0.47
20 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATATAAAAATTTA
Found at i:458975 original size:26 final size:25
Alignment explanation
Indices: 458934--458993 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
458924 AAAAATTATA
458934 AAAAAAGTATTAAATTTTAATAAAAAT
1 AAAAAA-T-TTAAATTTTAATAAAAAT
*
458961 ATAAAAATTTAAATTTTATTAAAAAT
1 A-AAAAATTTAAATTTTAATAAAAAT
458987 AAAAAAT
1 AAAAAAT
458994 CATAANNNNN
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 6 0.19
26 18 0.58
27 2 0.06
28 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAAAATTTAAATTTTAATAAAAAT
Found at i:469225 original size:19 final size:18
Alignment explanation
Indices: 469203--469249 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
469193 TTTGATACAC
*
469203 TTTATATTTTTTTACGATT
1 TTTATATTTTTATA-GATT
469222 TTTATAATTTTTATAGATT
1 TTTAT-ATTTTTATAGATT
469241 TTTAT-TTTT
1 TTTATATTTT
469250 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTATAGATT
Found at i:469259 original size:10 final size:10
Alignment explanation
Indices: 469208--469245 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
469198 TACACTTTAT
*
469208 ATTTTTTTACG
1 ATTTTTATA-G
469219 ATTTTTATA-
1 ATTTTTATAG
469228 ATTTTTATAG
1 ATTTTTATAG
469238 ATTTTTAT
1 ATTTTTAT
469246 TTTTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 8 0.32
11 8 0.32
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (10 bp):
ATTTTTATAG
Found at i:469562 original size:62 final size:60
Alignment explanation
Indices: 469485--469614 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 60
469475 TTTTTTAAAC
* * ** * *
469485 TTTTAGAATTTGAACTAAATTG-GTAATTTTTTGTAAATGTTTAGGGTTAAATTTATTGATTT
1 TTTTAGAATTAGAACTAAAATGAG-AA--TTTTGTAAACATTGAGGGTTAAATTTATTGAATT
*
469547 TTTTAGAATTAGAACTAAAATGACGAATTTTGTAAACATTGAGGGTTAAATTTGTTGAATT
1 TTTTAGAATTAGAACTAAAATGA-GAATTTTGTAAACATTGAGGGTTAAATTTATTGAATT
469608 TTTTAGA
1 TTTTAGA
469615 TTTAAGATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
61 36 0.61
62 20 0.34
63 2 0.03
64 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (60 bp):
TTTTAGAATTAGAACTAAAATGAGAATTTTGTAAACATTGAGGGTTAAATTTATTGAATT
Found at i:469642 original size:61 final size:62
Alignment explanation
Indices: 469527--469664 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 62
469517 GTAAATGTTT
* * *
469527 AGGGTTAAATTTATTGATTTTTTTAGAATTAGAACTAAAATGACGAATTTTGTAAACATT-G
1 AGGGTTAAATTTATTGAATTTTTTAGAATTAGAACTAAAATGAAGAATTATGTAAACATTAG
* * *
469588 AGGGTTAAATTTGTTGAATTTTTTAGATTTA-AGA-TAAAATTGATAGAA-TATGTAAATATTAG
1 AGGGTTAAATTTATTGAATTTTTTAGAATTAGA-ACTAAAA-TGA-AGAATTATGTAAACATTAG
* *
469650 AGGGCTGAATTTATT
1 AGGGTTAAATTTATT
469665 ATTAAGCTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
60 6 0.09
61 42 0.66
62 16 0.25
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (62 bp):
AGGGTTAAATTTATTGAATTTTTTAGAATTAGAACTAAAATGAAGAATTATGTAAACATTAG
Found at i:470145 original size:17 final size:17
Alignment explanation
Indices: 470123--470164 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
470113 ATTCAAGTTT
*
470123 TTAATTAAAAGCTACAA
1 TTAATTAAAAGCTAAAA
* *
470140 TTAATTGAACGCTAAAA
1 TTAATTAAAAGCTAAAA
470157 TT-ATTAAA
1 TTAATTAAA
470165 TATTACAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAGCTAAAA
Found at i:470180 original size:20 final size:20
Alignment explanation
Indices: 470157--470194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
470147 AACGCTAAAA
470157 TTATTAAATATTAC-AAAATG
1 TTATT-AATATTACGAAAATG
470177 TTATTAATATTACGAAAA
1 TTATTAATATTACGAAAA
470195 CCATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
TTATTAATATTACGAAAATG
Found at i:470258 original size:21 final size:22
Alignment explanation
Indices: 470234--470287 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
470224 AAAACTTAGA
470234 ATTATAAAAAAAGTATTAA-AT
1 ATTATAAAAAAAGTATTAATAT
* * *
470255 ATTAT-AAAATATTGTTAATAT
1 ATTATAAAAAAAGTATTAATAT
470276 ATTATAAAAAAA
1 ATTATAAAAAAA
470288 TGAAAGAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTATAAAAAAAGTATTAATAT
Found at i:477504 original size:30 final size:32
Alignment explanation
Indices: 477470--477542 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
477460 TTATATAAAA
477470 ATATTAAAATGATA-AAAAAAT-TAAAAATAT
1 ATATTAAAATGATATAAAAAATATAAAAATAT
* *
477500 ATATT-AAATAGTTATGAAAAATATAAAAATAT
1 ATATTAAAAT-GATATAAAAAATATAAAAATAT
*
477532 ATATAAAAATG
1 ATATTAAAATG
477543 TTTGTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 4 0.11
30 8 0.22
31 6 0.17
32 14 0.39
33 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (32 bp):
ATATTAAAATGATATAAAAAATATAAAAATAT
Found at i:478756 original size:11 final size:12
Alignment explanation
Indices: 478726--478758 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
478716 GTCACAAGTG
478726 AATTAATTCACA
1 AATTAATTCACA
*
478738 AATGAATTCA-A
1 AATTAATTCACA
478749 AATTAATTCA
1 AATTAATTCA
478759 TCTTGGGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (12 bp):
AATTAATTCACA
Found at i:479314 original size:114 final size:113
Alignment explanation
Indices: 479090--479409 Score: 376
Period size: 113 Copynumber: 2.8 Consensus size: 113
479080 CGTAAAAGAA
* * * *
479090 TATCATTAGCGGCG-TTTACAACCACGCGCCACAAAATCTCCTATCCAAAACGCAACGTTTTCGT
1 TATC-TTAGCGGCGTTTTACAACAACGCGCCGCAAAATCTCCTAACCAAAACGCATCGTTTTCGT
* * * * *
479154 CTTTATGTATGCAAGAATTAGTGGCGCCTCAAAAAACACGCCGCTAAAG
65 GTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAACACGCCGCTAAAG
* * ** *
479203 TGTCTTAGCGGCGTTTTACAACAACGCGCCGTAATTTCTCCTAACCAAAATGCATCGTTTTCAGT
1 TATCTTAGCGGCGTTTTACAACAACGCGCCGCAAAATCTCCTAACCAAAACGCATCGTTTTC-GT
479268 GTTGATGTATCCTAGAATTAGTGGCGCTTCGAAAAAA-ACGCCGCTAAAG
65 GTTGATGTATCCTAGAATTAGTGGCGCTTC-AAAAAACACGCCGCTAAAG
* * * * * * * *
479317 TATCTTAGCGGCATTTTGCGA-TATGCGCCGCAAAATATCTTAACCAAAACGCATCGTTTTTGGT
1 TATCTTAGCGGCGTTTTACAACAACGCGCCGCAAAATCTCCTAACCAAAACGCATCG-TTTTCGT
*
479381 GTTGATGTATCCTAGATTTAGTGGCGCTT
65 GTTGATGTATCCTAGAATTAGTGGCGCTT
479410 TTTGATATGC
Statistics
Matches: 175, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
112 9 0.05
113 100 0.57
114 60 0.34
115 6 0.03
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (113 bp):
TATCTTAGCGGCGTTTTACAACAACGCGCCGCAAAATCTCCTAACCAAAACGCATCGTTTTCGTG
TTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAACACGCCGCTAAAG
Found at i:480017 original size:77 final size:76
Alignment explanation
Indices: 479903--480048 Score: 177
Period size: 77 Copynumber: 1.9 Consensus size: 76
479893 GCTTATATGA
* **
479903 AAACGCCGCAAAATATCTGAACCAAAACACACCGTTTTGGTCTCGATGTATACTTCA-ATTAGTG
1 AAACGCCGCAAAATATCTGAACCAAAACACACAGTTTTAATCTCGATGTATACTT-ATATTAGTG
479967 GCGCTGACGTTG
65 GCGCTGACGTTG
* * * ** * *
479979 AAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGTG
1 AAACGCCGC-AAAATATCTGAACCAAAACACACAGTTTTAATCTCGATGTATACTTATATTAGTG
480044 GCGCT
65 GCGCT
480049 TACTAGAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
76 10 0.17
77 48 0.83
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (76 bp):
AAACGCCGCAAAATATCTGAACCAAAACACACAGTTTTAATCTCGATGTATACTTATATTAGTGG
CGCTGACGTTG
Found at i:480158 original size:266 final size:266
Alignment explanation
Indices: 479452--480258 Score: 1344
Period size: 266 Copynumber: 3.1 Consensus size: 266
479442 GGCATTTCGT
* *
479452 TTAAAGCGCCGC-AAAATATCTTTACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTA
1 TTAAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTA
* ** * * *
479516 GTGGCACTTACTAGAAAACGCCGTTAAAGAATATCTTTAGCGGCG-ATTGAGCCAAAGCGCCGCA
66 GTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGATTTAGCGGCGCTTTGGGTC-AAGCGCCGCA
* * *
479580 ACATATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAA
130 ACGTATCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATATGAA
* * *
479645 AACGCCGCAAAAAATCTGAACCAAAACGCACCGTTTTGGTCTTGATGTATACTTTAATTAGTGGC
195 AACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGC
479710 GCTGACG
260 GCTGACG
479717 TTAAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAA-TTT--TG---A-TTATATTA
1 TTAAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTA
479775 GTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGATTTAGCGGCGCTTTGGGTCAAGCGCCGCAA
66 GTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGATTTAGCGGCGCTTTGGGTCAAGCGCCGCAA
*
479840 AGTATCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATATGAAA
131 CGTATCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATATGAAA
*
479905 ACGCCGCAAAATATCTGAACCAAAACACACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCG
196 ACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCG
479970 CTGACG
261 CTGACG
*
479976 TTGAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTA
1 TTAAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTA
*
480041 GTGGCGCTTACTAGAAAATGCCGTTAAAGAATAGATTTAGCGGCGCTTTGGGTCAAGCGCCGCAA
66 GTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGATTTAGCGGCGCTTTGGGTCAAGCGCCGCAA
480106 CGTATCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATATGAAA
131 CGTATCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATATGAAA
* * *
480171 ATGCCGTAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGTG
196 ACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCG
480236 CTGACG
261 CTGACG
*
480242 TTAAAACGCCACAAAAA
1 TTAAAACGCCGCAAAAA
480259 AGCAAAATAC
Statistics
Matches: 508, Mismatches: 25, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
259 232 0.46
260 9 0.02
262 2 0.00
263 2 0.00
265 15 0.03
266 248 0.49
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (266 bp):
TTAAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTA
GTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGATTTAGCGGCGCTTTGGGTCAAGCGCCGCAA
CGTATCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATATGAAA
ACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCG
CTGACG
Found at i:480846 original size:15 final size:14
Alignment explanation
Indices: 480826--480875 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
480816 TAAGGTTTGT
480826 AGTTTAGGGTTTAA
1 AGTTTAGGGTTTAA
**
480840 GAGTTTAAAGTTTAA
1 -AGTTTAGGGTTTAA
*
480855 AGGTTACGGGTTTAA
1 AGTTTA-GGGTTTAA
480870 AGTTTA
1 AGTTTA
480876 AAGGTTACGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (14 bp):
AGTTTAGGGTTTAA
Found at i:480851 original size:22 final size:21
Alignment explanation
Indices: 480826--480882 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
480816 TAAGGTTTGT
*
480826 AGTTTAGGGTTTAAGAGTTTAA
1 AGTTTAAGG-TTAAGAGTTTAA
* *
480848 AGTTTAAAGGTTACGGGTTTAA
1 AGTTT-AAGGTTAAGAGTTTAA
480870 AGTTTAAAGGTTA
1 AGTTT-AAGGTTA
480883 CGGGTTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (21 bp):
AGTTTAAGGTTAAGAGTTTAA
Found at i:480852 original size:29 final size:30
Alignment explanation
Indices: 480796--480878 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 30
480786 TTTTGAGTGT
* * *
480796 AAGGTTACGGGTTT-AGAGTGTAAGGTTTG
1 AAGGTTACGGGTTTAAGAGTTTAAAGTTTA
* *
480825 TAGTTTA-GGGTTTAAGAGTTTAAAGTTTA
1 AAGGTTACGGGTTTAAGAGTTTAAAGTTTA
480854 AAGGTTACGGGTTTAA-AGTTTAAAG
1 AAGGTTACGGGTTTAAGAGTTTAAAG
480879 GTTACGGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
28 6 0.13
29 31 0.69
30 8 0.18
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.37
Consensus pattern (30 bp):
AAGGTTACGGGTTTAAGAGTTTAAAGTTTA
Found at i:480881 original size:15 final size:15
Alignment explanation
Indices: 480833--480881 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
480823 TGTAGTTTAG
480833 GGTTTAAGAGTTTAAA
1 GGTTTAA-AGTTTAAA
* **
480849 -GTTTAAAGGTTACG
1 GGTTTAAAGTTTAAA
480863 GGTTTAAAGTTTAAA
1 GGTTTAAAGTTTAAA
480878 GGTT
1 GGTT
480882 ACGGGTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.39
Consensus pattern (15 bp):
GGTTTAAAGTTTAAA
Found at i:480883 original size:22 final size:22
Alignment explanation
Indices: 480842--480894 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
480832 GGGTTTAAGA
480842 GTTTAAAGTTTAAAGGTTACGG
1 GTTTAAAGTTTAAAGGTTACGG
480864 GTTTAAAGTTTAAAGGTTACGG
1 GTTTAAAGTTTAAAGGTTACGG
480886 G-TTAAAGTT
1 GTTTAAAGTT
480895 AGGGGCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (22 bp):
GTTTAAAGTTTAAAGGTTACGG
Found at i:481125 original size:40 final size:40
Alignment explanation
Indices: 481068--481147 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
481058 TCCCTAATTT
* * *
481068 CCCATTTCGTATTCCCCCCA-ATTCCCCGATTTCATTTCCC
1 CCCAATTCCTATT-CCCCCAGATTCCCCGATTTAATTTCCC
*
481108 CCCAATTCCTATTCCCCCAGTTTCCCCGATTTAATTTCCC
1 CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
481148 TAAATCCCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.16, C:0.44, G:0.05, T:0.35
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
Found at i:489503 original size:43 final size:42
Alignment explanation
Indices: 489210--489522 Score: 337
Period size: 42 Copynumber: 7.4 Consensus size: 42
489200 GTTTGTGAAA
* **
489210 TAAGCACCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTC
* * * * * *
489253 -AAGCGCCGCTATAGAACATTA-CTTTTAGAGGTGTTTTCCTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTTC
*
489295 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-C
* *
489338 TAAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTGTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
489380 TAAGCGCTGCTAAAGAACATGATCTCTAGCGGTGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
489422 TAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * * *
489464 TAAGCGCTGCTAAAAAACATGATCTTTAGCGGTGTTTTTTTATG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTT-TC
*
489508 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
489523 TTAGCGACGT
Statistics
Matches: 230, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.00
42 139 0.60
43 76 0.33
44 14 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:490319 original size:314 final size:315
Alignment explanation
Indices: 489750--490378 Score: 1233
Period size: 314 Copynumber: 2.0 Consensus size: 315
489740 GCAAAATATG
489750 AAAGACAGAAATACAAAAGACATAACAGTGAATGTGAAATTTATTTATTAATTATTTAAATACAT
1 AAAGACAGAAATACAAAAGACATAACAGTGAATGTGAAATTTATTTATTAATTATTTAAATACAT
489815 AGAAAATAATTACATGTTTACTACAATATGAACATATTTCCCAACACTTGAATGGGATGTCGAGT
66 AGAAAATAATTACATGTTTACTACAATATGAACATATTTCCCAACACTTGAATGGGATGTCGAGT
489880 AAAATGTTTGAGTGACAATGAGTTTAATGTTTAGTGGCTTAAGGTAAGCAATGAGTAATATTTTG
131 AAAATGTTTGAGTGACAATGAGTTTAATGTTTAGTGGCTTAAGGTAAGCAATGAGTAATATTTTG
489945 GTTGAAGAGAGGTTTGTGAGGGAACTCGATAAGGATGAACTAAGGTATGACGTAAGATAGTGTGT
196 GTTGAAGAGAGGTTTGTGAGGGAACTCGATAAGGATGAACTAAGGTATGACGTAAGATAGTGTGT
* *
490010 GAAGGAAAATAAAAAAGAGCTTTAATTTTTTATTAAAAAAG-TTTTAAATTTTAT
261 GAAGGAAAATAAAAAAGAGCTGTAATCTTTTATTAAAAAAGTTTTTAAATTTTAT
490064 AAAGACAGAAATACAAAAGACATAACAGTGAATGTGAAATTTATTTATTAATTATTTAAATACAT
1 AAAGACAGAAATACAAAAGACATAACAGTGAATGTGAAATTTATTTATTAATTATTTAAATACAT
490129 AGAAAATAATTACATGTTTACTACAATATGAACATATTTCCCAACACTTGAATGGGATGTCGAGT
66 AGAAAATAATTACATGTTTACTACAATATGAACATATTTCCCAACACTTGAATGGGATGTCGAGT
490194 AAAATGTTTGAGTGACAATGAGTTTAATGTTTAGTGGCTTAAGGTAAGCAATGAGTAATATTTTG
131 AAAATGTTTGAGTGACAATGAGTTTAATGTTTAGTGGCTTAAGGTAAGCAATGAGTAATATTTTG
490259 GTTGAAGAGAGGTTTGTGAGGGAACTCGATAAGGATGAACTAAGGTATGACGTAAGATAGTGTGT
196 GTTGAAGAGAGGTTTGTGAGGGAACTCGATAAGGATGAACTAAGGTATGACGTAAGATAGTGTGT
490324 GAAGGAAAATAAAAAAGAGCTGTAATCTTTTATTAAAAAAGTTTTTAAATTTTAT
261 GAAGGAAAATAAAAAAGAGCTGTAATCTTTTATTAAAAAAGTTTTTAAATTTTAT
490379 TAAAATTTAT
Statistics
Matches: 312, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
314 299 0.96
315 13 0.04
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (315 bp):
AAAGACAGAAATACAAAAGACATAACAGTGAATGTGAAATTTATTTATTAATTATTTAAATACAT
AGAAAATAATTACATGTTTACTACAATATGAACATATTTCCCAACACTTGAATGGGATGTCGAGT
AAAATGTTTGAGTGACAATGAGTTTAATGTTTAGTGGCTTAAGGTAAGCAATGAGTAATATTTTG
GTTGAAGAGAGGTTTGTGAGGGAACTCGATAAGGATGAACTAAGGTATGACGTAAGATAGTGTGT
GAAGGAAAATAAAAAAGAGCTGTAATCTTTTATTAAAAAAGTTTTTAAATTTTAT
Found at i:490386 original size:11 final size:11
Alignment explanation
Indices: 490370--490449 Score: 112
Period size: 11 Copynumber: 7.5 Consensus size: 11
490360 AAAAGTTTTT
490370 AAATTTTATTA
1 AAATTTTATTA
490381 AAA-TTTATTA
1 AAATTTTATTA
490391 AAATTTTA-TA
1 AAATTTTATTA
*
490401 AAAATTTATTA
1 AAATTTTATTA
490412 AAATTTTA-TA
1 AAATTTTATTA
*
490422 AAAATTTATTA
1 AAATTTTATTA
*
490433 AAATTTTATAA
1 AAATTTTATTA
490444 AAATTT
1 AAATTT
490450 AAAAATTACA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
10 28 0.46
11 33 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATTTTATTA
Found at i:490387 original size:10 final size:10
Alignment explanation
Indices: 490368--490450 Score: 103
Period size: 10 Copynumber: 8.0 Consensus size: 10
490358 AAAAAAGTTT
*
490368 TTAAATTTTA
1 TTAAAATTTA
490378 TTAAAATTTA
1 TTAAAATTTA
490388 TTAAAATTTTA
1 TTAAAA-TTTA
*
490399 TAAAAATTTA
1 TTAAAATTTA
490409 TTAAAATTTTA
1 TTAAAA-TTTA
*
490420 TAAAAATTTA
1 TTAAAATTTA
490430 TTAAAATTTTA
1 TTAAAA-TTTA
*
490441 TAAAAATTTA
1 TTAAAATTTA
490451 AAAATTACAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
10 37 0.58
11 27 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:490394 original size:21 final size:21
Alignment explanation
Indices: 490370--490450 Score: 153
Period size: 21 Copynumber: 3.9 Consensus size: 21
490360 AAAAGTTTTT
*
490370 AAATTTTATTAAAATTTATTA
1 AAATTTTATAAAAATTTATTA
490391 AAATTTTATAAAAATTTATTA
1 AAATTTTATAAAAATTTATTA
490412 AAATTTTATAAAAATTTATTA
1 AAATTTTATAAAAATTTATTA
490433 AAATTTTATAAAAATTTA
1 AAATTTTATAAAAATTTA
490451 AAAATTACAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTTATAAAAATTTATTA
Found at i:490404 original size:42 final size:43
Alignment explanation
Indices: 490351--490450 Score: 145
Period size: 42 Copynumber: 2.4 Consensus size: 43
490341 AGCTGTAATC
*
490351 TTTTATTAAAAAAGTTT-TT-AAATTTTATTAAAATTTATTAAAA
1 TTTTA-TAAAAAA-TTTATTAAAATTTTATAAAAATTTATTAAAA
490394 TTTTAT-AAAAATTTATTAAAATTTTATAAAAATTTATTAAAA
1 TTTTATAAAAAATTTATTAAAATTTTATAAAAATTTATTAAAA
490436 TTTTAT-AAAAATTTA
1 TTTTATAAAAAATTTA
490451 AAAATTACAA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
40 3 0.06
41 7 0.13
42 39 0.72
43 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (43 bp):
TTTTATAAAAAATTTATTAAAATTTTATAAAAATTTATTAAAA
Found at i:494252 original size:21 final size:21
Alignment explanation
Indices: 494200--494252 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
494190 GATTTTGTAG
* *
494200 TTAACAAAAAAAGTAATATTT
1 TTAATAAAAAAAGCAATATTT
* * *
494221 TTATTGTAAAAAAGCATTATTT
1 TTAAT-AAAAAAAGCAATATTT
494243 TTAATAAAAA
1 TTAATAAAAA
494253 TTGGCTAAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (21 bp):
TTAATAAAAAAAGCAATATTT
Found at i:496884 original size:24 final size:24
Alignment explanation
Indices: 496857--496905 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
496847 ATATTAGAAT
* *
496857 TCATACAAAATTATAACAAATAAA
1 TCATACAAAATTATAAAAAAAAAA
* *
496881 TCATATAAATTTATAAAAAAAAAA
1 TCATACAAAATTATAAAAAAAAAA
496905 T
1 T
496906 AGAAGTATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
TCATACAAAATTATAAAAAAAAAA
Done.