Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 35
Found at i:309043 original size:17 final size:19
Alignment explanation
Indices: 309006--309043 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
308996 TTCTTTTTTC
*
309006 TTTCGAACAGTCTATCTTT
1 TTTCGAACAGTCTAGCTTT
309025 TTTCGAACAG-CT-GCTTT
1 TTTCGAACAGTCTAGCTTT
309042 TT
1 TT
309044 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTCGAACAGTCTAGCTTT
Found at i:314296 original size:3 final size:3
Alignment explanation
Indices: 314288--314317 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
314278 TAAATATAAA
314288 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
314318 CATATTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:314311 original size:13 final size:13
Alignment explanation
Indices: 314288--314323 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
314278 TAAATATAAA
314288 TATTA-TTATTAT
1 TATTACTTATTAT
314300 TATTACTTATTAT
1 TATTACTTATTAT
*
314313 TATTACATATT
1 TATTACTTATT
314324 TTACAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Found at i:315974 original size:16 final size:17
Alignment explanation
Indices: 315935--315986 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 17
315925 TTTAAGTTCC
*
315935 ATTATTATTTATAGTATAA
1 ATTATTATTT-T-GTTTAA
315954 TATTATTATTTT-TTTAA
1 -ATTATTATTTTGTTTAA
315971 ATTATTATTTTGTTTA
1 ATTATTATTTTGTTTA
315987 CATTCAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.37
17 8 0.27
19 1 0.03
20 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
ATTATTATTTTGTTTAA
Found at i:324805 original size:5 final size:5
Alignment explanation
Indices: 324785--324834 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
324775 ACACACACCC
324785 ATAT- ATATA TATATA ATATA AGTAATA AT-T- ATATA ATATA ATATA
1 ATATA ATATA -ATATA ATATA A-T-ATA ATATA ATATA ATATA ATATA
324830 ATATA
1 ATATA
324835 TAATCTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 21 0.52
6 7 0.17
7 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:330071 original size:69 final size:69
Alignment explanation
Indices: 329944--330125 Score: 249
Period size: 69 Copynumber: 2.6 Consensus size: 69
329934 TTTTTTTTTT
* * * * * *
329944 AAAACAATCTCACATGGCTAATAAACATAGAAGAACATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAACCACACATAGCTAAGAAACATAGAAG-TCATCCCAAAAATCTAAAGAGTAAAAATATG
330009 AGAAC
65 AGAAC
* *
330014 AAAATAACC-CATATAGCTAAGAAACATAGAAGTGCATCCCAAAAATCTAAAGAGTAAAAATATG
1 AAAACAACCACACATAGCTAAGAAACATAGAAGT-CATCCCAAAAATCTAAAGAGTAAAAATATG
330078 AGAAC
65 AGAAC
*
330083 AAAACAACCACACATGGCTAAGAAACATAGAAGATCATCCCAA
1 AAAACAACCACACATAGCTAAGAAACATAGAAG-TCATCCCAA
330126 CTAACTTCTA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
69 62 0.63
70 36 0.36
71 1 0.01
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.16
Consensus pattern (69 bp):
AAAACAACCACACATAGCTAAGAAACATAGAAGTCATCCCAAAAATCTAAAGAGTAAAAATATGA
GAAC
Found at i:332548 original size:23 final size:23
Alignment explanation
Indices: 332517--332569 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
332507 TCCTGAAGGA
* **
332517 CCACTTAGGTTTACATTGAAGTG
1 CCACATAGGTTTACACCGAAGTG
* *
332540 CTACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTACACCGAAGTG
332563 CCACATA
1 CCACATA
332570 ATTGTCCCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (23 bp):
CCACATAGGTTTACACCGAAGTG
Found at i:333349 original size:18 final size:18
Alignment explanation
Indices: 333326--333399 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
333316 CTGAATATTT
333326 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
* *
333344 GTCCCGAAGGATCACTGGATAT
1 GTCCCGAAGGACCAC----TAC
333366 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
* *
333384 ATCCCGAAAGACCACT
1 GTCCCGAAGGACCACT
333400 GGATATGTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 30 0.65
22 16 0.35
ACGTcount: A:0.30, C:0.34, G:0.22, T:0.15
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAC
Found at i:333369 original size:40 final size:40
Alignment explanation
Indices: 333325--333420 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
333315 ACTGAATATT
* * *
333325 TGTCCCGAAGGACCACTACGTCCCGAAGGATCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
333365 TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
333405 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
333421 AAGATATATG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
Found at i:333372 original size:22 final size:22
Alignment explanation
Indices: 333325--333443 Score: 110
Period size: 22 Copynumber: 5.8 Consensus size: 22
333315 ACTGAATATT
333325 TGTCCCGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGGATA
* *
333343 CGTCCCGAAGGATCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
*
333365 TGTCCCGAAGGACCACT--ACA
1 TGTCCCGAAGGACCACTGGATA
*
333385 --TCCCGAAAGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
**
333405 TGTCCCGAAGGACCACAAGATA
1 TGTCCCGAAGGACCACTGGATA
* *
333427 TATGCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
333444 ATAACCCTCG
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
18 28 0.35
20 4 0.05
22 48 0.60
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.16
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGGATA
Found at i:333723 original size:2 final size:2
Alignment explanation
Indices: 333677--333704 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
333667 TATAACAATA
333677 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
333705 GCATGTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334120 original size:64 final size:64
Alignment explanation
Indices: 334011--334148 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
334001 TTCATAACGT
* *
334011 GTGCATCGATGCACTACCTGTGCATTGGTACACAAATCACCTTCGATGTTTTAATCTTAAAGG-
1 GTGCATCGATGCACTACCTGTGCATTGATACACAAATCACATTCGATGTTTTAATCTTAAAGGA
* ** ** * * *
334074 GATGCATCGATGCACTACTTGTGCATAT-ATACACTTATGGCATTCGATGTTTTTATTTTGAAGG
1 G-TGCATCGATGCACTACCTGTGCAT-TGATACACAAATCACATTCGATGTTTTAATCTTAAAGG
334138 A
64 A
334139 GTGCATCGAT
1 GTGCATCGAT
334149 ACACCTGCCC
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.02
64 59 0.95
65 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATTGATACACAAATCACATTCGATGTTTTAATCTTAAAGGA
Found at i:340263 original size:40 final size:40
Alignment explanation
Indices: 340217--340312 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
340207 ACTGAATATT
*
340217 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
* * *
340257 TGTCCCGAAGGACCACTACGTCCTGAAATACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
340297 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
340313 AAGATATGTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.17
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACATCCCGAAAGACCACTGGATA
Found at i:340265 original size:22 final size:21
Alignment explanation
Indices: 340217--340335 Score: 115
Period size: 22 Copynumber: 5.8 Consensus size: 21
340207 ACTGAATATT
*
340217 TGTCCCGAAGGACCACT-ACA
1 TGTCCCGAAGGACCACTGATA
340237 --TCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACT-GATA
340257 TGTCCCGAAGGACCAC---TA
1 TGTCCCGAAGGACCACTGATA
* * **
340275 CGTCCTGAAATACCACTGGATA
1 TGTCCCGAAGGACCACT-GATA
*
340297 TGTCCCGAAGGACCACAAGATA
1 TGTCCCGAAGGACCAC-TGATA
340319 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
340336 ATAACCCTCG
Statistics
Matches: 79, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
18 29 0.37
20 2 0.03
22 48 0.61
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:347822 original size:20 final size:20
Alignment explanation
Indices: 347799--347836 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
347789 TCGCAACACG
347799 AATATGTAAATCACAACGAT
1 AATATGTAAATCACAACGAT
*
347819 AATATGTAAATCGCAACG
1 AATATGTAAATCACAACG
347837 CGGTTTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
AATATGTAAATCACAACGAT
Found at i:347851 original size:21 final size:21
Alignment explanation
Indices: 347826--347886 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
347816 GATAATATGT
*
347826 AAATCGCAACGCGGTTTTCCA
1 AAATCGCAACGCGATTTTCCA
*
347847 AAATCGCAACGCCATTTTCCA
1 AAATCGCAACGCGATTTTCCA
*
347868 AATTCGCAACGCGATTTTC
1 AAATCGCAACGCGATTTTC
347887 GATTTTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (21 bp):
AAATCGCAACGCGATTTTCCA
Found at i:347900 original size:28 final size:28
Alignment explanation
Indices: 347860--347914 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
347850 TCGCAACGCC
*
347860 ATTTTCCAAATTCGCAACGCGATTTTCG
1 ATTTTCCAAATTCGCAACGAGATTTTCG
*
347888 ATTTTTCAAATTCGCAACGAGATTTTC
1 ATTTTCCAAATTCGCAACGAGATTTTC
347915 AAATTCGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (28 bp):
ATTTTCCAAATTCGCAACGAGATTTTCG
Found at i:347989 original size:57 final size:57
Alignment explanation
Indices: 347899--348236 Score: 466
Period size: 57 Copynumber: 5.9 Consensus size: 57
347889 TTTTTCAAAT
* * *
347899 TCGCAACG-AGATTTTCAAATTCGCAACGCTAATTACTGATATAAGTAAACAGTATTA
1 TCGCAACGCA-ATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTA
*
347956 TTGCAACGCAATTTACAAATTCGCAACGCTAATTACCGATAT-AGATAAACAGTACTA
1 TCGCAACGCAATTTACAAATTCGCAACGCTAATTACCGATATAAG-TAAACAGTACTA
* * * * * *
348013 TCGCAACACGATTTACAAATTCGCAACGCTTATTACCAATATAGGTAAATAGTACTA
1 TCGCAACGCAATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTA
* * * *
348070 TCGTAACGCGATTTACAAATTCGCAACGCTGATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCAATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTA
*
348127 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTA
1 TCGCAACGCAATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTA
* * *
348184 TCGCAACG-AGATTTATAAATTCGCAACGCTAATTATCGATATAGGTAAACAGT
1 TCGCAACGCA-ATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGT
348237 GTTGCGAAAA
Statistics
Matches: 254, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
56 2 0.01
57 250 0.98
58 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27
Consensus pattern (57 bp):
TCGCAACGCAATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTA
Found at i:348099 original size:114 final size:114
Alignment explanation
Indices: 347899--348236 Score: 516
Period size: 114 Copynumber: 3.0 Consensus size: 114
347889 TTTTTCAAAT
* * * *
347899 TCGCAACGA-GATTTTCAAATTCGCAACGCTAATTACTGATATAAGTAAACAGTATTATTGCAAC
1 TCGCAAC-ACGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAAC
* *
347963 GCAATTTACAAATTCGCAACGCTAATTACCGATATAGATAAACAGTACTA
65 GCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * * * *
348013 TCGCAACACGATTTACAAATTCGCAACGCTTATTACCAATATAGGTAAATAGTACTATCGTAACG
1 TCGCAACACGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACG
*
348078 CGATTTACAAATTCGCAACGCTGATTACCGATATAGGTAAACAGTACTA
66 CGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
348127 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACG
1 TCGCAACACGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACG
* * *
348192 AGATTTATAAATTCGCAACGCTAATTATCGATATAGGTAAACAGT
66 CGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
348237 GTTGCGAAAA
Statistics
Matches: 201, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
113 1 0.00
114 200 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27
Consensus pattern (114 bp):
TCGCAACACGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACG
CGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:348143 original size:171 final size:171
Alignment explanation
Indices: 347903--348232 Score: 520
Period size: 171 Copynumber: 1.9 Consensus size: 171
347893 TCAAATTCGC
* * * *
347903 AACGAGATTTTCAAATTCGCAACGCTAATTACTGATATAAGTAAACAGTATTATTGCAACGCAAT
1 AACGAGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACGCAAT
347968 TTACAAATTCGCAACGCTAATTACCGATAT-AGATAAACAGTACTATCGCAAC-ACGATTTACAA
66 TTACAAATTCGCAACGCTAATTACCGATATAAG-TAAACAGTACTATCGCAACGA-GATTTACAA
*
348031 ATTCGCAACGCTTATTACCAATATAGGTAAATAGTACTATCGT
129 ATTCGCAACGCTAATTACCAATATAGGTAAATAGTACTATCGT
* * * *
348074 AACGCGATTTACAAATTCGCAACGCTGATTACCGATATAGGTAAACAGTACTATCGCAACGCGAT
1 AACGAGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACGCAAT
*
348139 TTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACGAGATTTATAAAT
66 TTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACGAGATTTACAAAT
* *
348204 TCGCAACGCTAATTATCGATATAGGTAAA
131 TCGCAACGCTAATTACCAATATAGGTAAA
348233 CAGTGTTGCG
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
171 142 0.98
172 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (171 bp):
AACGAGATTTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACGCAAT
TTACAAATTCGCAACGCTAATTACCGATATAAGTAAACAGTACTATCGCAACGAGATTTACAAAT
TCGCAACGCTAATTACCAATATAGGTAAATAGTACTATCGT
Found at i:348282 original size:20 final size:19
Alignment explanation
Indices: 348257--348407 Score: 149
Period size: 20 Copynumber: 7.6 Consensus size: 19
348247 TAAACGCGCT
*
348257 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACT-TCGTG
*
348277 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGAC-TTCGTG
*
348297 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACT-TCGTG
*
348317 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGAC-TTCGTG
*
348337 TTGCAAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GTG
*
348357 TTGCAAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GTG
* * * *
348377 TTGCGATTTATAAATTCGCG
1 TTGCGAATT-TGACTTCGTG
348397 TTGCGAATTTG
1 TTGCGAATTTG
348408 TTGGTAATTA
Statistics
Matches: 111, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.04
20 100 0.90
21 7 0.06
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (19 bp):
TTGCGAATTTGACTTCGTG
Found at i:348304 original size:40 final size:39
Alignment explanation
Indices: 348257--348407 Score: 203
Period size: 40 Copynumber: 3.8 Consensus size: 39
348247 TAAACGCGCT
348257 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTTTGTG
348297 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTTTGTG
* * * *
348337 TTGCAAATTTGACTTCTGTGTTGCAAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GCGTTGCGAATTTGACTTTTGTG
* * *
348377 TTGCGATTTATAAATTCGCGTTGCGAATTTG
1 TTGCGAATT-TGACTTCGCGTTGCGAATTTG
348408 TTGGTAATTA
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
39 2 0.02
40 92 0.93
41 5 0.05
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (39 bp):
TTGCGAATTTGACTTCGCGTTGCGAATTTGACTTTTGTG
Found at i:348327 original size:60 final size:59
Alignment explanation
Indices: 348257--348407 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 59
348247 TAAACGCGCT
* *
348257 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTCTGTGTTGCAAATTTGACT-TCTGCG
* * * *
348317 TTGCGAATTTGACTTTTGTGTTGCAAATTTGACTTCTGTGTTGCAAATTTGACTTCTGTG
1 TTGCGAATTTGAC-TTCGCGTTGCGAATTTGACTTCTGTGTTGCAAATTTGACTTCTGCG
* * *
348377 TTGCGATTTATAAATTCGCGTTGCGAATTTG
1 TTGCGAATT-TGACTTCGCGTTGCGAATTTG
348408 TTGGTAATTA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 2 0.03
60 71 0.93
61 3 0.04
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (59 bp):
TTGCGAATTTGACTTCGCGTTGCGAATTTGACTTCTGTGTTGCAAATTTGACTTCTGCG
Found at i:348510 original size:13 final size:13
Alignment explanation
Indices: 348492--348516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348482 AGGTAAACAG
348492 TGTTGCGAAAATT
1 TGTTGCGAAAATT
348505 TGTTGCGAAAAT
1 TGTTGCGAAAAT
348517 AAAAGCGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
TGTTGCGAAAATT
Found at i:348568 original size:20 final size:20
Alignment explanation
Indices: 348545--348648 Score: 122
Period size: 20 Copynumber: 5.2 Consensus size: 20
348535 TGATTATCAC
348545 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
348565 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
**
348585 GTTGTAAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* *
348605 GTTGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGAC-T-TTTGT
*
348625 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
348645 GTTG
1 GTTG
348649 TAATTTACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.03
19 5 0.07
20 55 0.80
21 5 0.07
22 2 0.03
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:348573 original size:40 final size:40
Alignment explanation
Indices: 348526--348676 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
348516 TAAAAGCGCT
* *
348526 TTGCGAATTTGATTATCACGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGAATATCGCGTTGCGAATTTGACTTTTGTG
* * **
348566 TTGCGAATTTGACT-TCTGTGTTGTAAATTTGACTTTTGTG
1 TTGCGAATTTGAATATC-GCGTTGCGAATTTGACTTTTGTG
*
348606 TTGCG-ATTT-ACATATTCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGA-ATA-TCGCGTTGCGAATTTGACTTTTGTG
* *
348646 TTG-TAATTT-ACAAATTCGCGTTGCGAATTTG
1 TTGCGAATTTGA-ATA-TCGCGTTGCGAATTTG
348677 GAAGCTGAGT
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 7 0.07
40 84 0.89
41 2 0.02
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (40 bp):
TTGCGAATTTGAATATCGCGTTGCGAATTTGACTTTTGTG
Found at i:348708 original size:20 final size:21
Alignment explanation
Indices: 348660--348714 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
348650 AATTTACAAA
*
348660 TTCGCGTTGCGAATTTGGAAG
1 TTCGCGTTGCGAAATTGGAAG
* *
348681 CT-GAGTTGCGAAATTGG-AG
1 TTCGCGTTGCGAAATTGGAAG
348700 TTCGCGTTGC-AAATT
1 TTCGCGTTGCGAAATT
348715 TGTTGGTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 8 0.29
20 19 0.68
21 1 0.04
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGAAATTGGAAG
Found at i:350114 original size:21 final size:22
Alignment explanation
Indices: 350082--350123 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
350072 ATTTTGATTA
*
350082 TTAATCTATT-AATTTTATCAC
1 TTAATCTATTAAATATTATCAC
350103 TTAAT-TATTTAAATATTATCA
1 TTAATCTA-TTAAATATTATCA
350124 ATCTAGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 7 0.39
22 9 0.50
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATCTATTAAATATTATCAC
Found at i:350408 original size:15 final size:15
Alignment explanation
Indices: 350357--350409 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
350347 AAAAAAATAA
*
350357 TTAATTAATAA-ATT
1 TTAATAAATAATATT
* *
350371 TAAATAAATAATAAT
1 TTAATAAATAATATT
*
350386 TTATATAAATATTATT
1 TTA-ATAAATAATATT
350402 TTAATAAA
1 TTAATAAA
350410 AAAATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 9 0.29
15 9 0.29
16 13 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATAAATAATATT
Found at i:350416 original size:32 final size:32
Alignment explanation
Indices: 350347--350449 Score: 83
Period size: 32 Copynumber: 3.3 Consensus size: 32
350337 TAATTAGCAC
* * *
350347 AAAAAAATAA-TTA-ATTAATA-AATTTAAAT
1 AAAAAAATAATTTATATAAATATTATTTTAAT
*
350376 -AAATAATAATTTATATAAATATTATTTTAAT
1 AAAAAAATAATTTATATAAATATTATTTTAAT
* *
350407 AAAAAAATAATATT-TATATA-ATTATATTAAT
1 AAAAAAATAAT-TTATATAAATATTATTTTAAT
*
350438 ATAAAATATAAT
1 A-AAAAAATAAT
350450 AACTATGTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 8 0.13
29 3 0.05
30 6 0.10
31 18 0.30
32 23 0.38
33 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
AAAAAAATAATTTATATAAATATTATTTTAAT
Found at i:350431 original size:31 final size:33
Alignment explanation
Indices: 350371--350450 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 33
350361 TTAATAAATT
* *
350371 TAAATAAATAATAATTTATATAAATATTATTTTAA
1 TAAAAAAATAAT-ATTTATAT-AATATTATATTAA
350406 TAAAAAAATAATATTTATAT-A-ATTATATTAA
1 TAAAAAAATAATATTTATATAATATTATATTAA
*
350437 TATAAAATATAATA
1 TA-AAAAAATAATA
350451 ACTATGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.27
32 11 0.27
34 8 0.20
35 11 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAAAAAATAATATTTATATAATATTATATTAA
Found at i:355787 original size:21 final size:21
Alignment explanation
Indices: 355736--355788 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
355726 ATTATGACTA
355736 TCGCAATGCGATTTTACAATT
1 TCGCAATGCGATTTTACAATT
** *
355757 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-ACAATT
355778 TCGCAATGCGA
1 TCGCAATGCGA
355789 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTACAATT
Found at i:355803 original size:20 final size:21
Alignment explanation
Indices: 355778--355829 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
355768 TTTTCCCAAT
*
355778 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
355798 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
355819 TCGCAATGCGA
1 TCGCAATGCGA
355830 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:355891 original size:41 final size:41
Alignment explanation
Indices: 355815--355892 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
355805 GCGAATTTGG
*
355815 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
355856 AAAATCGTAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
355893 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:355919 original size:20 final size:20
Alignment explanation
Indices: 355819--355927 Score: 121
Period size: 20 Copynumber: 5.4 Consensus size: 20
355809 ATTTGGAAAA
* *
355819 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
355839 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
*
355860 TCGTAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
355880 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
355900 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
355920 TCACAACG
1 TCGCAACG
355928 AGATTCTGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:355932 original size:20 final size:20
Alignment explanation
Indices: 355864--355936 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
355854 ACAAAATCGT
*
355864 AACGCGATACTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
*
355884 AACGCGATACTGACTTTCGC
1 AACGCGATTCTGACTTTCGC
*
355904 AACGCGATTCTGACTTTCAC
1 AACGCGATTCTGACTTTCGC
*
355924 AACGAGATTCTGA
1 AACGCGATTCTGA
355937 AAATCGCAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
AACGCGATTCTGACTTTCGC
Found at i:355944 original size:40 final size:40
Alignment explanation
Indices: 355814--355945 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 40
355804 TGCGAATTTG
* * *
355814 GAAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
* *
355854 ACAAAATCGTAACGCGATACTGACTTTCGCAACGCGATACT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
*** * * * *
355895 GACTTTCGCAACGCGATTCTGACTTTCACAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
355935 GAAAATCGCAA
1 GAAAATCGCAA
355946 TCATCTTCAA
Statistics
Matches: 74, Mismatches: 17, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
40 39 0.53
41 35 0.47
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
Found at i:356259 original size:19 final size:19
Alignment explanation
Indices: 356232--356274 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
356222 GATTTTGTCG
* *
356232 TTGCAATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
356251 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
356270 TTGCG
1 TTGCG
356275 TTTCTCTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:357910 original size:46 final size:42
Alignment explanation
Indices: 357860--357956 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 42
357850 CCTCTTCAAC
* * *
357860 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAT----GGGAGGGGACTCTTGAGG
* *
357906 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
357948 GATGACAGG
1 GATGACAGG
357957 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 24 0.53
46 21 0.47
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:357921 original size:21 final size:21
Alignment explanation
Indices: 357892--357952 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
357882 GTGGGGGGGG
*
357892 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
357913 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
357934 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
357953 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:358319 original size:20 final size:20
Alignment explanation
Indices: 358294--358332 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
358284 GAAGAATAGT
358294 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
358314 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
358333 ATGACTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:358345 original size:20 final size:20
Alignment explanation
Indices: 358322--358372 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
358312 ACTTACTTTC
358322 GCAACGCGAAAATGACTATA
1 GCAACGCGAAAATGACTATA
* * *
358342 GCAACGCGGAAATGGCTATC
1 GCAACGCGAAAATGACTATA
*
358362 GCAATGCGAAA
1 GCAACGCGAAA
358373 TGAAATCGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATA
Found at i:358382 original size:18 final size:16
Alignment explanation
Indices: 358359--358404 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
358349 GGAAATGGCT
358359 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAA--AA
*
358377 ATCGCAA--CGACAAA
1 ATCGCAATGCGAAAAA
358391 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
358405 CACAAATCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 9 0.38
16 8 0.33
18 7 0.29
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.13
Consensus pattern (16 bp):
ATCGCAATGCGAAAAA
Found at i:358433 original size:19 final size:19
Alignment explanation
Indices: 358411--358513 Score: 117
Period size: 19 Copynumber: 5.6 Consensus size: 19
358401 GAAACACAAA
358411 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
358430 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
358449 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
358465 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
358482 TCGCATTGCGATAACCATT
1 TCGCATTGCGATTTTCATT
358501 TCCGCATTGCGAT
1 T-CGCATTGCGAT
358514 AGTCATTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 4 0.06
17 4 0.06
18 3 0.04
19 40 0.56
20 11 0.15
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:359090 original size:18 final size:18
Alignment explanation
Indices: 359067--359114 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
359057 CGGGTCGATC
*
359067 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTA
*
359085 AGGTGATAGCTCTGGGTA
1 AGGTGATGGCTCTGGGTA
359103 AGGTGATGGCTC
1 AGGTGATGGCTC
359115 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTA
Found at i:360941 original size:20 final size:20
Alignment explanation
Indices: 360913--360965 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
360903 GATTATATAT
*
360913 TATCTCGTTGCGAAAGTCAG
1 TATCACGTTGCGAAAGTCAG
360933 TATCACGTTGCGAAAGTCAG
1 TATCACGTTGCGAAAGTCAG
*
360953 TATCGCGTTGCGA
1 TATCACGTTGCGA
360966 TTTTCCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCACGTTGCGAAAGTCAG
Found at i:361064 original size:21 final size:21
Alignment explanation
Indices: 360955--361052 Score: 187
Period size: 21 Copynumber: 4.7 Consensus size: 21
360945 AAAGTCAGTA
*
360955 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
360976 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
360997 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
361018 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
361039 TCGCATTGCGATTT
1 TCGCATTGCGATTT
361053 GGGAAAATCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:361064 original size:42 final size:42
Alignment explanation
Indices: 360955--361064 Score: 157
Period size: 42 Copynumber: 2.6 Consensus size: 42
360945 AAAGTCAGTA
* * *
360955 TCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTGCCAAAATCGCATTGCGATTTTCCAAAT
* *
360997 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTGCCAAAATCGCATTGCGATTTTCCAAAT
**
361039 TCGCATTGCGATTTGGGAAAATCGCA
1 TCGCATTGCGATTTGCCAAAATCGCA
361065 ACGCGAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (42 bp):
TCGCATTGCGATTTGCCAAAATCGCATTGCGATTTTCCAAAT
Found at i:361085 original size:63 final size:63
Alignment explanation
Indices: 360954--361092 Score: 170
Period size: 63 Copynumber: 2.2 Consensus size: 63
360944 GAAAGTCAGT
* * * ** **
360954 ATCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTGCCAAAATCGCAACGCGAAATTCCAAA
* ** **
361017 TTCGCATTGCGATTTTCCAAATTCGCATTGCGATTTGGGAAAATCGCAACGCGAAATTGGAAA
1 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTGCCAAAATCGCAACGCGAAATTCCAAA
361080 ATCGCATTGCGAT
1 ATCGCATTGCGAT
361093 AGTCATAATC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (63 bp):
ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTGCCAAAATCGCAACGCGAAATTCCAAA
Found at i:361091 original size:21 final size:22
Alignment explanation
Indices: 361039--361091 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
361029 TTTTCCAAAT
*
361039 TCGCATTGCG-ATTTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
361060 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
361081 TCGCATTGCGA
1 TCGCATTGCGA
361092 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:365003 original size:10 final size:10
Alignment explanation
Indices: 364990--365017 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
364980 GTTAACCGGC
364990 GTTGACCACT
1 GTTGACCACT
365000 GTTGACCACT
1 GTTGACCACT
365010 GTTGACCA
1 GTTGACCA
365018 AAACTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (10 bp):
GTTGACCACT
Found at i:367478 original size:46 final size:47
Alignment explanation
Indices: 367428--367540 Score: 158
Period size: 46 Copynumber: 2.4 Consensus size: 47
367418 TTGATTTGAT
*
367428 TTCTGATATGATACTTGACATGGATTCTGATCTGATA-TCTG-ATGGA
1 TTCTGATATGATACTTGACATGGATTCTGATATGATACT-TGAATGGA
* *
367474 TTCTGATCTGATACTTGACTTGGATTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGATTCTGATATGATACTTGA-ATGGA
*
367522 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
367541 GTGAATTATG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
46 36 0.61
47 1 0.02
48 22 0.37
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (47 bp):
TTCTGATATGATACTTGACATGGATTCTGATATGATACTTGAATGGA
Found at i:367552 original size:24 final size:24
Alignment explanation
Indices: 367428--367540 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
367418 TTGATTTGAT
367428 TTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
367452 TTCTGATCTGATA-TCTG--ATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
367474 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
367498 TTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
367522 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
367541 GTGAATTATG
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
22 20 0.25
23 2 0.03
24 58 0.73
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:367557 original size:24 final size:24
Alignment explanation
Indices: 367431--367557 Score: 134
Period size: 24 Copynumber: 5.4 Consensus size: 24
367421 ATTTGATTTC
*
367431 TGATATGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTA
* *
367455 TGATCTGATA-TCTG--ATGGATTC
1 TGATATGATACT-TGACATGGATTA
* * *
367477 TGATCTGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTA
*
367501 TGATATGATACTTGACATGGATTT
1 TGATATGATACTTGACATGGATTA
* *
367525 TGATATGATACTTGACGTGAATTA
1 TGATATGATACTTGACATGGATTA
*
367549 TGATTTGAT
1 TGATATGAT
367558 TTTTGATATA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
22 20 0.22
23 2 0.02
24 68 0.76
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTA
Found at i:369763 original size:27 final size:28
Alignment explanation
Indices: 369720--369795 Score: 100
Period size: 27 Copynumber: 2.6 Consensus size: 28
369710 TCTTGTTCCT
*
369720 TTCACTTTATTCATTTCATAGAATGTATTA
1 TTCAC-TT-TTCATTTCATAGAATATATTA
*
369750 TTCAC-TTTCATTTCATAGCATATATTA
1 TTCACTTTTCATTTCATAGAATATATTA
369777 TTCACTTTTTCATTTCATA
1 TTCAC-TTTTCATTTCATA
369796 TCCCAACGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 24 0.57
28 1 0.02
29 12 0.29
30 5 0.12
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.51
Consensus pattern (28 bp):
TTCACTTTTCATTTCATAGAATATATTA
Found at i:370130 original size:144 final size:144
Alignment explanation
Indices: 369904--370217 Score: 430
Period size: 144 Copynumber: 2.2 Consensus size: 144
369894 ACCATTGATT
* * * * * * *
369904 GTAGCACCACCGTCACATGGACGTCAGACGTGTTGGGTACCATTGATAGTAGCACCACCGTTACA
1 GTAGCACCACCGTCACATAGACGTCAGACATGATAGGTACCAATGATAATAGCACCACCGTCACA
* ** * * *
369969 TAGACGTTAGACGTGCTAATTATCATTAATAGTAGCACCACCGTCACACAGACGCCAGACATGTT
66 CAGACGCCAAACATGCTAATTATCATTAATAGTAGCACCACCGTCACACAGACGCCAGACATGCT
370034 AATTATCATTAATA
131 AATTATCATTAATA
370048 GTAGCACCACCGTCACATAGACGTCAGACATGATAGGTACCAATGATAATAGCACCACCGTCACA
1 GTAGCACCACCGTCACATAGACGTCAGACATGATAGGTACCAATGATAATAGCACCACCGTCACA
* * * **
370113 CATACGCCAAACATGCTAATTATCATTAATAGTAGCACCACTGTCACACAGACGTCAGATGTGCT
66 CAGACGCCAAACATGCTAATTATCATTAATAGTAGCACCACCGTCACACAGACGCCAGACATGCT
370178 AATTATCATTAATA
131 AATTATCATTAATA
* * * *
370192 GTAGTACCAACGTCACACAAACGTCA
1 GTAGCACCACCGTCACATAGACGTCA
370218 AACGTGCCAA
Statistics
Matches: 148, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
144 148 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (144 bp):
GTAGCACCACCGTCACATAGACGTCAGACATGATAGGTACCAATGATAATAGCACCACCGTCACA
CAGACGCCAAACATGCTAATTATCATTAATAGTAGCACCACCGTCACACAGACGCCAGACATGCT
AATTATCATTAATA
Found at i:370230 original size:48 final size:48
Alignment explanation
Indices: 369904--370245 Score: 369
Period size: 48 Copynumber: 7.1 Consensus size: 48
369894 ACCATTGATT
** * * *** * *
369904 GTAGCACCACCGTCACATGGACGTCAGACGTGTTGGGTACCATTGATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
* * * *
369952 GTAGCACCACCGTTACATAGACGTTAGACGTGCTAATTATCATTAATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
* *
370000 GTAGCACCACCGTCACACAGACGCCAGACATGTTAATTATCATTAATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
* * ** * * *
370048 GTAGCACCACCGTCACATAGACGTCAGACATGATAGGTACCAATGATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
* * * *
370096 ATAGCACCACCGTCACACATACGCCAAACATGCTAATTATCATTAATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
* **
370144 GTAGCACCACTGTCACACAGACGTCAGATGTGCTAATTATCATTAATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
* * * * * *
370192 GTAGTACCAACGTCACACAAACGTCAAACGTGCCAATTATCATTAATA
1 GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
370240 GTAGCA
1 GTAGCA
370246 TAATTGTCAC
Statistics
Matches: 245, Mismatches: 49, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 245 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (48 bp):
GTAGCACCACCGTCACACAGACGTCAGACATGCTAATTATCATTAATA
Found at i:372403 original size:15 final size:16
Alignment explanation
Indices: 372383--372414 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
372373 CAATTTAGGC
372383 ATCGAA-TTTATATTT
1 ATCGAATTTTATATTT
372398 ATCGAATTTTATATTT
1 ATCGAATTTTATATTT
372414 A
1 A
372415 AGTTTAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
ATCGAATTTTATATTT
Found at i:373342 original size:20 final size:21
Alignment explanation
Indices: 373303--373342 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
373293 ACCTCATTTT
**
373303 ATTTTCCAGTATGATTTATAA
1 ATTTTCCAGTATGAAATATAA
373324 ATTTT-CAGTATGAAATATA
1 ATTTTCCAGTATGAAATATA
373343 TCTATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (21 bp):
ATTTTCCAGTATGAAATATAA
Found at i:373458 original size:18 final size:18
Alignment explanation
Indices: 373432--373471 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
373422 AATTCTAAAT
373432 ATTTACAGTTATCAGATG
1 ATTTACAGTTATCAGATG
* *
373450 ATTTTCAGTTATTAGATG
1 ATTTACAGTTATCAGATG
373468 -TTTA
1 ATTTA
373472 TTGTTACCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (18 bp):
ATTTACAGTTATCAGATG
Found at i:374359 original size:21 final size:21
Alignment explanation
Indices: 374333--374379 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
374323 AAAATCAAGC
374333 GATATTAGGCAGTTGTATTTG
1 GATATTAGGCAGTTGTATTTG
374354 GATATTAGGCAGTTGTATTTG
1 GATATTAGGCAGTTGTATTTG
374375 GATAT
1 GATAT
374380 GAAACAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.04, G:0.28, T:0.43
Consensus pattern (21 bp):
GATATTAGGCAGTTGTATTTG
Found at i:378736 original size:37 final size:37
Alignment explanation
Indices: 378660--378736 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
378650 TTTTTATATT
*
378660 TTTAATTTTGTAAAAAAAAATATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAAATATATAAATATTATCAA
* * *
378697 TTTAATTTT-TTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAAATATATAAATATTAT-CAA
378734 TTT
1 TTT
378737 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 21 0.60
37 14 0.40
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAAATATATAAATATTATCAA
Found at i:379340 original size:114 final size:115
Alignment explanation
Indices: 379140--379371 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 115
379130 TTAATCACTC
* * *
379140 AAATATCTTTTTCACTCTTATATTTTCTTGTACGAATGATTAAATTGTTTGATTGTGAGTAGAAA
1 AAATATCTTTTTCACTCCTATATTCTCATGTACGAATGATTAAATTGTTTGATTGTGAGTAGAAA
* * * *
379205 TATCAACGGTGAGAAAATGATTAGTTATTTGGAAGATGACAAAAGA-TAA
66 AATCAAAGGTGAGAAAATGATTAGTCATTTGAAAGATGACAAAAGATTAA
*
379254 AAATATCTTCTTT-ACTCCTATATTCTCATGTATGAATGATTAAATTGTTTGATTGTGAGTAGAA
1 AAATATCTT-TTTCACTCCTATATTCTCATGTACGAATGATTAAATTGTTTGATTGTGAGTAGAA
*
379318 AAATCAAAGGTGCGAAAATGATTAGTCATTTGAAAGATGACAAAAGATTAA
65 AAATCAAAGGTGAGAAAATGATTAGTCATTTGAAAGATGACAAAAGATTAA
379369 AAA
1 AAA
379372 AAAAAAGAGA
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
114 98 0.92
115 9 0.08
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (115 bp):
AAATATCTTTTTCACTCCTATATTCTCATGTACGAATGATTAAATTGTTTGATTGTGAGTAGAAA
AATCAAAGGTGAGAAAATGATTAGTCATTTGAAAGATGACAAAAGATTAA
Found at i:379952 original size:21 final size:20
Alignment explanation
Indices: 379913--379953 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
379903 AAATTAAATT
* *
379913 TATTTTTTGTTAAATTATTA
1 TATTTTTTGTAAAAGTATTA
379933 TATTTTTTAGTAAAAGTATTA
1 TATTTTTT-GTAAAAGTATTA
379954 ATTAAACCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TATTTTTTGTAAAAGTATTA
Found at i:382465 original size:40 final size:40
Alignment explanation
Indices: 382415--382494 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
382405 TTTAAAAAAA
*
382415 TAGTTAAATGATCAAAAC-ATAATTGTAGGAATATGTAGGT
1 TAGTTAAATGATAAAAACGA-AATTGTAGGAATATGTAGGT
*
382455 TAGTTGAATGATAAAAACGAAATTGTAGGAATATGTAGGT
1 TAGTTAAATGATAAAAACGAAATTGTAGGAATATGTAGGT
382495 GAATAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (40 bp):
TAGTTAAATGATAAAAACGAAATTGTAGGAATATGTAGGT
Found at i:382896 original size:18 final size:19
Alignment explanation
Indices: 382854--382896 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
382844 AACGCTATTA
* * *
382854 ATTTTATTATTTTTTATCG
1 ATTTTATTATTGTTAAACG
382873 ATTTTATTATTGTTAAAC-
1 ATTTTATTATTGTTAAACG
382891 ATTTTA
1 ATTTTA
382897 CTAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
ATTTTATTATTGTTAAACG
Found at i:384450 original size:2 final size:2
Alignment explanation
Indices: 384443--384468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
384433 CACGTGTCCC
384443 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
384469 TATGATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:398942 original size:7 final size:7
Alignment explanation
Indices: 398924--399070 Score: 186
Period size: 7 Copynumber: 21.0 Consensus size: 7
398914 TGAAGATGAA
398924 GAAGAAG
1 GAAGAAG
* *
398931 AAAGAAT
1 GAAGAAG
398938 GAAGAAG
1 GAAGAAG
* *
398945 AAATAAG
1 GAAGAAG
*
398952 AAAGAAG
1 GAAGAAG
*
398959 AAAGAAG
1 GAAGAAG
398966 GAAGAAG
1 GAAGAAG
*
398973 AAAGAAG
1 GAAGAAG
398980 GAAGAAG
1 GAAGAAG
*
398987 AAAGAAG
1 GAAGAAG
*
398994 GAGGAAG
1 GAAGAAG
*
399001 AAAGAAG
1 GAAGAAG
*
399008 GAGGAAG
1 GAAGAAG
399015 GAAGAAG
1 GAAGAAG
*
399022 AAAGAAG
1 GAAGAAG
399029 GAAGAAG
1 GAAGAAG
399036 GAAGAAG
1 GAAGAAG
399043 GAAGAAG
1 GAAGAAG
399050 GAAGAAG
1 GAAGAAG
399057 GAAGAAG
1 GAAGAAG
399064 GAAGAAG
1 GAAGAAG
399071 AGGAGGAAGA
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 120 1.00
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.01
Consensus pattern (7 bp):
GAAGAAG
Found at i:398943 original size:14 final size:14
Alignment explanation
Indices: 398924--399071 Score: 206
Period size: 14 Copynumber: 10.6 Consensus size: 14
398914 TGAAGATGAA
*
398924 GAAGAAGAAAGAAT
1 GAAGAAGAAAGAAG
*
398938 GAAGAAGAAATAAG
1 GAAGAAGAAAGAAG
*
398952 AAAGAAGAAAGAAG
1 GAAGAAGAAAGAAG
398966 GAAGAAGAAAGAAG
1 GAAGAAGAAAGAAG
398980 GAAGAAGAAAGAAG
1 GAAGAAGAAAGAAG
*
398994 GAGGAAGAAAGAAG
1 GAAGAAGAAAGAAG
* *
399008 GAGGAAGGAAGAAG
1 GAAGAAGAAAGAAG
* *
399022 AAAGAAGGAAGAAG
1 GAAGAAGAAAGAAG
*
399036 GAAGAAGGAAGAAG
1 GAAGAAGAAAGAAG
*
399050 GAAGAAGGAAGAAG
1 GAAGAAGAAAGAAG
399064 GAAGAAGA
1 GAAGAAGA
399072 GGAGGAAGAA
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 123 1.00
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.01
Consensus pattern (14 bp):
GAAGAAGAAAGAAG
Found at i:409468 original size:29 final size:29
Alignment explanation
Indices: 409431--409496 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
409421 TAGGTCCAAA
409431 CAAC-TTTAAAACTTGCAATACAGTCCCC
1 CAACATTTAAAACTTGCAATACAGTCCCC
* * *
409459 TAACTTTTAAAACTTGCAATACGGTCCCC
1 CAACATTTAAAACTTGCAATACAGTCCCC
409488 CAACATTTA
1 CAACATTTA
409497 GTCTGTTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.29
Consensus pattern (29 bp):
CAACATTTAAAACTTGCAATACAGTCCCC
Found at i:409510 original size:31 final size:31
Alignment explanation
Indices: 409472--409549 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
409462 CTTTTAAAAC
*
409472 TTGCAATACGGTCCCCCAACATTTAGTCTGT
1 TTGCAATATGGTCCCCCAACATTTAGTCTGT
*
409503 TTGCAATATGGTGCCCCAACATTTAGTCTGT
1 TTGCAATATGGTCCCCCAACATTTAGTCTGT
409534 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
409550 GACGTAACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCTGT
Found at i:416542 original size:2 final size:2
Alignment explanation
Indices: 416535--416560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
416525 TAAAATTTGC
416535 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
416561 TATTTTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:430297 original size:16 final size:17
Alignment explanation
Indices: 430259--430291 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
430249 TTACAGGATT
430259 AAAAACTAGTTTTTTTA
1 AAAAACTAGTTTTTTTA
430276 AAAAACTAGTTTTTTT
1 AAAAACTAGTTTTTTT
430292 TCAAACCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
AAAAACTAGTTTTTTTA
Found at i:446875 original size:86 final size:85
Alignment explanation
Indices: 446703--446880 Score: 302
Period size: 85 Copynumber: 2.1 Consensus size: 85
446693 TCAATTAACG
*
446703 ATTTTCATCCAATAGGTTTATTTTGACAAAAAATTAAAATATTGAGAGTTAAAATACTCTAATAA
1 ATTTT-ATCCAATAGGTTTATTTTGACAAAAAATTAAAACATTGAGAGTTAAAATACTCTAATAA
446768 AGAATAGAGTCTAAAATAATC
65 AGAATAGAGTCTAAAATAATC
* * *
446789 ATTTTATCTAATAGGTTTATTTTGACAAAATATTAAAACATTGAGAGTTAAAATAGTCTAAATAA
1 ATTTTATCCAATAGGTTTATTTTGACAAAAAATTAAAACATTGAGAGTTAAAATACTCT-AATAA
446854 AGAATAGAGTCTAAAATAATC
65 AGAATAGAGTCTAAAATAATC
446875 ATTTTA
1 ATTTTA
446881 ACAAATATTG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 50 0.57
86 37 0.43
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (85 bp):
ATTTTATCCAATAGGTTTATTTTGACAAAAAATTAAAACATTGAGAGTTAAAATACTCTAATAAA
GAATAGAGTCTAAAATAATC
Found at i:451887 original size:13 final size:13
Alignment explanation
Indices: 451869--451898 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
451859 TAGTCAAGGG
451869 ACTCAACAAAGCA
1 ACTCAACAAAGCA
*
451882 ACTCAACAAAGTA
1 ACTCAACAAAGCA
451895 ACTC
1 ACTC
451899 TCTATAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.30, G:0.07, T:0.13
Consensus pattern (13 bp):
ACTCAACAAAGCA
Found at i:459660 original size:23 final size:23
Alignment explanation
Indices: 459634--459681 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
459624 ATAAAGTACA
*
459634 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
459657 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
459680 AT
1 AT
459682 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:460088 original size:21 final size:20
Alignment explanation
Indices: 460058--460111 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
460048 GATAGACACT
*
460058 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
460079 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
460102 TTACATTATA
1 TTACATTATA
460112 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:460099 original size:23 final size:23
Alignment explanation
Indices: 460073--460135 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
460063 ATATAACCAT
460073 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
460096 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
460119 TACCTATTACATCATAT
1 TACCTATTACATTATAT
460136 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:460516 original size:21 final size:20
Alignment explanation
Indices: 460486--460539 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
460476 GATAGACACT
*
460486 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
460507 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
460530 TTACATTATA
1 TTACATTATA
460540 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:460527 original size:23 final size:23
Alignment explanation
Indices: 460501--460558 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
460491 ATATAACCAT
460501 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
460524 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
460547 TACCTATTACAT
1 TACCTATTACAT
460559 CTTATGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:463479 original size:184 final size:184
Alignment explanation
Indices: 463052--463913 Score: 1573
Period size: 184 Copynumber: 4.7 Consensus size: 184
463042 TTTTAAATGG
*
463052 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* *
463117 TAAAACCAGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
463182 GATGTGTAAAATGTCGACAC-TTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
463235 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
463300 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
463365 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
463419 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
463484 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
463549 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
463603 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
463668 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
463733 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
463787 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGGTTGTAGACCTAT
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCG--ATA-----TAGGTTGTAGACCTAT
**
463852 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
59 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
463914 ATGTTGAAAG
Statistics
Matches: 662, Mismatches: 9, Indels: 8
0.97 0.01 0.01
Matches are distributed among these distances:
183 147 0.22
184 436 0.66
186 3 0.00
191 76 0.11
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
Found at i:465290 original size:3 final size:3
Alignment explanation
Indices: 465282--465332 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
465272 ACTTGTTTGG
* * * *
465282 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
465330 ATC
1 ATC
465333 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:465299 original size:12 final size:12
Alignment explanation
Indices: 465282--465344 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
465272 ACTTGTTTGG
465282 ATCATCATCTTC
1 ATCATCATCTTC
*
465294 ATCATCATCGTC
1 ATCATCATCTTC
*
465306 ATCATCATCATC
1 ATCATCATCTTC
*
465318 ATCGTCATCTTC
1 ATCATCATCTTC
* *
465330 ATCGTCAGCTTC
1 ATCATCATCTTC
465342 ATC
1 ATC
465345 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:465343 original size:18 final size:18
Alignment explanation
Indices: 465286--465347 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
465276 GTTTGGATCA
465286 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
465304 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
465322 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
465340 TCATCTTC
1 TCATCTTC
465348 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:465347 original size:6 final size:6
Alignment explanation
Indices: 465286--465347 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
465276 GTTTGGATCA
* * * * * *
465286 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
465334 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
465348 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:467149 original size:198 final size:199
Alignment explanation
Indices: 466810--468407 Score: 2119
Period size: 198 Copynumber: 8.1 Consensus size: 199
466800 TTTAAATTAG
* * *
466810 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
466875 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
466940 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAAA
467005 AAAA
196 AAAA
467009 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
467073 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
467138 CGACACTTTTTATATATGGATCAACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAAA
467201 AAAA
196 AAAA
467205 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
467270 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
467335 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAA
467400 AAAAA
195 AAAAA
467405 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
467470 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
467535 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAAA
467599 AAAA
196 AAAA
467603 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
467668 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * *
467733 CGACAC----T-T-TATGGGT-G-CAC---CTTG-T-----TT-TTAATTCATTC--T-GGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTT-ATTAATTCATTCTGGAAA
467777 AAAATA
195 AAAA-A
* * * * *
467783 TCGA-C-ACA-AACTA-TATTAGT-GTCGAC-ACATTATTTAGACTT--A-TT-CTCTCAT-A-A
1 T--ATCGACACAA--ACTA-TATTAGT-GTCGACA-CA-TT--ATTTAGACTTATTCTC-TCATA
* * * * * * ***
467836 AACCGGTATA-ATTGTACCGGTTA--GATTA-A-AAAATTACATATTACAT-TATAC-TT-TTGG
55 AAACCG-GTATAAT-T----G-TACCGGTTAGATTAAA--A-A-ATTACATAT-TACATTATACT
* * * * * *
467893 GTT-CGAT-GAT--TTTGGG-ATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACC
108 TTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACC
* *
467953 TTGTTTTTAATTCATTCTGGGAAAAAAA
172 TTGTTATTAATTCATTCTGGAAAAAAAA
467981 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
468046 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
468111 CGACACGTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAAA
468176 AAAA
196 AAAA
468180 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
468245 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
** *
468310 CGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTAGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAA
468374 AAAAA
195 AAAAA
*
468379 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
468408 TGACCCTTAA
Statistics
Matches: 1236, Mismatches: 85, Indels: 156
0.84 0.06 0.11
Matches are distributed among these distances:
178 8 0.01
179 23 0.02
180 21 0.02
181 20 0.02
182 12 0.01
183 9 0.01
184 9 0.01
185 18 0.01
186 2 0.00
187 6 0.00
190 5 0.00
191 2 0.00
192 6 0.00
193 13 0.01
194 9 0.01
195 8 0.01
196 22 0.02
197 165 0.13
198 378 0.31
199 313 0.25
200 187 0.15
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTATTAATTCATTCTGGAAAA
AAAA
Found at i:467850 original size:178 final size:178
Alignment explanation
Indices: 467552--467919 Score: 675
Period size: 178 Copynumber: 2.1 Consensus size: 178
467542 TTTTATATAT
* * * *
467552 GGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGATGCACCTTGTTTATAATTCATTCTGGGAAAAAAATATCGACACAAAC
467616 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
467681 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
131 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
* *
467729 GGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGATGCACCTTGTTTATAATTCATTCTGGGAAAAAAATATCGACACAAAC
467794 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
467859 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
131 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
467907 GGATCGACACTTT
1 GGATCGACACTTT
467920 TTTATATATG
Statistics
Matches: 184, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
177 25 0.14
178 159 0.86
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (178 bp):
GGATCGACACTTTATGGATGCACCTTGTTTATAATTCATTCTGGGAAAAAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
Found at i:468259 original size:199 final size:200
Alignment explanation
Indices: 467729--468407 Score: 1227
Period size: 199 Copynumber: 3.4 Consensus size: 200
467719 GATGATTTTG
* *
467729 GGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
467794 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
467859 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
131 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
467924 TATAT
196 TATAT
* *
467929 GGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
467994 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
* *
468059 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-GTTTTA
131 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
468123 TATAT
196 TATAT
*
468128 GGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
468193 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
468258 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
131 GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
468323 TATAT
196 TATAT
* *** *
468328 GGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTAGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
*
468392 TATATTAGTATCGACA
66 TATATTAGTGTCGACA
468408 TGACCCTTAA
Statistics
Matches: 466, Mismatches: 12, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
199 242 0.52
200 224 0.48
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (200 bp):
GGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
GATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTA
TATAT
Found at i:468514 original size:37 final size:38
Alignment explanation
Indices: 468473--468552 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
468463 TCTCATTCAT
*
468473 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
468510 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
468548 AATTA
1 AATTA
468553 ACTCGACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:468516 original size:19 final size:19
Alignment explanation
Indices: 468489--468552 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
468479 ATTCACATAA
*
468489 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
468508 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
468527 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
468546 AAAATTA
1 AAAATTA
468553 ACTCGACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:470381 original size:33 final size:33
Alignment explanation
Indices: 470344--470409 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
470334 CATCTTAATA
*
470344 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
470377 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
470410 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:472550 original size:24 final size:24
Alignment explanation
Indices: 472513--472565 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
472503 CCGTTCTATC
472513 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
472537 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
472561 TATTT
1 TATTT
472566 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:472756 original size:20 final size:19
Alignment explanation
Indices: 472710--472756 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
472700 TCCGGTATCA
*
472710 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
472729 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
472750 TTTTACC
1 TTTTACC
472757 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:472903 original size:20 final size:20
Alignment explanation
Indices: 472876--472922 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
472866 ACACTTTTAA
472876 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
472895 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
472916 TTTTACC
1 TTTTACC
472923 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:474577 original size:32 final size:31
Alignment explanation
Indices: 474538--474641 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 31
474528 GTTATCACTT
474538 TGAACATGTGGCACATATTATGTTAGTGCTTA
1 TGAACATGTGGCACATATTATGTTA-TGCTTA
* * * * * *
474570 TGCACATGTAGCA-TTTTTCACGTTATCACTT-
1 TGAACATGTGGCACATATT-ATGTTAT-GCTTA
*
474601 TGAACATGTGGCACATACTATGTTATTGCTTA
1 TGAACATGTGGCACATATTATGTTA-TGCTTA
*
474633 TGTACATGT
1 TGAACATGT
474642 AGCATTTGTC
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
31 23 0.43
32 30 0.57
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (31 bp):
TGAACATGTGGCACATATTATGTTATGCTTA
Found at i:474600 original size:63 final size:63
Alignment explanation
Indices: 474525--474668 Score: 245
Period size: 63 Copynumber: 2.3 Consensus size: 63
474515 AGACACATGC
* *
474525 CACGTTATCACTTTGAACATGTGGCACATATTATGTTAGTGCTTATGCACATGTAGCATTTTT
1 CACGTTATCACTTTGAACATGTGGCACATACTATGTTAGTGCTTATGCACATGTAGCATTTGT
* *
474588 CACGTTATCACTTTGAACATGTGGCACATACTATGTTATTGCTTATGTACATGTAGCATTTGT
1 CACGTTATCACTTTGAACATGTGGCACATACTATGTTAGTGCTTATGCACATGTAGCATTTGT
474651 CACGTTAT-ACTTTGAACA
1 CACGTTATCACTTTGAACA
474669 CATGACACAT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
62 10 0.13
63 67 0.87
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (63 bp):
CACGTTATCACTTTGAACATGTGGCACATACTATGTTAGTGCTTATGCACATGTAGCATTTGT
Found at i:474609 original size:31 final size:30
Alignment explanation
Indices: 474525--474668 Score: 78
Period size: 32 Copynumber: 4.6 Consensus size: 30
474515 AGACACATGC
* *
474525 CACGTTATCACTTTGAACATGTGGCACATATT
1 CACGTTAT-ACTTTGAACATGTAGCA-TTATT
* * * *
474557 -ATGTTAGTGCTTATGCACATGTAGCATTTTT
1 CACGTTA-TACTT-TGAACATGTAGCATTATT
* * *
474588 CACGTTATCACTTTGAACATGTGGCA-CATA
1 CACGTTAT-ACTTTGAACATGTAGCATTATT
* * *
474618 CTATGTTATTGCTTATGTACATGTAGCATT-TGT
1 C-ACGTTA-TACTT-TGAACATGTAGCATTAT-T
474651 CACGTTATACTTTGAACA
1 CACGTTATACTTTGAACA
474669 CATGACACAT
Statistics
Matches: 81, Mismatches: 22, Indels: 20
0.66 0.18 0.16
Matches are distributed among these distances:
30 7 0.09
31 35 0.43
32 38 0.47
33 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (30 bp):
CACGTTATACTTTGAACATGTAGCATTATT
Found at i:474694 original size:31 final size:31
Alignment explanation
Indices: 474659--474723 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
474649 GTCACGTTAT
474659 ACTTTGAACACATGACACATGTCATGGCATC
1 ACTTTGAACACATGACACATGTCATGGCATC
* *
474690 ACTTTGAATACATGACACATGTCATGTCATC
1 ACTTTGAACACATGACACATGTCATGGCATC
474721 ACT
1 ACT
474724 CATGTACACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (31 bp):
ACTTTGAACACATGACACATGTCATGGCATC
Found at i:477036 original size:18 final size:17
Alignment explanation
Indices: 477013--477050 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
477003 TTTAATATTA
477013 AAAATAGT-AAACTAACAT
1 AAAATAGTCAAA-TAA-AT
477031 AAAATAGTCAAATAAAT
1 AAAATAGTCAAATAAAT
477048 AAA
1 AAA
477051 TGATAAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 11 0.58
19 3 0.16
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATAGTCAAATAAAT
Found at i:482531 original size:65 final size:65
Alignment explanation
Indices: 482395--482557 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
482385 CGGTGCACCA
* *
482395 AGTGTGCATCGATGCATGAAATACATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGG
** * **
482459 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATG
482523 G
65 G
* *
482524 AGTGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
482558 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGG
Found at i:482597 original size:65 final size:64
Alignment explanation
Indices: 482397--482606 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 64
482387 GTGCACCAAG
* * * ** *
482397 TGTGCATCGATGCATGAAATACATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-C
1 TGTGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC
* * *
482460 TTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA
1 -TGTGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGA
*
482525 G
64 C
* *
482526 TGTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGG
1 TGTGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGG
482588 AC
63 AC
482590 TGATGCATCGGTGCATG
1 TG-TGCATCGGTGCATG
482607 CCTTTGAATA
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
62 3 0.02
63 7 0.06
64 54 0.43
65 62 0.49
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TGTGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGAC
Found at i:482797 original size:20 final size:21
Alignment explanation
Indices: 482774--482813 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
482764 GAATCGAATA
482774 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATAT-TAAAATTCATTTG
482794 TAAAATATTAAAATTCATTT
1 TAAAATATTAAAATTCATTT
482814 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATATTAAAATTCATTTG
Found at i:488032 original size:22 final size:21
Alignment explanation
Indices: 487990--488029 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
487980 GAGTTTGTTT
*
487990 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
488011 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
488030 ACAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:490110 original size:65 final size:64
Alignment explanation
Indices: 489974--490132 Score: 212
Period size: 65 Copynumber: 2.5 Consensus size: 64
489964 CGGTGCACCA
* *
489974 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGACGTTTGAAAAATAGCCAGGTGCATCGATGCATGG
** * **
490038 CTTGTGCATCGATGCATCAAATGCATTCGACGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGACG-TTTGAAAAATAGCCAG-GTGCATCGATGCATG
490102 G
64 G
* *
490103 AGTGTGCATCGGTGCATGGAATGCATTCGA
1 AGTGTGCATCGATGCATGAAATGCATTCGA
490133 TGTTCAATTA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
64 36 0.44
65 45 0.56
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGACGTTTGAAAAATAGCCAGGTGCATCGATGCATGG
Found at i:490376 original size:20 final size:21
Alignment explanation
Indices: 490353--490392 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
490343 GAATCGAATA
490353 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
490373 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
490393 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:490617 original size:15 final size:15
Alignment explanation
Indices: 490597--490628 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
490587 AAAATCTTTC
*
490597 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
490612 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
490627 TT
1 TT
490629 GGATTTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:493136 original size:37 final size:36
Alignment explanation
Indices: 493081--493164 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
493071 TGACAACCAA
493081 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
493118 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
493155 -GTTGAAAAAT
1 CTTTGAAAAAT
493165 TGTAATGAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:494942 original size:16 final size:16
Alignment explanation
Indices: 494917--494948 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
494907 CAGTTCCATC
*
494917 CCTTGTAGGCTCACTA
1 CCTTGCAGGCTCACTA
494933 CCTTGCAGGCTCACTA
1 CCTTGCAGGCTCACTA
494949 TATTATGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.34, G:0.19, T:0.28
Consensus pattern (16 bp):
CCTTGCAGGCTCACTA
Found at i:497540 original size:37 final size:36
Alignment explanation
Indices: 497442--497559 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 36
497432 TGACAACCAA
**
497442 CTTTGAAAAAATTATTTTCAAAGTTTGGTAAATG-TT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
497478 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
497513 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
*
497550 -GTTGAAAAAT
1 CTTTGAAAAAT
497560 TGTAATGGGA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
34 25 0.33
35 7 0.09
36 21 0.28
37 22 0.29
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:504791 original size:108 final size:108
Alignment explanation
Indices: 504602--504818 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 108
504592 AAAAATCACC
504602 AAAAGCAAAAGAGAGAGAGTGACTGAATATGAACTTACCTGTCGAAATATCCTTCAAGAAACCAA
1 AAAAGCAAAAGAGAGAGAGTGACTGAATATGAACTTACCTGTCGAAATATCCTTCAAGAAACCAA
*
504667 CAGAGTTTCAGCAAACAGCAAAGTAAAAAAGCGCGTTTGTTTT
66 CAAAGTTTCAGCAAACAGCAAAGTAAAAAAGCGCGTTTGTTTT
504710 AAAAGCAAAAGAGAGAGAGTGACTGAATATGAACTTACCTGTCGAAATATCCTTCAAGAAACCAA
1 AAAAGCAAAAGAGAGAGAGTGACTGAATATGAACTTACCTGTCGAAATATCCTTCAAGAAACCAA
504775 CAAAGTTTCAGCAAACAGCAAAGTAAAAAAGCGCGTTTGTTTT
66 CAAAGTTTCAGCAAACAGCAAAGTAAAAAAGCGCGTTTGTTTT
504818 A
1 A
504819 GTTTTCAACT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (108 bp):
AAAAGCAAAAGAGAGAGAGTGACTGAATATGAACTTACCTGTCGAAATATCCTTCAAGAAACCAA
CAAAGTTTCAGCAAACAGCAAAGTAAAAAAGCGCGTTTGTTTT
Found at i:505205 original size:32 final size:32
Alignment explanation
Indices: 505169--505230 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
505159 AATCTAATGG
* *
505169 GAGTTAATGGTTGTTAGACTAAAATTGAACAT
1 GAGTTAATGGTTGTGAGACTAAAATCGAACAT
*
505201 GAGTTAATGGTTGTGGGACTAAAATCGAAC
1 GAGTTAATGGTTGTGAGACTAAAATCGAAC
505231 GAATCATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (32 bp):
GAGTTAATGGTTGTGAGACTAAAATCGAACAT
Found at i:506469 original size:28 final size:28
Alignment explanation
Indices: 506427--506499 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
506417 GTCTTTGTTT
**
506427 ACATTATGTCATCGAGCTAGTTCTTGAA
1 ACATTATGTTGTCGAGCTAGTTCTTGAA
*
506455 ACATTATGTTGTCGAACTAGTTCTTGAA
1 ACATTATGTTGTCGAGCTAGTTCTTGAA
506483 ACATTATGTTGTCGAGC
1 ACATTATGTTGTCGAGC
506500 CAATACTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (28 bp):
ACATTATGTTGTCGAGCTAGTTCTTGAA
Found at i:506508 original size:28 final size:28
Alignment explanation
Indices: 506449--506511 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
506439 CGAGCTAGTT
* * *
506449 CTTGAAACATTATGTTGTCGAACTAGTT
1 CTTGAAACATTATGTTGTCGAACCAATA
*
506477 CTTGAAACATTATGTTGTCGAGCCAATA
1 CTTGAAACATTATGTTGTCGAACCAATA
506505 CTTGAAA
1 CTTGAAA
506512 GCAACGACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (28 bp):
CTTGAAACATTATGTTGTCGAACCAATA
Found at i:510019 original size:22 final size:22
Alignment explanation
Indices: 509991--510035 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
509981 TCAAACAGGC
509991 ATAGTTTTTGAACCATAAAAGT
1 ATAGTTTTTGAACCATAAAAGT
510013 ATAGTTTTTGAACCATAAAAGT
1 ATAGTTTTTGAACCATAAAAGT
510035 A
1 A
510036 ATCTTTTCTG
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:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
ATAGTTTTTGAACCATAAAAGT
Found at i:512027 original size:32 final size:32
Alignment explanation
Indices: 511991--512052 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
511981 TTATCTTATG
511991 ATCATCTTAGACTATTAAAAAAAATATTTGTA
1 ATCATCTTAGACTATTAAAAAAAATATTTGTA
512023 ATCATCTTAGACTATTAAAAAAAATATTTG
1 ATCATCTTAGACTATTAAAAAAAATATTTG
512053 CATGGTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (32 bp):
ATCATCTTAGACTATTAAAAAAAATATTTGTA
Found at i:513044 original size:2 final size:2
Alignment explanation
Indices: 513037--513080 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
513027 TAAAAATAAT
513037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
513078 TA T
1 TA T
513081 TAATAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:513084 original size:6 final size:7
Alignment explanation
Indices: 513038--513085 Score: 53
Period size: 8 Copynumber: 6.4 Consensus size: 7
513028 AAAAATAATT
513038 ATATATA
1 ATATATA
513045 TATATATA
1 -ATATATA
513053 TATATATA
1 -ATATATA
513061 TATATATA
1 -ATATATA
513069 TATATATA
1 -ATATATA
513077 ATAT-TA
1 ATATATA
513083 ATA
1 ATA
513086 AATTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 5 0.12
7 4 0.10
8 31 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATATATA
Found at i:515462 original size:39 final size:39
Alignment explanation
Indices: 515378--515463 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
515368 CTTATTAGTT
* * * *
515378 TGAAGACGCCATACACTCCTGAGGTCTTCTCCATTTGCT
1 TGAAGACGCCATAAAATCCTGAAGTCTTCTCCATTTGCC
* * * *
515417 TAAAGACGCCATAAAATCGTGAAGTCTTCTTCATTTTCC
1 TGAAGACGCCATAAAATCCTGAAGTCTTCTCCATTTGCC
515456 TGAAGACG
1 TGAAGACG
515464 TCATGCAGTC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (39 bp):
TGAAGACGCCATAAAATCCTGAAGTCTTCTCCATTTGCC
Found at i:520751 original size:22 final size:23
Alignment explanation
Indices: 520723--520770 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
520713 GTTTTTCTGC
520723 TTTCGAAT-GGAAAAATAATAG-T
1 TTTCGAATAGG-AAAATAATAGCT
520745 TTTCGAATAGGAAAATAATAGCT
1 TTTCGAATAGGAAAATAATAGCT
520768 TTT
1 TTT
520771 GAAAACGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (23 bp):
TTTCGAATAGGAAAATAATAGCT
Found at i:522162 original size:21 final size:21
Alignment explanation
Indices: 522138--522223 Score: 145
Period size: 21 Copynumber: 4.0 Consensus size: 21
522128 TAGTAGCGGA
522138 AGCACAAAGAGAAGCATCGAC
1 AGCACAAAGAGAAGCATCGAC
522159 AGCACAAAGAGAAGCATCGAC
1 AGCACAAAGAGAAGCATCGAC
522180 AGCACAAAGAGAAGCATCGAC
1 AGCACAAAGAGAAGCATCGAC
* *
522201 ATCACAAAAGAGAAGCAGCGAC
1 AGCAC-AAAGAGAAGCATCGAC
522223 A
1 A
522224 CAGAGAGAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 46 0.74
22 16 0.26
ACGTcount: A:0.49, C:0.23, G:0.23, T:0.05
Consensus pattern (21 bp):
AGCACAAAGAGAAGCATCGAC
Done.