Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 53 of 125
Found at i:16249210 original size:26 final size:26
Alignment explanation
Indices: 16249157--16249210 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
16249147 GCATAGTCGT
* *
16249157 CTCTTTTTCTGTTAGTGACGGTTGTA
1 CTCTTTTTCTGTTAGTGACGGCTATA
*
16249183 CTCTTTTTTTGTTAGTGACGGCTATA
1 CTCTTTTTCTGTTAGTGACGGCTATA
16249209 CT
1 CT
16249211 TGAGTTGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.17, G:0.20, T:0.50
Consensus pattern (26 bp):
CTCTTTTTCTGTTAGTGACGGCTATA
Found at i:16254903 original size:16 final size:16
Alignment explanation
Indices: 16254882--16254917 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16254872 TAAAAGTACA
*
16254882 ATATATATGTATGTGT
1 ATATATATATATGTGT
*
16254898 ATATATATATATTTGT
1 ATATATATATATGTGT
16254914 ATAT
1 ATAT
16254918 GCATATGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
ATATATATATATGTGT
Found at i:16257958 original size:32 final size:32
Alignment explanation
Indices: 16257922--16257992 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
16257912 TTTGTCGTGT
16257922 TATTTTTGGTGGTGACAACATGGTTATTTGTG
1 TATTTTTGGTGGTGACAACATGGTTATTTGTG
*
16257954 TATTTTTGGTGGTGACAGCATGGTTATTTGTG
1 TATTTTTGGTGGTGACAACATGGTTATTTGTG
16257986 TATTTTT
1 TATTTTT
16257993 CAGTATCAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.17, C:0.06, G:0.27, T:0.51
Consensus pattern (32 bp):
TATTTTTGGTGGTGACAACATGGTTATTTGTG
Found at i:16267924 original size:33 final size:32
Alignment explanation
Indices: 16267853--16267928 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
16267843 AATATTTTTG
16267853 TAAAATAAAAATATGTAAAAATTAAAAAATAA
1 TAAAATAAAAATATGTAAAAATTAAAAAATAA
*
16267885 TAAAATAAAAATATTTTGTAAAAA-T-AAAAATGA
1 TAAAATAAAAATA---TGTAAAAATTAAAAAATAA
*
16267918 TGAAATAAAAA
1 TAAAATAAAAA
16267929 GTTAAAAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 13 0.33
33 17 0.44
34 1 0.03
35 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (32 bp):
TAAAATAAAAATATGTAAAAATTAAAAAATAA
Found at i:16273270 original size:25 final size:26
Alignment explanation
Indices: 16273236--16273287 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
16273226 TGTAAATCTC
16273236 GAATTCCACTT-TCAAGAAGAGATTT
1 GAATTCCACTTATCAAGAAGAGATTT
*
16273261 GAATTCCACTTATCGAGAAGAGATTT
1 GAATTCCACTTATCAAGAAGAGATTT
16273287 G
1 G
16273288 TGAAATTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (26 bp):
GAATTCCACTTATCAAGAAGAGATTT
Found at i:16275206 original size:3 final size:3
Alignment explanation
Indices: 16275198--16275240 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
16275188 GTACCCTTAA
16275198 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16275241 TATTTTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16275429 original size:7 final size:7
Alignment explanation
Indices: 16275417--16275441 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16275407 GAATGAGAAC
16275417 TGATAAA
1 TGATAAA
16275424 TGATAAA
1 TGATAAA
16275431 TGATAAA
1 TGATAAA
16275438 TGAT
1 TGAT
16275442 TTATATGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (7 bp):
TGATAAA
Found at i:16285970 original size:36 final size:36
Alignment explanation
Indices: 16285886--16285970 Score: 84
Period size: 36 Copynumber: 2.3 Consensus size: 36
16285876 ATTTTTTAAA
* *
16285886 AATATTTATTTTATTTTATTTAATATTTAATAATTTT
1 AATA-TTATTTTATTTTATTGAATATTTAATAATCTT
* * *
16285923 ATACATT-TTTTA-TTTATTGATTTTTTATATAATCTT
1 A-ATATTATTTTATTTTATTGAATATTTA-ATAATCTT
16285959 AATATTATTTTA
1 AATATTATTTTA
16285971 ATGTTTACGT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
35 16 0.41
36 18 0.46
37 3 0.08
38 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (36 bp):
AATATTATTTTATTTTATTGAATATTTAATAATCTT
Found at i:16292851 original size:27 final size:27
Alignment explanation
Indices: 16292796--16292854 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
16292786 AATTAATAAA
* **
16292796 AATATTTAAATATTATTTTTAGAAAAT
1 AATATTAAAATATTATTTAAAGAAAAT
**
16292823 AATATTAAAATATTATTTAAAGACTAT
1 AATATTAAAATATTATTTAAAGAAAAT
16292850 AATAT
1 AATAT
16292855 ATTAAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (27 bp):
AATATTAAAATATTATTTAAAGAAAAT
Found at i:16296758 original size:37 final size:37
Alignment explanation
Indices: 16296672--16296855 Score: 185
Period size: 37 Copynumber: 5.0 Consensus size: 37
16296662 AACATTCATT
* * *
16296672 CTTGAA-TCACCGACACTAGAGCCTGCTAGACACATAG
1 CTTGAATTCACCGGCAC-AAAGCCTGCTAGGCACATAG
* * *
16296709 -TCCG-ATTACACCGGCACGAAGCTTGCTAGGCACATAG
1 CT-TGAATT-CACCGGCACAAAGCCTGCTAGGCACATAG
* *
16296746 CTTGAATTCACCGGTACAAAGCCTGCTAGGCGCATAG
1 CTTGAATTCACCGGCACAAAGCCTGCTAGGCACATAG
** *
16296783 CTTGAATTCACTAGCATAAAGCCTGCTAGGCACATAG
1 CTTGAATTCACCGGCACAAAGCCTGCTAGGCACATAG
* * **
16296820 CTCGAATACATTGGCACAAAGCCTGCTAGGCACATA
1 CTTGAATTCACCGGCACAAAGCCTGCTAGGCACATA
16296856 ACCCGAATTT
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
36 2 0.02
37 107 0.88
38 12 0.10
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (37 bp):
CTTGAATTCACCGGCACAAAGCCTGCTAGGCACATAG
Found at i:16306481 original size:16 final size:16
Alignment explanation
Indices: 16306462--16306498 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
16306452 AATTATCATA
*
16306462 TTAGGTTAAATTGCAT
1 TTAGGATAAATTGCAT
16306478 TTAGGGATAAATTGCAT
1 TTA-GGATAAATTGCAT
16306495 TTAG
1 TTAG
16306499 TTATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (16 bp):
TTAGGATAAATTGCAT
Found at i:16308130 original size:27 final size:27
Alignment explanation
Indices: 16308098--16308151 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16308088 TCATTTAACT
*
16308098 TTATTTTTTA-GGTATTTTATATATTTA
1 TTATTTTTTATGCTA-TTTATATATTTA
*
16308125 TTATTTTTTATGCTATTTATATCTTTA
1 TTATTTTTTATGCTATTTATATATTTA
16308152 CCTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (27 bp):
TTATTTTTTATGCTATTTATATATTTA
Found at i:16308189 original size:66 final size:65
Alignment explanation
Indices: 16308043--16308189 Score: 147
Period size: 67 Copynumber: 2.2 Consensus size: 65
16308033 ATTTAATTTT
*
16308043 TTATTTATTATATTTATTATATTCATGTATTTTATATTCTTACATTCATTTAACTTTATTTTTTA
1 TTATTTATT-TATTTATTATATTCATGTATTTTATATTCTTACATTCATTTAACTTTATTTTTCA
16308108 G
65 G
* * * * * * *
16308109 GTATTTTATATATTTATTATTTTTTATGCTA-TTTATA-TCTTTACCTTTATTTAATTTTATTTG
1 TTA-TTTATTTATTTATTA-TATTCATG-TATTTTATATTC-TTACATTCATTTAACTTTATTT-
16308172 TTCA-
61 TTCAG
16308176 TTATTTATTTATTT
1 TTATTTATTTATTT
16308190 TCTTTTTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
66 23 0.35
67 38 0.58
68 5 0.08
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (65 bp):
TTATTTATTTATTTATTATATTCATGTATTTTATATTCTTACATTCATTTAACTTTATTTTTCAG
Found at i:16308318 original size:8 final size:8
Alignment explanation
Indices: 16308301--16308360 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
16308291 TATTACTATC
*
16308301 ATTATATT
1 ATTATTTT
16308309 ATTATTTT
1 ATTATTTT
*
16308317 ATT-TATT
1 ATTATTTT
*
16308324 ACTA-TTT
1 ATTATTTT
16308331 ATTATTTT
1 ATTATTTT
*
16308339 ATTATGTT
1 ATTATTTT
16308347 ATTAATTGTT
1 ATT-ATT-TT
16308357 ATTA
1 ATTA
16308361 ATTGTATTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
7 10 0.24
8 23 0.56
9 3 0.07
10 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (8 bp):
ATTATTTT
Found at i:16308341 original size:30 final size:29
Alignment explanation
Indices: 16308291--16308349 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
16308281 TTATTACAAC
*
16308291 TATTACTATCATTATATTATTATTTTATT
1 TATTACTATCATTATATTATTATGTTATT
* *
16308320 TATTACTATTTATTATTTTATTATGTTATT
1 TATTACTA-TCATTATATTATTATGTTATT
16308350 AATTGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (29 bp):
TATTACTATCATTATATTATTATGTTATT
Found at i:16323292 original size:11 final size:11
Alignment explanation
Indices: 16323264--16323306 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
16323254 CTTCATATTA
*
16323264 TTTATTTTATT
1 TTTATTTAATT
*
16323275 TAGTATTTAATT
1 T-TTATTTAATT
16323287 TTTATTTAATTT
1 TTTATTTAA-TT
16323299 TTTATTTA
1 TTTATTTA
16323307 TCGTATTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTTAATT
Found at i:16327261 original size:7 final size:7
Alignment explanation
Indices: 16327251--16327359 Score: 59
Period size: 7 Copynumber: 15.9 Consensus size: 7
16327241 AATATAATAT
16327251 CTTAAAC
1 CTTAAAC
16327258 CTTAAAC
1 CTTAAAC
*
16327265 CCTAAAC
1 CTTAAAC
16327272 TCTT-AA-
1 -CTTAAAC
*
16327278 CTTGTAAC
1 CTT-AAAC
*
16327286 CTTGAAC
1 CTTAAAC
16327293 C-TAAAC
1 CTTAAAC
*
16327299 ATTAAAC
1 CTTAAAC
*
16327306 ATTAAAAC
1 CTT-AAAC
*
16327314 CTTCAAC
1 CTTAAAC
*
16327321 CTTAAAT
1 CTTAAAC
16327328 C-TAAA-
1 CTTAAAC
16327333 CTTAAAAC
1 CTT-AAAC
**
16327341 CCAAAAC
1 CTTAAAC
16327348 CTTAAA-
1 CTTAAAC
16327354 CTTAAA
1 CTTAAA
16327360 TTTGAACCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
5 4 0.05
6 15 0.19
7 49 0.61
8 12 0.15
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (7 bp):
CTTAAAC
Found at i:16327314 original size:28 final size:27
Alignment explanation
Indices: 16327254--16327341 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 27
16327244 ATAATATCTT
* * * *
16327254 AAACCTTAAACCCTAAACTCTTAACTTG
1 AAACCTTCAA-CCTAAAATCTAAACTTA
* *
16327282 TAACCTTGAACCTAAACAT-TAAACATTA
1 AAACCTTCAACCTAAA-ATCTAAAC-TTA
*
16327310 AAACCTTCAACCTTAAATCTAAACTTA
1 AAACCTTCAACCTAAAATCTAAACTTA
16327337 AAACC
1 AAACC
16327342 CAAAACCTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
27 20 0.41
28 29 0.59
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.27
Consensus pattern (27 bp):
AAACCTTCAACCTAAAATCTAAACTTA
Found at i:16327359 original size:27 final size:28
Alignment explanation
Indices: 16327290--16327359 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
16327280 TGTAACCTTG
***
16327290 AACC-TAAACATTAAACATTAAAACCTTC
1 AACCTTAAAC-TTAAACATTAAAACCCAA
16327318 AACCTTAAA-TCTAAAC-TTAAAACCCAA
1 AACCTTAAACT-TAAACATTAAAACCCAA
16327345 AACCTTAAACTTAAA
1 AACCTTAAACTTAAA
16327360 TTTGAACCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 22 0.61
28 10 0.28
29 4 0.11
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (28 bp):
AACCTTAAACTTAAACATTAAAACCCAA
Found at i:16327379 original size:20 final size:20
Alignment explanation
Indices: 16327345--16327388 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
16327335 TAAAACCCAA
*
16327345 AACCTTAAACTTAAATT-TG
1 AACCATAAACTTAAATTCTG
16327364 AACCATAAATCTTAAATTCTG
1 AACCATAAA-CTTAAATTCTG
16327385 AACC
1 AACC
16327389 CAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (20 bp):
AACCATAAACTTAAATTCTG
Found at i:16327614 original size:17 final size:18
Alignment explanation
Indices: 16327592--16327625 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16327582 TTATTTATAA
16327592 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
16327609 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
16327626 GAGAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:16330795 original size:16 final size:15
Alignment explanation
Indices: 16330775--16330815 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
16330765 TAATCAAGCC
16330775 ATTATATTTATTAAGT
1 ATTATATTTATT-AGT
*
16330791 TTTATATTT-TTAGT
1 ATTATATTTATTAGT
16330805 ATT-TATTTATT
1 ATTATATTTATT
16330816 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 2 0.09
16 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
ATTATATTTATTAGT
Found at i:16330817 original size:17 final size:18
Alignment explanation
Indices: 16330795--16330843 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
16330785 TTAAGTTTTA
*
16330795 TATTTTTAGTATTTA-TT
1 TATTTTTAGTATTTAGGT
*
16330812 TATTTTTAAT-TTTAGGT
1 TATTTTTAGTATTTAGGT
16330829 TATTTTTAAGTATTT
1 TATTTTT-AGTATTT
16330844 TAAGTTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 17 0.65
18 2 0.08
19 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TATTTTTAGTATTTAGGT
Found at i:16339115 original size:21 final size:21
Alignment explanation
Indices: 16339081--16339136 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
16339071 TTACAGGGGT
*
16339081 CACACGCCCATGTGG-CTCTCC
1 CACACACCCATGTGGCCT-TCC
*
16339102 CACACACCCGTGTGGCCTTCC
1 CACACACCCATGTGGCCTTCC
**
16339123 CACATGCCCATGTG
1 CACACACCCATGTG
16339137 CTTAATCGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.20
Consensus pattern (21 bp):
CACACACCCATGTGGCCTTCC
Found at i:16342701 original size:99 final size:99
Alignment explanation
Indices: 16342569--16343173 Score: 636
Period size: 99 Copynumber: 6.1 Consensus size: 99
16342559 AAGGTACTAG
* *
16342569 GTTCGCCGTTCCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGC
*
16342634 CTCAACCTTTCCCTTTATATCTTCACGGTATCAA
66 CTCAACCTTTCCCTTCATATCTTCACGGTATCAA
* * * * *
16342668 GCTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCACCGTTGCTGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGC
* * *** **
16342733 CTCAACCTTTCCCATCACATCTTCTTAGTATCGG
66 CTCAACCTTTCCCTTCATATCTTCACGGTATCAA
*
16342767 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGTGGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGC
* * *
16342832 CTCAACCTTTCCCTTCATATATTCACGATACCGAA
66 CTCAACCTTTCCCTTCATATCTTCACGGTATC-AA
** * * * *
16342867 -TTCGTTGTTGCGGCCTCATCCTTTCCCATCATATCTTCTAAGGTATCGGGTTCGTCGTTGCAGC
1 GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGC
* *
16342931 CTCAACCTTTCCCTT--TATGCCTCTAGGGTATC-A
66 CTCAACCTTTCCCTTCATAT-CTTC-ACGGTATCAA
* * * * * * * * ** *
16342964 GATTCGTCGTTACAGCCTCAATCTTTCCCATAACATTTTCTAAGGTACCAGGTTAACCGTTGCGA
1 G-TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGG
* *
16343029 CCTCAACCTTTCCCTTCATATCTTCATGGTA-CCA
65 CCTCAACCTTTCCCTTCATATCTTCACGGTATCAA
* * * *
16343063 GATTCGCCGTTGCGGCCTCAATCC-TTCCCATAACATCTTCTAAGGTA-CAGAGTTTGCTGTTGC
1 G-TTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTATC-GGGTTCGCCGTTGC
* * *
16343126 GGTCTCAACCTTTCCCTT--TATCTCCAGGGTATC-A
63 GGCCTCAACCTTTCCCTTCATATCTTCACGGTATCAA
*
16343160 GATTCACCGTTGCG
1 G-TTCGCCGTTGCG
16343174 ATCTCAATCT
Statistics
Matches: 420, Mismatches: 75, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
97 29 0.07
98 5 0.01
99 379 0.90
100 4 0.01
101 3 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (99 bp):
GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGC
CTCAACCTTTCCCTTCATATCTTCACGGTATCAA
Found at i:16343071 original size:297 final size:297
Alignment explanation
Indices: 16342580--16343143 Score: 769
Period size: 297 Copynumber: 1.9 Consensus size: 297
16342570 TTCGCCGTTC
* *
16342580 CGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTC
1 CGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTC
* *** *
16342645 CCTTTATATCTTCACGGTATCAAGCTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCTTCTAA
66 CCTTTATACCTTCACGGTATCAAGCTCGCCGTTACAGCCTCAACCTTTCCCATAACATCTTCTAA
* * * * * *
16342710 GGTACCGGGTTCACCGTTGCTGCCTCAACCTTTCCCATCACATCTTCTTAGTATCGGGTTCGCCG
131 GGTACCAGGTTAACCGTTGCTGCCTCAACCTTTCCCATCACATCTTCATAGTACCAGATTCGCCG
* * *
16342775 TTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTATC-GGGTTCGCCGTTGTGGCCTCAAC
196 TTGCGGCCTCAATCC-TTCCCATAACATCTTCTAAGGTA-CAGAGTTCGCCGTTGCGGCCTCAAC
16342838 CTTTCCCTTCATATATTCACGATACCGAATTCGTTGTTG
259 CTTTCCCTTCATATATTCACGATACCGAATTCGTTGTTG
* * *
16342877 CGGCCTCATCCTTTCCCATCATATCTTCTAAGGTATCGGGTTCGTCGTTGCAGCCTCAACCTTTC
1 CGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTC
* * * * * *
16342942 CCTTTATGCC-TCTAGGGTATC-AGATTCGTCGTTACAGCCTCAATCTTTCCCATAACATTTTCT
66 CCTTTATACCTTC-ACGGTATCAAG-CTCGCCGTTACAGCCTCAACCTTTCCCATAACATCTTCT
* * *
16343005 AAGGTACCAGGTTAACCGTTGC-GACCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTCG
129 AAGGTACCAGGTTAACCGTTGCTG-CCTCAACCTTTCCCATCACATCTTCATAGTACCAGATTCG
* * *
16343069 CCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACAGAGTTTGCTGTTGCGGTCTCAA
193 CCGTTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACAGAGTTCGCCGTTGCGGCCTCAA
16343134 CCTTTCCCTT
258 CCTTTCCCTT
16343144 TATCTCCAGG
Statistics
Matches: 231, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
296 6 0.03
297 223 0.97
298 2 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (297 bp):
CGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCAGCCTCAACCTTTC
CCTTTATACCTTCACGGTATCAAGCTCGCCGTTACAGCCTCAACCTTTCCCATAACATCTTCTAA
GGTACCAGGTTAACCGTTGCTGCCTCAACCTTTCCCATCACATCTTCATAGTACCAGATTCGCCG
TTGCGGCCTCAATCCTTCCCATAACATCTTCTAAGGTACAGAGTTCGCCGTTGCGGCCTCAACCT
TTCCCTTCATATATTCACGATACCGAATTCGTTGTTG
Found at i:16344213 original size:88 final size:88
Alignment explanation
Indices: 16344060--16344234 Score: 298
Period size: 88 Copynumber: 2.0 Consensus size: 88
16344050 GAAAGCTTTC
* * *
16344060 TTCACTACATAAGGTCCCTCCCAATTGGGCATCCATTTTCCTCGAGAGTCCTTGAGTATGGGAAG
1 TTCACTACATAAGGTCCCGCCCAATTGGGCATCCATTTTCCTCAAGAGTCCTTGAGTATGAGAAG
*
16344125 TATCTTTTTCAGAACTAGATCTA
66 TATCTTTTTCAAAACTAGATCTA
16344148 TTCACTACATAAGGTCCCGCCCAATTGGGCATCCATTTTCCTCAAGAGTCCTT-ATGTATGAGAA
1 TTCACTACATAAGGTCCCGCCCAATTGGGCATCCATTTTCCTCAAGAGTCCTTGA-GTATGAGAA
16344212 GTATCTTTTTCAAAACTAGATCT
65 GTATCTTTTTCAAAACTAGATCT
16344235 CCCTCATAGA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 1 0.01
88 81 0.99
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (88 bp):
TTCACTACATAAGGTCCCGCCCAATTGGGCATCCATTTTCCTCAAGAGTCCTTGAGTATGAGAAG
TATCTTTTTCAAAACTAGATCTA
Found at i:16348805 original size:12 final size:12
Alignment explanation
Indices: 16348788--16348813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16348778 GTACTAGAAA
16348788 ACAAATTCTTTT
1 ACAAATTCTTTT
16348800 ACAAATTCTTTT
1 ACAAATTCTTTT
16348812 AC
1 AC
16348814 TAGTAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (12 bp):
ACAAATTCTTTT
Found at i:16351715 original size:19 final size:19
Alignment explanation
Indices: 16351691--16351737 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
16351681 GACAAAAATC
16351691 AGATTTTGAAGGAAAGAAG
1 AGATTTTGAAGGAAAGAAG
16351710 AGATTTTGAAGGAAAGAAG
1 AGATTTTGAAGGAAAGAAG
16351729 AGATTTTGA
1 AGATTTTGA
16351738 TGCTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.26
Consensus pattern (19 bp):
AGATTTTGAAGGAAAGAAG
Found at i:16353207 original size:34 final size:34
Alignment explanation
Indices: 16353167--16353310 Score: 155
Period size: 34 Copynumber: 4.2 Consensus size: 34
16353157 AGTTAACCAT
* *
16353167 CCAACACACCATATGCTCGAATGAGCCAATCTAA
1 CCAACACACCAAATGCTCGAATGAGCCAATCCAA
* * * *
16353201 CCAACACACCAAATGCTC-ATAAGAGCTAGTCCAT
1 CCAACACACCAAATGCTCGA-ATGAGCCAATCCAA
* * *
16353235 CCAACATACCATATGCTTGAATGAGCCAATCCAA
1 CCAACACACCAAATGCTCGAATGAGCCAATCCAA
* * * *
16353269 CCAACACACCAAATGCTCGTATGAGCTAGTCCAT
1 CCAACACACCAAATGCTCGAATGAGCCAATCCAA
16353303 CCAACACA
1 CCAACACA
16353311 TCGTATAAAC
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
33 1 0.01
34 86 0.98
35 1 0.01
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.18
Consensus pattern (34 bp):
CCAACACACCAAATGCTCGAATGAGCCAATCCAA
Found at i:16353272 original size:68 final size:68
Alignment explanation
Indices: 16353163--16353310 Score: 251
Period size: 68 Copynumber: 2.2 Consensus size: 68
16353153 ACACAGTTAA
*
16353163 CCATCCAACACACCATATGCTCGAATGAGCCAATCTAACCAACACACCAAATGCTCATAAGAGCT
1 CCATCCAACACACCATATGCTCGAATGAGCCAATCCAACCAACACACCAAATGCTCATAAGAGCT
16353228 AGT
66 AGT
* * * *
16353231 CCATCCAACATACCATATGCTTGAATGAGCCAATCCAACCAACACACCAAATGCTCGTATGAGCT
1 CCATCCAACACACCATATGCTCGAATGAGCCAATCCAACCAACACACCAAATGCTCATAAGAGCT
16353296 AGT
66 AGT
16353299 CCATCCAACACA
1 CCATCCAACACA
16353311 TCGTATAAAC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
68 74 1.00
ACGTcount: A:0.37, C:0.33, G:0.11, T:0.18
Consensus pattern (68 bp):
CCATCCAACACACCATATGCTCGAATGAGCCAATCCAACCAACACACCAAATGCTCATAAGAGCT
AGT
Found at i:16357965 original size:342 final size:342
Alignment explanation
Indices: 16357333--16358017 Score: 1244
Period size: 342 Copynumber: 2.0 Consensus size: 342
16357323 GCAACTCTTT
*
16357333 AATCCGATGAAGGAATAACAGTCTAGCCCTAAGCTCAGCAATAACAAAACCATCACCTTTCAGAG
1 AATCCGATGAAGGAATAAAAGTCTAGCCCTAAGCTCAGCAATAACAAAACCATCACCTTTCAGAG
* *
16357398 TTAATTATGCATTTAATGCTTTCAGTGTAAACAACGGTTTCCAACTTCAAGCATCTACGACAACA
66 TTAATTATGCATTTAATGCTTTCAGTGTAAACAACGATTTCCAACTTCAAGCATCTACGAAAACA
16357463 TTCACTTTCTCAAGAAGATAATCAATCACAAGATCATAATCTTTTAGTAACTCTAACCATCGTTG
131 TTCACTTTCTCAAGAAGATAATCAATCACAAGATCATAATCTTTTAGTAACTCTAACCATCGTTG
* *
16357528 TTGTCTTAAGTTTAACTTTTTTTGAGTCATCAACTATTTCAGGCTTTTATGATCTGTAAATATAT
196 TTGTCTTAAGTTTAACTCTTTTTAAGTCATCAACTATTTCAGGCTTTTATGATCTGTAAATATAT
*
16357593 GACACTTTTCATTGTAGAGGTAATGACGCCAAATTTTCAGAGCAAAAATAAAGACGGCTAGCTCT
261 GACACTTTTCATTGTAGAGGTAATGACGCCAAATCTTCAGAGCAAAAATAAAGACGGCTAGCTCT
16357658 AAATCATGCATCGGATA
326 AAATCATGCATCGGATA
* *
16357675 AATCCGCTGAAGGAATAAAAGTCTAGCCCTGAGCTCAGCAATAACAAAACCATCACCTTTCAGAG
1 AATCCGATGAAGGAATAAAAGTCTAGCCCTAAGCTCAGCAATAACAAAACCATCACCTTTCAGAG
*
16357740 TTAATTATGCATTTAATGCTTTTAGTGTAAACAACGATTTCCAACTTCAAGCATCTACGAAAACA
66 TTAATTATGCATTTAATGCTTTCAGTGTAAACAACGATTTCCAACTTCAAGCATCTACGAAAACA
* **
16357805 TTCACTTTCTCTAGAAGATAATCAATCACATTATCATAATCTTTTAGTAACTCTAACCATCGTTG
131 TTCACTTTCTCAAGAAGATAATCAATCACAAGATCATAATCTTTTAGTAACTCTAACCATCGTTG
*
16357870 TTGTCTTAAGTTTAACTCTTTTTAAGTCATCAACTATTTCATGCTTTTATGATCTGTAAATATAT
196 TTGTCTTAAGTTTAACTCTTTTTAAGTCATCAACTATTTCAGGCTTTTATGATCTGTAAATATAT
*
16357935 GACACTTTTCATTGTAGAGGTAATGACGCCAAATCTTCAGAGCAAAAATAATGACGGCTAGCTCT
261 GACACTTTTCATTGTAGAGGTAATGACGCCAAATCTTCAGAGCAAAAATAAAGACGGCTAGCTCT
16358000 AAATCATGCATCGGATA
326 AAATCATGCATCGGATA
16358017 A
1 A
16358018 TTCCTTTCAT
Statistics
Matches: 329, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
342 329 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (342 bp):
AATCCGATGAAGGAATAAAAGTCTAGCCCTAAGCTCAGCAATAACAAAACCATCACCTTTCAGAG
TTAATTATGCATTTAATGCTTTCAGTGTAAACAACGATTTCCAACTTCAAGCATCTACGAAAACA
TTCACTTTCTCAAGAAGATAATCAATCACAAGATCATAATCTTTTAGTAACTCTAACCATCGTTG
TTGTCTTAAGTTTAACTCTTTTTAAGTCATCAACTATTTCAGGCTTTTATGATCTGTAAATATAT
GACACTTTTCATTGTAGAGGTAATGACGCCAAATCTTCAGAGCAAAAATAAAGACGGCTAGCTCT
AAATCATGCATCGGATA
Found at i:16362147 original size:68 final size:67
Alignment explanation
Indices: 16362035--16362187 Score: 227
Period size: 68 Copynumber: 2.3 Consensus size: 67
16362025 ACACAGTTAA
* * * *
16362035 CCATCAAATACACCATATGCTCGAATGAGCCAATCCAACCAACATACCAAATGC-CCATAAGAGC
1 CCATCCAACACACCATACGCTCGAATGAGCCAATCCAACAAACATACCAAATGCTCCAT-A-AGC
16362099 TAGT
64 TAGT
*
16362103 CCATCCAACACACCATACGCTCGAATGAGCCAATCCAACAAACATACCAAATGCTTGCATAAGCT
1 CCATCCAACACACCATACGCTCGAATGAGCCAATCCAACAAACATACCAAATGC-TCCATAAGCT
16362168 AGT
65 AGT
16362171 CCATCCAACACACCATA
1 CCATCCAACACACCATA
16362188 TAAACTGTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
68 74 0.95
69 1 0.01
70 3 0.04
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.17
Consensus pattern (67 bp):
CCATCCAACACACCATACGCTCGAATGAGCCAATCCAACAAACATACCAAATGCTCCATAAGCTA
GT
Found at i:16363675 original size:22 final size:21
Alignment explanation
Indices: 16363637--16363682 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
16363627 CTTCAAAAAT
*
16363637 AATTTTTTTAATTTATTTTACA
1 AATTTTTTTAATATATTTTA-A
16363659 AATTTTATTTAA-ATATTTTAA
1 AATTTT-TTTAATATATTTTAA
16363680 AAT
1 AAT
16363683 AACTTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 13 0.59
23 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTTTTAATATATTTTAA
Found at i:16363758 original size:24 final size:23
Alignment explanation
Indices: 16363731--16363784 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
16363721 ATATAATAAC
**
16363731 AAAAATAATTCATTAAAATGTAA
1 AAAAATAATAAATTAAAATGTAA
16363754 AAAAATATATAAATTAAAATGTAA
1 AAAAATA-ATAAATTAAAATGTAA
*
16363778 AATAATA
1 AAAAATA
16363785 TAATCAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAAATAATAAATTAAAATGTAA
Found at i:16367702 original size:11 final size:11
Alignment explanation
Indices: 16367689--16367779 Score: 60
Period size: 11 Copynumber: 8.0 Consensus size: 11
16367679 ACCCACATTT
*
16367689 TTTAAATTTAT
1 TTTAAATTTAA
*
16367700 TTTAAGATTAAA
1 TTTAA-ATTTAA
*
16367712 TTT-ATTTTAAA
1 TTTAAATTT-AA
16367723 TTTAAATTTAA
1 TTTAAATTTAA
*
16367734 TTTAAGTTTAAA
1 TTTAAATTT-AA
**
16367746 TTTATTTTTAA
1 TTTAAATTTAA
*
16367757 TTTTAAAATT-A
1 -TTTAAATTTAA
16367768 TTCTAAATTTAA
1 TT-TAAATTTAA
16367780 ATTATTAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
10 4 0.07
11 30 0.49
12 27 0.44
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:16367726 original size:6 final size:6
Alignment explanation
Indices: 16367689--16367782 Score: 65
Period size: 6 Copynumber: 16.3 Consensus size: 6
16367679 ACCCACATTT
* *
16367689 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
16367734 TTTAAG TTTAAA TTTATT TTTAAT TTTAAA ATT--A TTCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
16367781 TT
1 TT
16367783 ATTAAAAAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
4 2 0.03
5 15 0.22
6 48 0.71
7 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:16367727 original size:34 final size:35
Alignment explanation
Indices: 16367689--16367782 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
16367679 ACCCACATTT
16367689 TTTAAATTTATTTTAAGATTAAATTTA-TTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTTAAA
* * *
16367723 TTTAAATTTAATTTAAGTTTAAATTTATTTTTAAT
1 TTTAAATTTATTTTAAGATTAAATTTATTTTTAAA
* *
16367758 TTTAAAATTATTCTAA-ATTTAAATT
1 TTTAAATTTATTTTAAGA-TTAAATT
16367783 ATTAAAAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 25 0.49
35 26 0.51
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTTAAA
Found at i:16367780 original size:17 final size:17
Alignment explanation
Indices: 16367689--16367782 Score: 118
Period size: 17 Copynumber: 5.5 Consensus size: 17
16367679 ACCCACATTT
16367689 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
16367707 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
16367723 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
16367740 TTTAAATTTATTTTTAAT
1 TTTAAATTTA-TTTTAAA
* *
16367758 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
16367775 TTTAAATT
1 TTTAAATT
16367783 ATTAAAAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
16 1 0.02
17 51 0.77
18 14 0.21
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:16368518 original size:3 final size:3
Alignment explanation
Indices: 16368510--16368555 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
16368500 ATAATGACTT
* *
16368510 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAT TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
16368556 AAAAGGAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16369599 original size:30 final size:30
Alignment explanation
Indices: 16369560--16369818 Score: 192
Period size: 30 Copynumber: 8.8 Consensus size: 30
16369550 AAAGGTCCCT
*
16369560 AAAC-TTCAAAAAATCATATTTTAACCCCC
1 AAACTTTCAAAAAATTATATTTTAACCCCC
* * *
16369589 AAACTTTCAAAAAAATACATTTTAACCCCT
1 AAACTTTCAAAAAATTATATTTTAACCCCC
* * *
16369619 AAACTTTCTAAAAGTTATATTTTAACCCCT
1 AAACTTTCAAAAAATTATATTTTAACCCCC
* * *
16369649 AAAATTTCCAAAAATTACATTTTAACCCCC
1 AAACTTTCAAAAAATTATATTTTAACCCCC
* * *
16369679 AAACTTTCTAAAAGTTATATTTTAACCCTC
1 AAACTTTCAAAAAATTATATTTTAACCCCC
* * * *
16369709 GAGCTTTTC-AAAAATTACCATTTT-ACCCTC
1 AAAC-TTTCAAAAAATTA-TATTTTAACCCCC
* *
16369739 AAAC-TTCTTAAAAATTACATTTT-ACCCCC
1 AAACTTTC-AAAAAATTATATTTTAACCCCC
* * ** *
16369768 GAAC-TTCCAAAAATTGCATTTT-ACCCTC
1 AAACTTTCAAAAAATTATATTTTAACCCCC
* *
16369796 GAACTTCTC-AAAAATTACATTTT
1 AAACTT-TCAAAAAATTATATTTT
16369819 GCCCTCGAAC
Statistics
Matches: 193, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
28 25 0.13
29 35 0.18
30 124 0.64
31 9 0.05
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (30 bp):
AAACTTTCAAAAAATTATATTTTAACCCCC
Found at i:16369802 original size:57 final size:56
Alignment explanation
Indices: 16369568--16370020 Score: 266
Period size: 60 Copynumber: 7.8 Consensus size: 56
16369558 CTAAACTTCA
* * * * * *
16369568 AAAAATCATATTTTAACCCCCAAACTTTCAAAAAAATACATTTTAACCC-CTAAACTTTC
1 AAAAATTACATTTT-ACCCCCGAAC-TTCCAAAAATTACATTTT-ACCCTC-GAACTTTC
* * ** * * *
16369627 TAAAAGTTATATTTTAACCCCTAAAATTTCCAAAAATTACATTTTAACCCCCAAACTTTC
1 -AAAAATTACATTTT-ACCCC-CGAACTTCCAAAAATTACATTTT-ACCCTCGAACTTTC
* * * * * * *
16369687 TAAAAGTTATATTTTAACCCTCGAGCTTTTCAAAAATTACCATTTTACCCTCAAACTTCTT
1 -AAAAATTACATTTT-ACCCCCGAAC-TTCCAAAAATTA-CATTTTACCCTCGAACTT-TC
*
16369748 AAAAATTACATTTTACCCCCGAACTTCCAAAAATTGCATTTTACCCTCGAACTTCTC
1 AAAAATTACATTTTACCCCCGAACTTCCAAAAATTACATTTTACCCTCGAACTT-TC
* * * * *
16369805 AAAAATTACATTTTGCCCTCGAACTTCTCACAAATTACTTTTTGCCC-CTGAACTTTC
1 AAAAATTACATTTTACCCCCGAACTTC-CAAAAATTACATTTTACCCTC-GAACTTTC
* * * * * * *
16369862 AAAAATTACATTTTTCCCTCAAACTTCTTAAAAATTACATTTTTACCCTTGATCTTCC
1 AAAAATTACATTTTACCCCCGAACTTC-CAAAAATTACA-TTTTACCCTCGAACTTTC
* * * * * *
16369920 AAAAATTACATTTTTGCCCCCTATCTTCCCAAAATGACATTTTTA-CCTCGAAAACTTTT
1 AAAAATTACA-TTTTACCCCCGAACTTCCAAAAATTACA-TTTTACCCTCG--AACTTTC
* * * * * *
16369979 TAAAATTATATTTTAACCCCAAACTCTCCGAAACTT-CATTTT
1 AAAAATTACATTTTACCCCCGAACT-TCCAAAAATTACATTTT
16370021 CGACCCCGAT
Statistics
Matches: 323, Mismatches: 57, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
57 89 0.28
58 81 0.25
59 41 0.13
60 101 0.31
61 11 0.03
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (56 bp):
AAAAATTACATTTTACCCCCGAACTTCCAAAAATTACATTTTACCCTCGAACTTTC
Found at i:16369823 original size:29 final size:29
Alignment explanation
Indices: 16369657--16369933 Score: 294
Period size: 29 Copynumber: 9.5 Consensus size: 29
16369647 CTAAAATTTC
* *
16369657 CAAAAATTACATTTTAACCCCCAAACTT-T
1 CAAAAATTACATTTT-ACCCTCGAACTTCT
* * * *
16369686 CTAAAAGTTATATTTTAACCCTCGAGCTTTT
1 C-AAAAATTACATTTT-ACCCTCGAACTTCT
*
16369717 CAAAAATTACCATTTTACCCTCAAACTTCT
1 CAAAAATTA-CATTTTACCCTCGAACTTCT
* *
16369747 TAAAAATTACATTTTACCCCCGAACTTC-
1 CAAAAATTACATTTTACCCTCGAACTTCT
*
16369775 CAAAAATTGCATTTTACCCTCGAACTTCT
1 CAAAAATTACATTTTACCCTCGAACTTCT
*
16369804 CAAAAATTACATTTTGCCCTCGAACTTCT
1 CAAAAATTACATTTTACCCTCGAACTTCT
* * *
16369833 CACAAATTACTTTTTGCCC-CTGAACTT-T
1 CAAAAATTACATTTTACCCTC-GAACTTCT
* *
16369861 CAAAAATTACATTTTTCCCTCAAACTTCT
1 CAAAAATTACATTTTACCCTCGAACTTCT
* * *
16369890 TAAAAATTACATTTTTACCCTTGATCTTC-
1 CAAAAATTACA-TTTTACCCTCGAACTTCT
16369919 CAAAAATTACATTTT
1 CAAAAATTACATTTT
16369934 TGCCCCCTAT
Statistics
Matches: 210, Mismatches: 30, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
28 52 0.25
29 90 0.43
30 61 0.29
31 7 0.03
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (29 bp):
CAAAAATTACATTTTACCCTCGAACTTCT
Found at i:16369840 original size:86 final size:86
Alignment explanation
Indices: 16369657--16369971 Score: 328
Period size: 86 Copynumber: 3.6 Consensus size: 86
16369647 CTAAAATTTC
* * * * * *
16369657 CAAAAATTACATTTTAACCCCCAAACTTTCTAAAAGTTATATTTTAACCCTCGAGCTTTTCAAAA
1 CAAAAATTACATTTT-ACCCCCGAAC-TTCCAAAAATTACATTTT-ACCCTCGAACTTCTCAAAA
*
16369722 ATTACCATTTTACCCTCAAACTTCT
63 ATTA-CATTTTACCCTCGAACTTCT
* *
16369747 TAAAAATTACATTTTACCCCCGAACTTCCAAAAATTGCATTTTACCCTCGAACTTCTCAAAAATT
1 CAAAAATTACATTTTACCCCCGAACTTCCAAAAATTACATTTTACCCTCGAACTTCTCAAAAATT
*
16369812 ACATTTTGCCCTCGAACTTCT
66 ACATTTTACCCTCGAACTTCT
* * * * * * * *
16369833 CACAAATTACTTTTTGCCCCTGAACTTTCAAAAATTACATTTTTCCCTCAAACTTCTTAAAAATT
1 CAAAAATTACATTTTACCCCCGAACTTCCAAAAATTACATTTTACCCTCGAACTTCTCAAAAATT
* *
16369898 ACATTTTTACCCTTGATCTTC-
66 ACA-TTTTACCCTCGAACTTCT
* * * * *
16369919 CAAAAATTACATTTTTGCCCCCTATCTTCCCAAAATGACATTTTTA-CCTCGAA
1 CAAAAATTACA-TTTTACCCCCGAACTTCCAAAAATTACA-TTTTACCCTCGAA
16369972 AACTTTTTAA
Statistics
Matches: 189, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
86 85 0.45
87 63 0.33
88 18 0.10
89 9 0.05
90 14 0.07
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (86 bp):
CAAAAATTACATTTTACCCCCGAACTTCCAAAAATTACATTTTACCCTCGAACTTCTCAAAAATT
ACATTTTACCCTCGAACTTCT
Found at i:16369934 original size:29 final size:29
Alignment explanation
Indices: 16369654--16369971 Score: 265
Period size: 29 Copynumber: 11.0 Consensus size: 29
16369644 CCCCTAAAAT
* * *
16369654 TTCCAAAAATTACATTTTAACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* * * * *
16369683 TTTCTAAAAGTTATATTTTAACCCTCGAGC
1 -TTCCAAAAATTACATTTTTACCCTCGAAC
* *
16369713 TTTTCAAAAATTACCA-TTTTACCCTCAAAC
1 -TTCCAAAAATTA-CATTTTTACCCTCGAAC
* *
16369743 TTCTTAAAAATTACA-TTTTACCCCCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
*
16369772 TTCCAAAAATTGCA-TTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
16369800 TTCTCAAAAATTACA-TTTTGCCCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
* *
16369829 TTCTCACAAATTAC-TTTTTGCCC-CTGAAC
1 TTC-CAAAAATTACATTTTTACCCTC-GAAC
* *
16369858 TTTCAAAAATTACATTTTT-CCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* * *
16369886 TTCTTAAAAATTACATTTTTACCCTTGATC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
* * * *
16369916 TTCCAAAAATTACATTTTTGCCCCCTATC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* *
16369945 TTCCCAAAATGACATTTTTA-CCTCGAA
1 TTCCAAAAATTACATTTTTACCCTCGAA
16369972 AACTTTTTAA
Statistics
Matches: 237, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
28 47 0.20
29 128 0.54
30 61 0.26
31 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCGAAC
Found at i:16370412 original size:97 final size:97
Alignment explanation
Indices: 16370246--16370430 Score: 282
Period size: 97 Copynumber: 1.9 Consensus size: 97
16370236 ATTTAAAATT
* * *
16370246 GAGGCAATATTCATTTATTTCGGGTTTTGAAAATTTGTGCTTTAACTTACTAGGCGCGATTTTTC
1 GAGGCAATATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTTC
16370311 TTCAAACCGGGATAATCGAATACCCTTAAAAC
66 TTCAAACCGGGATAATCGAATACCCTTAAAAC
* * *
16370343 GAGGCAATGTTTC-TTTATCTCTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGTGCGACTTTT
1 GAGGCAAT-ATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTT
* *
16370407 CTTCAAATCGGGATAATTGAATAC
65 CTTCAAACCGGGATAATCGAATAC
16370431 TCTTTTCTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 76 0.96
98 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (97 bp):
GAGGCAATATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGACTTTTC
TTCAAACCGGGATAATCGAATACCCTTAAAAC
Found at i:16378120 original size:18 final size:18
Alignment explanation
Indices: 16378099--16378139 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16378089 TTATCAGAAG
16378099 ATATATTACTTA-ATAATA
1 ATATATTA-TTATATAATA
*
16378117 ATATTTTATTATATAATA
1 ATATATTATTATATAATA
16378135 ATATA
1 ATATA
16378140 AAATATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATTATTATATAATA
Found at i:16379192 original size:17 final size:19
Alignment explanation
Indices: 16379165--16379203 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
16379155 GATATGGGAC
*
16379165 AAAAATAAGAA-TGATGTG
1 AAAAATAAGAATTGAAGTG
16379183 AAAAAT-AGAATTGAAGTG
1 AAAAATAAGAATTGAAGTG
16379201 AAA
1 AAA
16379204 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAAATAAGAATTGAAGTG
Found at i:16395492 original size:21 final size:20
Alignment explanation
Indices: 16395442--16395492 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
16395432 ATATTTGGAA
16395442 TTTAATTTTATGAATTTAATT
1 TTTAATTTTATGAATTTAA-T
*
16395463 TATTTATTTT-TGAATTTAAAT
1 T-TTAATTTTATGAATTT-AAT
16395484 TTTAGATTT
1 TTTA-ATTT
16395493 ATTTGTTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (20 bp):
TTTAATTTTATGAATTTAAT
Found at i:16395859 original size:35 final size:35
Alignment explanation
Indices: 16395793--16395864 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
16395783 TTATAATCTC
* * *
16395793 AAAACATTGAAAGATTAAAATTGAAATTTTACCAT
1 AAAACAATGAAAGATTAAAATTGAAAATTTACAAT
16395828 AAAACAATGAAAAGATTAAAATT-AAAATTTACAAT
1 AAAACAATG-AAAGATTAAAATTGAAAATTTACAAT
16395863 AA
1 AA
16395865 TCTTTTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 20 0.61
36 13 0.39
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (35 bp):
AAAACAATGAAAGATTAAAATTGAAAATTTACAAT
Found at i:16402176 original size:452 final size:458
Alignment explanation
Indices: 16401148--16402258 Score: 1864
Period size: 452 Copynumber: 2.4 Consensus size: 458
16401138 TTCAATCATA
*
16401148 CTCTGAATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAA
1 CTCTGGATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAA
* *
16401213 -TCGTATGCTAAGCAAATGGCTTAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGA
66 CT-GTATGCTAAGCAAATTGCTTAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGC
* *
16401277 AAATGGATACAATTAAGTCAAAGTTTATTTCATACAAAATTTCATTTCATTTATCTCAACTACTT
130 AAATGGATACAATTAAGTC-AAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTT
16401342 CAAATTTTAAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACC
194 CAAATTTTAAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACC
16401407 TATTCATTTGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACTCATCAA
259 --TTCATTTGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACTCATCAA
*
16401472 CATGTCAAAATCATAACAACAATTTTTTATCATATAGTACATATTCATATTTACTTAATTCCAGA
322 CATGTCAAAAGCATAACAACAATTTTTTATCATATAGTACATATTCATATTTACTTAATTCCAGA
*
16401537 TATCATAATAAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCGGGGCTCATT
387 TATCATAATAAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCGGGGCTCACT
16401602 TTCAATC
452 TTCAATC
* * *
16401609 CTCTGGATGTTGAGATCTACTAGATGCTTGCTCAAGAATCTATTAATCC-ACACACGAAAAAATA
1 CTCTGGATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAA-CCTACACACGAAAAAACA
* *
16401673 ACTTTATGCTAAGCAAATTGCTTAGTGGTAAACAATGATTCAAATTAACATAAAAATGAAAATGC
65 ACTGTATGCTAAGCAAATTGCTTAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGC
* *
16401738 AAATGGATACAATTTAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTAATTC
130 AAATGGATACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTC
*
16401803 AAATTTTAAGTAGCATACTTATGCATGTCTCAATTTCTTACTCAAGTACATGATGATGCTAACC-
195 AAATTTTAAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACCT
16401867 T-A-TT-CATTTGCATTTTCATTTT-ATTTCCATACCTTATCCATATAAATAAACTCATCAACAT
260 TCATTTGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACTCATCAACAT
* * * *
16401928 GTCACAAGCATAACAACAATTTTTTATCATGTAGTACATATTCATATTTTCTTATTTCCAGATAT
325 GTCAAAAGCATAACAACAATTTTTTATCATATAGTACATATTCATATTTACTTAATTCCAGATAT
* *
16401993 CATAATAACAATCTTCGAGTCTATAAGTT-GGATT-TTGATCTATTAGCCCTCGGGGCTCACTTT
390 CATAATAAAAATCTTCGAGACTATAAGTTAGG-TTCTTGATCTATTAGCCCTCGGGGCTCACTTT
16402056 CAATC
454 CAATC
* * * *
16402061 CTTTGGATGTTGAGATATATTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGGAAAAACAA
1 CTCTGGATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAA
16402126 CTGTATGCTAAGCAAATTGCTTAGTGGTAAACTATGATTCAAATTAACAT-AAAATGAAAATGCA
66 CTGTATGCTAAGCAAATTGCTTAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCA
*
16402190 AATGGATACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGCCATTCATCTCAACTACTTCA
131 AATGGATACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCA
16402255 AATT
196 AATT
16402259 AACATAAAAA
Statistics
Matches: 613, Mismatches: 33, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
451 82 0.13
452 138 0.23
453 128 0.21
454 18 0.03
455 2 0.00
456 1 0.00
457 1 0.00
460 106 0.17
461 134 0.22
462 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (458 bp):
CTCTGGATGTTGAGATCTACTAGTTGCTTGCTCAAGAATCTACTAACCTACACACGAAAAAACAA
CTGTATGCTAAGCAAATTGCTTAGTGGTAAACTATGATTCAAATTAACATAAAAATGAAAATGCA
AATGGATACAATTAAGTCAAGTTTATTTCATACAAAATTTCATGTCATTCATCTCAACTACTTCA
AATTTTAAGTAGCATACTTATGCATATCTCAATTTCTTACTCAAGTACATGATGATGCTAACCTT
CATTTGCATTTGCATTTTCATTTTCATTTCCATACCTTATCCATATAAATAAACTCATCAACATG
TCAAAAGCATAACAACAATTTTTTATCATATAGTACATATTCATATTTACTTAATTCCAGATATC
ATAATAAAAATCTTCGAGACTATAAGTTAGGTTCTTGATCTATTAGCCCTCGGGGCTCACTTTCA
ATC
Found at i:16402367 original size:89 final size:89
Alignment explanation
Indices: 16402163--16402347 Score: 318
Period size: 89 Copynumber: 2.1 Consensus size: 89
16402153 TAAACTATGA
* * *
16402163 TTCAAATTAACAT-AAAATGAAAATGCAAATGGATACAATTAAGTCAAGTTTATTTCATACAAAA
1 TTCAAATTAACATAAAAATGAAAATGCAAATGGATACAATTAAATCAAGTTTATCTCATAAAAAA
16402227 TTTCATGCCATTCATCTCAACTAC
66 TTTCATGCCATTCATCTCAACTAC
16402251 TTCAAATTAACATAAAAATGAAAATGCAAATGGATACAATTAAATCAAGTTTATCTCATAAAAAA
1 TTCAAATTAACATAAAAATGAAAATGCAAATGGATACAATTAAATCAAGTTTATCTCATAAAAAA
* *
16402316 TTTCATGTCATTCATCTCAAGTAC
66 TTTCATGCCATTCATCTCAACTAC
16402340 TTCAAATT
1 TTCAAATT
16402348 TTAAGTAGCA
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 13 0.14
89 78 0.86
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (89 bp):
TTCAAATTAACATAAAAATGAAAATGCAAATGGATACAATTAAATCAAGTTTATCTCATAAAAAA
TTTCATGCCATTCATCTCAACTAC
Found at i:16404299 original size:21 final size:21
Alignment explanation
Indices: 16404273--16404326 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
16404263 GAAACATTTA
16404273 TTTTAATGTATTTAGTGTATT
1 TTTTAATGTATTTAGTGTATT
16404294 TTTTAATGTATTTAGTGTATT
1 TTTTAATGTATTTAGTGTATT
16404315 TTTTAATGTATT
1 TTTTAATGTATT
16404327 ATATTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (21 bp):
TTTTAATGTATTTAGTGTATT
Found at i:16404640 original size:3 final size:3
Alignment explanation
Indices: 16404632--16404664 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16404622 TATTTCTGTC
16404632 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16404665 AAGAGATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16406569 original size:29 final size:30
Alignment explanation
Indices: 16406512--16406569 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16406502 ATTCCTCCTT
*
16406512 ATTTTTAATTAATTTTAAATATATTTTTAG
1 ATTTTTAATTAATTTTAAATATATATTTAG
*
16406542 ATTTTTTA-TAATTTCTAAATA-ATATTTA
1 ATTTTTAATTAATTT-TAAATATATATTTA
16406570 AAGAATAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (30 bp):
ATTTTTAATTAATTTTAAATATATATTTAG
Found at i:16411555 original size:26 final size:26
Alignment explanation
Indices: 16411516--16411687 Score: 184
Period size: 26 Copynumber: 6.7 Consensus size: 26
16411506 CTCTAGTAGT
16411516 GTAAACGTATATTCATGCTGACGAGC
1 GTAAACGTATATTCATGCTGACGAGC
* * *
16411542 GTAAACGTACATTCATGCTAACGAGT
1 GTAAACGTATATTCATGCTGACGAGC
* * *
16411568 GTAAACGTATATCCATGCTCACCAGC
1 GTAAACGTATATTCATGCTGACGAGC
* * * *
16411594 ATTAATGTATATTCATGCTGGCGAGC
1 GTAAACGTATATTCATGCTGACGAGC
* * *
16411620 GTAAACGTA-ATTCATGCTGGCAAGA
1 GTAAACGTATATTCATGCTGACGAGC
* *
16411645 GTAAACGCATAATCATGCTGACGAGC
1 GTAAACGTATATTCATGCTGACGAGC
* *
16411671 GTAAACTTATAATCATG
1 GTAAACGTATATTCATG
16411688 TTGGCGAACG
Statistics
Matches: 118, Mismatches: 27, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
25 22 0.19
26 96 0.81
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (26 bp):
GTAAACGTATATTCATGCTGACGAGC
Found at i:16411687 original size:77 final size:78
Alignment explanation
Indices: 16411516--16411700 Score: 205
Period size: 77 Copynumber: 2.4 Consensus size: 78
16411506 CTCTAGTAGT
* * * * *
16411516 GTAAACGTATATTCATGCTGACGAGCGTAAACGTACATTCATGCTAACGAGTGTAAACGTATATC
1 GTAAACTTATATTCATGCTGGCGAGCGTAAACGTACATTCATGCTAACAAGAGTAAACGCATATC
16411581 CATGCTCACCAGC
66 CATGCTCACCAGC
* * **
16411594 ATTAA-TGTATATTCATGCTGGCGAGCGTAAACGTA-ATTCATGCTGGCAAGAGTAAACGCATAA
1 GTAAACT-TATATTCATGCTGGCGAGCGTAAACGTACATTCATGCTAACAAGAGTAAACGCAT-A
* *
16411657 T-CATGCTGACGAGC
64 TCCATGCTCACCAGC
* * *
16411671 GTAAACTTATAATCATGTTGGCGAACGTAA
1 GTAAACTTATATTCATGCTGGCGAGCGTAA
16411701 TTGCATGTTA
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
77 55 0.62
78 33 0.38
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (78 bp):
GTAAACTTATATTCATGCTGGCGAGCGTAAACGTACATTCATGCTAACAAGAGTAAACGCATATC
CATGCTCACCAGC
Found at i:16418839 original size:26 final size:26
Alignment explanation
Indices: 16418803--16419030 Score: 296
Period size: 26 Copynumber: 8.8 Consensus size: 26
16418793 GAGCTTTAGT
*
16418803 AGCGTAAACGTATATTCATGCTAACG
1 AGCGTAAACGTATATTCATGCTGACG
*
16418829 AGCGTAAACGTATATCCATGCTGACG
1 AGCGTAAACGTATATTCATGCTGACG
16418855 AGCGTAAACGTATATTCATGCTGACG
1 AGCGTAAACGTATATTCATGCTGACG
* *
16418881 AGCGTAAACGTACATACATGCTGACG
1 AGCGTAAACGTATATTCATGCTGACG
* *
16418907 AGCGTAAACGTATATCCATGCTGACC
1 AGCGTAAACGTATATTCATGCTGACG
* *
16418933 AGTGTAAACGTATATTCATGTTGGA-G
1 AGCGTAAACGTATATTCATGCT-GACG
* *
16418959 AGCGTAAACGTATATTCATGTTGTCG
1 AGCGTAAACGTATATTCATGCTGACG
* * * *
16418985 AGCATAAACGCATAATCATGCTAACG
1 AGCGTAAACGTATATTCATGCTGACG
* *
16419011 AACGTAAACGTATAATCATG
1 AGCGTAAACGTATATTCATG
16419031 TTGGCGAACG
Statistics
Matches: 177, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
25 1 0.01
26 174 0.98
27 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (26 bp):
AGCGTAAACGTATATTCATGCTGACG
Found at i:16421407 original size:20 final size:20
Alignment explanation
Indices: 16421382--16421423 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
16421372 GTTTGACCAA
*
16421382 ACCTATTGATTGACCCGTTG
1 ACCTATTGATCGACCCGTTG
16421402 ACCTATTGATCGACCCGTTG
1 ACCTATTGATCGACCCGTTG
16421422 AC
1 AC
16421424 TTTGACCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
ACCTATTGATCGACCCGTTG
Found at i:16423302 original size:39 final size:39
Alignment explanation
Indices: 16423259--16423346 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
16423249 ATCGAAATAG
**
16423259 GAAAACTACTCCTATT-TGCATACTACTTC-TAATAATATA
1 GAAAACTACTCCTATTCACCAT-CTACTTCAT-ATAATATA
*
16423298 GAAAACTACTCCTATTCACCCTCTACTTCATATAATATA
1 GAAAACTACTCCTATTCACCATCTACTTCATATAATATA
16423337 GAAAACTACT
1 GAAAACTACT
16423347 TCTAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 41 0.93
40 3 0.07
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.33
Consensus pattern (39 bp):
GAAAACTACTCCTATTCACCATCTACTTCATATAATATA
Found at i:16428899 original size:26 final size:26
Alignment explanation
Indices: 16428835--16428899 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
16428825 TTTCATCCCT
*
16428835 ATTTTACCCTTAGCAAAATTTTGACG
1 ATTTTACCCTTGGCAAAATTTTGACG
** *
16428861 ATTTTACTTTTGGTAAAATTTTGACG
1 ATTTTACCCTTGGCAAAATTTTGACG
*
16428887 ATTTTGCCCTTGG
1 ATTTTACCCTTGG
16428900 GAAATTTCCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (26 bp):
ATTTTACCCTTGGCAAAATTTTGACG
Found at i:16429163 original size:9 final size:10
Alignment explanation
Indices: 16429143--16429171 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
16429133 CATTTATAAT
16429143 TTTCTATTCA
1 TTTCTATTCA
16429153 TTTCT-TTCA
1 TTTCTATTCA
16429162 TTTCTATTCA
1 TTTCTATTCA
16429172 AATACACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:16431031 original size:28 final size:28
Alignment explanation
Indices: 16430999--16431053 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
16430989 GATATCTAAT
*
16430999 TTACTACTTATTGACCCAAAGGTCATGC
1 TTACTACCTATTGACCCAAAGGTCATGC
* *
16431027 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTACCTATTGACCCAAAGGTCATG
16431054 ATGCTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (28 bp):
TTACTACCTATTGACCCAAAGGTCATGC
Found at i:16431077 original size:36 final size:36
Alignment explanation
Indices: 16431027--16431125 Score: 164
Period size: 36 Copynumber: 2.8 Consensus size: 36
16431017 AAGGTCATGC
*
16431027 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
*
16431063 TTACTCCTTATTGACCCAAAGGTTC-TGATGCTCATT
1 TTACTCCCTATTGACCCAAAGG-TCATGATGCTCATT
16431099 TTACTCCCTATTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
16431126 CCTGTTACCA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 2 0.03
36 54 0.93
37 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.34
Consensus pattern (36 bp):
TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
Found at i:16433056 original size:13 final size:13
Alignment explanation
Indices: 16433035--16433068 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16433025 ACAATATAAT
16433035 AATAATAATCCTA
1 AATAATAATCCTA
*
16433048 AATATTAATCCTA
1 AATAATAATCCTA
*
16433061 AAAAATAA
1 AATAATAA
16433069 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:16440646 original size:5 final size:5
Alignment explanation
Indices: 16440609--16440648 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
16440599 ACCTACAAGC
16440609 AAAAG -AAA- AAAA- AAAAG AAAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AA
16440649 CAAAAGTCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 10 0.31
5 17 0.53
6 5 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:16440653 original size:23 final size:19
Alignment explanation
Indices: 16440608--16440654 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 19
16440598 GACCTACAAG
16440608 CAAAAGAAAAAAAAAAAGA
1 CAAAAGAAAAAAAAAAAGA
16440627 -AAAAGAAAAGAAAAGAAAAGAA
1 CAAAAG-AAA-AAAA-AAAAG-A
16440649 CAAAAG
1 CAAAAG
16440655 TCCCTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.22
19 3 0.13
20 4 0.17
21 5 0.22
22 1 0.04
23 5 0.22
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (19 bp):
CAAAAGAAAAAAAAAAAGA
Found at i:16441138 original size:2 final size:2
Alignment explanation
Indices: 16441131--16441177 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
16441121 TAAACTGTAC
16441131 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16441173 AG AG A
1 AG AG A
16441178 AATCCTAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16448042 original size:14 final size:14
Alignment explanation
Indices: 16448020--16448049 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16448010 CACCATCAAA
*
16448020 TTCGGGTATAACAT
1 TTCGAGTATAACAT
16448034 TTCGAGTATAACAT
1 TTCGAGTATAACAT
16448048 TT
1 TT
16448050 AGTATTGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
TTCGAGTATAACAT
Found at i:16453797 original size:236 final size:236
Alignment explanation
Indices: 16453380--16453852 Score: 883
Period size: 236 Copynumber: 2.0 Consensus size: 236
16453370 AGCTGTGGAG
*
16453380 AATCCGCAACACATGCTGGATCTCAGCCATTGGTAGGACCTTCAAGACCAGCCCCCGATACATAT
1 AATCCGCAACACATGCTGGATCTCAGCCATCGGTAGGACCTTCAAGACCAGCCCCCGATACATAT
*
16453445 ACTTCCTAATGACATGTCATTTGTATCCTAAGTATTCTCTAGGTTCAAACGGGAATTCATACCTT
66 ACTTCCTAATGACATGTCATTTGTATCCTAAGTATTCTCTAGGTTCAAACAGGAATTCATACCTT
* * *
16453510 CGGTTATACAAATCCCTTAGCATCATGATTCGATTTATAATCAATAACTTGTCAAACACCAACAT
131 CGGTTATACAAATCCCTTAGCATCATGATTCAATTTATAATCAACAACTTGTCAAACACAAACAT
16453575 CTATAATATACATAATACAAATCCAAAAATTTATAACTCAT
196 CTATAATATACATAATACAAATCCAAAAATTTATAACTCAT
16453616 AATCCGCAACACATGCTGGATCTCAGCCATCGGTAGGACCTTCAAGACCAGCCCCCGATACATAT
1 AATCCGCAACACATGCTGGATCTCAGCCATCGGTAGGACCTTCAAGACCAGCCCCCGATACATAT
*
16453681 ACTTCCTAATGGCATGTCATTTGTATCCTAAGTATTCTCTAGGTTCAAACAGGAATTCATACCTT
66 ACTTCCTAATGACATGTCATTTGTATCCTAAGTATTCTCTAGGTTCAAACAGGAATTCATACCTT
*
16453746 CGGTTATACAAATCCCTTAGCATCATGATTCAATTTATAATCAACAACTTGTCAAACATAAACAT
131 CGGTTATACAAATCCCTTAGCATCATGATTCAATTTATAATCAACAACTTGTCAAACACAAACAT
16453811 CTATAATATACATAATACAAATCCAAAAATTTATAACTCAT
196 CTATAATATACATAATACAAATCCAAAAATTTATAACTCAT
16453852 A
1 A
16453853 CGAACTTACC
Statistics
Matches: 230, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
236 230 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (236 bp):
AATCCGCAACACATGCTGGATCTCAGCCATCGGTAGGACCTTCAAGACCAGCCCCCGATACATAT
ACTTCCTAATGACATGTCATTTGTATCCTAAGTATTCTCTAGGTTCAAACAGGAATTCATACCTT
CGGTTATACAAATCCCTTAGCATCATGATTCAATTTATAATCAACAACTTGTCAAACACAAACAT
CTATAATATACATAATACAAATCCAAAAATTTATAACTCAT
Found at i:16454648 original size:31 final size:28
Alignment explanation
Indices: 16454591--16454648 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
16454581 GTATTTATTA
* *
16454591 GAAATTAAAATAGAGAAATATTACAAAT
1 GAAATTAAAATAGAGAAAAATAACAAAT
16454619 GAAATTAAAATGTAGCAGAAAAATAACAAA
1 GAAATTAAAA--TAG-AGAAAAATAACAAA
16454649 ACAAAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
30 3 0.12
31 12 0.48
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (28 bp):
GAAATTAAAATAGAGAAAAATAACAAAT
Found at i:16455051 original size:23 final size:23
Alignment explanation
Indices: 16454997--16455055 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
16454987 TATAAAGCAG
*
16454997 AAGTGTGCCACAAGGTAGAGGAA
1 AAGTGTGCCACAAGATAGAGGAA
**
16455020 AAGCATGCCACAAGATAGA-GAA
1 AAGTGTGCCACAAGATAGAGGAA
16455042 CAAGTGTGCCACAA
1 -AAGTGTGCCACAA
16455056 AGGCAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (23 bp):
AAGTGTGCCACAAGATAGAGGAA
Found at i:16493657 original size:39 final size:39
Alignment explanation
Indices: 16493603--16493726 Score: 230
Period size: 39 Copynumber: 3.2 Consensus size: 39
16493593 TAAACATTAA
16493603 GAAATGGTATAGCATTTAATTGTTAAATTACCTCGAATT
1 GAAATGGTATAGCATTTAATTGTTAAATTACCTCGAATT
*
16493642 GAAATGGTATAGCATTTAATTGTTAAATTACCTCAAATT
1 GAAATGGTATAGCATTTAATTGTTAAATTACCTCGAATT
16493681 GAAATGGTATAGCATTTAATTGTTAAATTACCTCGAATT
1 GAAATGGTATAGCATTTAATTGTTAAATTACCTCGAATT
16493720 GCAAATG
1 G-AAATG
16493727 TTCAAGACCT
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
39 77 0.94
40 5 0.06
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (39 bp):
GAAATGGTATAGCATTTAATTGTTAAATTACCTCGAATT
Found at i:16496022 original size:27 final size:27
Alignment explanation
Indices: 16495984--16496038 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
16495974 ATCACTATCC
*
16495984 CTATCTCCCTCTGGAACAGCTTCCTCT
1 CTATCTCCCTCTGGAACAACTTCCTCT
16496011 CTATCTCCCTCTGGAACAACTTCCTCT
1 CTATCTCCCTCTGGAACAACTTCCTCT
16496038 C
1 C
16496039 CCCTTCCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.42, G:0.09, T:0.33
Consensus pattern (27 bp):
CTATCTCCCTCTGGAACAACTTCCTCT
Found at i:16497507 original size:27 final size:27
Alignment explanation
Indices: 16497445--16497497 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
16497435 TTAAAATCTC
*
16497445 AATTTTTTTCAACCTTCTCTTATTTCA
1 AATTTTTTTAAACCTTCTCTTATTTCA
* *
16497472 AAATTTTTTAAACTTTCTCTTATTTC
1 AATTTTTTTAAACCTTCTCTTATTTC
16497498 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.57
Consensus pattern (27 bp):
AATTTTTTTAAACCTTCTCTTATTTCA
Found at i:16503211 original size:18 final size:18
Alignment explanation
Indices: 16503166--16503211 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
16503156 ATTCTCAAAC
*
16503166 TATT-AATTAATTTATTT
1 TATTCAATTAAATTATTT
*
16503183 TATTTAATTAAATTATTT
1 TATTCAATTAAATTATTT
16503201 T-TTCAACTTAA
1 TATTCAA-TTAA
16503212 TTACAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTCAATTAAATTATTT
Found at i:16505282 original size:157 final size:157
Alignment explanation
Indices: 16504996--16505309 Score: 610
Period size: 157 Copynumber: 2.0 Consensus size: 157
16504986 GTCTATCCGG
16504996 GCCTCTGTAAGGCAACGTTTGCAAGTCCAAGATAGTTCCGAGCACGTACTCCATCATCACTGAAA
1 GCCTCTGTAAGGCAACGTTTGCAAGTCCAAGATAGTTCCGAGCACGTACTCCATCATCACTGAAA
16505061 ACCACCCTTGAAGTTCATTGAATGACTCATACTAGTCGTCGTACAATTGTTGCATGGCCATTTAT
66 ACCACCCTTGAAGTTCATTGAATGACTCATACTAGTCGTCGTACAATTGTTGCATGGCCATTTAT
*
16505126 TTCGTCCGCCATGCTTTCTTATACAAC
131 TTCGTCCGCCATGCTTTCCTATACAAC
*
16505153 GCCTCTGTAAGGCAACGTTTGCAAGTCCAAGATAGTTCCGGGCACGTACTCCATCATCACTGAAA
1 GCCTCTGTAAGGCAACGTTTGCAAGTCCAAGATAGTTCCGAGCACGTACTCCATCATCACTGAAA
16505218 ACCACCCTTGAAGTTCATTGAATGACTCATACTAGTCGTCGTACAATTGTTGCATGGCCATTTAT
66 ACCACCCTTGAAGTTCATTGAATGACTCATACTAGTCGTCGTACAATTGTTGCATGGCCATTTAT
16505283 TTCGTCCGCCATGCTTTCCTATACAAC
131 TTCGTCCGCCATGCTTTCCTATACAAC
16505310 ACTTTAAACT
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (157 bp):
GCCTCTGTAAGGCAACGTTTGCAAGTCCAAGATAGTTCCGAGCACGTACTCCATCATCACTGAAA
ACCACCCTTGAAGTTCATTGAATGACTCATACTAGTCGTCGTACAATTGTTGCATGGCCATTTAT
TTCGTCCGCCATGCTTTCCTATACAAC
Found at i:16508060 original size:9 final size:9
Alignment explanation
Indices: 16508046--16508079 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16508036 GCTCGAAGAA
16508046 TTTTTTTTC
1 TTTTTTTTC
*
16508055 TTTTTTTTA
1 TTTTTTTTC
*
16508064 TTTGTTTTC
1 TTTTTTTTC
16508073 TTTTTTT
1 TTTTTTT
16508080 AAACAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:16508071 original size:18 final size:18
Alignment explanation
Indices: 16508045--16508079 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16508035 AGCTCGAAGA
*
16508045 ATTTTTTTTCTTTTTTTT
1 ATTTGTTTTCTTTTTTTT
16508063 ATTTGTTTTCTTTTTTT
1 ATTTGTTTTCTTTTTTT
16508080 AAACAAAATA
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:0.06, C:0.06, G:0.03, T:0.86
Consensus pattern (18 bp):
ATTTGTTTTCTTTTTTTT
Found at i:16510029 original size:98 final size:96
Alignment explanation
Indices: 16509803--16510092 Score: 233
Period size: 98 Copynumber: 3.0 Consensus size: 96
16509793 TAAACTATCA
* *** * * **
16509803 TTTTTAAAATTTTTAAATTAAAAAACACATTT-AAAA-AAATCTAGACACAGTACATTGGTGA-C
1 TTTTTATAATTTTTAAA-TAAAAAACA-ATTTAAAAATAAAAAAAGACACAATACACTAATGATC
** *
16509865 ACC-ATTCTATATGGTTCCATCAAATAAAATAACATT
64 -CCTATTCTATATGACTCCACCAAATAAAAT-A-A-T
* ** *
16509901 TTTTTATAATTTTTAAATAAAAAACTATTTAAAAATTAAAAAAA-ACACGGTACACTAATGA-CG
1 TTTTTATAATTTTTAAATAAAAAACAATTTAAAAA-TAAAAAAAGACACAATACACTAATGATCC
16509964 CTATTCTATATGACTCCACCAAATAAAATAAT
65 CTATTCTATATGACTCCACCAAATAAAATAAT
*
16509996 TTTTT-T-ATTTTTAAATGTTAAAAAATCAAATTTAAAAATAAAAAAAGACACAATACACTTATG
1 TTTTTATAATTTTTAAA---TAAAAAA-C-AATTTAAAAATAAAAAAAGACACAATACACTAATG
*
16510059 ATCCCT-TTCTATAT-ACTCCTCC-AATAAAAATAAT
61 ATCCCTATTCTATATGACTCCACCAAAT-AAAATAAT
16510093 ATTTGTTTCT
Statistics
Matches: 161, Mismatches: 19, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
93 9 0.06
94 1 0.01
95 6 0.04
96 15 0.09
97 38 0.24
98 85 0.53
99 7 0.04
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (96 bp):
TTTTTATAATTTTTAAATAAAAAACAATTTAAAAATAAAAAAAGACACAATACACTAATGATCCC
TATTCTATATGACTCCACCAAATAAAATAAT
Found at i:16512632 original size:33 final size:33
Alignment explanation
Indices: 16512588--16512654 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
16512578 CATCTAATCC
*
16512588 TCTAAATTTAGATTTCGTTAAACATTTTAGTTA
1 TCTAAACTTAGATTTCGTTAAACATTTTAGTTA
16512621 TCTAAACTTAGATTTCGTTAAACATTTTAGTTA
1 TCTAAACTTAGATTTCGTTAAACATTTTAGTTA
16512654 T
1 T
16512655 TTTCAACATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (33 bp):
TCTAAACTTAGATTTCGTTAAACATTTTAGTTA
Found at i:16513094 original size:22 final size:21
Alignment explanation
Indices: 16513063--16513107 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
16513053 TGTATTTACA
*
16513063 AAATAATTATGTGTTAAATAT
1 AAATAATTATGTGATAAATAT
*
16513084 AAATAAATTATTTGATAAATAT
1 AAAT-AATTATGTGATAAATAT
16513106 AA
1 AA
16513108 CTTTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATAATTATGTGATAAATAT
Found at i:16513678 original size:18 final size:20
Alignment explanation
Indices: 16513657--16513699 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
16513647 TTTTTTCTAA
16513657 TTTTAATAAAATTT-AT-AT
1 TTTTAATAAAATTTAATAAT
*
16513675 TTTTATTAAAATTTAATAAT
1 TTTTAATAAAATTTAATAAT
16513695 TTTTA
1 TTTTA
16513700 TTGATGTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAATAAAATTTAATAAT
Found at i:16513984 original size:90 final size:89
Alignment explanation
Indices: 16513889--16514073 Score: 221
Period size: 90 Copynumber: 2.1 Consensus size: 89
16513879 GTTTTAAGAC
* * * * * * ***
16513889 CTTTTTTATACATTTTGAAATTTTAAGTA-CCGAATTGAGTGCAGAATAAAGGTAAGGGTTTAAT
1 CTTTTTGATACATTTTGAAAGTTTAAGTATCC-AAGTGAGTGCAAAAAAAAAGTAAGACCTTAAT
**
16513953 TG-TTTTTTTTTAAATAGTTTGAGGGT
65 TGCTTTTTTTGAAAAT-GTTTGA-GGT
*
16513979 CTTTTTGATGCATTTTGAAAGTTTAAGTATCCAAGTGAGTGCAAAAAAAAAGTAAGACCTTAATT
1 CTTTTTGATACATTTTGAAAGTTTAAGTATCCAAGTGAGTGCAAAAAAAAAGTAAGACCTTAATT
16514044 GCTTTTTTTGAAAATGTTTGAGGT
66 GCTTTTTTTGAAAATGTTTGAGGT
16514068 CTTTTT
1 CTTTTT
16514074 ACACTCTTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
89 9 0.11
90 59 0.73
91 13 0.16
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.43
Consensus pattern (89 bp):
CTTTTTGATACATTTTGAAAGTTTAAGTATCCAAGTGAGTGCAAAAAAAAAGTAAGACCTTAATT
GCTTTTTTTGAAAATGTTTGAGGT
Found at i:16515512 original size:16 final size:16
Alignment explanation
Indices: 16515491--16515543 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
16515481 AAATTATTTT
16515491 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
**
16515507 TTAAAAT-TATTATT-
1 TTAAAATATAAAATTA
*
16515521 TTGAAATATAAAATTA
1 TTAAAATATAAAATTA
16515537 TTAAAAT
1 TTAAAAT
16515544 TATTAAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 6 0.21
15 10 0.34
16 13 0.45
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:16515513 original size:9 final size:9
Alignment explanation
Indices: 16515491--16515550 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
16515481 AAATTATTTT
16515491 TTAAAA-TA
1 TTAAAATTA
16515499 -TAAAATTA
1 TTAAAATTA
16515507 TTAAAATTA
1 TTAAAATTA
16515516 TT---ATT-
1 TTAAAATTA
*
16515521 TTGAAA-TA
1 TTAAAATTA
16515529 -TAAAATTA
1 TTAAAATTA
16515537 TTAAAATTA
1 TTAAAATTA
16515546 TTAAA
1 TTAAA
16515551 TAATTTTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
5 2 0.05
6 3 0.07
7 10 0.23
8 5 0.12
9 23 0.53
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
TTAAAATTA
Found at i:16515530 original size:30 final size:30
Alignment explanation
Indices: 16515478--16515548 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
16515468 ACAAATTATT
16515478 TTAAAATTATT-TTTTAAAATATAAAATTA
1 TTAAAATTATTATTTTAAAATATAAAATTA
*
16515507 TTAAAATTATTATTTTGAAATATAAAATTA
1 TTAAAATTATTATTTTAAAATATAAAATTA
16515537 TTAAAATTATTA
1 TTAAAATTATTA
16515549 AATAATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 11 0.28
30 29 0.73
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TTAAAATTATTATTTTAAAATATAAAATTA
Found at i:16524338 original size:23 final size:23
Alignment explanation
Indices: 16524262--16524328 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
16524252 AGAGTTAGCA
*
16524262 CGCACTTTGGTCAGCTTGCAAGCT
1 CGCAC-TTGGTCAGCTCGCAAGCT
*
16524286 CGCACTTGGTCAACTCGCAAGCT
1 CGCACTTGGTCAGCTCGCAAGCT
16524309 CGCACTTGGTCAGCTCGCAA
1 CGCACTTGGTCAGCTCGCAA
16524329 ACTCATACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 35 0.88
24 5 0.12
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (23 bp):
CGCACTTGGTCAGCTCGCAAGCT
Found at i:16524599 original size:22 final size:21
Alignment explanation
Indices: 16524559--16524599 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16524549 AATTCTGCTT
*
16524559 GATTAAAAAATAATCAAAAGA
1 GATTAAAAAATAAGCAAAAGA
*
16524580 GATTAAAAAACTAAGGAAAA
1 GATTAAAAAA-TAAGCAAAA
16524600 CATAGATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (21 bp):
GATTAAAAAATAAGCAAAAGA
Found at i:16537378 original size:17 final size:17
Alignment explanation
Indices: 16537356--16537403 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
16537346 TGATATATGG
*
16537356 AAATGCAATGACAATGT
1 AAATGCAATGACAATAT
16537373 AAATGCAATGACAATAT
1 AAATGCAATGACAATAT
16537390 AAATGCAATGACAA
1 AAATGCAATGACAA
16537404 AGGAAATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAT
Found at i:16537410 original size:17 final size:17
Alignment explanation
Indices: 16537354--16537411 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
16537344 AATGATATAT
*
16537354 GGAAATGCAATGACAAT
1 GGAAATGCAATGACAAA
*
16537371 GTAAATGCAATGACAATA
1 GGAAATGCAATGACAA-A
*
16537389 -TAAATGCAATGACAAA
1 GGAAATGCAATGACAAA
16537405 GGAAATG
1 GGAAATG
16537412 TGATGCCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 1 0.03
17 35 0.97
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (17 bp):
GGAAATGCAATGACAAA
Found at i:16538508 original size:49 final size:49
Alignment explanation
Indices: 16538436--16538542 Score: 214
Period size: 49 Copynumber: 2.2 Consensus size: 49
16538426 GCGCTTAATG
16538436 GAGGCATCATTAATAGGTCCTTTGTTGTCCAACATTTCTTCTCCCTCAC
1 GAGGCATCATTAATAGGTCCTTTGTTGTCCAACATTTCTTCTCCCTCAC
16538485 GAGGCATCATTAATAGGTCCTTTGTTGTCCAACATTTCTTCTCCCTCAC
1 GAGGCATCATTAATAGGTCCTTTGTTGTCCAACATTTCTTCTCCCTCAC
16538534 GAGGCATCA
1 GAGGCATCA
16538543 CTCTTCGTCG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (49 bp):
GAGGCATCATTAATAGGTCCTTTGTTGTCCAACATTTCTTCTCCCTCAC
Found at i:16539734 original size:21 final size:21
Alignment explanation
Indices: 16539687--16539726 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16539677 AATACTAAGA
*
16539687 AAAAT-AACTGAAATATAAAT
1 AAAATAAACTGAAAAATAAAT
16539707 AAAATAAACT-AAAAATAAAT
1 AAAATAAACTGAAAAATAAAT
16539727 TATAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAAACTGAAAAATAAAT
Found at i:16549743 original size:123 final size:121
Alignment explanation
Indices: 16549514--16549866 Score: 528
Period size: 123 Copynumber: 2.9 Consensus size: 121
16549504 CTTTTCATTT
* *
16549514 TAATATCTCATATTAAAATGGAAATATATATCTTTAGAGAAATATATTGAAGGTTTATT-AAATA
1 TAATATCTCATATTAAAATGGAAATAT-T-TCTTTAAAGAAATATA-TGAAGGTTTATTAAAACA
* *
16549578 TTATATCCTTTTCAAAAGGATATCATCTTCCATGTTTTAATATTAAATTTCCTTTTATA
63 TTATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATTAAATTTCCTTTTATA
* *
16549637 TAATATATCATATTAAAATGGAAATATTTCTTTAAAGAAATATATGAAAGGTCTATTAAAACATT
1 TAATATCTCATATTAAAATGGAAATATTTCTTTAAAGAAATATATG-AAGGTTTATTAAAACATT
* * * *
16549702 ATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAGTTTTCTTTTATA
65 ATATCCTTTCCAAAAGGATATTATCTTCCATG-TTTTAATATTAAATTTCCTTTTATA
* * *
16549760 TAATATCTAATATTAAAATGAAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTAAAACATT
1 TAATATCTCATATTAAAATGGAAATATTTCTTTAAAGAAATATAT-GAAGGTTTATTAAAACATT
16549825 ATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATT
65 ATATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATT
16549867 TAATGAAATC
Statistics
Matches: 210, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
120 2 0.01
121 24 0.11
122 46 0.22
123 137 0.65
124 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (121 bp):
TAATATCTCATATTAAAATGGAAATATTTCTTTAAAGAAATATATGAAGGTTTATTAAAACATTA
TATCCTTTCCAAAAGGATATTATCTTCCATGTTTTAATATTAAATTTCCTTTTATA
Found at i:16549973 original size:8 final size:8
Alignment explanation
Indices: 16549960--16549985 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
16549950 ATTAACTTCC
16549960 ATGTTTTA
1 ATGTTTTA
16549968 ATGTTTTA
1 ATGTTTTA
16549976 ATGTTTTA
1 ATGTTTTA
16549984 AT
1 AT
16549986 ATTTAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATGTTTTA
Found at i:16549992 original size:15 final size:16
Alignment explanation
Indices: 16549960--16549993 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16549950 ATTAACTTCC
*
16549960 ATGTTTTAATGTTTTA
1 ATGTTTTAATGATTTA
16549976 ATGTTTTAAT-ATTTA
1 ATGTTTTAATGATTTA
16549991 ATG
1 ATG
16549994 AAATCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
ATGTTTTAATGATTTA
Found at i:16556806 original size:122 final size:125
Alignment explanation
Indices: 16556569--16556812 Score: 370
Period size: 122 Copynumber: 2.0 Consensus size: 125
16556559 TTCTGCTATC
* * *
16556569 TTTCCTTTTATTTTAATATCTCATATTAAAATGGAAATATATATCTTTAGAAAAATATATGAAAG
1 TTTCCTTTTATTATAATATCTAATATTAAAATGGAAATATATACCTTTAGAAAAATATATGAAAG
* *
16556634 GTTTATTAAAACATTATATCGTTTCCAAACGGATATTATCTTCAACGTTTTAATATTCAA
66 GTTTATTAAAACATTATATCGTTTCCAAAAGAATATTATCTTCAACGTTTTAATATTCAA
*
16556694 TTTCCTTTTA-TATAATATCTAATATTAAAATGGAAATAT-T-CCTTTA-AACAAATATATGGAA
1 TTTCCTTTTATTATAATATCTAATATTAAAATGGAAATATATACCTTTAGAA-AAATATATGAAA
* * *
16556755 GGTTTATTAAAACATTATATCTTTTCCAAAAGAATATTATCTTCCATGTTTTAATATT
65 GGTTTATTAAAACATTATATCGTTTCCAAAAGAATATTATCTTCAACGTTTTAATATT
16556813 TAACAAAATC
Statistics
Matches: 109, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
121 2 0.02
122 69 0.63
123 1 0.01
124 27 0.25
125 10 0.09
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (125 bp):
TTTCCTTTTATTATAATATCTAATATTAAAATGGAAATATATACCTTTAGAAAAATATATGAAAG
GTTTATTAAAACATTATATCGTTTCCAAAAGAATATTATCTTCAACGTTTTAATATTCAA
Found at i:16567936 original size:18 final size:18
Alignment explanation
Indices: 16567889--16567937 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
16567879 ATCTTGATCA
*
16567889 AATGCAGGCACATAGCTAG
1 AATGCAGCCACA-AGCTAG
**
16567908 -ATGCAATCACAAGCTAG
1 AATGCAGCCACAAGCTAG
16567925 AATGCAGCCACAA
1 AATGCAGCCACAA
16567938 CAGACTGCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AATGCAGCCACAAGCTAG
Found at i:16578633 original size:30 final size:30
Alignment explanation
Indices: 16578597--16578657 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
16578587 CACGGTCTTA
* *
16578597 CACATGGCCGTGTGCCCATCCCGTGTGGCT
1 CACATGGCCATGTGCCCAGCCCGTGTGGCT
* *
16578627 CACATGGCCATGTGTCCAGCTCGTGTGGCT
1 CACATGGCCATGTGCCCAGCCCGTGTGGCT
16578657 C
1 C
16578658 CTAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.11, C:0.34, G:0.30, T:0.25
Consensus pattern (30 bp):
CACATGGCCATGTGCCCAGCCCGTGTGGCT
Found at i:16579005 original size:13 final size:13
Alignment explanation
Indices: 16578987--16579011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16578977 GTTAGGGTCG
16578987 AATCTTATGTATT
1 AATCTTATGTATT
16579000 AATCTTATGTAT
1 AATCTTATGTAT
16579012 ATTATCATTT
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:0.08, T:0.52
Consensus pattern (13 bp):
AATCTTATGTATT
Found at i:16584594 original size:29 final size:29
Alignment explanation
Indices: 16584550--16584637 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
16584540 TCGTGGAAGA
* * * * *
16584550 GGTGGAGAACTTGTTCATTAAGAGTTCGT
1 GGTGAAGAACTCGTTCGTTGAGAATTCGT
*
16584579 GGTGAAGAACTCGTTCGTTGAGAATTTGT
1 GGTGAAGAACTCGTTCGTTGAGAATTCGT
* *
16584608 GATCAAGAACTCGTTCGTTGAGAATTCGT
1 GGTGAAGAACTCGTTCGTTGAGAATTCGT
16584637 G
1 G
16584638 TCAAGGTGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (29 bp):
GGTGAAGAACTCGTTCGTTGAGAATTCGT
Found at i:16588634 original size:13 final size:13
Alignment explanation
Indices: 16588616--16588640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16588606 TAAAAATTCA
16588616 AAATTCTTTTATT
1 AAATTCTTTTATT
16588629 AAATTCTTTTAT
1 AAATTCTTTTAT
16588641 GTGACATTTT
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:0.00, T:0.60
Consensus pattern (13 bp):
AAATTCTTTTATT
Found at i:16590626 original size:13 final size:13
Alignment explanation
Indices: 16590574--16590628 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
16590564 TTAATAACAC
16590574 TATAAAAATATAAA
1 TATAAAAAT-TAAA
* *
16590588 -AAAAAAATTATA
1 TATAAAAATTAAA
*
16590600 T-TAGAAATTTAAA
1 TATA-AAAATTAAA
16590613 TATAAAAATTAAA
1 TATAAAAATTAAA
16590626 TAT
1 TAT
16590629 CAAATTTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
12 4 0.12
13 26 0.81
14 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TATAAAAATTAAA
Found at i:16595967 original size:41 final size:41
Alignment explanation
Indices: 16595862--16596121 Score: 306
Period size: 41 Copynumber: 6.3 Consensus size: 41
16595852 TGTATAAAAA
*** * ** *
16595862 AAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTG-ATTAA-GG
*
16595905 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGA
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGG
* * * *
16595946 AAGACTCATGTCTCGAGATGAGAATGATATTATGAATAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGG
* * * *
16595987 AAGACTCATGTATCAAAATGAGAACGAGATTTTAATTAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGG
* * *
16596028 AAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGG
* *
16596069 AAGATTCATGTTTC-AAATGAGAATGAGATTTTGATTAAGG
1 AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGG
16596109 AAGACTCATGTCT
1 AAGACTCATGTCT
16596122 TTAGATAAGA
Statistics
Matches: 182, Mismatches: 35, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
40 34 0.19
41 116 0.64
42 4 0.02
43 28 0.15
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (41 bp):
AAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGG
Found at i:16596151 original size:123 final size:124
Alignment explanation
Indices: 16595898--16596156 Score: 306
Period size: 123 Copynumber: 2.1 Consensus size: 124
16595888 AGAAATTGTA
* * *
16595898 TAAATGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAG
1 TAAA-GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAAGAAAGACTCATGTCTCGAA
* * * * *
16595963 ATGAGAATGATATTATGAATAAGGAAGACTCATGTATCAAAATGAGAACGAGATTTTAAT
65 ATGAGAATGAGATTATGAATAAGGAAGACTCATGTATCAAAATAAGAACAAGAATATAAT
* * * *
16596023 T-AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGGAAGATTCATGTTTC-AAA
1 TAAAGGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAAGAAAGACTCATGTCTCGAAA
* * * ** * * **
16596086 TGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTTTAGATAAGAATAAGAATATGGT
66 TGAGAATGAGATTATGAATAAGGAAGACTCATGTATCAAAATAAGAACAAGAATATAAT
16596145 TAAAGGAAGACT
1 TAAAGGAAGACT
16596157 TATGATTCGA
Statistics
Matches: 112, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
122 48 0.43
123 61 0.54
124 2 0.02
125 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (124 bp):
TAAAGGAAGACTCATGTCTCGAAATGAGAATGAGATTATGAATAAGAAAGACTCATGTCTCGAAA
TGAGAATGAGATTATGAATAAGGAAGACTCATGTATCAAAATAAGAACAAGAATATAAT
Found at i:16596153 original size:82 final size:82
Alignment explanation
Indices: 16595862--16596121 Score: 362
Period size: 82 Copynumber: 3.2 Consensus size: 82
16595852 TGTATAAAAA
* * * * * * *
16595862 AAGACTCATGTCTCGGGTTGAGCATGAGA-AATTGTATAAATGGAAGACTCATGTCTCGAAATGA
1 AAGACTCATGTCTCGAGATGAGAATGAGATTA-TGAAT-AA-GGAAGACTCATGTATCAAAATGA
*
16595926 GAATGAGATTTTGATTAAGA
63 GAATGAGATTTTGATTAAGG
*
16595946 AAGACTCATGTCTCGAGATGAGAATGATATTATGAATAAGGAAGACTCATGTATCAAAATGAGAA
1 AAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGGAAGACTCATGTATCAAAATGAGAA
* *
16596011 CGAGATTTTAATTAAGG
66 TGAGATTTTGATTAAGG
* *
16596028 AAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGGAAGATTCATGTTTC-AAATGAGAA
1 AAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGGAAGACTCATGTATCAAAATGAGAA
16596092 TGAGATTTTGATTAAGG
66 TGAGATTTTGATTAAGG
16596109 AAGACTCATGTCT
1 AAGACTCATGTCT
16596122 TTAGATAAGA
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
81 37 0.23
82 90 0.57
83 2 0.01
84 29 0.18
85 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (82 bp):
AAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAGGAAGACTCATGTATCAAAATGAGAA
TGAGATTTTGATTAAGG
Found at i:16602208 original size:22 final size:21
Alignment explanation
Indices: 16602183--16602230 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
16602173 CAAATATTGA
*
16602183 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
16602205 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
16602226 TTAAT
1 TTAAT
16602231 TATGAAAGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:16603104 original size:43 final size:44
Alignment explanation
Indices: 16603022--16603105 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
16603012 GAATACGTGG
** *
16603022 TGTATAAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAAAT
1 TGTATAAAAAGGAAGACTCATGTCTCGAAATGAGAATGAGAAAT
*
16603066 TGTAT-AAATGGAAGACTCATGTCTCGAAATGAGAATGAGA
1 TGTATAAAAAGGAAGACTCATGTCTCGAAATGAGAATGAGA
16603106 TCGGGTCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (44 bp):
TGTATAAAAAGGAAGACTCATGTCTCGAAATGAGAATGAGAAAT
Found at i:16603275 original size:231 final size:231
Alignment explanation
Indices: 16602872--16603336 Score: 885
Period size: 231 Copynumber: 2.0 Consensus size: 231
16602862 TGATAGATCA
* *
16602872 AGATCGGGTCATAGATCGCGGAAAGGGGAAAATCATAGAATAGTCCTTAAAGTTTTGCCTGAACT
1 AGATCGGGTCATAGATCGCAGAAAGGGGAAAATCATAGAATAGTCCTTAAAGTTTCGCCTGAACT
* *
16602937 GCAATTTCATCCGGTAAGTTCGTTGTTAGATTTCCTATTTGAACTGCTGATTATTACCTATTGAG
66 GCAATTTCATCCGGTAAGTTCGTTGTTAGATTTCCTATTTGAACTACTGATTATTACCGATTGAG
16603002 GATGTGCTTGGAATACGTGGTGTATAAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAAATT
131 GATGTGCTTGGAATACGTGGTGTATAAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAAATT
16603067 GTATAAATGGAAGACTCATGTCTCGAAATGAGAATG
196 GTATAAATGGAAGACTCATGTCTCGAAATGAGAATG
16603103 AGATCGGGTCATAGATCGCAGAAAGGGGAAAATCATAGAATAGTCCTTAAAGTTTCGCCTGAACT
1 AGATCGGGTCATAGATCGCAGAAAGGGGAAAATCATAGAATAGTCCTTAAAGTTTCGCCTGAACT
16603168 GCAATTTCATCCGGTAAGTTCGTTGTTAGATTTCCTATTTGAACTACTGATTATTACCGATTGAG
66 GCAATTTCATCCGGTAAGTTCGTTGTTAGATTTCCTATTTGAACTACTGATTATTACCGATTGAG
16603233 GATGTGCTTGGAATACGTGGTGTATAAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAAATT
131 GATGTGCTTGGAATACGTGGTGTATAAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAAATT
*
16603298 GTATAAATGGAAGACTCATGTCTCGAGATGAGAATG
196 GTATAAATGGAAGACTCATGTCTCGAAATGAGAATG
16603334 AGA
1 AGA
16603337 ATATGGTTAA
Statistics
Matches: 229, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 229 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (231 bp):
AGATCGGGTCATAGATCGCAGAAAGGGGAAAATCATAGAATAGTCCTTAAAGTTTCGCCTGAACT
GCAATTTCATCCGGTAAGTTCGTTGTTAGATTTCCTATTTGAACTACTGATTATTACCGATTGAG
GATGTGCTTGGAATACGTGGTGTATAAAAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAAATT
GTATAAATGGAAGACTCATGTCTCGAAATGAGAATG
Found at i:16603315 original size:43 final size:43
Alignment explanation
Indices: 16603260--16603365 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
16603250 TGGTGTATAA
* *
16603260 AAAGGAAGACTCATGTCTCGAGTTGAGCATGAGAA-ATTGTAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATTGTAT
*
16603302 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGT-T
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAATATTGTAT
* *
16603345 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
16603366 AAGAGCATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 19 0.33
43 34 0.60
44 4 0.07
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATTGTAT
Found at i:16612625 original size:209 final size:209
Alignment explanation
Indices: 16612258--16612675 Score: 773
Period size: 209 Copynumber: 2.0 Consensus size: 209
16612248 TCTTGGTCCA
16612258 AAAAACCAAATCTTGGAGTTGGTACAAATTGGATCACACTAATGAGCTTAAACGAGCTCAACCTT
1 AAAAACCAAATCTTGGAGTTGGTACAAATTGGATCACACTAATGAGCTTAAACGAGCTCAACCTT
* *
16612323 GCAATAAACGAATCATAAATTCAGGTTCTTGAAAATTAGCCCATGGGACATCCACAAGCCCATTT
66 GCAATAAACGAATAATAAATTCAGGTTCTTGAAAATTAGCCCATGGGACATCCACAAACCCATTT
*
16612388 GGATGATTTACCATTGATGCAATCGAAACTAACTAAAAATATGACTAAGGTAAGTACACCTATCA
131 GGATGATTTACCATTGATGCAATCGAAACTAACTAAAAATATGACTAAGGTAAGTACACCTATAA
16612453 ATTAATAGTATAGT
196 ATTAATAGTATAGT
*
16612467 AAAATCCAAATCTTGGAGTTGGTACAAATTGGATCACACTAATGAGCTTAAACGAGCTCAACCTT
1 AAAAACCAAATCTTGGAGTTGGTACAAATTGGATCACACTAATGAGCTTAAACGAGCTCAACCTT
**
16612532 GCAATAAACGAATAATAAATTTGGGTTCTTGAAAATTAGCCCATGGGACATCCACAAACCCATTT
66 GCAATAAACGAATAATAAATTCAGGTTCTTGAAAATTAGCCCATGGGACATCCACAAACCCATTT
*
16612597 GGATGATTTACCATTGATGCAGTCGAAACTAACTAAAAATATGACTAAGGTAAGTACACCTATAA
131 GGATGATTTACCATTGATGCAATCGAAACTAACTAAAAATATGACTAAGGTAAGTACACCTATAA
16612662 ATTAATAGTATAGT
196 ATTAATAGTATAGT
16612676 TGCGGTGAGC
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 202 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (209 bp):
AAAAACCAAATCTTGGAGTTGGTACAAATTGGATCACACTAATGAGCTTAAACGAGCTCAACCTT
GCAATAAACGAATAATAAATTCAGGTTCTTGAAAATTAGCCCATGGGACATCCACAAACCCATTT
GGATGATTTACCATTGATGCAATCGAAACTAACTAAAAATATGACTAAGGTAAGTACACCTATAA
ATTAATAGTATAGT
Found at i:16616908 original size:25 final size:25
Alignment explanation
Indices: 16616871--16617063 Score: 178
Period size: 25 Copynumber: 7.7 Consensus size: 25
16616861 GACATTGAAG
* *
16616871 GATATTCTATTTGGCTCGCAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* * *
16616896 TATATTTTGTTTGGCTCGCAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* **
16616921 GATATTCT-TTCTAGCTTATAAGAGC
1 GATATTCTGTT-TGGCTCGTAAGAGC
* *
16616946 G-TATTCTGTCTGGCTCATAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* *
16616970 GATATTCTATCTGGCTCGTAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
*
16616995 GATATTCTGTGTT-GCTCGTGAGAGC
1 GATATTCTGT-TTGGCTCGTAAGAGC
* * *
16617020 GATATTTTGTTTGACTC-TCAAGAGT
1 GATATTCTGTTTGGCTCGT-AAGAGC
16617045 GATATTCTGTTTGGGCTCG
1 GATATTCTGTTT-GGCTCG
16617064 AAAAAGCTAA
Statistics
Matches: 137, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
24 24 0.18
25 108 0.79
26 5 0.04
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (25 bp):
GATATTCTGTTTGGCTCGTAAGAGC
Found at i:16623387 original size:35 final size:35
Alignment explanation
Indices: 16623341--16623411 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
16623331 CAAGGATGTC
*
16623341 TCTGCGGTTAGATTTGCTCTTTTGTTTTCTGCTTT
1 TCTGCGATTAGATTTGCTCTTTTGTTTTCTGCTTT
16623376 TCTGCGATTAGATTTGCTCTTTTGTTTTCTGCTTT
1 TCTGCGATTAGATTTGCTCTTTTGTTTTCTGCTTT
16623411 T
1 T
16623412 ACTTTGCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.07, C:0.17, G:0.18, T:0.58
Consensus pattern (35 bp):
TCTGCGATTAGATTTGCTCTTTTGTTTTCTGCTTT
Found at i:16624725 original size:21 final size:24
Alignment explanation
Indices: 16624696--16624743 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 24
16624686 GTAAAAAAAC
*
16624696 AAAGTGAAACAAACTTG-A-AATA
1 AAAGTGAAACAAAATTGCATAATA
*
16624718 AAAG-GAAATAAAATTGCATAATA
1 AAAGTGAAACAAAATTGCATAATA
16624741 AAA
1 AAA
16624744 ATTTCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 7 0.32
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (24 bp):
AAAGTGAAACAAAATTGCATAATA
Found at i:16633121 original size:26 final size:25
Alignment explanation
Indices: 16633072--16633122 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16633062 AGACACTGAA
**
16633072 GCATATTCTGTCTGGCTCGTAAGAG
1 GCATATTCTGTCTGGCTCAAAAGAG
*
16633097 GCATATTCTGTCTAGGCTTAAAAGAG
1 GCATATTCTGTCT-GGCTCAAAAGAG
16633123 CTAAAACTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (25 bp):
GCATATTCTGTCTGGCTCAAAAGAG
Found at i:16633324 original size:21 final size:22
Alignment explanation
Indices: 16633295--16633336 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
16633285 TAAGCTTATC
*
16633295 TGTACATTTTGTTTTT-TGTTT
1 TGTACATTTTATTTTTCTGTTT
*
16633316 TGTAGATTTTATTTTTCTGTT
1 TGTACATTTTATTTTTCTGTT
16633337 GAAGATCGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (22 bp):
TGTACATTTTATTTTTCTGTTT
Found at i:16646663 original size:3 final size:3
Alignment explanation
Indices: 16646655--16646772 Score: 61
Period size: 3 Copynumber: 38.7 Consensus size: 3
16646645 GAAGAAAACC
*
16646655 ATA ATA ATA ATA ATA ATA ATA ATAA AGA ACTA A-A CA-A GATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA A-TA ATA -ATA -ATA ATA ATA
* * * *
16646700 ATA ATA AAA AGA ATA A-A ATAA ATAA ACA ACTAA ATA A-A GAAA ATA
1 ATA ATA ATA ATA ATA ATA AT-A AT-A ATA A-T-A ATA ATA -ATA ATA
16646745 ATA ATA ATA A-A ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
16646773 GAGTCGAACG
Statistics
Matches: 94, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
2 10 0.11
3 69 0.73
4 13 0.14
5 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (3 bp):
ATA
Found at i:16646724 original size:45 final size:45
Alignment explanation
Indices: 16646646--16646765 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 45
16646636 ACAGTGAATG
** * *
16646646 AAGAAAACCATAATAATAATAATAATAAT-AATAAAGAACTAAA-C
1 AAGAAAAAAATAATAATAA-AATAATAATAAATAAACAACTAAATA
*
16646690 AAGATAAAAAATAATAAAAAGAATAA-AATAAATAAACAACTAAATA
1 AAGA-AAAAAATAATAATAA-AATAATAATAAATAAACAACTAAATA
*
16646736 AAGAAAATAATAATAATAAAATAATAATAA
1 AAGAAAAAAATAATAATAAAATAATAATAA
16646766 TAATAATGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
44 12 0.19
45 48 0.75
46 4 0.06
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (45 bp):
AAGAAAAAAATAATAATAAAATAATAATAAATAAACAACTAAATA
Found at i:16647552 original size:35 final size:35
Alignment explanation
Indices: 16647493--16647560 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
16647483 AATATTAAGC
* * *
16647493 TCTAGTGGTCATACGGTCTGGCACACGCTCGTGTG
1 TCTAGTGGTCACACGGTCTAGCACACGCCCGTGTG
* *
16647528 TCTAGTGGTCACATGGTTTAGCACACGCCCGTG
1 TCTAGTGGTCACACGGTCTAGCACACGCCCGTG
16647561 CATCTAGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.28
Consensus pattern (35 bp):
TCTAGTGGTCACACGGTCTAGCACACGCCCGTGTG
Found at i:16653232 original size:13 final size:13
Alignment explanation
Indices: 16653215--16653257 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
16653205 ATTTAGTTCG
16653215 TTTGTTTATTT-T
1 TTTGTTTATTTAT
16653227 TCTTGTTTATTTAT
1 T-TTGTTTATTTAT
*
16653241 TTTATTTATTTAAT
1 TTTGTTTATTT-AT
16653255 TTT
1 TTT
16653258 CTCTCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 19 0.70
14 7 0.26
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTGTTTATTTAT
Done.