Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 131 of 202
Found at i:40495992 original size:24 final size:22
Alignment explanation
Indices: 40495964--40496049 Score: 95
Period size: 24 Copynumber: 3.8 Consensus size: 22
40495954 TTTTTGTTAA
40495964 AATTTAATATAGTAAATAAATTAT
1 AATTTAA-ATA-TAAATAAATTAT
40495988 AATTTAAATATAAATAAGGATTAT
1 AATTTAAATATAAATAA--ATTAT
* *
40496012 TATTTAAATATAAAATAATTTA-
1 AATTTAAATAT-AAATAAATTAT
40496034 AATTTAAATA-AAATAA
1 AATTTAAATATAAATAA
40496050 TAAAATAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
20 6 0.11
22 16 0.29
23 6 0.11
24 22 0.39
25 6 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
AATTTAAATATAAATAAATTAT
Found at i:40498808 original size:23 final size:25
Alignment explanation
Indices: 40498754--40498802 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
40498744 TACACATATA
40498754 TATATTTTTTAAACGAATATTTTCC
1 TATATTTTTTAAACGAATATTTTCC
* *
40498779 TATATTTTTTTAATGAATATTTTC
1 TATATTTTTTAAACGAATATTTTC
40498803 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATTTTTTAAACGAATATTTTCC
Found at i:40504924 original size:45 final size:45
Alignment explanation
Indices: 40504793--40504924 Score: 112
Period size: 45 Copynumber: 3.0 Consensus size: 45
40504783 TCAGTGAAAG
* * * *
40504793 AGCAGATCTTGTCTTCCTGCATCGACAGCGAAGCAGATCGAA-A-
1 AGCAGATCTTGCCTTCCTGCATTGACAGTGGAGCAGATCGAAGAT
* * * * * **
40504836 A-CAAAGCCTTGCCTTCCT-CGTTTG-TAGTGGAGCAGGTTAAAGAT
1 AGCAGA-TCTTGCCTTCCTGC-ATTGACAGTGGAGCAGATCGAAGAT
40504880 AGCAGATCTTGCCTTCCTGCATTGACAGTGGAGCAGATCGAAGAT
1 AGCAGATCTTGCCTTCCTGCATTGACAGTGGAGCAGATCGAAGAT
40504925 GACGGATTTT
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
42 15 0.23
43 14 0.22
44 15 0.23
45 20 0.31
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (45 bp):
AGCAGATCTTGCCTTCCTGCATTGACAGTGGAGCAGATCGAAGAT
Found at i:40505351 original size:132 final size:132
Alignment explanation
Indices: 40505104--40505356 Score: 384
Period size: 132 Copynumber: 1.9 Consensus size: 132
40505094 NNNNNNNNNN
* *
40505104 GAGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
1 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
40505169 TTCTACTTTCCTGGACAACAGTGGAATAGACTGAAGATTTTAGATCTTATCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGACAACAGTGAAATAGACTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAG
40505234 TG
131 TG
*
40505236 GAGCAGATCGAAGATTGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * *
40505301 TTCTACTTCCCTAGG-CAATAGTGAAATAGATTGGAGATTGTAAG-TTTTATCTCCCT
66 TTCTACTTCCCT-GGACAACAGTGAAATAGACTGAAGATT-TAAGATCTTATCTCCCT
40505357 GCAGTTGCAG
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
132 104 0.95
133 5 0.05
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (132 bp):
GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
TTCTACTTCCCTGGACAACAGTGAAATAGACTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAG
TG
Found at i:40506855 original size:23 final size:25
Alignment explanation
Indices: 40506801--40506849 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
40506791 TGTACACATA
40506801 TATATTTTTTAAACGAATATTTTCC
1 TATATTTTTTAAACGAATATTTTCC
* *
40506826 TATATTTTTTTAATGAATATTTTC
1 TATATTTTTTAAACGAATATTTTC
40506850 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATTTTTTAAACGAATATTTTCC
Found at i:40509213 original size:71 final size:72
Alignment explanation
Indices: 40509138--40509280 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
40509128 CCGGTTAAGT
*
40509138 ATATAGAAATATCAAAT-AATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
1 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
40509202 AGTTGAA
66 AGTTGAA
**
40509209 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTGGGGTGTGCCTCATATTTTC
1 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
40509274 AGTTGAA
66 AGTTGAA
40509281 TAGACGACGA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 16 0.24
72 52 0.76
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (72 bp):
ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
AGTTGAA
Found at i:40512416 original size:28 final size:28
Alignment explanation
Indices: 40512376--40512431 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
40512366 TTGTCTTCAC
40512376 ATCCATTTGATGTACCAACAAATTGTGA
1 ATCCATTTGATGTACCAACAAATTGTGA
*
40512404 ATCCATTTGATGTACCAGCAAATTGTGA
1 ATCCATTTGATGTACCAACAAATTGTGA
40512432 TTGAAATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (28 bp):
ATCCATTTGATGTACCAACAAATTGTGA
Found at i:40516745 original size:35 final size:35
Alignment explanation
Indices: 40516699--40516770 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
40516689 ACCTTTAAAG
40516699 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
1 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
40516734 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
1 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
40516769 TT
1 TT
40516771 CAATTATGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (35 bp):
TTGAAATCCACATTCTCTCAAACATCTACAATTTC
Found at i:40526725 original size:58 final size:58
Alignment explanation
Indices: 40526631--40526746 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
40526621 TGTGGCGTTA
*
40526631 GCTATACCTTTGGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
1 GCTATACCTTTAGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
* * * * *
40526689 GCTATACCTTTAGTTGCTTTCTTGTTAGATAGTGGGTCAAGGTTTATTTGCTGATTTC
1 GCTATACCTTTAGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
40526747 ATTTTTTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (58 bp):
GCTATACCTTTAGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
Found at i:40532102 original size:42 final size:41
Alignment explanation
Indices: 40531973--40532123 Score: 196
Period size: 41 Copynumber: 3.7 Consensus size: 41
40531963 TTAAATAGAT
* * * *
40531973 TCACCGGCACTTAGTCTGTTAGACTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAACCTGATTCAGA
*
40532014 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAACCTGATTCAGA
*
40532055 TCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATTCAG-
1 TCACCGGCACTTAGCCTGCTAGG-CTTAAAACCTGATTCAGA
** *
40532096 TACACCGGCTTTTAGCCTGCTAGACTTA
1 T-CACCGGCACTTAGCCTGCTAGGCTTA
40532124 TAGTCCGAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
41 63 0.65
42 34 0.35
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAACCTGATTCAGA
Found at i:40532111 original size:83 final size:82
Alignment explanation
Indices: 40531973--40532125 Score: 209
Period size: 83 Copynumber: 1.9 Consensus size: 82
40531963 TTAAATAGAT
* * * *
40531973 TCACCGGCACTTAGTCTGTTAGACTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGC
1 TCACCGGCACTTAGCCTGCTAGACTTAAAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGAC
40532038 TTATAACCTGATTCAGA
66 TTATAACCTGATTCAGA
** **
40532055 TCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATTCAG-TACACCGGCTTTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTA-GACTTAAAACCTGATTCAGAT-CACCGGCACTTAGCCTGCTAG
40532119 ACTTATA
64 ACTTATA
40532126 GTCCGAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 20 0.33
83 41 0.67
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (82 bp):
TCACCGGCACTTAGCCTGCTAGACTTAAAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGAC
TTATAACCTGATTCAGA
Found at i:40532563 original size:77 final size:77
Alignment explanation
Indices: 40532460--40532674 Score: 231
Period size: 77 Copynumber: 2.8 Consensus size: 77
40532450 TACATTTAAC
* *
40532460 ATTCGAATCT-CACATATACCTATATAATTTCATA-TCCCATTTCAATACAAGAACTTATACATG
1 ATTCGAATCTACACATATACATATATAATTTCATACTCACA-TTCAATACAAGAACTTATACATG
* * *
40532523 TACATATATACAT
65 CACACACATACAT
* * * * *
40532536 ATTCGAATCTACATATATACATATATAATTTTATACTTACATTCAATACAAGTACTTATACTTGC
1 ATTCGAATCTACACATATACATATATAATTTCATACTCACATTCAATACAAGAACTTATACATGC
* *
40532601 ATACACATGCAT
66 ACACACATACAT
* * * * *
40532613 ATTCGAATTTA-ACATATACATATATAATTTCATACTTATACTCAATATAAGCAA-TTATACAT
1 ATTCGAATCTACACATATACATATATAATTTCATACTCACATTCAATACAAG-AACTTATACAT
40532675 ATGTATACAT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
76 52 0.45
77 61 0.53
78 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (77 bp):
ATTCGAATCTACACATATACATATATAATTTCATACTCACATTCAATACAAGAACTTATACATGC
ACACACATACAT
Found at i:40532685 original size:76 final size:74
Alignment explanation
Indices: 40532460--40532714 Score: 230
Period size: 76 Copynumber: 3.4 Consensus size: 74
40532450 TACATTTAAC
* * **
40532460 ATTCGAATCTCACATATACCTATATAATTTCATATCCCAT-TTCAATACAAGAACTTATACA-TG
1 ATTCGAATCTAACATATACATATATAATTTCATA-CTTATATTCAATACAAGAA-TTATACATTG
* *
40532523 TACATATATACAT
64 T--ATACATGCAT
* * * *
40532536 ATTCGAATCTACATATATACATATATAATTTTATACTTACATTCAATACAAGTACTTATAC-TTG
1 ATTCGAATCTA-ACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACATTG
*
40532600 CATACACATGCAT
64 --TATACATGCAT
* * *
40532613 ATTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAATTATACATATG
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACAT-TG
*
40532678 TATACATGCTT
64 TATACATGCAT
* *
40532689 ATTCG-ATCCAAACATATACAAATATA
1 ATTCGAAT-CTAACATATACATATATA
40532715 TTATACATAT
Statistics
Matches: 146, Mismatches: 24, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
75 2 0.01
76 83 0.57
77 57 0.39
78 3 0.02
79 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (74 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAGAATTATACATTGTA
TACATGCAT
Found at i:40535332 original size:51 final size:51
Alignment explanation
Indices: 40535268--40535368 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
40535258 CGATGCCTAA
* * * *
40535268 CAGGTTTAATGCCGGTGAATTATTTCAGACTTTATGTCTAGTAGGCTTTAG
1 CAGGCTTAATGCCGGTGAATTATTTCAAACTTTATGACTAGCAGGCTTTAG
*
40535319 CAGGCTTAATGCCGGTGAATTATTTTAAACTTTATGACTAGCAGGCTTTA
1 CAGGCTTAATGCCGGTGAATTATTTCAAACTTTATGACTAGCAGGCTTTA
40535369 TGCCGGTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (51 bp):
CAGGCTTAATGCCGGTGAATTATTTCAAACTTTATGACTAGCAGGCTTTAG
Found at i:40542676 original size:87 final size:87
Alignment explanation
Indices: 40542471--40542676 Score: 288
Period size: 87 Copynumber: 2.4 Consensus size: 87
40542461 AAAAACACAA
* * * *
40542471 GTTTTTGAGAAAAGAATCAATGGAAAAGAAGACATTTTTTTGTCTTTAAAATTATAGGTTTTCTT
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATATAGGTTTTCTT
*
40542536 TTTTCAGTTCTCAAAAATCATG
66 TTTTCAGTTCACAAAAATCATG
* *
40542558 GTTTTTAAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATCTAGGTTTT-TT
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATATAGGTTTTCTT
* ***
40542622 TTTTCAGTTCACTAGGTTCAATG
66 TTTTCAGTTCACAAAAATC-ATG
*
40542645 GTTTTTGAGATAAGAATCAATGGAGAAGAAGG
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGG
40542677 TTTGAATTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
86 16 0.15
87 89 0.85
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (87 bp):
GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATATAGGTTTTCTT
TTTTCAGTTCACAAAAATCATG
Found at i:40545196 original size:21 final size:21
Alignment explanation
Indices: 40545155--40545210 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
40545145 GTGGAAATCT
* *
40545155 CACACACCCGTGTGGCTAAGG
1 CACACAGCCGTGTGGCCAAGG
* *
40545176 GACACAGCCGTGTGTCCAAGG
1 CACACAGCCGTGTGGCCAAGG
40545197 CACAC-GCCTGTGTG
1 CACACAGCC-GTGTG
40545211 AAAATTGACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.16
Consensus pattern (21 bp):
CACACAGCCGTGTGGCCAAGG
Found at i:40545323 original size:12 final size:13
Alignment explanation
Indices: 40545297--40545329 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
40545287 TTTCACACAG
40545297 CCGTGTGGACCAC
1 CCGTGTGGACCAC
40545310 CCGTGTGG-CCAC
1 CCGTGTGGACCAC
*
40545322 CCATGTGG
1 CCGTGTGG
40545330 TCACGAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.12, C:0.36, G:0.33, T:0.18
Consensus pattern (13 bp):
CCGTGTGGACCAC
Found at i:40548673 original size:20 final size:20
Alignment explanation
Indices: 40548636--40548676 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40548626 TAAAAAGACA
* *
40548636 TATAATTATTCATCTAATAT
1 TATAAATATTCAACTAATAT
*
40548656 TATAAATATTCAAGTAATAT
1 TATAAATATTCAACTAATAT
40548676 T
1 T
40548677 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAAATATTCAACTAATAT
Found at i:40560593 original size:14 final size:15
Alignment explanation
Indices: 40560571--40560599 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40560561 GGCTGGAGAG
40560571 TGAGTATATGAGATA
1 TGAGTATATGAGATA
40560586 TGAG-ATATGAGATA
1 TGAGTATATGAGATA
40560600 GAGCTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (15 bp):
TGAGTATATGAGATA
Found at i:40567122 original size:25 final size:24
Alignment explanation
Indices: 40567094--40567290 Score: 121
Period size: 25 Copynumber: 8.0 Consensus size: 24
40567084 ATCTCGTTAT
*
40567094 ATGGCTCTCACGAGCTTCCCGATTA
1 ATGGCTCTCATGAGCTTCCCGA-TA
* * *
40567119 ATGGTTCTCTTGAGCTTTCC-ATA
1 ATGGCTCTCATGAGCTTCCCGATA
* *
40567142 TATGGCTCGTAATAAGCTTCCCGATA
1 -ATGGCTC-TCATGAGCTTCCCGATA
*
40567168 ATTGGCTCTCATGAGCTTCCTGATTA
1 A-TGGCTCTCATGAGCTTCCCGA-TA
*
40567194 ATGGATCTC-TGGAGC-TCCCGATA
1 ATGGCTCTCAT-GAGCTTCCCGATA
* * * * *
40567217 TTGGGTCACATGAGCTTCCCGGTT
1 ATGGCTCTCATGAGCTTCCCGATA
* * ** *
40567241 ATGACCTCTTATGAGCTTTTCGTTA
1 ATG-GCTCTCATGAGCTTCCCGATA
* *
40567266 CATAGCTCACATGAGCTTCCCGATA
1 -ATGGCTCTCATGAGCTTCCCGATA
40567291 TATATATGGC
Statistics
Matches: 127, Mismatches: 35, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
23 14 0.11
24 22 0.17
25 77 0.61
26 14 0.11
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (24 bp):
ATGGCTCTCATGAGCTTCCCGATA
Found at i:40570062 original size:54 final size:54
Alignment explanation
Indices: 40569980--40570100 Score: 233
Period size: 54 Copynumber: 2.2 Consensus size: 54
40569970 TCCCTCTCTT
*
40569980 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTC
1 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
40570034 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
1 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
40570088 CTAATTCAACTAG
1 CTAATTCAACTAG
40570101 GGTTCCTCTA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (54 bp):
CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
Found at i:40570243 original size:20 final size:19
Alignment explanation
Indices: 40570204--40570243 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
40570194 AAATAGTGAG
* *
40570204 AATTTATTTTCTAAGTATA
1 AATTTATTTTCCAAGAATA
40570223 AATTCTATTTTCCAAGAATA
1 AATT-TATTTTCCAAGAATA
40570243 A
1 A
40570244 TAATTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTTATTTTCCAAGAATA
Found at i:40570271 original size:2 final size:2
Alignment explanation
Indices: 40570264--40570306 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
40570254 AGTTTCTATA
*
40570264 AG AG AG AG AG AA 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
40570306 A
1 A
40570307 TTTACTTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40570415 original size:70 final size:70
Alignment explanation
Indices: 40570302--40570437 Score: 272
Period size: 70 Copynumber: 1.9 Consensus size: 70
40570292 AGAGAGAGAG
40570302 AGAGATTTACTTTCCTACTGAAAGTAAGAAAATTAATTTTGATTCTGCATTTGATTCGTAATTGT
1 AGAGATTTACTTTCCTACTGAAAGTAAGAAAATTAATTTTGATTCTGCATTTGATTCGTAATTGT
40570367 TAGAT
66 TAGAT
40570372 AGAGATTTACTTTCCTACTGAAAGTAAGAAAATTAATTTTGATTCTGCATTTGATTCGTAATTGT
1 AGAGATTTACTTTCCTACTGAAAGTAAGAAAATTAATTTTGATTCTGCATTTGATTCGTAATTGT
40570437 T
66 T
40570438 CGAACCCACA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (70 bp):
AGAGATTTACTTTCCTACTGAAAGTAAGAAAATTAATTTTGATTCTGCATTTGATTCGTAATTGT
TAGAT
Found at i:40577163 original size:20 final size:20
Alignment explanation
Indices: 40577140--40577202 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
40577130 TATCAAAGTA
40577140 CAATCAGGGGCACGTATGTG
1 CAATCAGGGGCACGTATGTG
* * *
40577160 CAATCAGGGGTACCG-AAGTA
1 CAATCAGGGGCA-CGTATGTG
*
40577180 CAATCAGGGGCACATATGTG
1 CAATCAGGGGCACGTATGTG
40577200 CAA
1 CAA
40577203 ACATTCAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.91
21 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.17
Consensus pattern (20 bp):
CAATCAGGGGCACGTATGTG
Found at i:40577180 original size:40 final size:40
Alignment explanation
Indices: 40577125--40577202 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
40577115 AAATGCGTTT
* *
40577125 AGGGGTATCAAAGTACAATCAGGGGCACGTATGTGCAATC
1 AGGGGTACCAAAGTACAATCAGGGGCACATATGTGCAATC
*
40577165 AGGGGTACCGAAGTACAATCAGGGGCACATATGTGCAA
1 AGGGGTACCAAAGTACAATCAGGGGCACATATGTGCAA
40577203 ACATTCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (40 bp):
AGGGGTACCAAAGTACAATCAGGGGCACATATGTGCAATC
Found at i:40584486 original size:20 final size:20
Alignment explanation
Indices: 40584463--40584575 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 20
40584453 GGGTATCGAA
40584463 GTACAAACAGGGGCACACAT
1 GTACAAACAGGGGCACACAT
* * *
40584483 GTACAAACAAGGGTAC-CGAA
1 GTACAAACAGGGGCACAC-AT
* **
40584503 GAACAAACAGGGGCACTTAT
1 GTACAAACAGGGGCACACAT
* * *
40584523 GTGCGAACAGGGGTACTA-AT
1 GTACAAACAGGGGCAC-ACAT
* **
40584543 GTACAGACAGGGGCACGTAT
1 GTACAAACAGGGGCACACAT
*
40584563 GTACAATCAGGGG
1 GTACAAACAGGGG
40584576 TACCGAAGTA
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 68 0.99
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.14
Consensus pattern (20 bp):
GTACAAACAGGGGCACACAT
Found at i:40584503 original size:40 final size:40
Alignment explanation
Indices: 40584451--40584604 Score: 175
Period size: 40 Copynumber: 3.9 Consensus size: 40
40584441 AAATGCGTTT
* *
40584451 AGGGGTATCGAAGTACAAACAGGGGCACACATGTACAAAC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTACAAAC
* * * * *
40584491 AAGGGTACCGAAGAACAAACAGGGGCACTTATGTGCGAAC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTACAAAC
* * * *
40584531 AGGGGTA-CTAATGTACAGACAGGGGCACGTATGTACAATC
1 AGGGGTACCGAA-GTACAAACAGGGGCACATATGTACAAAC
* *
40584571 AGGGGTACCGAAGTACAATCAGGGACACATATGT
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGT
40584605 GCAGACATTC
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
39 3 0.03
40 86 0.93
41 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (40 bp):
AGGGGTACCGAAGTACAAACAGGGGCACATATGTACAAAC
Found at i:40587264 original size:15 final size:15
Alignment explanation
Indices: 40587241--40587271 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40587231 ATATTTTTTC
*
40587241 TTTTGAAAAATAATT
1 TTTTAAAAAATAATT
40587256 TTTTAAAAAATAATT
1 TTTTAAAAAATAATT
40587271 T
1 T
40587272 ATGAGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAATAATT
Found at i:40593517 original size:40 final size:39
Alignment explanation
Indices: 40593428--40593530 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 39
40593418 CGTGATTCAG
* **
40593428 GTGGATCAGCTCTTATGATCTTCTGTTGGCGTGTTTCGA
1 GTGGATCAGCTCTTATGAGCTTCTGTTGGCGCATTTCGA
* * * *
40593467 GTGAACCAGCTCTTATGAGCTTTTGTTTGGCGCATTTCTA
1 GTGGATCAGCTCTTATGAGCTTCTG-TTGGCGCATTTCGA
* *
40593507 TTGGATCAGCTCTTATAAGCTTCT
1 GTGGATCAGCTCTTATGAGCTTCT
40593531 ATTTGGTGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
39 21 0.41
40 30 0.59
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (39 bp):
GTGGATCAGCTCTTATGAGCTTCTGTTGGCGCATTTCGA
Found at i:40594414 original size:103 final size:103
Alignment explanation
Indices: 40594235--40594444 Score: 402
Period size: 103 Copynumber: 2.0 Consensus size: 103
40594225 GTATAATGTT
*
40594235 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTGATAGACTTACTCATTTATGA
1 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
40594300 GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
66 GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
40594338 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
1 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
*
40594403 GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
66 GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
40594441 TATA
1 TATA
40594445 GGTTTATATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (103 bp):
TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
Found at i:40597412 original size:25 final size:24
Alignment explanation
Indices: 40597384--40597448 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 24
40597374 TTGTACATTG
40597384 TACTGACAACACTGTAGATAGTGTA
1 TACTGA-AACACTGTAGATAGTGTA
*
40597409 TACTGAAAACACTATAGATAGTGTA
1 TACTG-AAACACTGTAGATAGTGTA
40597434 TACTGAAA-ACTGTAG
1 TACTGAAACACTGTAG
40597449 CAAAATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 6 0.16
24 3 0.08
25 27 0.73
26 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
TACTGAAACACTGTAGATAGTGTA
Found at i:40601228 original size:35 final size:35
Alignment explanation
Indices: 40601189--40601258 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
40601179 GTGGATCGAT
40601189 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
1 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
40601224 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
1 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
40601259 GACTTTTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
Found at i:40602148 original size:28 final size:28
Alignment explanation
Indices: 40602100--40602156 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
40602090 CTATTCCCTT
* *
40602100 AGTGAAGGTTCTACCGTGTAAAGGTAGC
1 AGTGAAGGTTCTACCGCGTAAAGATAGC
**
40602128 AGTGAAGGTTCTGTCGCGTAAAGATAGC
1 AGTGAAGGTTCTACCGCGTAAAGATAGC
40602156 A
1 A
40602157 CTGAGGAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.25
Consensus pattern (28 bp):
AGTGAAGGTTCTACCGCGTAAAGATAGC
Found at i:40604890 original size:35 final size:35
Alignment explanation
Indices: 40604844--40604913 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
40604834 ATTGAGTTTG
40604844 AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
1 AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
*
40604879 AGGTGCCTTTTGGCATATTTGTTGTATGGATAAAT
1 AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
40604914 GACCTTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (35 bp):
AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
Found at i:40611121 original size:7 final size:7
Alignment explanation
Indices: 40611109--40611134 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40611099 AATTGCTAAA
40611109 TGATATG
1 TGATATG
40611116 TGATATG
1 TGATATG
40611123 TGATATG
1 TGATATG
40611130 TGATA
1 TGATA
40611135 CGAAATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
TGATATG
Found at i:40617303 original size:34 final size:34
Alignment explanation
Indices: 40617244--40617318 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
40617234 TTCATATAAC
* *
40617244 AAATCAAGTATTTCATGTAGCTTATAAACCATGT
1 AAATCATGTATTTCATGTAACTTATAAACCATGT
* * *
40617278 AAATCATGTATTTCATGTAATTTATAATCTATGT
1 AAATCATGTATTTCATGTAACTTATAAACCATGT
*
40617312 GAATCAT
1 AAATCAT
40617319 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (34 bp):
AAATCATGTATTTCATGTAACTTATAAACCATGT
Found at i:40617524 original size:22 final size:22
Alignment explanation
Indices: 40617494--40617549 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
40617484 TCAGCTGGTA
*
40617494 AACGGTAAGCTCTATCGAGCTG
1 AACGATAAGCTCTATCGAGCTG
40617516 AACGATAAGCTCTATCGAGCTG
1 AACGATAAGCTCTATCGAGCTG
40617538 AACGATAAGCTC
1 AACGATAAGCTC
40617550 CGTAAAGCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (22 bp):
AACGATAAGCTCTATCGAGCTG
Found at i:40617558 original size:22 final size:22
Alignment explanation
Indices: 40617511--40617561 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
40617501 AGCTCTATCG
* **
40617511 AGCTGAACGATAAGCTCTATCG
1 AGCTGAACGATAAGCTCCATAA
*
40617533 AGCTGAACGATAAGCTCCGTAA
1 AGCTGAACGATAAGCTCCATAA
40617555 AGCTGAA
1 AGCTGAA
40617562 ATGGTCAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (22 bp):
AGCTGAACGATAAGCTCCATAA
Found at i:40624816 original size:34 final size:34
Alignment explanation
Indices: 40624769--40624846 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
40624759 AAATGATCCG
* *
40624769 TGTAAGTCATGTATTTTATGCAACTTATAAACCA
1 TGTAAATCATGTATTTCATGCAACTTATAAACCA
* * * * *
40624803 TGTAAATCGTGTATTTCATGTAATTTATAATCCT
1 TGTAAATCATGTATTTCATGCAACTTATAAACCA
40624837 TGTAAATCAT
1 TGTAAATCAT
40624847 ATAACTCTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
TGTAAATCATGTATTTCATGCAACTTATAAACCA
Found at i:40625108 original size:23 final size:23
Alignment explanation
Indices: 40625021--40625127 Score: 87
Period size: 23 Copynumber: 4.7 Consensus size: 23
40625011 TTCAGCTGGT
*
40625021 AAACGGTAAGCTC-TATCGAGCT-
1 AAACGGTAAGCTCATA-AGAGCTA
* *
40625043 GAATGGTAAGCTCCAT-AGAGCTA
1 AAACGGTAAGCT-CATAAGAGCTA
* *
40625066 AAACGGTAAGATCCGT-AGAGCTA
1 AAACGGTAAGCT-CATAAGAGCTA
* *
40625089 AAACGGTAACCTCATAAGAGCTG
1 AAACGGTAAGCTCATAAGAGCTA
*
40625112 AAATGGTAAGCTCATA
1 AAACGGTAAGCTCATA
40625128 CAAGGTGTAG
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.25
23 50 0.74
24 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (23 bp):
AAACGGTAAGCTCATAAGAGCTA
Found at i:40626774 original size:27 final size:27
Alignment explanation
Indices: 40626744--40626831 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
40626734 AAGGCATTTC
* * *
40626744 TTTCAGAGTTAACCACAAGGGCTTCCT
1 TTTCAAAGTTAGCCACAAAGGCTTCCT
40626771 TTTCAAAGTTAGCCACAAAGGCTTCCT
1 TTTCAAAGTTAGCCACAAAGGCTTCCT
*
40626798 TTTCATAGTTAGCCACAAAGGCTTCCT
1 TTTCAAAGTTAGCCACAAAGGCTTCCT
*
40626825 CTTCAAA
1 TTTCAAA
40626832 CATTTTTATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (27 bp):
TTTCAAAGTTAGCCACAAAGGCTTCCT
Found at i:40628725 original size:17 final size:17
Alignment explanation
Indices: 40628695--40628727 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40628685 ACAAAGAACG
40628695 AATAAAAATCATAAATA
1 AATAAAAATCATAAATA
40628712 AATAAGAAAT-ATAAAT
1 AATAA-AAATCATAAAT
40628728 TATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AATAAAAATCATAAATA
Found at i:40629954 original size:12 final size:13
Alignment explanation
Indices: 40629931--40629960 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
40629921 AATCTCAGAC
40629931 ATACCTTGATTCT
1 ATACCTTGATTCT
40629944 ATACC-TGATTCT
1 ATACCTTGATTCT
40629956 ATACC
1 ATACC
40629961 ATACATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (13 bp):
ATACCTTGATTCT
Found at i:40636803 original size:28 final size:28
Alignment explanation
Indices: 40636749--40636839 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 28
40636739 TATTCAGTAT
* *
40636749 CAGT-ACAGTGTGGGCC-TAGCCCGATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
40636775 CAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
* * *
40636803 CAGTAATAGTGT-GGCCTTAGCTCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
40636830 CAGTAACAAT
1 CAGTAACAAT
40636840 ATAGTGCCCT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
26 4 0.07
27 33 0.59
28 19 0.34
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
CAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:40637186 original size:27 final size:27
Alignment explanation
Indices: 40637154--40637214 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
40637144 TGATCTCCTA
*
40637154 GAGGTATAATAGTTATTTTACCCTATG
1 GAGGTATAATAGTCATTTTACCCTATG
* ** * *
40637181 GGGGTATTTTGGTCATTTTACCTTATG
1 GAGGTATAATAGTCATTTTACCCTATG
40637208 GAGGTAT
1 GAGGTAT
40637215 TTTGATCATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (27 bp):
GAGGTATAATAGTCATTTTACCCTATG
Found at i:40637215 original size:27 final size:27
Alignment explanation
Indices: 40637168--40637253 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
40637158 TATAATAGTT
*
40637168 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCTTATGGGGGTATTTTGGTC
* *
40637195 ATTTTACCTTATGGAGGTATTTTGATC
1 ATTTTACCTTATGGGGGTATTTTGGTC
* *
40637222 ATTTTACCTTATGGGGGTCTTTCGGTC
1 ATTTTACCTTATGGGGGTATTTTGGTC
40637249 -TTTTA
1 ATTTTA
40637254 TTGACCCCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
26 5 0.10
27 47 0.90
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.48
Consensus pattern (27 bp):
ATTTTACCTTATGGGGGTATTTTGGTC
Found at i:40641165 original size:52 final size:52
Alignment explanation
Indices: 40641087--40641194 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
40641077 TTTCAAGGAT
40641087 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
1 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
40641139 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
1 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
40641191 CAAC
1 CAAC
40641195 TAAAACTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.24
Consensus pattern (52 bp):
CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
Found at i:40644529 original size:28 final size:28
Alignment explanation
Indices: 40644479--40644551 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
40644469 GTATTAGTAC
* *
40644479 AGTGTGGGCC-TAGCCCGATACAGTAAA
1 AGTGTGGGCCTTAGCCCAACACAGTAAA
* *
40644506 ATTGTGGGCCTTAGCCCAACACAGTAAT
1 AGTGTGGGCCTTAGCCCAACACAGTAAA
*
40644534 AGTAT-GGCCTTAGCCCAA
1 AGTGTGGGCCTTAGCCCAA
40644552 TACAATAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAACACAGTAAA
Found at i:40644563 original size:27 final size:27
Alignment explanation
Indices: 40644512--40644564 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
40644502 TAAAATTGTG
*
40644512 GGCCTTAGCCCAACACAGTAATAGTAT
1 GGCCTTAGCCCAACACAATAATAGTAT
* *
40644539 GGCCTTAGCCCAATACAATAGTAGTA
1 GGCCTTAGCCCAACACAATAATAGTA
40644565 CAGTGCCATA
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:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (27 bp):
GGCCTTAGCCCAACACAATAATAGTAT
Found at i:40644695 original size:26 final size:26
Alignment explanation
Indices: 40644666--40644716 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
40644656 AACACACCAA
40644666 TATCGAAACAAAGCTGCCAGTAATAG
1 TATCGAAACAAAGCTGCCAGTAATAG
* ***
40644692 TATCGCAGTGAAGCTGCCAGTAATA
1 TATCGAAACAAAGCTGCCAGTAATA
40644717 ATATATGTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
TATCGAAACAAAGCTGCCAGTAATAG
Found at i:40644935 original size:27 final size:27
Alignment explanation
Indices: 40644905--40644963 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
40644895 ATCTCCTAGA
*
40644905 GGTATAACAGTCATTTTACCCTATGTG
1 GGTATAACAGTCATTTTACCCTATGGG
** *
40644932 GGTATTTCGGTCATTTTACCCTATGGG
1 GGTATAACAGTCATTTTACCCTATGGG
40644959 GGTAT
1 GGTAT
40644964 TTTGATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
GGTATAACAGTCATTTTACCCTATGGG
Found at i:40644964 original size:27 final size:27
Alignment explanation
Indices: 40644914--40645002 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
40644904 AGGTATAACA
* *
40644914 GTCATTTTACCCTATGTGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTTG
*
40644941 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTTG
* *
40644968 ATAATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTTG
40644995 GTC-TTTTA
1 GTCATTTTA
40645003 ATGATCGCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 5 0.09
27 50 0.91
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTTG
Found at i:40660032 original size:4 final size:4
Alignment explanation
Indices: 40660023--40660053 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
40660013 ATGCATTTGA
40660023 TATT TATT TATT TATT TATT TATT TAGTT TA
1 TATT TATT TATT TATT TATT TATT TA-TT TA
40660054 CTTAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:40663990 original size:17 final size:17
Alignment explanation
Indices: 40663939--40663990 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
40663929 ATGGAAACAT
* *
40663939 AATCTTCGAGGATATGC
1 AATCTTAGAAGATATGC
*
40663956 AATCTTATATATGATATGC
1 AATCTTAGA-A-GATATGC
40663975 AATCTTAGAAGATATG
1 AATCTTAGAAGATATG
40663991 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 1 0.03
19 15 0.52
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (17 bp):
AATCTTAGAAGATATGC
Found at i:40664009 original size:22 final size:23
Alignment explanation
Indices: 40663979--40664024 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
40663969 ATATGCAATC
40663979 TTAGAAGATATGATTTTGTA-ATA
1 TTAGAAGATATGA-TTTGTAGATA
*
40664002 TTAG-AGATTTGATTTGTAGATA
1 TTAGAAGATATGATTTGTAGATA
40664024 T
1 T
40664025 CTTTTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.46
Consensus pattern (23 bp):
TTAGAAGATATGATTTGTAGATA
Found at i:40664846 original size:28 final size:27
Alignment explanation
Indices: 40664807--40664875 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
40664797 TGATTCACTG
* *
40664807 CAAAGGCATTTTCTTTCAGATTTAGCCA
1 CAAAGGC-TTTTTTTTCAGAGTTAGCCA
*
40664835 CAAAGGCTTTTTTTTCATAGTTAGCCA
1 CAAAGGCTTTTTTTTCAGAGTTAGCCA
*
40664862 CAAAGGCTTCTTTT
1 CAAAGGCTTTTTTT
40664876 ATTGACATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (27 bp):
CAAAGGCTTTTTTTTCAGAGTTAGCCA
Found at i:40667396 original size:61 final size:61
Alignment explanation
Indices: 40667300--40667433 Score: 187
Period size: 61 Copynumber: 2.2 Consensus size: 61
40667290 AAAGGATAGT
* * * *
40667300 CTTTGTGGAAAAACCTTGGATAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGGCAAC
1 CTTTGTGGCAAAACCTTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAAC
* * * * *
40667361 TTTTGTGGCAAAACTTTGAACAGGAAAGCCTTTGTGGCGAGTACTGGATGTAAATGACAAC
1 CTTTGTGGCAAAACCTTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAAC
40667422 CTTTGTGGCAAA
1 CTTTGTGGCAAA
40667434 TCTCAGGAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (61 bp):
CTTTGTGGCAAAACCTTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAAC
Found at i:40667430 original size:32 final size:31
Alignment explanation
Indices: 40667326--40667430 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 31
40667316 TGGATAGGAA
* *
40667326 AACCTTTGTGGCGAGTACTGAAAGTAAATGGC
1 AACCTTTGTGGCGAGTACTG-ATGTAAATGAC
* ** * *
40667358 AACTTTTGTGGC-AAAACT-TTG-AACAGGA-
1 AACCTTTGTGGCGAGTACTGATGTAA-ATGAC
40667386 AAGCCTTTGTGGCGAGTACTGGATGTAAATGAC
1 AA-CCTTTGTGGCGAGTACT-GATGTAAATGAC
40667419 AACCTTTGTGGC
1 AACCTTTGTGGC
40667431 AAATCTCAGG
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
28 4 0.07
29 12 0.22
30 4 0.07
31 4 0.07
32 26 0.48
33 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (31 bp):
AACCTTTGTGGCGAGTACTGATGTAAATGAC
Found at i:40667451 original size:61 final size:61
Alignment explanation
Indices: 40667323--40667461 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 61
40667313 CCTTGGATAG
* * * ** *
40667323 GAAAACCTTTGTGGCGAGTACTGAAAGTAAATGGCAACTTTTGTGGCAAAACTTTGAACAG
1 GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACTAGGAACAC
* * *
40667384 GAAAGCCTTTGTGGCGAGTACTGGATGTAAATGACAACCTTTGTGGCAAATCTCAGGAA-AC
1 GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACT-AGGAACAC
* **
40667445 GTAAGCCTAGGTGGCGA
1 GAAAGCCTTTGTGGCGA
40667462 ACCTCTACAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 62 0.95
62 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACTAGGAACAC
Found at i:40687657 original size:28 final size:28
Alignment explanation
Indices: 40687626--40687705 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
40687616 TATTTTACAA
**
40687626 ATTTTACAGTTTTATCCCTATTTTTTTT
1 ATTTTACAGTTTTATCCCTATTTTTTAG
*
40687654 ATTTTACAATTTTA-CTCCTATTTTTTAG
1 ATTTTACAGTTTTATC-CCTATTTTTTAG
* *
40687682 ATTTTACAGTTTTGTTCCTATTTT
1 ATTTTACAGTTTTATCCCTATTTT
40687706 ACAAAAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.20, C:0.14, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTTTACAGTTTTATCCCTATTTTTTAG
Found at i:40689470 original size:3 final size:3
Alignment explanation
Indices: 40689462--40689493 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
40689452 CTTGACTTTC
*
40689462 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40689494 ATGGTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:40694060 original size:23 final size:23
Alignment explanation
Indices: 40694029--40694079 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
40694019 ACCTACTTTC
*
40694029 TTACTGTAGTAATTTTCAGGG-TA
1 TTACAGTAGTAATTTTC-GGGATA
40694052 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
40694075 TTACA
1 TTACA
40694080 CTTCACCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:40701166 original size:23 final size:23
Alignment explanation
Indices: 40701139--40701185 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40701129 ACTATATCAG
* * *
40701139 TGAGAAATTCACTTATTGTGAAT
1 TGAGAAACTCACCTATTGAGAAT
*
40701162 TGAGATACTCACCTATTGAGAAT
1 TGAGAAACTCACCTATTGAGAAT
40701185 T
1 T
40701186 TATGTTGCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (23 bp):
TGAGAAACTCACCTATTGAGAAT
Found at i:40702775 original size:14 final size:14
Alignment explanation
Indices: 40702756--40702795 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40702746 TTGATTGCCA
40702756 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
40702770 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
40702784 GGAAAATGTTTT
1 GTAAAATGTTTT
40702796 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:40702811 original size:34 final size:35
Alignment explanation
Indices: 40702764--40702830 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
40702754 CAGTAAAATG
* *
40702764 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
40702798 TTTTCTGTGAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
40702831 CTGCTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:40704931 original size:54 final size:54
Alignment explanation
Indices: 40704861--40705035 Score: 138
Period size: 54 Copynumber: 3.4 Consensus size: 54
40704851 TTTCCCTGGC
*
40704861 GTTGTAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
* * * ** * * * *
40704915 GTTGTAGTGGAGCAGATTGAAGC--C--ACCA--GC----CTTATTTCCCTAG-C
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCT-TCTTGAA
*
40704959 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
* * *
40705013 GTTACAGTGGAGCAGATTTAAGC
1 GTTGCAGTGGAACAGATTAAAGC
40705036 CACCAACCTT
Statistics
Matches: 88, Mismatches: 21, Indels: 24
0.66 0.16 0.18
Matches are distributed among these distances:
44 26 0.30
45 3 0.03
46 1 0.01
48 4 0.05
50 4 0.05
52 1 0.01
53 2 0.02
54 47 0.53
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (54 bp):
GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
Found at i:40704973 original size:98 final size:97
Alignment explanation
Indices: 40704801--40705072 Score: 355
Period size: 98 Copynumber: 2.8 Consensus size: 97
40704791 AAGCTACCAG
* * * * * * * * *
40704801 TCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGT
1 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCA-CCAACCTTATTTCCCT-GCGTTGC
40704866 AGTGGAACAGATTAAAGCTACAAATTATGGCGGA
64 AGTGGAACAGATTAAAGCTACAAATTATGGCGGA
* ** *
40704900 TCTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATTTCCCTAGCGTTGCA
1 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATTTCCCT-GCGTTGCA
40704965 GTGGAACAGATTAAAGCTACAAATTATGGCGGA
65 GTGGAACAGATTAAAGCTACAAATTATGGCGGA
* * *
40704998 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTTAAGCCACCAACCTTATCTCCCTGAAGTTGCA
1 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATTTCCCTG-CGTTGCA
*
40705063 GTGGAGCAGA
65 GTGGAACAGA
40705073 ATGAAGATAG
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
97 1 0.01
98 118 0.78
99 33 0.22
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (97 bp):
TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATTTCCCTGCGTTGCAG
TGGAACAGATTAAAGCTACAAATTATGGCGGA
Found at i:40705158 original size:143 final size:143
Alignment explanation
Indices: 40704901--40705639 Score: 815
Period size: 143 Copynumber: 5.2 Consensus size: 143
40704891 TATGGCGGAT
* * * * ** * ** *
40704901 CTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGAAGCCA-CCAGCCTTATTTCCCTAGCGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
40704965 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
*
40705030 TTAAGCCACCAAC
131 TGAAGCCACCAAC
* * * * *
40705043 CTTATCTCCCTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATTTTATCTCCTTAGTGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
* * **
40705108 GTGGAACAAATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTTGTAGTGGAGCAGAT
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
* *
40705173 TGAAGCTACCATC
131 TGAAGCCACCAAC
* * * * ** *
40705186 CTTATCTCCCTGAAGATACAATGGAGCAGACTGAAGAAAATGAATCTTATCTCCCTGGCGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
* * * * * *
40705251 GTGGAACAAATTAAAGCTATAAGTTATGGCAGATCTTATATTCTTGAAGTTGA-AGTGGAGCAGA
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTT-ACAGTGGAGCAGA
*
40705315 TTGAAGCCACCAGC
130 TTGAAGCCACCAAC
* * * * * * * * *
40705329 CTTATCTCCCTGAAGTTGTA-TCAGAGTAGACTGAAGACT-GCAAATCTTATTTCTCTGGCATTA
1 CTTATCTCCCTGAAGTTGCAGT-GGAGCAGACTGAAGA-TAGCGAATCTTATCTCCCTAGCGTTG
* * * * *
40705392 CAGTGGAACAGATTAAAGCTACAAGTTATGGCGAATCTTATCCTCCTGAAGTTGCAGTGGAGTAG
64 CAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAG
*
40705457 ATTGAAGCCACCAGC
129 ATTGAAGCCACCAAC
* * * * *
40705472 CTTATCTCTCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGCGTTG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
* * * *
40705536 GTGGAACAGATTAAAACTACAAATCATGGAGGATCTTATCTTCCTGAAGTTACAGTGGAACAGAT
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
** * *
40705601 CAAAGACA-TAATC
131 TGAAGCCACCAA-C
*
40705614 CTTATCTCTCTGAAGTTGCAGTGGAG
1 CTTATCTCCCTGAAGTTGCAGTGGAG
40705640 TAGGTTGAAA
Statistics
Matches: 500, Mismatches: 89, Indels: 16
0.83 0.15 0.03
Matches are distributed among these distances:
141 1 0.00
142 121 0.24
143 378 0.76
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (143 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
TGAAGCCACCAAC
Found at i:40708632 original size:87 final size:86
Alignment explanation
Indices: 40708392--40708693 Score: 347
Period size: 86 Copynumber: 3.5 Consensus size: 86
40708382 TGGCGGCTAG
* * * * **
40708392 TCCACAAAACCCAGTAGCAATTTGTTTAATCTGCGAATATGTTATGCACCCACAGTAAGTGACAG
1 TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACAG
*
40708457 TAACTGCAAACATGTGGCTCA
66 TAACTGCAAATATGTGGCTCA
* * *
40708478 TCCACAAAACCTAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACATCAAGTGACAG
1 TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACAG
*
40708543 TAACTACAAATATGTGGCTCA
66 TAACTGCAAATATGTGGCTCA
* * ** * **
40708564 TCTACAAAACCCAGTGGCTAATTTGTATAATCTATAAATATGTTGTGCACTCATAACAAGTGGTA
1 TCCACAAAACCCAGTGGC-AATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACA
*
40708629 GTAACTGCAAATATGTGGCTCG
65 GTAACTGCAAATATGTGGCTCA
* * * * * **
40708651 TCC-CCAAACCTAGTGAC-TTTTGTTTAATTTGCAACCATGTTGT
1 TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGT
40708694 CACAACAAGT
Statistics
Matches: 182, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
84 19 0.10
86 103 0.57
87 60 0.33
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (86 bp):
TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACAG
TAACTGCAAATATGTGGCTCA
Found at i:40710159 original size:26 final size:24
Alignment explanation
Indices: 40710076--40710165 Score: 85
Period size: 26 Copynumber: 3.6 Consensus size: 24
40710066 TCGAGCCATG
**
40710076 ATCGGTAAGCTCATTCTGAGCTGAA
1 ATCGGTAAGCTCA-TAAGAGCTGAA
*
40710101 GAACGGTAAGCTCTATAA-AGCTGAA
1 -ATCGGTAAGCTC-ATAAGAGCTGAA
40710126 AT-GGTAAGCTCATAAGAGCTGATA
1 ATCGGTAAGCTCATAAGAGCTGA-A
*
40710150 TATCGGTAAGCACATA
1 -ATCGGTAAGCTCATA
40710166 CGGGTTGTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
22 4 0.07
23 15 0.28
24 2 0.04
25 9 0.17
26 23 0.43
27 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (24 bp):
ATCGGTAAGCTCATAAGAGCTGAA
Found at i:40712100 original size:25 final size:26
Alignment explanation
Indices: 40712053--40712102 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
40712043 AAGAATAAAT
40712053 AAATTAACTAAGTTTTCAAAAATAGC
1 AAATTAACTAAGTTTTCAAAAATAGC
40712079 AAATTAACTAAG-TTTCAAAAATAG
1 AAATTAACTAAGTTTTCAAAAATAG
40712103 TTATCATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (26 bp):
AAATTAACTAAGTTTTCAAAAATAGC
Found at i:40713494 original size:29 final size:30
Alignment explanation
Indices: 40713448--40713506 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
40713438 TTTGGTCAAA
*
40713448 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
* *
40713477 TGTGCAATTTTATTCATGAAATTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
40713507 GATCCTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTTTATACATGAAACTTTGATTT
Found at i:40719980 original size:16 final size:17
Alignment explanation
Indices: 40719948--40719981 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40719938 CAATTCAGTC
40719948 CAAAATTCATACTTTTG
1 CAAAATTCATACTTTTG
*
40719965 CAAAATT-ATGCTTTTG
1 CAAAATTCATACTTTTG
40719981 C
1 C
40719982 CTCTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
CAAAATTCATACTTTTG
Found at i:40723119 original size:40 final size:41
Alignment explanation
Indices: 40723057--40723173 Score: 116
Period size: 40 Copynumber: 2.9 Consensus size: 41
40723047 GTTTGGAACA
* * *
40723057 AAAGCGCCAC-AACAAATCGAGCATTAGCGGCGATTTA-GCC
1 AAAGCGCCGCTAA-AAATAGAGCATTAGCGGCGATTTATCCC
** *
40723097 AAAGCGCCGCTAAAGGTAGAGCATCAGCGGCGA-TTATCCC
1 AAAGCGCCGCTAAAAATAGAGCATTAGCGGCGATTTATCCC
* * *
40723137 GAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTAT
1 AAAGCGCCGCTAAAAATAGAGCATTAGCGGCGATTTAT
40723174 ATAAAGCGCC
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
39 13 0.21
40 47 0.76
41 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (41 bp):
AAAGCGCCGCTAAAAATAGAGCATTAGCGGCGATTTATCCC
Found at i:40723289 original size:41 final size:41
Alignment explanation
Indices: 40723231--40723511 Score: 246
Period size: 41 Copynumber: 6.8 Consensus size: 41
40723221 TTTTTTAAAC
*
40723231 CTTTAGCAGCGTTTTTGTCTATGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTCGGAT
* *
40723272 ATTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTCGGAT
* * * *
40723313 CTTTAGCGGCATTTTTTTTCTATGCGCCGCTAATGCTTGGGGT
1 CTTTAGCGGC-GTTTTTGTCTATGCGCCGCTAATGC-TCGGAT
* * *
40723356 CTTTAGCGGCGTTTTTATAC-AAGCGCCGCCAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGT-CTATGCGCCGCTAATGCTCGGAT
* ** * * *
40723397 CTTTAGCGGCGTTTCTAACTGA-GCGCCACTAATTCTCTTG-T
1 CTTTAGCGGCGTTTTTGTCT-ATGCGCCGCTAATGCTC-GGAT
* * * * ** *
40723438 CTTCAGCGGCGTTTGTATCTAAGCGCCGCTAATG-TATTGAC
1 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCT-CGGAT
* * *
40723479 CTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAAT
40723512 AGTAACAAAT
Statistics
Matches: 200, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
40 5 0.03
41 135 0.68
42 44 0.22
43 16 0.08
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.35
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTCGGAT
Found at i:40723382 original size:84 final size:83
Alignment explanation
Indices: 40723242--40723406 Score: 233
Period size: 84 Copynumber: 2.0 Consensus size: 83
40723232 TTTAGCAGCG
* * *
40723242 TTTTTGTCTATGCGCCGCTAATGCTCGGATATTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGC
1 TTTTTGTCTATGCGCCGCTAATGCTCGGATATTTAGCGGCGTTTTTATCTAAGCGCCGCCAATGC
*
40723307 TCGGGTCTTTAGCGGCAT
66 TCGGATCTTTAGCGGCAT
* * * *
40723325 TTTTTTTCTATGCGCCGCTAATGCTTGGGGTCTTTAGCGGCGTTTTTATAC-AAGCGCCGCCAAT
1 TTTTTGTCTATGCGCCGCTAATGC-TCGGATATTTAGCGGCGTTTTTAT-CTAAGCGCCGCCAAT
40723389 GCTCGGATCTTTAGCGGC
64 GCTCGGATCTTTAGCGGC
40723407 GTTTCTAACT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
83 23 0.32
84 48 0.67
85 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (83 bp):
TTTTTGTCTATGCGCCGCTAATGCTCGGATATTTAGCGGCGTTTTTATCTAAGCGCCGCCAATGC
TCGGATCTTTAGCGGCAT
Found at i:40728062 original size:43 final size:43
Alignment explanation
Indices: 40728025--40728233 Score: 307
Period size: 43 Copynumber: 4.9 Consensus size: 43
40728015 AGACTAATAC
*
40728025 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACTGGGGT
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACTAGGGT
*
40728068 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGA-TCAGGGT
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACT-AGGGT
* * *
40728111 CTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGT
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACTAGGGT
40728154 CTTTAGCGGCGTTTTTAGT-TAAAGCGCCGCTATAGA-TCAGGGT
1 CTTTAGCGGCGTTTTTAGTAT-AAGCGCCGCTATAGACT-AGGGT
* *
40728197 CTTTAGTGGCGTTTTTAGTATAAGCGCCGCTAAAGAC
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGAC
40728234 CCCAGTCTAT
Statistics
Matches: 149, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
42 3 0.02
43 144 0.97
44 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACTAGGGT
Found at i:40728247 original size:86 final size:86
Alignment explanation
Indices: 40728025--40728446 Score: 385
Period size: 86 Copynumber: 4.9 Consensus size: 86
40728015 AGACTAATAC
* **** * * ** *
40728025 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTATAGACTGGGGTCTTTAGCGGCGTTTTTAGTAAA
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
* * * * *
40728090 AGCGCCGCTATAGATCAGGGT
66 AACGCCACTAAAGACCAGGAT
* * * **** * * ** * *
40728111 CTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGTCTTTAGCGGCGTTTTTAGTTAA
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
* * * * *
40728176 AGCGCCGCTATAGATCAGGGT
66 AACGCCACTAAAGACCAGGAT
*
40728197 CTTTAGTGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
**
40728262 AACGCCACTAAAGACCCTGAT
66 AACGCCACTAAAGACCAGGAT
* * * * * *
40728283 CTATAGCGGCGCTTTAACTAAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
**
40728348 AACGCCACTAAAGACCCTGAT
66 AACGCCACTAAAGACCAGGAT
* * * * * *
40728369 CTATAGCGGCGCTTTTACTAAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTTATACTAAA
1 CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
*
40728434 AACGCCGCTAAAG
66 AACGCCACTAAAG
40728447 GTATTAGTCT
Statistics
Matches: 304, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 304 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGTTTTTAGTATAAGCGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAA
AACGCCACTAAAGACCAGGAT
Found at i:40728290 original size:129 final size:126
Alignment explanation
Indices: 40728028--40728422 Score: 335
Period size: 129 Copynumber: 3.1 Consensus size: 126
40728018 CTAATACCTT
*
40728028 TAGCGGCGTTTTTAG-TATAAGCGCCGCTATAGACTGGGGTCTTTAGCGGCGTTTTTAGTAAAAG
1 TAGCGGCGTTTTTAGTTA-AAGCGCCGCTATAGAC-AGGGTCTTTAGCGGCGTTTTTAGTAAAAG
* * * * * * ** * * ** *
40728092 CGCCGCTATAGA-TCAGGGTCTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGTCT
64 CGCCGCTAAAGACCCA--GTCTATAGCGGCGCTTTTACTAAAAACGCCGCTAAAGAC-CCGATCT
*
40728156 T
126 A
* *
40728157 TAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATAAGC
1 TAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGA-CAGGGTCTTTAGCGGCGTTTTTAGTAAAAGC
** *
40728222 GCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGATCTA
65 GCCGCTAAAGA-CCCAGTCTATAGCGGCGCTTTTACTAAAAACGCCGCTAAAGACCC-GATCTA
* * * * * * *** * * ** * *
40728286 TAGCGGCGCTTTAACTAAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAAC
1 TAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGA-CAGGGTCTTTAGCGGCGTTTTTAGTAAAAGC
* * *
40728351 GCCACTAAAGACCCTGATCTATAGCGGCGCTTTTACTAAAAACGCCGCTAAAGACCCCAGTCTA
65 GCCGCTAAAGACCCAG-TCTATAGCGGCGCTTTTACTAAAAACGCCGCTAAAGACCCGA-TCTA
40728415 TAGCGGCG
1 TAGCGGCG
40728423 CTTATACTAA
Statistics
Matches: 215, Mismatches: 44, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
128 5 0.02
129 205 0.95
130 3 0.01
131 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (126 bp):
TAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGACAGGGTCTTTAGCGGCGTTTTTAGTAAAAGCG
CCGCTAAAGACCCAGTCTATAGCGGCGCTTTTACTAAAAACGCCGCTAAAGACCCGATCTA
Found at i:40728456 original size:43 final size:43
Alignment explanation
Indices: 40728221--40728446 Score: 332
Period size: 43 Copynumber: 5.3 Consensus size: 43
40728211 TTAGTATAAG
* *
40728221 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAA
1 CGCCGCTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
*
40728264 CGCCACTAAAGACCCT-GATCTATAGCGGCGCTT-TAACTAAAAA
1 CGCCGCTAAAGACCCTAG-TCTATAGCGGCGCTTAT-ACTAAAAA
* *
40728307 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAA
1 CGCCGCTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
* *
40728350 CGCCACTAAAGACCCT-GATCTATAGCGGCGCTTTTACTAAAAA
1 CGCCGCTAAAGACCCTAG-TCTATAGCGGCGCTTATACTAAAAA
*
40728393 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTTATACTAAAAA
1 CGCCGCTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
40728436 CGCCGCTAAAG
1 CGCCGCTAAAG
40728447 GTATTAGTCT
Statistics
Matches: 164, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
42 3 0.02
43 158 0.96
44 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.19
Consensus pattern (43 bp):
CGCCGCTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
Found at i:40728463 original size:43 final size:43
Alignment explanation
Indices: 40728221--40728488 Score: 321
Period size: 43 Copynumber: 6.3 Consensus size: 43
40728211 TTAGTATAAG
* * *
40728221 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAA
1 CGCCACTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
40728264 CGCCACTAAAGACCCT-GATCTATAGCGGCGCTT-TAACTAAAAA
1 CGCCACTAAAGACCCTAG-TCTATAGCGGCGCTTAT-ACTAAAAA
* * *
40728307 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAA
1 CGCCACTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
*
40728350 CGCCACTAAAGACCCT-GATCTATAGCGGCGCTTTTACTAAAAA
1 CGCCACTAAAGACCCTAG-TCTATAGCGGCGCTTATACTAAAAA
* *
40728393 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTTATACTAAAAA
1 CGCCACTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
* **** * *
40728436 CGCCGCTAAAGGTATTAGTCT-TCAGCGGCGCTTCTACT-AAAG
1 CGCCACTAAAGACCCTAGTCTAT-AGCGGCGCTTATACTAAAAA
40728478 CGCCACTAAAG
1 CGCCACTAAAG
40728489 CTCTTACTCT
Statistics
Matches: 197, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
42 17 0.09
43 177 0.90
44 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
CGCCACTAAAGACCCTAGTCTATAGCGGCGCTTATACTAAAAA
Found at i:40728468 original size:86 final size:86
Alignment explanation
Indices: 40728221--40728446 Score: 425
Period size: 86 Copynumber: 2.6 Consensus size: 86
40728211 TTAGTATAAG
40728221 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGATCTA
1 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGATCTA
*
40728286 TAGCGGCGCTTTAACTAAAAA
66 TAGCGGCGCTTTTACTAAAAA
40728307 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGATCTA
1 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGATCTA
40728372 TAGCGGCGCTTTTACTAAAAA
66 TAGCGGCGCTTTTACTAAAAA
* *
40728393 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTTATACTAAAAACGCCGCTAAAG
1 CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAG
40728447 GTATTAGTCT
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 137 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.19
Consensus pattern (86 bp):
CGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGATCTA
TAGCGGCGCTTTTACTAAAAA
Found at i:40728677 original size:22 final size:21
Alignment explanation
Indices: 40728644--40728688 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
40728634 TTCTGCGGCG
*
40728644 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
40728665 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
40728687 CT
1 CT
40728689 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:40729695 original size:27 final size:28
Alignment explanation
Indices: 40729642--40729701 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
40729632 CTTGGGAAAG
*
40729642 AAAAAATCATTTAAATACCACTTATGATA
1 AAAAAATCATTTAAATACCACTCATGA-A
*
40729671 AAAAAAT-ATTTAAGTACCAC-CATGAA
1 AAAAAATCATTTAAATACCACTCATGAA
40729697 AAAAA
1 AAAAA
40729702 GTTTATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 4 0.14
28 12 0.41
29 7 0.24
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAAAATCATTTAAATACCACTCATGAA
Found at i:40734312 original size:30 final size:30
Alignment explanation
Indices: 40734278--40734379 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
40734268 AAGTAGGATC
40734278 ACACGACCGTGTAACTCTCTGACTTGCCAT
1 ACACGACCGTGTAACTCTCTGACTTGCCAT
* * *
40734308 ACACGGCCGTATAACTCTCTGACTTACCAT
1 ACACGACCGTGTAACTCTCTGACTTGCCAT
* * *
40734338 ACACGGCTGTGTAACTCTCTGACTTGCTAT
1 ACACGACCGTGTAACTCTCTGACTTGCCAT
40734368 ACAC-AGCCGTGT
1 ACACGA-CCGTGT
40734380 CGCAGGCCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (30 bp):
ACACGACCGTGTAACTCTCTGACTTGCCAT
Found at i:40734405 original size:42 final size:42
Alignment explanation
Indices: 40734346--40734433 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
40734336 ATACACGGCT
* * *
40734346 GTGTAACTCTCTGACTTGCTATACACAGCCGTGTCGCAGGCC
1 GTGTAACTCTCTAACTTGCCACACACAGCCGTGTCGCAGGCC
*
40734388 GTGTAACTCTCTAACTTGCCACACACAGCCGTGTGGCAGGCC
1 GTGTAACTCTCTAACTTGCCACACACAGCCGTGTCGCAGGCC
40734430 GTGT
1 GTGT
40734434 GCTAGGCCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (42 bp):
GTGTAACTCTCTAACTTGCCACACACAGCCGTGTCGCAGGCC
Found at i:40737147 original size:37 final size:37
Alignment explanation
Indices: 40737089--40737159 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
40737079 ACTACATGTG
* *
40737089 AGCTGGGAACAGAAAGGTTGCGAACTGATGGAGTGCA
1 AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGTGCA
* * *
40737126 AGCTGCGAACAGAGAGCTTGCGCACTGGTGGAGT
1 AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGT
40737160 ACGAGTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.38, T:0.17
Consensus pattern (37 bp):
AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGTGCA
Found at i:40739034 original size:21 final size:22
Alignment explanation
Indices: 40739005--40739095 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 22
40738995 CTTCTCTCTC
40739005 AAAA-AATTTC-ATTATATAAT
1 AAAATAATTTCAATTATATAAT
* * *
40739025 AAAATAATTT-TATTTTAAAAT
1 AAAATAATTTCAATTATATAAT
*
40739046 AAGATAATTTCAATTTAATATAAT
1 AAAATAATTTCAA-TT-ATATAAT
* *
40739070 -TAATAAGTTTACTATTATATAAT
1 AAAATAA-TTT-CAATTATATAAT
40739093 AAA
1 AAA
40739096 TTGTTAAACG
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.08
21 22 0.42
22 1 0.02
23 13 0.25
24 11 0.21
25 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATAATTTCAATTATATAAT
Found at i:40739836 original size:2 final size:2
Alignment explanation
Indices: 40739831--40739861 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40739821 TTTCCTCTCT
40739831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40739862 TCCCCAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40745189 original size:12 final size:12
Alignment explanation
Indices: 40745172--40745204 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40745162 AAATCGGCAG
40745172 AAAAAGAGAAAA-
1 AAAAAGA-AAAAC
40745184 AAAAAGAAAAAC
1 AAAAAGAAAAAC
40745196 AAAAAGAAA
1 AAAAAGAAA
40745205 TAGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:40746467 original size:21 final size:21
Alignment explanation
Indices: 40746441--40746510 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
40746431 TTAATATACT
40746441 ATTATTATATGTATGTACATA
1 ATTATTATATGTATGTACATA
* ** *
40746462 ATTATTTTAAT-TACCCTCCACT-
1 ATTATTAT-ATGTA-TGTACA-TA
40746484 ATTATTATATGTATGTACATA
1 ATTATTATATGTATGTACATA
40746505 ATTATT
1 ATTATT
40746511 TTAATTACCC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 20 0.56
22 14 0.39
23 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTATTATATGTATGTACATA
Found at i:40746499 original size:43 final size:43
Alignment explanation
Indices: 40746438--40746537 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
40746428 TTTTTAATAT
40746438 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
40746481 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
* *
40746524 TCTATATTTTATAT
1 ACTAT-TATTATAT
40746538 ATTTTAACTT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 47 0.87
44 7 0.13
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (43 bp):
ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
Found at i:40751765 original size:30 final size:30
Alignment explanation
Indices: 40751729--40751788 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40751719 CTCGAGAAGA
40751729 AAGGAAAATGAAGTAAACAACGTGAATACG
1 AAGGAAAATGAAGTAAACAACGTGAATACG
40751759 AAGGAAAATGAAGTAAACAACGTGAATACG
1 AAGGAAAATGAAGTAAACAACGTGAATACG
40751789 TATAACAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13
Consensus pattern (30 bp):
AAGGAAAATGAAGTAAACAACGTGAATACG
Found at i:40758979 original size:44 final size:44
Alignment explanation
Indices: 40758924--40759245 Score: 156
Period size: 44 Copynumber: 7.3 Consensus size: 44
40758914 CAGTAAGGAT
* *
40758924 AGCAGATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* ** ** * *
40758968 GGCAAATCTTATCT-TTTCAAG-A-TAGTGGGAAGCAGATTTAGGCC
1 AGCAAATCTTATCTCCCT-AAGCAGTAGT-GG-AGCAGATCAAAGAC
* * * * * * * * ** **
40759012 ACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGGT
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
*
40759056 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * ** *
40759100 GGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCC
1 AGCAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGAC
** * * * * * * * *
40759144 TCCGAGTCTTGTCTCCCTGAGCAGCT-GCGGAGTAGGTTC-AAGAT
1 AGCAAATCTTATCTCCCTAAGCAG-TAGTGGAGCA-GATCAAAGAC
*
40759188 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
40759232 GGTAAATCTTATCT
1 AGCAAATCTTATCT
40759246 TTCTAGGATA
Statistics
Matches: 192, Mismatches: 70, Indels: 32
0.65 0.24 0.11
Matches are distributed among these distances:
42 8 0.04
43 14 0.07
44 154 0.80
45 12 0.06
46 3 0.02
47 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
Found at i:40759160 original size:132 final size:132
Alignment explanation
Indices: 40758918--40759316 Score: 654
Period size: 132 Copynumber: 3.0 Consensus size: 132
40758908 ACAGATCAGT
*
40758918 AAGGATAGCAGATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTT
1 AAGG-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTT
* * * *
40758983 TTCAAGATAGTGGGAAGCAGATTTAGGCCACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
65 TCCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
40759048 TTG
130 TTG
40759051 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
1 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* * *
40759116 CCAAGATAGTGGGAAGCAGATTTAAGCCTCCGAGTCTTGTCTCCCTGAGCAGCTGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
*
40759181 TC
131 TG
* *
40759183 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTT
1 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* * * *
40759248 CTAGGATAGTGGGAAGCAGATTTAAGCCACAGAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
40759313 TG
131 TG
40759315 AA
1 AA
40759317 AATTAGAAGT
Statistics
Matches: 247, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
132 243 0.98
133 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (132 bp):
AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
TG
Found at i:40759997 original size:12 final size:12
Alignment explanation
Indices: 40759980--40760012 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40759970 AAATCGGCAG
40759980 AAAAAGAGAAAA-
1 AAAAAGA-AAAAC
40759992 AAAAAGAAAAAC
1 AAAAAGAAAAAC
40760004 AAAAAGAAA
1 AAAAAGAAA
40760013 TAGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:40761270 original size:21 final size:21
Alignment explanation
Indices: 40761244--40761313 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
40761234 TTAATATACT
40761244 ATTATTATATGTATGTACATA
1 ATTATTATATGTATGTACATA
* ** *
40761265 ATTATTTTAAT-TACCCTCCACT-
1 ATTATTAT-ATGTA-TGTACA-TA
40761287 ATTATTATATGTATGTACATA
1 ATTATTATATGTATGTACATA
40761308 ATTATT
1 ATTATT
40761314 TTAATTACCC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 20 0.56
22 14 0.39
23 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTATTATATGTATGTACATA
Found at i:40761302 original size:43 final size:43
Alignment explanation
Indices: 40761241--40761340 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
40761231 TTTTTAATAT
40761241 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
40761284 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
* *
40761327 TCTATATTTTATAT
1 ACTAT-TATTATAT
40761341 ATTTTAACTT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 47 0.87
44 7 0.13
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (43 bp):
ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
Found at i:40769204 original size:2 final size:2
Alignment explanation
Indices: 40769197--40769222 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40769187 CGTTAAAACA
40769197 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40769223 TCGAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40772266 original size:9 final size:9
Alignment explanation
Indices: 40772252--40772285 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
40772242 GTTTTCGAAG
*
40772252 TCGAATAAC
1 TCGAATAAT
40772261 TCGAATAAT
1 TCGAATAAT
40772270 TCGAATAAT
1 TCGAATAAT
40772279 TCGAATA
1 TCGAATA
40772286 TCAAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (9 bp):
TCGAATAAT
Found at i:40777971 original size:14 final size:14
Alignment explanation
Indices: 40777929--40777971 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
40777919 AAAATCGTCG
*
40777929 AATAAAATTGAAGAA
1 AATAAAATAGAA-AA
* *
40777944 AATAAAAAATAAAA
1 AATAAAATAGAAAA
40777958 AATAAAATAGAAAA
1 AATAAAATAGAAAA
40777972 TCCCCTTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
AATAAAATAGAAAA
Found at i:40778766 original size:44 final size:44
Alignment explanation
Indices: 40778717--40779098 Score: 163
Period size: 44 Copynumber: 8.2 Consensus size: 44
40778707 TAACTTTAGA
* * *
40778717 GAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* * * **
40778761 GAGATAGGATTAC-TAGCTTCAATCTGCTCTGCTGTAATCTCAGG
1 GAGATAAGA-TACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* *
40778805 GAGATAAGAT--TTCTGGCTTCAATATGATGCGATCTACTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-GCTTC---A--ATCCG--CT-C-C-ACTGTAATC-TCAGG
* ** *
40778859 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* * * * *
40778903 GAGATAGGATTAC-TAGCTTCAATCTGCT-TAGCTGTAATATCAGG
1 GAGATAAGA-TACTTTGCTTCAATCCGCTCCA-CTGTAATCTCAGG
*
40778947 GAGATAAGAT--TTCTGGCTTCAATCCGGTGCGATCTATTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-GCTTCAATCC---GC--TC----C-ACTGTAATC-TCAGG
* ** * *
40779001 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGA
1 GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* * * *
40779045 GAGATAGGATTAC-TAGCTTCAATCTGCTCCGCTGTAATCTCAGG
1 GAGATAAGA-TACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
40779089 GAGATAAGAT
1 GAGATAAGAT
40779099 TTCTGGCTTT
Statistics
Matches: 251, Mismatches: 48, Indels: 79
0.66 0.13 0.21
Matches are distributed among these distances:
42 2 0.01
43 4 0.02
44 156 0.62
45 10 0.04
46 1 0.00
47 5 0.02
49 10 0.04
51 5 0.02
52 1 0.00
53 1 0.00
54 49 0.20
55 3 0.01
56 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
Found at i:40778847 original size:142 final size:142
Alignment explanation
Indices: 40778678--40779198 Score: 900
Period size: 142 Copynumber: 3.7 Consensus size: 142
40778668 TGCTGTTGTA
* *
40778678 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTGTTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
40778743 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAG
40778808 ATAAGATTTCTG
131 ATAAGATTTCTG
*
40778820 GCTTCAATATGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
*
40778885 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT-TAGCTGTAATATCAGGGA
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCT-GCTGTAATCTCAGGGA
40778949 GATAAGATTTCTG
130 GATAAGATTTCTG
* * *
40778962 GCTTCAATCCGGTGCGATCTATTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
* *
40779027 CTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAG
40779092 ATAAGATTTCTG
131 ATAAGATTTCTG
* * * *
40779104 GCTTTAATCTGATGCAATCTACTCTACTATAACTTTAGAGAGATAAGATCCTTTTATTTTAATCC
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC-TTTATTTTAATCC
40779169 GCTCCACTGTAATCTCAGGGAGATAGGATT
65 GCTCCACTGTAATCTCAGGGAGATAGGATT
40779199 TCTTCTATCT
Statistics
Matches: 357, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
141 1 0.00
142 314 0.88
143 42 0.12
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (142 bp):
GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAG
ATAAGATTTCTG
Found at i:40779113 original size:44 final size:44
Alignment explanation
Indices: 40779018--40779114 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
40779008 GATCCTTTAT
* *
40779018 TTTAATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGC
1 TTTAATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGC
* * * * *
40779062 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGC
1 TTTAATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGC
40779106 TTTAATCTG
1 TTTAATCTG
40779115 ATGCAATCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGC
Found at i:40793315 original size:30 final size:30
Alignment explanation
Indices: 40793281--40793344 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
40793271 TGGTTTTTGG
* *
40793281 GTTTAGGCT-AGCTAGGTTTGGGTTAAAGCT
1 GTTTAGGCTAATC-AGGTTTGAGTTAAAGCT
*
40793311 GTTTAGGCTAATCGGGTTTGAGTTAAAGCT
1 GTTTAGGCTAATCAGGTTTGAGTTAAAGCT
40793341 GTTT
1 GTTT
40793345 TTTTTTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.39
Consensus pattern (30 bp):
GTTTAGGCTAATCAGGTTTGAGTTAAAGCT
Found at i:40808885 original size:85 final size:85
Alignment explanation
Indices: 40808742--40808911 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
40808732 TCACTTTTGG
40808742 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
1 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
*
40808807 AGAGCCAAAGTGAGATTTTA
66 AGAGCCAAACTGAGATTTTA
*
40808827 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCTAGAAA
1 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
*
40808892 ATAGCCAAACTGAGATTTTA
66 AGAGCCAAACTGAGATTTTA
40808912 ATTACTCATG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.33
Consensus pattern (85 bp):
GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCGAGAAA
AGAGCCAAACTGAGATTTTA
Found at i:40814552 original size:16 final size:16
Alignment explanation
Indices: 40814513--40814552 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
40814503 TCTTCAACTG
*
40814513 AAGAAAGAATATGCCT
1 AAGAAAGAATACGCCT
*
40814529 AATAAAGAATACGCCT
1 AAGAAAGAATACGCCT
*
40814545 AAGGAAGA
1 AAGAAAGA
40814553 GTATGCCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (16 bp):
AAGAAAGAATACGCCT
Found at i:40815848 original size:25 final size:25
Alignment explanation
Indices: 40815805--40815858 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40815795 TTGTAGCGAG
* **
40815805 TTATTTGTAAGGCTTTTATGAAAAA
1 TTATTTGTAAAGCCCTTATGAAAAA
**
40815830 TTATTTGTAAAGCCCTTATGGTAAA
1 TTATTTGTAAAGCCCTTATGAAAAA
40815855 TTAT
1 TTAT
40815859 CTAAAAGGCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (25 bp):
TTATTTGTAAAGCCCTTATGAAAAA
Found at i:40819251 original size:23 final size:22
Alignment explanation
Indices: 40819208--40819251 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
40819198 TTCTAAGTTG
40819208 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
40819231 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
40819252 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:40819368 original size:45 final size:45
Alignment explanation
Indices: 40819299--40819384 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
40819289 AGATACTCAT
* *
40819299 TGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCAG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCAG
**
40819344 TGGAATCAGCACATATTAACCACCTTACTAATCAATGATGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
40819385 TCGGTTCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCAG
Found at i:40823066 original size:39 final size:39
Alignment explanation
Indices: 40823012--40823092 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
40823002 GAAAATAAGA
*
40823012 CGAATAACACGAGTAAGATTTTATAAAGTTTAGTAAGTT
1 CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
*
40823051 CGAATAACACGAGTAAGCTTTTATAAAGCTTAGTAAGTT
1 CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
40823090 CGA
1 CGA
40823093 TGATTAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (39 bp):
CGAATAACACGAGTAAGATTTTATAAAGCTTAGTAAGTT
Found at i:40825285 original size:23 final size:24
Alignment explanation
Indices: 40825245--40825291 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
40825235 TGATTCTGTG
40825245 ATGGGCTAAAGCCCTACTGCATAT
1 ATGGGCTAAAGCCCTACTGCATAT
*
40825269 ATGGGCT-ACGCCCTACTGCATAT
1 ATGGGCTAAAGCCCTACTGCATAT
40825292 TTGATACTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (24 bp):
ATGGGCTAAAGCCCTACTGCATAT
Found at i:40830417 original size:22 final size:22
Alignment explanation
Indices: 40830373--40830417 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40830363 TTAAGTGACT
* *
40830373 AAAATTGGTTTTTGGATGGTCG
1 AAAATAGGTTTTTGGATGCTCG
40830395 AAAATAGG-TTTTGGAGTGCTCG
1 AAAATAGGTTTTTGGA-TGCTCG
40830417 A
1 A
40830418 GGATCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.36
Consensus pattern (22 bp):
AAAATAGGTTTTTGGATGCTCG
Found at i:40831756 original size:40 final size:41
Alignment explanation
Indices: 40831668--40831848 Score: 231
Period size: 41 Copynumber: 4.5 Consensus size: 41
40831658 CAAACTGATT
* * * *
40831668 CTGTGATGGGCTAAGGCCCTACTGCGTATTTGAAACTAATT
1 CTGTGATGGGCTAAGACCCTACTGCATATTTGATACTAATA
* * * * *
40831709 CTATGATGGGCTAAGGCCTTA-TGGATATTTGATACTGATA
1 CTGTGATGGGCTAAGACCCTACTGCATATTTGATACTAATA
*
40831749 CTGTGATGGGCTAAGACCCTACTGCAGATTTGATACTAATA
1 CTGTGATGGGCTAAGACCCTACTGCATATTTGATACTAATA
* *
40831790 CTATGATGGGCTAAGACCCTACTACATATTTGATACT-ATA
1 CTGTGATGGGCTAAGACCCTACTGCATATTTGATACTAATA
*
40831830 CTGAGATGGGCTAAGACCC
1 CTGTGATGGGCTAAGACCC
40831849 AAATTGTTAC
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 52 0.43
41 69 0.57
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (41 bp):
CTGTGATGGGCTAAGACCCTACTGCATATTTGATACTAATA
Found at i:40831796 original size:81 final size:82
Alignment explanation
Indices: 40831661--40831848 Score: 265
Period size: 81 Copynumber: 2.3 Consensus size: 82
40831651 TAAGGCCCAA
* * * *
40831661 ACTGATTCTGTGATGGGCTAAGGCCCTACTGCGTATTTGAAACTAATTCTATGATGGGCTAAGGC
1 ACTGATACTGTGATGGGCTAAGACCCTACTGCGTATTTGAAACTAATACTATGATGGGCTAAGAC
* **
40831726 CTTA-TGGATATTTGAT
66 CCTACTACATATTTGAT
*
40831742 ACTGATACTGTGATGGGCTAAGACCCTACTGCAG-ATTTGATACTAATACTATGATGGGCTAAGA
1 ACTGATACTGTGATGGGCTAAGACCCTACTGC-GTATTTGAAACTAATACTATGATGGGCTAAGA
40831806 CCCTACTACATATTTGAT
65 CCCTACTACATATTTGAT
*
40831824 ACT-ATACTGAGATGGGCTAAGACCC
1 ACTGATACTGTGATGGGCTAAGACCC
40831849 AAATTGTTAC
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
81 82 0.85
82 14 0.15
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (82 bp):
ACTGATACTGTGATGGGCTAAGACCCTACTGCGTATTTGAAACTAATACTATGATGGGCTAAGAC
CCTACTACATATTTGAT
Found at i:40839476 original size:23 final size:23
Alignment explanation
Indices: 40839449--40839582 Score: 159
Period size: 23 Copynumber: 6.0 Consensus size: 23
40839439 GCTATGCCGA
*
40839449 TCAGGAACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
40839472 TCAGGCACTTTATGTGTCATATT
1 TCAGGCACTTTATGTGTCGTATT
* **
40839495 TCAGGCACCTCGTGTGTCGTATAT
1 TCAGGCACTTTATGTGTCGTAT-T
40839519 T-AGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
40839541 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATT
40839562 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
40839583 ACTGATCAGG
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.11
21 8 0.09
22 2 0.02
23 72 0.77
24 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:40839511 original size:46 final size:46
Alignment explanation
Indices: 40839461--40839578 Score: 190
Period size: 46 Copynumber: 2.6 Consensus size: 46
40839451 AGGAACTTTA
40839461 TGTGTCGTATTTCAGGCACTTTATGTGTCATATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACTTTATGTGTCATATTTCAGGCACCTCG
*
40839507 TGTGTCGTATATT-AGGCACTTTATGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTAT-TTCAGGCACTTTATGTGTCATATTTCAGGCACCTCG
40839553 TGTGTCGTA--TCAGGCAC-TTATGTGTC
1 TGTGTCGTATTTCAGGCACTTTATGTGTC
40839579 GTATACTGAT
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
43 10 0.14
44 6 0.09
46 51 0.74
47 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (46 bp):
TGTGTCGTATTTCAGGCACTTTATGTGTCATATTTCAGGCACCTCG
Found at i:40840418 original size:47 final size:48
Alignment explanation
Indices: 40840305--40840425 Score: 138
Period size: 47 Copynumber: 2.6 Consensus size: 48
40840295 ATTGACGGAA
* * * * *
40840305 AAGACCATGGTTGGACCATGGCAAC-ATGTGATATGTGATTTCTGTAT
1 AAGACCATAGTTGGACTATGGCATCGATGTGATATGTGACTACTGTAT
* * * *
40840352 AAGACCATAGCTGGGCTATGGCATCGGTGTGATATGTG-CTACTGTGT
1 AAGACCATAGTTGGACTATGGCATCGATGTGATATGTGACTACTGTAT
*
40840399 AAGACCATAGTTGGACTATGACATCGA
1 AAGACCATAGTTGGACTATGGCATCGA
40840426 GAAAACGAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 49 0.82
48 11 0.18
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (48 bp):
AAGACCATAGTTGGACTATGGCATCGATGTGATATGTGACTACTGTAT
Found at i:40843173 original size:23 final size:22
Alignment explanation
Indices: 40843147--40843192 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
40843137 GAAATTAATT
40843147 TGAATTG-TGAACATGAGAAATGA
1 TGAATTGATGAA-ATG-GAAATGA
40843170 TGAATTGAATGAAATGGAAATGA
1 TGAATTG-ATGAAATGGAAATGA
40843193 AGCATTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 14 0.67
24 3 0.14
25 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.26
Consensus pattern (22 bp):
TGAATTGATGAAATGGAAATGA
Done.