Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 28 of 218
Found at i:9016313 original size:66 final size:66
Alignment explanation
Indices: 9016151--9016320 Score: 191
Period size: 66 Copynumber: 2.6 Consensus size: 66
9016141 CTTGCTGCTG
* * * * * *
9016151 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATACTTTCGTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TAGCTGGAGTTCTTCATACTTTCGTTG
9016215 AA
65 AA
* * * *
9016217 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATA-CTTTCGTTG
9016281 AA
65 AA
* * *
9016283 TCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
9016321 GTAATTTGGT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 85 0.94
67 4 0.04
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATACTTTCGTTGA
A
Found at i:9021726 original size:9 final size:9
Alignment explanation
Indices: 9021690--9021990 Score: 107
Period size: 9 Copynumber: 36.0 Consensus size: 9
9021680 AATTGCACGG
9021690 GTAAGTTAT
1 GTAAGTTAT
*
9021699 GT-A-TTGT
1 GTAAGTTAT
*
9021706 GTAAGCTAT
1 GTAAGTTAT
*
9021715 GTAAGTTGT
1 GTAAGTTAT
9021724 GT-A-TTAT
1 GTAAGTTAT
9021731 GTAAGTTAT
1 GTAAGTTAT
9021740 -T-A-TTAT
1 GTAAGTTAT
9021746 GCTTTAAGTTAT
1 G---TAAGTTAT
*
9021758 GTAAGTAAT
1 GTAAGTTAT
9021767 GT-A-TTAT
1 GTAAGTTAT
*
9021774 GTAAGTTGT
1 GTAAGTTAT
*
9021783 GT-A-TAAT
1 GTAAGTTAT
*
9021790 GTTAGTTAT
1 GTAAGTTAT
**
9021799 CAAAGTTAT
1 GTAAGTTAT
9021808 GT-A-TTAT
1 GTAAGTTAT
9021815 GTAAGTTAT
1 GTAAGTTAT
*
9021824 TTAAGTTAT
1 GTAAGTTAT
*
9021833 GTAA--CAT
1 GTAAGTTAT
*
9021840 GTAAATTAT
1 GTAAGTTAT
*
9021849 GTAAGTTGT
1 GTAAGTTAT
*
9021858 GT-A-TAAT
1 GTAAGTTAT
*
9021865 GTTAGTTAT
1 GTAAGTTAT
** *
9021874 CAAAGTAAT
1 GTAAGTTAT
9021883 GT-A-TTAT
1 GTAAGTTAT
*
9021890 GTAAGTTGT
1 GTAAGTTAT
*
9021899 GT-A-TAAT
1 GTAAGTTAT
*
9021906 GTTAGTTAT
1 GTAAGTTAT
**
9021915 CAAAGTTAT
1 GTAAGTTAT
*
9021924 GT-A-TTTT
1 GTAAGTTAT
***
9021931 GTGTTTCTAT
1 GTAAGT-TAT
*
9021941 TTAAGTTAT
1 GTAAGTTAT
*
9021950 GTAAGTTGT
1 GTAAGTTAT
9021959 GT-A-TTAT
1 GTAAGTTAT
*
9021966 GTAAGTTGT
1 GTAAGTTAT
9021975 GT-A-TTAT
1 GTAAGTTAT
9021982 GTAAGTTAT
1 GTAAGTTAT
9021991 TAAAAATTGA
Statistics
Matches: 207, Mismatches: 54, Indels: 62
0.64 0.17 0.19
Matches are distributed among these distances:
6 4 0.02
7 60 0.29
8 22 0.11
9 110 0.53
10 5 0.02
11 1 0.00
12 5 0.02
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:9021731 original size:16 final size:16
Alignment explanation
Indices: 9021712--9021990 Score: 86
Period size: 16 Copynumber: 17.8 Consensus size: 16
9021702 TTGTGTAAGC
*
9021712 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
9021728 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
*
9021743 TATGCT---TTAAG--T
1 TATG-TAAGTTATGTAT
*
9021755 TATGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
9021771 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
9021787 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
9021805 TATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
9021821 TATTTAAGTTATGTAA
1 TATGTAAGTTATGTAT
* *
9021837 CATGTAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
9021855 TGTGT-A-TAATGTTAGT
1 TATGTAAGTTATG-TA-T
** *
9021871 TATCAAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
9021887 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
9021903 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
* *
9021921 TATGT-A-TTTTGTGT
1 TATGTAAGTTATGTAT
* * *
9021935 T-TCT-ATTTAAG--T
1 TATGTAAGTTATGTAT
*
9021947 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
9021963 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
9021979 TATGTAAGTTAT
1 TATGTAAGTTAT
9021991 TAAAAATTGA
Statistics
Matches: 191, Mismatches: 48, Indels: 48
0.67 0.17 0.17
Matches are distributed among these distances:
11 1 0.01
12 7 0.04
13 8 0.04
14 12 0.06
15 7 0.04
16 120 0.63
17 12 0.06
18 24 0.13
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:9021798 original size:25 final size:25
Alignment explanation
Indices: 9021750--9021901 Score: 121
Period size: 25 Copynumber: 6.1 Consensus size: 25
9021740 TATTATGCTT
9021750 TAAGTTATGTAAGTAATG-TA-TTATG
1 TAAGTTATGT-A-TAATGTTAGTTATG
* *
9021775 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTTAGTTATG
* * * *
9021800 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATAATGTTAGTTATG
* *
9021825 TAAGTTATGTA-ACATGTAAATTATG
1 TAAGTTATGTATA-ATGTTAGTTATG
* *
9021850 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTTAGTTATG
* * * * *
9021875 AAAGTAATGTATTATGTAAGTTGTG
1 TAAGTTATGTATAATGTTAGTTATG
9021900 TA
1 TA
9021902 TAATGTTAGT
Statistics
Matches: 100, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
23 5 0.05
24 3 0.03
25 91 0.91
26 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (25 bp):
TAAGTTATGTATAATGTTAGTTATG
Found at i:9021810 original size:41 final size:41
Alignment explanation
Indices: 9021717--9021990 Score: 236
Period size: 41 Copynumber: 7.0 Consensus size: 41
9021707 TAAGCTATGT
* * * **
9021717 AAGTTGTGTATTATGTAAGTTAT-TATTATGCTTTAAGTTATGT
1 AAGTTATGTATTATGTAAGTTGTGTATAATG--TT-AGTTATCA
*
9021760 AAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
1 AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
* *
9021801 AAGTTATGTATTATGTAAGTTAT-T-TAA-GTTA-TGTAAC-
1 AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGT-TATCA
* *
9021838 ATG-TA--AATTATGTAAGTTGTGTATAATGTTAGTTATCA
1 AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
*
9021876 AAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
1 AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
* * * **
9021917 AAGTTATGTATTTTGT--GTT-TCTAT--T-TAAGTTATGT
1 AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
* * *
9021952 AAGTTGTGTATTATGTAAGTTGTGTATTATGTAAGTTAT
1 AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGTTAT
9021991 TAAAAATTGA
Statistics
Matches: 190, Mismatches: 25, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
34 13 0.07
35 22 0.12
36 6 0.03
37 13 0.07
38 18 0.09
39 7 0.04
40 2 0.01
41 81 0.43
42 2 0.01
43 20 0.11
44 6 0.03
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (41 bp):
AAGTTATGTATTATGTAAGTTGTGTATAATGTTAGTTATCA
Found at i:9021829 original size:75 final size:74
Alignment explanation
Indices: 9021748--9021896 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 74
9021738 ATTATTATGC
*
9021748 TTTAAGTTATGTAAGTAATGT-ATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTAT
1 TTTAAGTTATGTAA--AATGTAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTAATGTAT
9021812 TATGTAAGTTA
64 TATGTAAGTTA
*
9021823 TTTAAGTTATGTAACATGTAAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTAATGTATT
1 TTTAAGTTATGTAAAATGT-AATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTAATGTATT
9021888 ATGTAAGTT
65 ATGTAAGTT
9021897 GTGTATAATG
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
73 4 0.06
75 66 0.94
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (74 bp):
TTTAAGTTATGTAAAATGTAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTAATGTATTA
TGTAAGTTA
Found at i:9021977 original size:25 final size:25
Alignment explanation
Indices: 9021770--9021977 Score: 150
Period size: 25 Copynumber: 8.3 Consensus size: 25
9021760 AAGTAATGTA
* *
9021770 TTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTGTGTATTATGTAAG
** *
9021795 TTATCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* * ** *
9021820 TTATTTAAGTTATGTAACATGTAAA
1 TTATGTAAGTTGTGTATTATGTAAG
* *
9021845 TTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTGTGTATTATGTAAG
** **
9021870 TTATCAAAGTAATGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* * **
9021895 TTGTGTATA-ATGT-TAGTTATCAAAG
1 TTATGTA-AGTTGTGTA-TTATGTAAG
** * *
9021920 TTATGTATTTTGTGTTTCTATTTAAG
1 TTATGTAAGTTGTGTAT-TATGTAAG
9021946 TTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
*
9021971 TTGTGTA
1 TTATGTA
9021978 TTATGTAAGT
Statistics
Matches: 137, Mismatches: 41, Indels: 10
0.73 0.22 0.05
Matches are distributed among these distances:
24 2 0.01
25 113 0.82
26 22 0.16
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATTATGTAAG
Found at i:9022153 original size:121 final size:121
Alignment explanation
Indices: 9021993--9022270 Score: 495
Period size: 121 Copynumber: 2.3 Consensus size: 121
9021983 TAAGTTATTA
* *
9021993 AAAATTGAAATGTAGGATATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
*
9022058 AATATTTAAAAATAAAATTTACAATTATTTTTAAAATTATAAAATTCATTTG-TAAT
66 AATATTTAAAAATAAAATTTACAATTATTTTTAAAATTATAAAATTCA-TTGACAAT
9022114 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
* *
9022179 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTTATTGACAAT
66 AATATTTAAAAATAAAATTTACAATTATTTTTAAAATTATAAAATTCATTGACAAT
9022235 AAAATTGAAATATAGGTTATATATCCATACCATATA
1 AAAATTGAAATATAGGTTATATATCCATACCATATA
9022271 GCTAAATTTT
Statistics
Matches: 151, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 3 0.02
121 148 0.98
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (121 bp):
AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
AATATTTAAAAATAAAATTTACAATTATTTTTAAAATTATAAAATTCATTGACAAT
Found at i:9022322 original size:18 final size:18
Alignment explanation
Indices: 9022299--9022387 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
9022289 ATATATAAAG
9022299 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
9022317 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
**
9022339 TTTTTGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
9022356 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
9022374 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
9022388 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:9022382 original size:31 final size:31
Alignment explanation
Indices: 9022301--9022405 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
9022291 ATATAAAGTT
9022301 TAAGTAATGTAATATA--TT--TAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
* * *
9022328 TAAGT--TATAA-ATTTTTGTAAGTAA-TATATT
1 TAAGTAATGTAATATATTT-T-AGTAAGTA-ATG
9022358 TAAGTAATGTAATATATTTTAGTAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
9022389 TAAGTAATGTAATATAT
1 TAAGTAATGTAATATAT
9022406 ACTTTAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
24 2 0.03
25 4 0.07
26 1 0.02
27 6 0.10
29 2 0.03
30 10 0.16
31 24 0.39
32 7 0.11
33 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (31 bp):
TAAGTAATGTAATATATTTTAGTAAGTAATG
Found at i:9022462 original size:27 final size:27
Alignment explanation
Indices: 9022432--9022505 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
9022422 GTCATGTATT
*
9022432 TAAGTAATATATTTAA-TCCAATTCTAG
1 TAAGTAATATATTTAAGT-AAATTCTAG
* *
9022459 TAAGTAATGTATTTAAGTAAATTTTAG
1 TAAGTAATATATTTAAGTAAATTCTAG
*
9022486 TAATTAATATATTTAAGTAA
1 TAAGTAATATATTTAAGTAA
9022506 TGTAAGTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (27 bp):
TAAGTAATATATTTAAGTAAATTCTAG
Found at i:9022469 original size:40 final size:38
Alignment explanation
Indices: 9022344--9022478 Score: 116
Period size: 40 Copynumber: 3.6 Consensus size: 38
9022334 ATAAATTTTT
* * *
9022344 GTAAGTAATATATTTAAGT-A-ATGTAAT--ATATTTTA
1 GTAAGTAATGTATTTAAGTAATATATAATCCA-ATTCTA
** * ** *
9022379 GTAAGTAATGTAAGTAATGTAATATATACTTTAATTTTA
1 GTAAGTAATGTATTTAA-GTAATATATAATCCAATTCTA
*
9022418 GTAAGTCATGTATTTAAGTAATATATTTAATCCAATTCTA
1 GTAAGTAATGTATTTAAGTAATATA--TAATCCAATTCTA
9022458 GTAAGTAATGTATTTAAGTAA
1 GTAAGTAATGTATTTAAGTAA
9022479 ATTTTAGTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
35 14 0.17
36 2 0.03
37 1 0.01
38 13 0.16
39 20 0.25
40 30 0.38
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.43
Consensus pattern (38 bp):
GTAAGTAATGTATTTAAGTAATATATAATCCAATTCTA
Found at i:9026110 original size:7 final size:7
Alignment explanation
Indices: 9026098--9026198 Score: 55
Period size: 7 Copynumber: 14.0 Consensus size: 7
9026088 ATTAATTGAC
9026098 ACCCTAA
1 ACCCTAA
9026105 ACCCTAA
1 ACCCTAA
9026112 ATCCCT-A
1 A-CCCTAA
9026119 ACCCTTAA
1 ACCC-TAA
*
9026127 CCCCTAA
1 ACCCTAA
*
9026134 ATTCCTAA
1 A-CCCTAA
*
9026142 CCCCTAA
1 ACCCTAA
*
9026149 ATCC-ATA
1 ACCCTA-A
9026156 ACCACTAA
1 ACC-CTAA
*
9026164 CCCCTAA
1 ACCCTAA
*
9026171 CCCCTAA
1 ACCCTAA
*
9026178 ACCTTATA
1 ACCCTA-A
*
9026186 TCCC-AA
1 ACCCTAA
9026192 ACCCTAA
1 ACCCTAA
9026199 TAATCATATA
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
6 8 0.11
7 42 0.59
8 20 0.28
9 1 0.01
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.21
Consensus pattern (7 bp):
ACCCTAA
Found at i:9026119 original size:15 final size:15
Alignment explanation
Indices: 9026099--9026198 Score: 66
Period size: 14 Copynumber: 6.9 Consensus size: 15
9026089 TTAATTGACA
*
9026099 CCCTAAACCCTAAAT
1 CCCTAAACCCTAAAC
*
9026114 CCCT-AACCCTTAAC
1 CCCTAAACCCTAAAC
*
9026128 CCCTAAATTCCT-AAC
1 CCCTAAA-CCCTAAAC
*
9026143 CCCTAAATCC-ATAAC
1 CCCTAAACCCTA-AAC
* *
9026158 CACTAACCCCT-AAC
1 CCCTAAACCCTAAAC
* * *
9026172 CCCTAAACCTTATAT
1 CCCTAAACCCTAAAC
9026187 CCC-AAACCCTAA
1 CCCTAAACCCTAA
9026199 TAATCATATA
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
14 33 0.50
15 30 0.45
16 3 0.05
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAACCCTAAAC
Found at i:9026180 original size:22 final size:22
Alignment explanation
Indices: 9026099--9026178 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
9026089 TTAATTGACA
9026099 CCCTAAACCCTAAATCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
* * *
9026121 CCTTAACCCCTAAATTCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
*
9026143 CCCTAAATCC-ATAA-CCACTAAC
1 CCCTAAACCCTA-AATCC-CTAAC
*
9026165 CCCTAACCCCTAAA
1 CCCTAAACCCTAAA
9026179 CCTTATATCC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
21 2 0.04
22 43 0.93
23 1 0.02
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.20
Consensus pattern (22 bp):
CCCTAAACCCTAAATCCCTAAC
Found at i:9026880 original size:8 final size:8
Alignment explanation
Indices: 9026862--9026912 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
9026852 ATTAGAAAAA
9026862 TTATATTTT
1 TTAT-TTTT
9026871 TTATTTTT
1 TTATTTTT
9026879 TTATTTTT
1 TTATTTTT
9026887 TTATTTCATTT
1 TTA-TT--TTT
9026898 TTATTTTT
1 TTATTTTT
*
9026906 GTATTTT
1 TTATTTT
9026913 ATTTTTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 24 0.63
9 6 0.16
10 2 0.05
11 6 0.16
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (8 bp):
TTATTTTT
Found at i:9026898 original size:27 final size:27
Alignment explanation
Indices: 9026868--9026920 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
9026858 AAAATTATAT
*
9026868 TTTTTATTTTTTTATTTT-TTTATTTCA
1 TTTTTATTTTTGTATTTTATTT-TTTCA
9026895 TTTTTATTTTTGTATTTTATTTTTTC
1 TTTTTATTTTTGTATTTTATTTTTTC
9026921 TTATAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTTATTTTTGTATTTTATTTTTTCA
Found at i:9026900 original size:19 final size:19
Alignment explanation
Indices: 9026876--9026918 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
9026866 ATTTTTTATT
*
9026876 TTTTTATTTTTTTATTTCA
1 TTTTTATTTTTGTATTTCA
*
9026895 TTTTTATTTTTGTATTTTA
1 TTTTTATTTTTGTATTTCA
9026914 TTTTT
1 TTTTT
9026919 TCTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTTGTATTTCA
Found at i:9026912 original size:13 final size:12
Alignment explanation
Indices: 9026865--9026919 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 12
9026855 AGAAAAATTA
9026865 TATTTTTTATTT
1 TATTTTTTATTT
9026877 T-TTTATTT-TTT
1 TATTT-TTTATTT
**
9026888 TATTTCAT-TTT
1 TATTTTTTATTT
9026899 TATTTTTGTATTT
1 TATTTTT-TATTT
9026912 TATTTTTT
1 TATTTTTT
9026920 CTTATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
11 16 0.46
12 9 0.26
13 10 0.29
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.82
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:9027331 original size:21 final size:20
Alignment explanation
Indices: 9027301--9027341 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
9027291 CCTAACTCCT
*
9027301 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
9027322 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
9027342 TAAATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:9028321 original size:41 final size:41
Alignment explanation
Indices: 9028252--9028490 Score: 316
Period size: 41 Copynumber: 5.8 Consensus size: 41
9028242 TTATTATTAC
* * * *
9028252 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCACAGCAA
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGCAT
* * * * ** *
9028293 TACCGGCACTTCTTTAAAAACGCCGCTAAAGATCTGAGCAT
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
9028334 TAGCGGCGCTTATTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
9028375 TAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
9028416 TAGCAGCGCTTACTCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGCAT
*
9028457 TAGCGGCGTTTATTCAAAAACGCCGCTAAAGGCC
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCC
9028491 CCAAAAACCC
Statistics
Matches: 171, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 171 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (41 bp):
TAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGCAT
Found at i:9028870 original size:19 final size:19
Alignment explanation
Indices: 9028833--9028871 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9028823 TAAGAGCTTA
*
9028833 TAAATAATTATTAAATTAT
1 TAAATAATTAATAAATTAT
9028852 TAAATAA-TAATAAAGTTAT
1 TAAATAATTAATAAA-TTAT
9028871 T
1 T
9028872 GTGAAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TAAATAATTAATAAATTAT
Found at i:9030002 original size:13 final size:13
Alignment explanation
Indices: 9029984--9030008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9029974 ATAATGGCAA
9029984 AAAAAATAAAAAT
1 AAAAAATAAAAAT
9029997 AAAAAATAAAAA
1 AAAAAATAAAAA
9030009 AAACAAGCCA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:9034383 original size:20 final size:18
Alignment explanation
Indices: 9034346--9034388 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
9034336 AATAGTCTCC
9034346 ATTAAATTTTAATAATTT
1 ATTAAATTTTAATAATTT
*
9034364 ATTATAATTGTTAGTAATTT
1 ATTA-AATT-TTAATAATTT
9034384 -TTAAA
1 ATTAAA
9034389 ATATTTTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTAAATTTTAATAATTT
Found at i:9038217 original size:19 final size:19
Alignment explanation
Indices: 9038193--9038236 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
9038183 TAAAAGCAAC
9038193 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
9038212 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
9038231 ACAACA
1 ACAACA
9038237 AAAATAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.27, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:9040914 original size:90 final size:90
Alignment explanation
Indices: 9040810--9041208 Score: 647
Period size: 90 Copynumber: 4.4 Consensus size: 90
9040800 ATTAAAAATT
*
9040810 AATTAATATAATAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACATTTTAAAC
1 AATTAATATAATAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAC
9040875 TTTAAAGTTAGTTAATTGAAGCCTA
66 TTTAAAGTTAGTTAATTGAAGCCTA
* * *
9040900 AATTAATATAATAGTACAATAACATAAATTAAACAAAAAAAAGTCTGTTAAGCTATC-GTTTAAA
1 AATTAATATAATAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTA-CAGTTTAAA
9040964 CTTTAAAGTTAGTTAATTGAAGCCTA
65 CTTTAAAGTTAGTTAATTGAAGCCTA
9040990 AATTAATATAATAGTACAAGTACGACATCATAAATTAAACAAAAAAAAAGTATGTTAAACTACAG
1 AATTAATATAATAGTAC-A--AC-A-A-CATAAATTAAAC-AAAAAAAAGTATGTTAAACTACAG
9041055 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
59 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
* * *
9041087 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAGTATGTTAAACCACAGTTTAAAC
1 AATTAATATAATAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAC
9041152 TTTAAAGTTAGTTAATTGAAGCCTA
66 TTTAAAGTTAGTTAATTGAAGCCTA
*
9041177 AATTAATATAATAGTACAACAGCATAAATTAA
1 AATTAATATAATAGTACAACAACATAAATTAA
9041209 TTAATTGAAG
Statistics
Matches: 289, Mismatches: 11, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
90 187 0.65
91 14 0.05
93 2 0.01
94 2 0.01
95 1 0.00
96 14 0.05
97 69 0.24
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (90 bp):
AATTAATATAATAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAC
TTTAAAGTTAGTTAATTGAAGCCTA
Found at i:9041085 original size:187 final size:186
Alignment explanation
Indices: 9040805--9041195 Score: 664
Period size: 187 Copynumber: 2.1 Consensus size: 186
9040795 ATTAAATTAA
9040805 AAATTAAT-TAATA-TA-ATAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACA
1 AAATTAATATAATAGTACA-AGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACA
*
9040867 TTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAACATAAATTAA
65 GTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAACATAAATTAA
* * *
9040932 ACAAAAAAAAGTCTGTTAAGCTATC-GTTTAAACTTTAAAGTTAGTTAATTGAAGCCT
130 ACAAAAAAAAGTATGTTAAACCA-CAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCT
* *
9040989 AAATTAATATAATAGTACAAGTACGACATCATAAATTAAACAAAAAAAAAGTATGTTAAACTACA
1 AAATTAATATAATAGTACAAGTACAACAACATAAATTAAAC-AAAAAAAAGTATGTTAAACTACA
*
9041054 GTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAA
65 GTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAACATAAATTAA
9041119 ACAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCT
130 ACAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCT
9041176 AAATTAATATAATAGTACAA
1 AAATTAATATAATAGTACAA
9041196 CAGCATAAAT
Statistics
Matches: 195, Mismatches: 7, Indels: 7
0.93 0.03 0.03
Matches are distributed among these distances:
184 8 0.04
185 5 0.03
186 23 0.12
187 159 0.82
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (186 bp):
AAATTAATATAATAGTACAAGTACAACAACATAAATTAAACAAAAAAAAGTATGTTAAACTACAG
TTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAACATAAATTAAA
CAAAAAAAAGTATGTTAAACCACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCT
Found at i:9041535 original size:17 final size:17
Alignment explanation
Indices: 9041513--9041564 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
9041503 TTTTCTCTAT
*
9041513 TAATATTATGTTATTAC
1 TAATATTATATTATTAC
9041530 TAATATTATATTATTAC
1 TAATATTATATTATTAC
*
9041547 TAATATTACATTATTAC
1 TAATATTATATTATTAC
9041564 T
1 T
9041565 TTGGGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (17 bp):
TAATATTATATTATTAC
Found at i:9041975 original size:19 final size:18
Alignment explanation
Indices: 9041951--9042012 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 18
9041941 TGAGAAGGAA
9041951 AATAGAGCGAAAATCATTC
1 AATAGAGC-AAAATCATTC
9041970 AATAGAGCAAAA-CATATGC
1 AATAGAGCAAAATCAT-T-C
9041989 AAATAGAGCTAAAATCATTC
1 -AATAGAGC-AAAATCATTC
9042009 AATA
1 AATA
9042013 ATTCAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.08
18 5 0.13
19 13 0.34
20 9 0.24
21 5 0.13
22 3 0.08
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.21
Consensus pattern (18 bp):
AATAGAGCAAAATCATTC
Found at i:9041995 original size:20 final size:20
Alignment explanation
Indices: 9041950--9042010 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
9041940 ATGAGAAGGA
9041950 AAATAGAGCGAAAATCATTC
1 AAATAGAGCGAAAATCATTC
9041970 -AATAGAGC-AAAA-CATATGC
1 AAATAGAGCGAAAATCAT-T-C
*
9041989 AAATAGAGCTAAAATCATTC
1 AAATAGAGCGAAAATCATTC
9042009 AA
1 AA
9042011 TAATTCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 3 0.08
18 5 0.14
19 9 0.25
20 11 0.31
21 5 0.14
22 3 0.08
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (20 bp):
AAATAGAGCGAAAATCATTC
Found at i:9042982 original size:44 final size:44
Alignment explanation
Indices: 9042918--9043008 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
9042908 ATTGCTAAGA
*
9042918 TAATATTAAAATAATATACACTAATCAGAGTTTAAGTAAAAAAT
1 TAATATTAAAATAATATACACTAATCAAAGTTTAAGTAAAAAAT
* * *
9042962 TAATATTAAAATAATCTACACTAATCAAAGTTTAAGTGAGAAAT
1 TAATATTAAAATAATATACACTAATCAAAGTTTAAGTAAAAAAT
9043006 TAA
1 TAA
9043009 AAATAAAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAATATACACTAATCAAAGTTTAAGTAAAAAAT
Found at i:9048934 original size:17 final size:17
Alignment explanation
Indices: 9048899--9048941 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
9048889 AAATATTAAA
*
9048899 AAATATTAAA-TTGACT
1 AAATATAAAATTTGACT
*
9048915 AAATATAAAATTTGATT
1 AAATATAAAATTTGACT
9048932 AAATA-AAAAT
1 AAATATAAAAT
9048942 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (17 bp):
AAATATAAAATTTGACT
Found at i:9050571 original size:20 final size:20
Alignment explanation
Indices: 9050546--9050585 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9050536 AATATTTTCC
*
9050546 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
9050566 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
9050586 TCATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:9052081 original size:40 final size:40
Alignment explanation
Indices: 9052021--9052160 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
9052011 AACACACCAG
* * *
9052021 TTTGGCACCCAGTGCCTCATCGGATAATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * *
9052061 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
* * * * *
9052099 -TTGGCACCTAGTACCTCATTGAATTAATCCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATCCGAAGTAATAA
* *
9052139 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
9052161 ACTCAAAGTC
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 16 0.21
38 12 0.16
39 2 0.03
40 31 0.40
41 16 0.21
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATCCGAAGTAATAA
Found at i:9053129 original size:3 final size:3
Alignment explanation
Indices: 9053121--9053155 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9053111 TTATTTGTTT
9053121 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9053156 TATATTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9054470 original size:26 final size:26
Alignment explanation
Indices: 9054440--9054493 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
9054430 ATAAGCCACC
*
9054440 ACGTCCGGGTGTATTCAAAGCTTGAA
1 ACGTCCGGGTGTATTCAAAACTTGAA
9054466 ACGTCCGGGTGTATTCAAAACTTGAA
1 ACGTCCGGGTGTATTCAAAACTTGAA
9054492 AC
1 AC
9054494 CTCTATCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (26 bp):
ACGTCCGGGTGTATTCAAAACTTGAA
Found at i:9061651 original size:14 final size:14
Alignment explanation
Indices: 9061617--9061651 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9061607 CTACCATTTC
*
9061617 ACTATTATATTGTT
1 ACTATTTTATTGTT
9061631 ACTATTTTATTGTT
1 ACTATTTTATTGTT
*
9061645 ATTATTT
1 ACTATTT
9061652 GGATATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (14 bp):
ACTATTTTATTGTT
Found at i:9063368 original size:40 final size:40
Alignment explanation
Indices: 9063319--9063400 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
9063309 CTGGAATAAG
9063319 TATGTTTCCTCTCCGTTGACTGCAGAGGCCTAGGCTGGAT
1 TATGTTTCCTCTCCGTTGACTGCAGAGGCCTAGGCTGGAT
9063359 TATGTTTCCTCTCCGTTGACTGCAGAGGCCTAGGCTGGAT
1 TATGTTTCCTCTCCGTTGACTGCAGAGGCCTAGGCTGGAT
9063399 TA
1 TA
9063401 CAGAAGATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (40 bp):
TATGTTTCCTCTCCGTTGACTGCAGAGGCCTAGGCTGGAT
Found at i:9064312 original size:60 final size:60
Alignment explanation
Indices: 9064209--9064349 Score: 198
Period size: 60 Copynumber: 2.4 Consensus size: 60
9064199 CACCTAAATT
*
9064209 TGACATTTTTTCCTAATTTGGTACCTAAACTTTGTTTTGGCCCAATTCAGTACTTGAACG
1 TGACATTTTTTCCTAATTTGGTACCTAAACTTTGTTTTGGCCCAATTCAGTACCTGAACG
* *
9064269 TGACATATTTTT-CTAATTTGGTACCTAAA-TATT-TTTTGAGCCCAATTTAGTACCTGAACT
1 TGACAT-TTTTTCCTAATTTGGTACCTAAACT-TTGTTTTG-GCCCAATTCAGTACCTGAACG
*
9064329 TGACATTTTTTCCTAGTTTGG
1 TGACATTTTTTCCTAATTTGG
9064350 CACGTAAGCT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
59 11 0.15
60 57 0.78
61 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (60 bp):
TGACATTTTTTCCTAATTTGGTACCTAAACTTTGTTTTGGCCCAATTCAGTACCTGAACG
Found at i:9064842 original size:31 final size:31
Alignment explanation
Indices: 9064805--9064883 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
9064795 TGGACCCAAA
* *
9064805 AAATTTAAGTACCAACTTAAGAAAAAGTTTC
1 AAATTTAAGTACCAAATTAAGAAAAAGTGTC
*
9064836 AAATTTAGGTACCAAATTAAGAAAAAGTGTC
1 AAATTTAAGTACCAAATTAAGAAAAAGTGTC
* * *
9064867 AAGTTCAAATACCAAAT
1 AAATTTAAGTACCAAAT
9064884 ATTATATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (31 bp):
AAATTTAAGTACCAAATTAAGAAAAAGTGTC
Found at i:9065737 original size:6 final size:6
Alignment explanation
Indices: 9065726--9065752 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9065716 ATATTTATCA
9065726 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
9065753 GATTAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:9068265 original size:21 final size:20
Alignment explanation
Indices: 9068241--9068386 Score: 125
Period size: 21 Copynumber: 7.7 Consensus size: 20
9068231 CATCTTGAAG
9068241 GAGAAGGAGGAGGAGAAGATA
1 GAGAAGGAGGAGGAGAAGA-A
* *
9068262 GAGAAGGAGAAGAAGAAGAA
1 GAGAAGGAGGAGGAGAAGAA
9068282 GA-AA-GAGGA-G-G-AG--
1 GAGAAGGAGGAGGAGAAGAA
*
9068295 GAGAAGGAGGAGAAGAAGAA
1 GAGAAGGAGGAGGAGAAGAA
9068315 -AG-AGGAGGAGGAGAAGAA
1 GAGAAGGAGGAGGAGAAGAA
* *
9068333 GGAGGAGGAGGAGGAGGAGAA
1 -GAGAAGGAGGAGGAGAAGAA
* *
9068354 CGAGGAGGAGGAGGGGAAG--
1 -GAGAAGGAGGAGGAGAAGAA
9068373 GAGAAGGAGGAGGA
1 GAGAAGGAGGAGGA
9068387 AGGAAAGGAG
Statistics
Matches: 103, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
13 2 0.02
14 2 0.02
15 7 0.07
16 1 0.01
17 1 0.01
18 33 0.32
19 4 0.04
20 5 0.05
21 48 0.47
ACGTcount: A:0.47, C:0.01, G:0.52, T:0.01
Consensus pattern (20 bp):
GAGAAGGAGGAGGAGAAGAA
Found at i:9068269 original size:18 final size:17
Alignment explanation
Indices: 9068248--9068428 Score: 106
Period size: 18 Copynumber: 10.2 Consensus size: 17
9068238 AAGGAGAAGG
9068248 AGGAGGAGAAGATAGAGA
1 AGGAGGAGAAGA-AGAGA
*
9068266 AGGAGAAGAAGAAGAAGA
1 AGGAGGAGAAGAAG-AGA
* *
9068284 AAGAGGAG--GAGGAGA
1 AGGAGGAGAAGAAGAGA
9068299 AGGAGGAGAAGAAGAAAGA
1 AGGAGGAGAAGAAG--AGA
9068318 GGAGGAGGAGAAGAAGGAGGA
1 --AGGAGGAGAAGAA-GA-GA
* *
9068339 GGAGGAGGAGGAGAACGAGG
1 --AGGAGGAGAAGAA-GAGA
**
9068359 AGGAGGAGGGGAAGGAGA
1 AGGAGGAGAAGAA-GAGA
9068377 AGGAGGAG--GAAG-GAA
1 AGGAGGAGAAGAAGAG-A
9068392 AGGAGGAGAAGAA-AG-
1 AGGAGGAGAAGAAGAGA
* *
9068407 AGGAGGAAAAGGAGGAGA
1 AGGAGGAGAA-GAAGAGA
9068425 AGGA
1 AGGA
9068429 AAAGGAGGAG
Statistics
Matches: 133, Mismatches: 14, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.01
15 29 0.22
16 8 0.06
17 11 0.08
18 47 0.35
19 3 0.02
20 2 0.02
21 31 0.23
22 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.01
Consensus pattern (17 bp):
AGGAGGAGAAGAAGAGA
Found at i:9068292 original size:3 final size:3
Alignment explanation
Indices: 9068286--9068439 Score: 105
Period size: 3 Copynumber: 51.3 Consensus size: 3
9068276 GAAGAAGAAA
* * * * * * *
9068286 GAG GAG GAG GAG AAG GAG GAG AAG AAG AAA GAG GAG GAG GAG AAG AAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
* * *
9068334 GAG GAG GAG GAG GAG GAG AAC GAG GAG GAG GAG G-G GAAG GAG AAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G-AG GAG GAG
* * * * * *
9068379 GAG GAG GAAG GA- AAG GAG GAG AAG AAA GAG GAG GAA AAG GAG GAG
1 GAG GAG G-AG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
* * *
9068424 AAG GAA AAG GAG GAG G
1 GAG GAG GAG GAG GAG G
9068440 TTGAAGATGA
Statistics
Matches: 117, Mismatches: 30, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
2 3 0.03
3 109 0.93
4 5 0.04
ACGTcount: A:0.45, C:0.01, G:0.54, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:9068333 original size:33 final size:33
Alignment explanation
Indices: 9068263--9068339 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
9068253 GAGAAGATAG
* *
9068263 AGAAGGAGAAGAAGAAGAAGAAAGAGGAGGAGG
1 AGAAGGAGGAGAAGAAGAAGAAAGAGGAGGAGA
*
9068296 AGAAGGAGGAGAAGAAGAA-AGAGGAGGAGGAGA
1 AGAAGGAGGAGAAGAAGAAGA-AAGAGGAGGAGA
9068329 AGAAGGAGGAG
1 AGAAGGAGGAG
9068340 GAGGAGGAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (33 bp):
AGAAGGAGGAGAAGAAGAAGAAAGAGGAGGAGA
Found at i:9068337 original size:15 final size:15
Alignment explanation
Indices: 9068242--9068439 Score: 126
Period size: 15 Copynumber: 13.6 Consensus size: 15
9068232 ATCTTGAAGG
9068242 AGAAGGAGGAGGAGA
1 AGAAGGAGGAGGAGA
*
9068257 AGATA-GAGAAGGAGA
1 AGA-AGGAGGAGGAGA
* *
9068272 AGAA-GAAGAAGA-A
1 AGAAGGAGGAGGAGA
9068285 AG-AGGAGGAGGAGA
1 AGAAGGAGGAGGAGA
* * *
9068299 AGGAGGAGAAGAAGA
1 AGAAGGAGGAGGAGA
9068314 A-AGAGGAGGAGGAGA
1 AGA-AGGAGGAGGAGA
*
9068329 AGAAGGAGGAGGAGG
1 AGAAGGAGGAGGAGA
* * * *
9068344 AGGAGGAGAACGAGG
1 AGAAGGAGGAGGAGA
* *
9068359 AGGAGGAGG-GGAAGG
1 AGAAGGAGGAGG-AGA
9068374 AGAAGGAGGAGGA-A
1 AGAAGGAGGAGGAGA
*
9068388 GGAA--AGGAGGAGA
1 AGAAGGAGGAGGAGA
* *
9068401 AGAAAGAGGAGGAAA
1 AGAAGGAGGAGGAGA
* * *
9068416 AGGAGGAGAAGGAAA
1 AGAAGGAGGAGGAGA
*
9068431 AGGAGGAGG
1 AGAAGGAGG
9068440 TTGAAGATGA
Statistics
Matches: 146, Mismatches: 26, Indels: 22
0.75 0.13 0.11
Matches are distributed among these distances:
12 8 0.05
13 13 0.09
14 13 0.09
15 108 0.74
16 4 0.03
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.01
Consensus pattern (15 bp):
AGAAGGAGGAGGAGA
Found at i:9068343 original size:24 final size:24
Alignment explanation
Indices: 9068239--9068439 Score: 169
Period size: 24 Copynumber: 8.4 Consensus size: 24
9068229 ACCATCTTGA
*
9068239 AGGAGAAGGAGGAGGAGAAGATA-G
1 AGGAGGAGGAGGAGGAGAAGA-AGG
* * * * *
9068263 AGAAGGAGAAGAAGAAGAAGAAAG
1 AGGAGGAGGAGGAGGAGAAGAAGG
* * *
9068287 AGGAGGAGGAGAAGGAGGAGAAGA
1 AGGAGGAGGAGGAGGAGAAGAAGG
* *
9068311 AGAAAGAGGAGGAGGAGAAGAAGG
1 AGGAGGAGGAGGAGGAGAAGAAGG
9068335 AGGAGGAGGAGGAGGAGAACG-AGG
1 AGGAGGAGGAGGAGGAGAA-GAAGG
*
9068359 AGGAGGAGG-GGAAGGAGAAGGAGG
1 AGGAGGAGGAGG-AGGAGAAGAAGG
* *
9068383 AGGAAGGA-AAGGAGGAGAAGAAAG
1 AGG-AGGAGGAGGAGGAGAAGAAGG
** *
9068407 AGGAGGAAAAGGAGGAGAAGGAA-A
1 AGGAGGAGGAGGAGGAGAA-GAAGG
9068431 AGGAGGAGG
1 AGGAGGAGG
9068440 TTGAAGATGA
Statistics
Matches: 145, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
23 8 0.06
24 127 0.88
25 10 0.07
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.00
Consensus pattern (24 bp):
AGGAGGAGGAGGAGGAGAAGAAGG
Found at i:9072373 original size:91 final size:94
Alignment explanation
Indices: 9072255--9072436 Score: 230
Period size: 91 Copynumber: 1.9 Consensus size: 94
9072245 TCAAAAGTCA
** * *
9072255 TTTTTGATGCATTTTGGCAGATCAAGTACCTAATTGAGTG-GAAAA-AAAAAGCAGA-GGCTTAA
1 TTTTTGATGCATTTTGAAAGATCAAGTACCCAATTGAGTGAAAAAAGAAAAAGCA-ATGGCTTAA
*
9072317 TTGC-TTTTTTTTGAAAAAGTTTGAGGGCC
65 TTACTTTTTTTTTGAAAAAGTTTGAGGGCC
*
9072346 TTTTTTATGCATTTTGAAAG-TCTAAGTACCCAATTGAGTGCAAAAAAGAAAAAGCAATGGCTTA
1 TTTTTGATGCATTTTGAAAGATC-AAGTACCCAATTGAGTG-AAAAAAGAAAAAGCAATGGCTTA
9072410 ATTACTTTTTTTTTTTGAAAAAGTTTG
64 ATTAC--TTTTTTTTTGAAAAAGTTTG
9072437 TAGGTTTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
90 2 0.03
91 33 0.43
93 5 0.06
94 18 0.23
97 19 0.25
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (94 bp):
TTTTTGATGCATTTTGAAAGATCAAGTACCCAATTGAGTGAAAAAAGAAAAAGCAATGGCTTAAT
TACTTTTTTTTTGAAAAAGTTTGAGGGCC
Found at i:9073033 original size:29 final size:29
Alignment explanation
Indices: 9073001--9073056 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
9072991 TACCTAAATA
9073001 ATATA-AAAAAATAATTAATTACGAAAAAG
1 ATATAGAAAAAA-AATTAATTACGAAAAAG
* *
9073030 ATATAGAAAACAAGTTAATTACGAAAA
1 ATATAGAAAAAAAATTAATTACGAAAA
9073057 TAGGCATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.23
Consensus pattern (29 bp):
ATATAGAAAAAAAATTAATTACGAAAAAG
Found at i:9073277 original size:27 final size:28
Alignment explanation
Indices: 9073222--9073285 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
9073212 AATGGATAAA
*
9073222 TTCTTCATAAGCCCCCTTATTTATTATT
1 TTCTTCATAAGACCCCTTATTTATTATT
* *
9073250 TTCTTCATAA-ACCCTTTTTTTATTATT
1 TTCTTCATAAGACCCCTTATTTATTATT
*
9073277 TGCTTCATA
1 TTCTTCATA
9073286 TATAATTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCTTCATAAGACCCCTTATTTATTATT
Found at i:9073898 original size:28 final size:29
Alignment explanation
Indices: 9073845--9073908 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
9073835 GTGAATTACA
* *
9073845 TATGAAGCAAATAATAAAAAA-AGGGGTT
1 TATGAAGAAAATAATAAAAAAGAGGGGCT
** *
9073873 TATGAAGAAAATAATAAATTAGGGGGGCT
1 TATGAAGAAAATAATAAAAAAGAGGGGCT
9073902 TATGAAG
1 TATGAAG
9073909 GAATTTATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.48, C:0.03, G:0.25, T:0.23
Consensus pattern (29 bp):
TATGAAGAAAATAATAAAAAAGAGGGGCT
Found at i:9078985 original size:20 final size:20
Alignment explanation
Indices: 9078962--9078999 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9078952 TAGTTAATTT
* *
9078962 ATTTTTTTTTAAGTTTTAAG
1 ATTTTTTTATAAATTTTAAG
9078982 ATTTTTTTATAAATTTTA
1 ATTTTTTTATAAATTTTA
9079000 GTTATAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTTTTTATAAATTTTAAG
Found at i:9089417 original size:15 final size:15
Alignment explanation
Indices: 9089399--9089427 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9089389 TTGATGTTTG
9089399 GTATCATTTTGTTCA
1 GTATCATTTTGTTCA
9089414 GTATCATTTTGTTC
1 GTATCATTTTGTTC
9089428 GTGATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
GTATCATTTTGTTCA
Found at i:9099908 original size:20 final size:20
Alignment explanation
Indices: 9099883--9099922 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9099873 AATTCTTACT
9099883 ACTTTCTGGTAGAATAACAA
1 ACTTTCTGGTAGAATAACAA
9099903 ACTTTCTGGTAGAATAACAA
1 ACTTTCTGGTAGAATAACAA
9099923 TATATGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
ACTTTCTGGTAGAATAACAA
Found at i:9102886 original size:14 final size:12
Alignment explanation
Indices: 9102868--9102924 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 12
9102858 TTTGCTTTCA
9102868 AAATAAAAGAAAT
1 AAATAAAA-AAAT
*
9102881 AAAATAAGAAAAT
1 -AAATAAAAAAAT
9102894 AAATAAATAAAAAT
1 AAAT-AA-AAAAAT
* *
9102908 AAATAAATAAAC
1 AAATAAAAAAAT
9102920 AAATA
1 AAATA
9102925 GGCCGAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 13 0.35
13 8 0.22
14 16 0.43
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.18
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:9102923 original size:22 final size:22
Alignment explanation
Indices: 9102867--9102924 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
9102857 GTTTGCTTTC
*
9102867 AAAATAAAAGAAAT-AAAATAAG
1 AAAAT-AAACAAATAAAAATAAG
*
9102889 AAAATAAATAAATAAAAATAA-
1 AAAATAAACAAATAAAAATAAG
9102910 ATAAATAAACAAATA
1 A-AAATAAACAAATA
9102925 GGCCGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAATAAACAAATAAAAATAAG
Found at i:9109014 original size:43 final size:43
Alignment explanation
Indices: 9108957--9109267 Score: 313
Period size: 43 Copynumber: 7.3 Consensus size: 43
9108947 TTTTAAAAAT
*
9108957 AAACGTCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
9109000 AAACGCCGCAATAGACCATGACCTTTAGCGGCGC-TTCCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * **
9109042 AAATGCCGCTATAGACCATTACCTTTAGCGACGCTTTTATCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * **
9109085 AAACGCCGCTATAGACCATTACCTTTAGCGGCGCCTTTATCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * * *
9109128 AAACACCACTAAAGACCATTACCTTTAGCTGCGCTTCTCCCAT
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * **
9109171 AAACGCCGTTATAAATCATGACTTTTAGCGACGCTTTTTCGTAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGC-TTTTCCCAC
* * * *
9109215 AAACGCCACTATAGA--ATTGGCCTTTAGCAGCGCTTTTCACAC
1 AAACGCCGCTATAGACCA-TGACCTTTAGCGGCGCTTTTCCCAC
9109257 AAACGCCGCTA
1 AAACGCCGCTA
9109268 AAAACATATC
Statistics
Matches: 219, Mismatches: 46, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
42 55 0.25
43 147 0.67
44 17 0.08
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:9109109 original size:85 final size:86
Alignment explanation
Indices: 9108963--9109178 Score: 265
Period size: 85 Copynumber: 2.5 Consensus size: 86
9108953 AAATAAACGT
* * *
9108963 CGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCAATAGACCATGACCTTTAG
1 CGCTATAGACCATTACCTTTAGCGACGCTTTTACCACAAACGCCGCAATAGACCATGACCTTTAG
* **
9109028 CGGCG-CTTCCCCACAAATGC
66 CGGCGCCTTCACCACAAACAC
* * *
9109048 CGCTATAGACCATTACCTTTAGCGACGCTTTTATCACAAACGCCGCTATAGACCATTACCTTTAG
1 CGCTATAGACCATTACCTTTAGCGACGCTTTTACCACAAACGCCGCAATAGACCATGACCTTTAG
* *
9109113 CGGCGCCTTTATCACAAACAC
66 CGGCGCCTTCACCACAAACAC
* * * * *
9109134 CACTAAAGACCATTACCTTTAGCTG-CGCTTCTCCCATAAACGCCG
1 CGCTATAGACCATTACCTTTAGC-GACGCTTTTACCACAAACGCCG
9109179 TTATAAATCA
Statistics
Matches: 112, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
85 64 0.57
86 47 0.42
87 1 0.01
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (86 bp):
CGCTATAGACCATTACCTTTAGCGACGCTTTTACCACAAACGCCGCAATAGACCATGACCTTTAG
CGGCGCCTTCACCACAAACAC
Found at i:9109592 original size:43 final size:43
Alignment explanation
Indices: 9109544--9109634 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
9109534 ACATATGCAA
** * * *
9109544 GGTAATAAATTATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
9109587 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
9109630 -GTAAT
1 GGTAAT
9109635 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 5 0.12
43 37 0.88
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:9111315 original size:13 final size:13
Alignment explanation
Indices: 9111297--9111323 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9111287 ATGTAGCCCA
9111297 AGTGCTGTGCGAC
1 AGTGCTGTGCGAC
9111310 AGTGCTGTGCGAC
1 AGTGCTGTGCGAC
9111323 A
1 A
9111324 AAGCACCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.22
Consensus pattern (13 bp):
AGTGCTGTGCGAC
Found at i:9111712 original size:25 final size:25
Alignment explanation
Indices: 9111684--9111771 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
9111674 TAATAATATT
9111684 ATAATTTTCCTCAAAATATATACAA
1 ATAATTTTCCTCAAAATATATACAA
* * *
9111709 ATAATATTTGCATTGATTATATATAATA-ATA
1 ATAAT-TTT-C-CTCA--AAATAT-ATACA-A
9111740 TTATAATTTTCCTCAAAATATATACAA
1 --ATAATTTTCCTCAAAATATATACAA
9111767 ATAAT
1 ATAAT
9111772 ATTATTTGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
25 10 0.21
26 3 0.06
27 5 0.11
28 8 0.17
30 8 0.17
31 5 0.11
32 3 0.06
33 5 0.11
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (25 bp):
ATAATTTTCCTCAAAATATATACAA
Found at i:9111713 original size:33 final size:33
Alignment explanation
Indices: 9111675--9111776 Score: 98
Period size: 33 Copynumber: 3.3 Consensus size: 33
9111665 GATTATTTAT
9111675 AATAATATTATAATTTTCCTCAAAATATATACA
1 AATAATATTATAATTTTCCTCAAAATATATACA
* *
9111708 AATAATATT-TGCATTGAT--T----ATATAT---
1 AATAATATTAT-AATT-TTCCTCAAAATATATACA
9111733 AATAATATTATAATTTTCCTCAAAATATATACA
1 AATAATATTATAATTTTCCTCAAAATATATACA
9111766 AATAATATTAT
1 AATAATATTAT
9111777 TTGTGCATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 24
0.65 0.05 0.30
Matches are distributed among these distances:
24 1 0.02
25 12 0.23
26 2 0.04
28 6 0.11
30 6 0.11
32 2 0.04
33 23 0.43
34 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (33 bp):
AATAATATTATAATTTTCCTCAAAATATATACA
Found at i:9111722 original size:58 final size:58
Alignment explanation
Indices: 9111657--9111774 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
9111647 CCTTAAAAAT
*
9111657 TTTGCATTGATTATTTATAATAATATTATAATTTTCCTCAAAATATATACAAATAATA
1 TTTGCATTGATTATATATAATAATATTATAATTTTCCTCAAAATATATACAAATAATA
9111715 TTTGCATTGATTATATATAATAATATTATAATTTTCCTCAAAATATATACAAATAATA
1 TTTGCATTGATTATATATAATAATATTATAATTTTCCTCAAAATATATACAAATAATA
9111773 TT
1 TT
9111775 ATTTGTGCAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (58 bp):
TTTGCATTGATTATATATAATAATATTATAATTTTCCTCAAAATATATACAAATAATA
Found at i:9111760 original size:28 final size:28
Alignment explanation
Indices: 9111672--9111761 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
9111662 ATTGATTATT
9111672 TATAATAATATTATAATTTTCCTCAAAA
1 TATAATAATATTATAATTTTCCTCAAAA
* * * * * *
9111700 TAT-ATACAAATAAT-ATTTGCATTGATTATA
1 TATAATA-ATATTATAATTTTC-CTCA--AAA
9111730 TATAATAATATTATAATTTTCCTCAAAA
1 TATAATAATATTATAATTTTCCTCAAAA
9111758 TATA
1 TATA
9111762 TACAAATAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 12
0.65 0.18 0.18
Matches are distributed among these distances:
27 8 0.18
28 16 0.36
30 12 0.27
31 8 0.18
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (28 bp):
TATAATAATATTATAATTTTCCTCAAAA
Found at i:9111761 original size:30 final size:30
Alignment explanation
Indices: 9111672--9111763 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
9111662 ATTGATTATT
9111672 TATAATAATATTATAATTTTCCTCAAAATA
1 TATAATAATATTATAATTTTCCTCAAAATA
* * * **
9111702 TATACA-AATA--AT-ATTTGCATTGATTATA
1 TATA-ATAATATTATAATTTTC-CTCAAAATA
9111730 TATAATAATATTATAATTTTCCTCAAAATA
1 TATAATAATATTATAATTTTCCTCAAAATA
9111760 TATA
1 TATA
9111764 CAAATAATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
27 6 0.13
28 15 0.33
30 19 0.41
31 6 0.13
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (30 bp):
TATAATAATATTATAATTTTCCTCAAAATA
Found at i:9114387 original size:83 final size:81
Alignment explanation
Indices: 9114147--9114380 Score: 279
Period size: 83 Copynumber: 2.8 Consensus size: 81
9114137 TCTTTATTTA
** * * *
9114147 GTCAATGAAACAACGCCGTTTTGTTAAATCTTTAATTTATTTTTTTGTGGCATTTTTATAGAAAA
1 GTCAATGAAACGGCGCCGTTTTGTTAAAT-TTTAATATA-TTTTTTGCGGCATTTTT-TACAAAA
9114212 CGCCACTAATATTTAATTC
63 CGCCACTAATATTTAATTC
* * * * * *
9114231 ATCAATGAAATGGCACCGTTTTATTAAATTCTTAATATATTTTTTGCGGCGTTTGTATACAAAAC
1 GTCAATGAAACGGCGCCGTTTTGTTAAATT-TTAATATATTTTTTGCGGCATTT-TTTACAAAAC
9114296 GCCACTAATATTTAATTC
64 GCCACTAATATTTAATTC
* * * *
9114314 GTCAATGAAACGGTGCCGTTTGGTTAAATTTTAAATGTATTTTTTGCGGCATTTTTTACCAAACG
1 GTCAATGAAACGGCGCCGTTTTGTTAAATTTT-AATATATTTTTTGCGGCATTTTTTACAAAACG
9114379 CC
65 CC
9114381 CGCTAATGAT
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
82 13 0.10
83 82 0.65
84 31 0.25
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (81 bp):
GTCAATGAAACGGCGCCGTTTTGTTAAATTTTAATATATTTTTTGCGGCATTTTTTACAAAACGC
CACTAATATTTAATTC
Found at i:9114534 original size:14 final size:14
Alignment explanation
Indices: 9114515--9114542 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9114505 ACATCATTAT
9114515 TAATATTATTTAAA
1 TAATATTATTTAAA
9114529 TAATATTATTTAAA
1 TAATATTATTTAAA
9114543 ATTTTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:9114657 original size:17 final size:17
Alignment explanation
Indices: 9114612--9114658 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
9114602 CTTTTACAAT
*
9114612 TATATAATATATATCCA
1 TATAAAATATATATCCA
*
9114629 TATAAAAAATATATCCA
1 TATAAAATATATATCCA
* *
9114646 TATCAATTATATA
1 TATAAAATATATA
9114659 AATCTTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAATATATATCCA
Found at i:9115016 original size:21 final size:21
Alignment explanation
Indices: 9114992--9115032 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9114982 AACCCTAAAT
*
9114992 CCCTAACTATTAACCCCTAAC
1 CCCTAACTACTAACCCCTAAC
*
9115013 CCCTAACTCCTAACCCCTAA
1 CCCTAACTACTAACCCCTAA
9115033 ACCTTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCTAACTACTAACCCCTAAC
Found at i:9115019 original size:14 final size:14
Alignment explanation
Indices: 9115002--9115032 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9114992 CCCTAACTAT
9115002 TAACCCCTAACCCC
1 TAACCCCTAACCCC
*
9115016 TAACTCCTAACCCC
1 TAACCCCTAACCCC
9115030 TAA
1 TAA
9115033 ACCTTAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (14 bp):
TAACCCCTAACCCC
Found at i:9115048 original size:21 final size:21
Alignment explanation
Indices: 9115003--9115064 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
9114993 CCTAACTATT
* * * *
9115003 AACCCCTAACCCCTAACTCCT
1 AACCCCTAAACCATAAATCCC
*
9115024 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCATAAATCCC
*
9115045 AACCCTTAAACCAT-AATCCC
1 AACCCCTAAACCATAAATCCC
9115065 TAATCCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 6 0.17
21 29 0.83
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCCTAAACCATAAATCCC
Found at i:9115084 original size:15 final size:15
Alignment explanation
Indices: 9115051--9115088 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
9115041 TCCCAACCCT
9115051 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
9115065 T-AATCCATAATCCC
1 TAAATCCATAATCCC
9115079 TAAATCCATA
1 TAAATCCATA
9115089 TGTAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:9115347 original size:7 final size:7
Alignment explanation
Indices: 9115335--9115462 Score: 53
Period size: 7 Copynumber: 18.0 Consensus size: 7
9115325 ACTAGTTAAT
9115335 CTAAACC
1 CTAAACC
9115342 CTAAACC
1 CTAAACC
*
9115349 ATAAACC
1 CTAAACC
* *
9115356 CTTAACA
1 CTAAACC
9115363 C-ATAACC
1 CTA-AACC
9115370 TCT-AACC
1 -CTAAACC
9115377 CTTAAACC
1 C-TAAACC
* *
9115385 CCAAACT
1 CTAAACC
* *
9115392 TTTAACC
1 CTAAACC
* *
9115399 ATAAATC
1 CTAAACC
* *
9115406 ATAACCC
1 CTAAACC
9115413 CTAAACC
1 CTAAACC
*
9115420 CATAATCC
1 C-TAAACC
*
9115428 ATAAACC
1 CTAAACC
* *
9115435 TTAAACT
1 CTAAACC
9115442 CTAAACC
1 CTAAACC
* *
9115449 ATATACC
1 CTAAACC
9115456 CTAAACC
1 CTAAACC
9115463 AAAAAACCTA
Statistics
Matches: 85, Mismatches: 30, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
6 1 0.01
7 73 0.86
8 11 0.13
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:9115355 original size:14 final size:14
Alignment explanation
Indices: 9115336--9115475 Score: 93
Period size: 14 Copynumber: 9.9 Consensus size: 14
9115326 CTAGTTAATC
9115336 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
9115350 TAAACCCTTAACACA
1 TAAACCCTAAAC-CA
* *
9115365 T-AACCTCTAACCCT
1 TAAACC-CTAAACCA
* **
9115379 TAAACCCCAAACTT
1 TAAACCCTAAACCA
* * *
9115393 TTAACCATAAATCA
1 TAAACCCTAAACCA
*
9115407 TAACCCCTAAACCCA
1 TAAACCCTAAA-CCA
* * *
9115422 TAATCCATAAACCT
1 TAAACCCTAAACCA
*
9115436 TAAACTCTAAACCA
1 TAAACCCTAAACCA
*
9115450 TATACCCTAAACCA
1 TAAACCCTAAACCA
* *
9115464 AAAAACCTAAAC
1 TAAACCCTAAAC
9115476 TATAGTGATA
Statistics
Matches: 93, Mismatches: 29, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
14 71 0.76
15 22 0.24
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:9115713 original size:41 final size:41
Alignment explanation
Indices: 9115656--9115900 Score: 379
Period size: 41 Copynumber: 6.0 Consensus size: 41
9115646 ATTTTAAATC
9115656 CCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
1 CCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
* *
9115697 CCTGAGCATTAGCGGCGCTTAATT-ACAAACGCCGCTAAAGG
1 CCTGAGCATTAGCGGCGCTT-CTTCAAAAACGCCGCTAAAGG
9115738 CCTGAGCATTAGCGGCGCTT-TATCAAAAACGCCGCTAAAGG
1 CCTGAGCATTAGCGGCGCTTCT-TCAAAAACGCCGCTAAAGG
* *
9115779 CATGAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGG
1 CCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
*
9115820 CTTGAGCATTAGCGGCGCTT-TATCAAAAACGCCGCTAAAGG
1 CCTGAGCATTAGCGGCGCTTCT-TCAAAAACGCCGCTAAAGG
* *
9115861 CCTAAGCATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAG
1 CCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG
9115901 CCCCAAAAAC
Statistics
Matches: 188, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 184 0.98
42 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (41 bp):
CCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
Found at i:9116050 original size:40 final size:40
Alignment explanation
Indices: 9115997--9116072 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
9115987 TGTTTTTAAT
* *
9115997 AAAGCGCCACTAATGCTCGACCTTTAGTGGCGTTTTACAG
1 AAAGCGCCACTAATGCTCCACCTTTAGCGGCGTTTTACAG
* * * *
9116037 AAAGTGCCGCTAATTCTCCATCTTTAGCGGCGTTTT
1 AAAGCGCCACTAATGCTCCACCTTTAGCGGCGTTTT
9116073 TTATTGAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (40 bp):
AAAGCGCCACTAATGCTCCACCTTTAGCGGCGTTTTACAG
Found at i:9119529 original size:5 final size:5
Alignment explanation
Indices: 9119521--9119571 Score: 75
Period size: 5 Copynumber: 9.8 Consensus size: 5
9119511 TAGAGTGTGC
*
9119521 AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG AGCGAC AGGAG TAGGA
1 AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG AG-GAG AGGAG -AGGA
9119572 AGCGGCTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 34 0.81
6 8 0.19
ACGTcount: A:0.39, C:0.04, G:0.55, T:0.02
Consensus pattern (5 bp):
AGGAG
Found at i:9126868 original size:67 final size:67
Alignment explanation
Indices: 9126760--9126894 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
9126750 AGAAATTTTC
*
9126760 AACTGATTCTATAGTGCTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGAA
1 AACTGATTCTATAGTACTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGAA
9126825 GG
66 GG
*
9126827 AACTGATTCTATAGTACTTGTTGCATTATTAGTAGGATTGAGCTCATAAGCTCACGACAATGGAA
1 AACTGATTCTATAGTACTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGAA
9126892 GG
66 GG
9126894 A
1 A
9126895 TGAGTCAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (67 bp):
AACTGATTCTATAGTACTTGTTGCATTATTAATAGGATTGAGCTCATAAGCTCACGACAATGGAA
GG
Found at i:9127195 original size:3 final size:3
Alignment explanation
Indices: 9127187--9127213 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9127177 TCTAGTCAAG
9127187 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
9127214 GCAAAGTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9134943 original size:15 final size:14
Alignment explanation
Indices: 9134922--9134957 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
9134912 ATAATCCTTA
*
9134922 ATAATTATCTTAAT
1 ATAATTATCCTAAT
9134936 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
9134951 ATAATTA
1 ATAATTA
9134958 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:9140257 original size:21 final size:23
Alignment explanation
Indices: 9140217--9140262 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
9140207 CTTCGACACT
*
9140217 GGTTGAATTGTTCTGGAAATAGA
1 GGTTGAATTGTTCAGGAAATAGA
9140240 GGTTGAATT-TT-AGGAAATAGA
1 GGTTGAATTGTTCAGGAAATAGA
9140261 GG
1 GG
9140263 CTTCGGTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
23 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.33
Consensus pattern (23 bp):
GGTTGAATTGTTCAGGAAATAGA
Found at i:9142932 original size:15 final size:14
Alignment explanation
Indices: 9142911--9142946 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
9142901 ATAATCTTTA
*
9142911 ATAATTATCTTAAT
1 ATAATTATCCTAAT
9142925 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
9142940 ATAATTA
1 ATAATTA
9142947 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:9145854 original size:13 final size:13
Alignment explanation
Indices: 9145836--9145879 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
9145826 ATTATTATAT
9145836 TTACCATCATAAC
1 TTACCATCATAAC
9145849 TTACCATCATAAC
1 TTACCATCATAAC
9145862 TTACCATACA-AAC
1 TTACCAT-CATAAC
9145875 TTACC
1 TTACC
9145880 TGACCAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 28 0.93
14 2 0.07
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.30
Consensus pattern (13 bp):
TTACCATCATAAC
Found at i:9146576 original size:48 final size:48
Alignment explanation
Indices: 9146521--9146618 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
9146511 AAACTCTCGC
9146521 TTTCTTTCCACTTTTGTTTCTTTTAATTAATGTTTTGATTTCATTATT
1 TTTCTTTCCACTTTTGTTTCTTTTAATTAATGTTTTGATTTCATTATT
9146569 TTTCTTTCCACTTTTGTTTCTTTTAATTAATGTTTTGATTTCATTATT
1 TTTCTTTCCACTTTTGTTTCTTTTAATTAATGTTTTGATTTCATTATT
9146617 TT
1 TT
9146619 AACTTTAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.65
Consensus pattern (48 bp):
TTTCTTTCCACTTTTGTTTCTTTTAATTAATGTTTTGATTTCATTATT
Found at i:9155222 original size:9 final size:9
Alignment explanation
Indices: 9155208--9155234 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
9155198 ATCAGACAAT
9155208 TTTTCATTC
1 TTTTCATTC
9155217 TTTTCATTC
1 TTTTCATTC
9155226 TTTTCATTC
1 TTTTCATTC
9155235 AAATTCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTCATTC
Found at i:9155363 original size:21 final size:21
Alignment explanation
Indices: 9155339--9155382 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9155329 TATTCGTTTT
*
9155339 AATTAAATTCTT-ATGAATGAC
1 AATTAAATT-TTCACGAATGAC
9155360 AATTAAATTTTCACGAATGAC
1 AATTAAATTTTCACGAATGAC
9155381 AA
1 AA
9155383 CCTCTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
AATTAAATTTTCACGAATGAC
Found at i:9158037 original size:52 final size:49
Alignment explanation
Indices: 9157938--9158037 Score: 128
Period size: 52 Copynumber: 2.0 Consensus size: 49
9157928 TCCTATAGAG
* *
9157938 AACATATGGAAAGCATTAAACACGTTATATTATTTCCAAAAAGAATTAA
1 AACATATGGAAAGCATTAAAAACGTTATATTATTTCCAAAAAAAATTAA
* * *
9157987 AACATATGGAAAGTATTAAAAAAAACTTTATATTCTTTCCAAAAAAAATTA
1 AACATATGGAAAGCATT---AAAAACGTTATATTATTTCCAAAAAAAATTA
9158038 TAACTACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 16 0.37
52 27 0.63
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (49 bp):
AACATATGGAAAGCATTAAAAACGTTATATTATTTCCAAAAAAAATTAA
Found at i:9158091 original size:13 final size:13
Alignment explanation
Indices: 9158073--9158098 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9158063 CTAAATCATA
9158073 ATTATAATAATTT
1 ATTATAATAATTT
9158086 ATTATAATAATTT
1 ATTATAATAATTT
9158099 TAGCAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:9163592 original size:25 final size:25
Alignment explanation
Indices: 9163543--9163594 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
9163533 ATTCTAATTC
* *
9163543 TTAAAAAACTCTAACCCTAACAAAA
1 TTAAAAAAATCTAACCATAACAAAA
*
9163568 TTAAAAAAATCCTAACCATAAAAAAA
1 TTAAAAAAAT-CTAACCATAACAAAA
9163594 T
1 T
9163595 CCAATGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (25 bp):
TTAAAAAAATCTAACCATAACAAAA
Found at i:9164471 original size:22 final size:23
Alignment explanation
Indices: 9164431--9164481 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
9164421 TTATGAAAAC
*
9164431 AAAAAAAAACTCTTTAAAAT-TCA
1 AAAAAAAAACTCTTAAAAATAT-A
*
9164454 AAAAAAAAATTC-TAAAAATATA
1 AAAAAAAAACTCTTAAAAATATA
9164476 AAAAAA
1 AAAAAA
9164482 TCCAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAAAAAACTCTTAAAAATATA
Found at i:9164479 original size:23 final size:23
Alignment explanation
Indices: 9164431--9164481 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
9164421 TTATGAAAAC
* *
9164431 AAAAAAAAACTCTTTAAAATTCA
1 AAAAAAAAACTCTTAAAAATTAA
*
9164454 AAAAAAAAATTC-TAAAAATATAA
1 AAAAAAAAACTCTTAAAAAT-TAA
9164477 AAAAA
1 AAAAA
9164482 TCCAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAAAAAACTCTTAAAAATTAA
Found at i:9166022 original size:33 final size:33
Alignment explanation
Indices: 9165953--9166050 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
9165943 CTATACCCAT
* * *
9165953 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
9165990 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
9166023 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
9166051 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:9166310 original size:41 final size:41
Alignment explanation
Indices: 9166265--9166420 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
9166255 ACCGGCTCTT
*
9166265 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
9166306 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
9166347 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
9166388 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
9166421 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:9173661 original size:33 final size:33
Alignment explanation
Indices: 9173592--9173689 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
9173582 CTATACCCAT
* * *
9173592 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
9173629 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
9173662 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
9173690 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:9173949 original size:41 final size:41
Alignment explanation
Indices: 9173904--9174059 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
9173894 ACCGGCTCTT
*
9173904 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
9173945 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
9173986 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
9174027 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
9174060 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:9177068 original size:3 final size:3
Alignment explanation
Indices: 9177060--9177090 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
9177050 CCTCCTTCCC
9177060 CTT CTT CTT C-T CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
9177091 CATTTCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:9177083 original size:20 final size:19
Alignment explanation
Indices: 9177060--9177115 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
9177050 CCTCCTTCCC
*
9177060 CTTCTTCTTCTCTTCTTCTT
1 CTTCTTCTTCTCTT-TCCTT
9177080 CTTCTTCTTCTCATTTCCTT
1 CTTCTTCTTCTC-TTTCCTT
9177100 -TTCTTTCTTCTCTTTC
1 CTTC-TTCTTCTCTTTC
9177116 GTGCAGCTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 7 0.21
20 24 0.73
21 2 0.06
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (19 bp):
CTTCTTCTTCTCTTTCCTT
Found at i:9177338 original size:9 final size:10
Alignment explanation
Indices: 9177307--9177351 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
9177297 AATAAAATAG
9177307 TTGTATTATT
1 TTGTATTATT
9177317 TTGGTATTATT
1 TT-GTATTATT
*
9177328 TT-TATTTTT
1 TTGTATTATT
9177337 TTGTATTA-T
1 TTGTATTATT
9177346 TTGTAT
1 TTGTAT
9177352 AAAAAACTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 15 0.48
10 6 0.19
11 10 0.32
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (10 bp):
TTGTATTATT
Found at i:9177342 original size:19 final size:20
Alignment explanation
Indices: 9177310--9177347 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
9177300 AAAATAGTTG
9177310 TATTATTTTGGTATTATTTT
1 TATTATTTTGGTATTATTTT
*
9177330 TATT-TTTTTGTATTATTT
1 TATTATTTTGGTATTATTT
9177348 GTATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
TATTATTTTGGTATTATTTT
Found at i:9177874 original size:9 final size:9
Alignment explanation
Indices: 9177833--9177900 Score: 57
Period size: 10 Copynumber: 7.0 Consensus size: 9
9177823 TTCATATTTT
9177833 TAAAAAAT-
1 TAAAAAATA
*
9177841 TAAAAAAAA
1 TAAAAAATA
9177850 TTATAAAAATA
1 -TA-AAAAATA
*
9177861 TTAAAAAATC
1 -TAAAAAATA
9177871 TAAAGAATATA
1 TAAA-AA-ATA
9177882 TAAAAAATA
1 TAAAAAATA
9177891 TAAAATAATA
1 TAAAA-AATA
9177901 ATTTTTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
8 7 0.14
9 12 0.24
10 16 0.32
11 15 0.30
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (9 bp):
TAAAAAATA
Found at i:9177883 original size:29 final size:28
Alignment explanation
Indices: 9177832--9177895 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
9177822 ATTCATATTT
9177832 TTAAAAAATTAAAAAAAATTATAAAAATA
1 TTAAAAAATTAAAAAAAATTATAAAAA-A
* *
9177861 TTAAAAAATCTAAAGAATA-TATAAAAAA
1 TTAAAAAAT-TAAAAAAAATTATAAAAAA
9177889 TATAAAA
1 T-TAAAA
9177896 TAATAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 22 0.71
30 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (28 bp):
TTAAAAAATTAAAAAAAATTATAAAAAA
Found at i:9177885 original size:11 final size:10
Alignment explanation
Indices: 9177845--9177895 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
9177835 AAAAATTAAA
9177845 AAAAAT-TAT
1 AAAAATATAT
9177854 AAAAATAT-T
1 AAAAATATAT
*
9177863 AAAAA-ATCT
1 AAAAATATAT
9177872 AAAGAATATAT
1 AAA-AATATAT
9177883 AAAAA-ATAT
1 AAAAATATAT
9177892 AAAA
1 AAAA
9177896 TAATAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 2 0.05
9 24 0.65
10 5 0.14
11 6 0.16
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (10 bp):
AAAAATATAT
Found at i:9177885 original size:20 final size:18
Alignment explanation
Indices: 9177844--9177900 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
9177834 AAAAAATTAA
9177844 AAAAAATTATAAAAATATT
1 AAAAAATTA-AAAAATATT
*
9177863 AAAAAATCTAAAGAATATAT
1 AAAAAAT-TAAAAAATAT-T
9177883 AAAAAATATAAAATAATA
1 AAAAAAT-TAAAA-AATA
9177901 ATTTTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
20 14 0.44
21 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAAATTAAAAAATATT
Found at i:9178114 original size:18 final size:18
Alignment explanation
Indices: 9178091--9178128 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9178081 TAATTTAATT
*
9178091 TTAAAA-AATTAAATCAAA
1 TTAAAATAATAAAAT-AAA
9178109 TTAAAATAATAAAATAAA
1 TTAAAATAATAAAATAAA
9178127 TT
1 TT
9178129 TATCAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAATAATAAAATAAA
Found at i:9178395 original size:5 final size:5
Alignment explanation
Indices: 9178381--9178420 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
9178371 TTGTCTATGT
* * *
9178381 GTTGA GTTGA ATTGA GTTGA GTTGA GTTGG GTTGG GTTGA
1 GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA
9178421 AGAGGTTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.40
Consensus pattern (5 bp):
GTTGA
Found at i:9186624 original size:19 final size:19
Alignment explanation
Indices: 9186602--9186645 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
9186592 TTGATTCATT
9186602 CTATTTAATTATGAATTCA
1 CTATTTAATTATGAATTCA
* * *
9186621 CTATTTATTTATTATTTCA
1 CTATTTAATTATGAATTCA
9186640 CTATTT
1 CTATTT
9186646 TCAATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (19 bp):
CTATTTAATTATGAATTCA
Found at i:9191874 original size:27 final size:27
Alignment explanation
Indices: 9191838--9191910 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
9191828 CGAATATAAT
* *
9191838 AAATATTTTTTTTATTTTTTAATTTTA
1 AAATACTTTTTTAATTTTTTAATTTTA
*
9191865 AAATACTTTTTTAATTTTTTATTTTTA
1 AAATACTTTTTTAATTTTTTAATTTTA
** *
9191892 AAATAAATTTTTAGTTTTT
1 AAATACTTTTTTAATTTTT
9191911 ATTAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (27 bp):
AAATACTTTTTTAATTTTTTAATTTTA
Found at i:9194719 original size:19 final size:19
Alignment explanation
Indices: 9194692--9194729 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9194682 TCACATGTAT
9194692 AAATGCATGTACCAAATTA
1 AAATGCATGTACCAAATTA
* *
9194711 AAATTCATGTATCAAATTA
1 AAATGCATGTACCAAATTA
9194730 CACATTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (19 bp):
AAATGCATGTACCAAATTA
Found at i:9202343 original size:169 final size:169
Alignment explanation
Indices: 9202063--9202403 Score: 529
Period size: 169 Copynumber: 2.0 Consensus size: 169
9202053 GGCCTCCCCA
** *
9202063 AATTCAACGCTACAGATTAAAGTATGTCAACAACTAAGATTAAAAGCTATCTACAAATCAAACCT
1 AATTCAACGCTACAGATTAAAGTACATCAACAACTAAAATTAAAAGCTATCTACAAATCAAACCT
*
9202128 CTAATATTACAAAATCATATATTTTAAGATTACAAGTAAAATCTAAGATTGCATATCTTCAAAGA
66 CTAATATTACAAAATCATATATTCTAAGATTACAAGTAAAATCTAAGATTGCATATCTTCAAAGA
* *
9202193 TTACGTTCCATAATTGTCACGCTTTGTAGATGGGCCTTC
131 TTACGTTCCATAATTATCACGCTTTGTAGATGAGCCTTC
* * ** *
9202232 AATTCAATGCTACAGATTAAAGTCCATCAACGGCTAAAATTAAAAGCTATCTACAAATCAAATCT
1 AATTCAACGCTACAGATTAAAGTACATCAACAACTAAAATTAAAAGCTATCTACAAATCAAACCT
* * * * *
9202297 CTAATATTACAAAATCTTATCTTCTAAGGTTACAAGTAATATCTAAGATTGCATATCTTCGAAGA
66 CTAATATTACAAAATCATATATTCTAAGATTACAAGTAAAATCTAAGATTGCATATCTTCAAAGA
*
9202362 TTACGTTCCATAATTATCATGCTTTGTAGATGAGCCTTC
131 TTACGTTCCATAATTATCACGCTTTGTAGATGAGCCTTC
9202401 AAT
1 AAT
9202404 CTCTCCAAGC
Statistics
Matches: 155, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
169 155 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (169 bp):
AATTCAACGCTACAGATTAAAGTACATCAACAACTAAAATTAAAAGCTATCTACAAATCAAACCT
CTAATATTACAAAATCATATATTCTAAGATTACAAGTAAAATCTAAGATTGCATATCTTCAAAGA
TTACGTTCCATAATTATCACGCTTTGTAGATGAGCCTTC
Found at i:9203843 original size:2 final size:2
Alignment explanation
Indices: 9203836--9203869 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9203826 CCTCCCATTC
9203836 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9203870 GTGCTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9212983 original size:11 final size:11
Alignment explanation
Indices: 9212969--9213008 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
9212959 TTTGTTTTCT
9212969 TTATTTGTTTA
1 TTATTTGTTTA
*
9212980 TTATTTGTTTTT
1 TTATTTG-TTTA
9212992 TTATTTGTTTA
1 TTATTTGTTTA
9213003 TTATTT
1 TTATTT
9213009 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTATTTGTTTA
Found at i:9212997 original size:12 final size:12
Alignment explanation
Indices: 9212959--9213001 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
9212949 TCCGCTACTT
9212959 TTTGTTTTCTTTA
1 TTTGTTTT-TTTA
*
9212972 TTTG-TTTATTA
1 TTTGTTTTTTTA
9212983 TTTGTTTTTTTA
1 TTTGTTTTTTTA
9212995 TTTGTTT
1 TTTGTTT
9213002 ATTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 7 0.26
12 16 0.59
13 4 0.15
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTGTTTTTTTA
Found at i:9212998 original size:23 final size:24
Alignment explanation
Indices: 9212959--9213013 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
9212949 TCCGCTACTT
9212959 TTTGTTTTCTTTATTTGTTTATTA
1 TTTGTTTTCTTTATTTGTTTATTA
9212983 TTTGTTTT-TTTATTTGTTTATTA
1 TTTGTTTTCTTTATTTGTTTATTA
*
9213006 TTTATTTT
1 TTTGTTTT
9213014 ATAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTGTTTTCTTTATTTGTTTATTA
Found at i:9214382 original size:67 final size:68
Alignment explanation
Indices: 9214236--9214383 Score: 262
Period size: 68 Copynumber: 2.2 Consensus size: 68
9214226 CCCATTCAAA
9214236 TATTTTGTATTTTGTAGAAGAGAAGGAAGAAAGGAGAAAAAAAAACTTGTAAGGTATATAATAGT
1 TATTTTGTATTTTGTAGAAGAGAAGGAAGAAAGGAGAAAAAAAAACTTGTAAGGTATATAATAGT
9214301 ATG
66 ATG
*
9214304 TATTTTGTATTTTGTAGAAGAGAATGAAGAAAGGAGAAAAAAAAACTTGTAAGGTATAT-ATAGT
1 TATTTTGTATTTTGTAGAAGAGAAGGAAGAAAGGAGAAAAAAAAACTTGTAAGGTATATAATAGT
*
9214368 TTG
66 ATG
*
9214371 TATTTTATATTTT
1 TATTTTGTATTTT
9214384 ATAGTTATTG
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 19 0.25
68 58 0.75
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.35
Consensus pattern (68 bp):
TATTTTGTATTTTGTAGAAGAGAAGGAAGAAAGGAGAAAAAAAAACTTGTAAGGTATATAATAGT
ATG
Found at i:9215726 original size:10 final size:10
Alignment explanation
Indices: 9215706--9215775 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 10
9215696 GAATGAATAA
9215706 AAAAAGAAAAG
1 AAAAAG-AAAG
9215717 AAAAAGAAAG
1 AAAAAGAAAG
9215727 CCAACGAAACAGAAAG
1 --AA--AAA--GAAAG
9215743 AAAAAGAAAG
1 AAAAAGAAAG
*
9215753 AAAAGAAAAAG
1 AAAA-AGAAAG
*
9215764 AGAAAGAAAG
1 AAAAAGAAAG
9215774 AA
1 AA
9215776 GGAGAAAGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 19 0.40
11 14 0.29
12 5 0.10
14 5 0.10
16 5 0.10
ACGTcount: A:0.74, C:0.06, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:9216488 original size:24 final size:26
Alignment explanation
Indices: 9216434--9216488 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
9216424 GTGTTTTGCA
* *
9216434 ATTGAAATGAATTGATTTTGTATGTG
1 ATTGAAATGAATTGAATTTATATGTG
*
9216460 A-TGAAAT-TATTGAATTTATAT-TG
1 ATTGAAATGAATTGAATTTATATGTG
9216483 ATTGAA
1 ATTGAA
9216489 TTGGTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 15 0.60
25 6 0.24
26 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (26 bp):
ATTGAAATGAATTGAATTTATATGTG
Found at i:9219716 original size:25 final size:25
Alignment explanation
Indices: 9219631--9219790 Score: 167
Period size: 25 Copynumber: 6.6 Consensus size: 25
9219621 TTGTTATGCA
9219631 CTAATGAA-CAGAGAGCACTGAA-GTG
1 CTAAT-AATCAGAGAGCACT-AATGTG
9219656 CT-AT-A-CAGAGAGCAC-AGATGTG
1 CTAATAATCAGAGAGCACTA-ATGTG
*
9219678 CT-A-AA-CAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTAATGTG
* * *
9219700 CTAGTAATCAGAGAGCATTAACGTG
1 CTAATAATCAGAGAGCACTAATGTG
9219725 CTAATAATCAGAGAGCACTAATGTG
1 CTAATAATCAGAGAGCACTAATGTG
* *
9219750 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACTAATGTG
*
9219775 CTAATATTCAGAGAGC
1 CTAATAATCAGAGAGC
9219791 GCGCTAAAGT
Statistics
Matches: 117, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 35 0.30
24 4 0.03
25 76 0.65
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAATGTG
Found at i:9223449 original size:3 final size:3
Alignment explanation
Indices: 9223443--9223481 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
9223433 ACCACCACTG
9223443 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
9223482 CTCTCTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:9230332 original size:15 final size:15
Alignment explanation
Indices: 9230314--9230371 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
9230304 GAAAATATTC
9230314 AATATTTTAATAATA
1 AATATTTTAATAATA
*
9230329 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
9230348 AATATATTAATAATA
1 AATATTTTAATAATA
*
9230363 AATGTTTTA
1 AATATTTTA
9230372 TAGTATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:9230766 original size:32 final size:34
Alignment explanation
Indices: 9230728--9230800 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
9230718 CAACTTTTAT
*
9230728 AAAATATTTTTA-A-GAAATCTACCAAACAACAG
1 AAAATATTTTTACACGAAATCAACCAAACAACAG
* * *
9230760 AAAATA-TTTTACACGGATTCAACCAAACACCAG
1 AAAATATTTTTACACGAAATCAACCAAACAACAG
9230793 AAAATATT
1 AAAATATT
9230801 AACTTTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 5 0.15
32 7 0.21
33 21 0.62
34 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.25
Consensus pattern (34 bp):
AAAATATTTTTACACGAAATCAACCAAACAACAG
Done.