Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold40
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: 1915636
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 67970 characters in sequence are not A, C, G, or T
File 1 of 6
Found at i:1435 original size:16 final size:17
Alignment explanation
Indices: 1400--1438 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1390 ATTTATGAAA
1400 TATAAATTTTAATTACT
1 TATAAATTTTAATTACT
* *
1417 TATAATTTTTAA-TATT
1 TATAAATTTTAATTACT
1433 TATAAA
1 TATAAA
1439 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAAATTTTAATTACT
Found at i:2176 original size:90 final size:89
Alignment explanation
Indices: 2016--2232 Score: 219
Period size: 90 Copynumber: 2.4 Consensus size: 89
2006 GGACTATCTT
* * * * * *
2016 AAAAAGCCCTTAAACTTTTTTCAAAAAAAAATAATTAAACCTCTCTTTTTTTACACTCAATTGAG
1 AAAAAGCCCTCAAACTTTCTTCAAAAAAAAACAATTAAACCCCTATTTTTTTACACTCAATTGAA
2081 CATTTGAA-TTTTCAAAATGCATCG
66 CATTTGAACTTTT-AAAATGCATCG
* * *
2105 AAAAAGCCCTCAAAC-TTCTTCAAAAATAAAAGCAATTAAGCCCCTATTTTTTTTCACTTAATTG
1 AAAAAGCCCTCAAACTTTCTTCAAAAA-AAAA-CAATTAAACCCCTATTTTTTTACACTCAATTG
* * **
2169 AATATTTGAACTTTTAAAATACATAAAA
64 AACATTTGAACTTTTAAAATGCAT--CG
*
2197 AAAAAGACCCTCAAAATTT-TTC--AAAAAAACAATTAA
1 AAAAAG-CCCTCAAACTTTCTTCAAAAAAAAACAATTAA
2233 GCCTAAGCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
88 10 0.09
89 25 0.23
90 46 0.43
91 7 0.07
92 6 0.06
93 11 0.10
94 2 0.02
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.33
Consensus pattern (89 bp):
AAAAAGCCCTCAAACTTTCTTCAAAAAAAAACAATTAAACCCCTATTTTTTTACACTCAATTGAA
CATTTGAACTTTTAAAATGCATCG
Found at i:2649 original size:20 final size:21
Alignment explanation
Indices: 2624--2664 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2614 TATCTTTTAT
*
2624 TTATTT-TAATTTTTTATAAA
1 TTATTTCTAATTTTTAATAAA
2644 TTATTTCTAATTTTTAATAAA
1 TTATTTCTAATTTTTAATAAA
2665 AGCAGGGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTCTAATTTTTAATAAA
Found at i:2826 original size:89 final size:91
Alignment explanation
Indices: 2671--2842 Score: 231
Period size: 89 Copynumber: 1.9 Consensus size: 91
2661 TAAAAGCAGG
* *
2671 GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGGGTCTTTTTGATACATTTTAAAAATTCAAGTAC
1 GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATAC
*
2736 CCAATTGAGTGCAAAAAAAAAGTATA
66 CCAAATGAGTGCAAAAAAAAAGTATA
** * * * * *
2762 GGCTTAATTG-TTTTTTTG-AAAAGGTTTGAGAGTCTTTTTTATGCATTTTGAAAGTTTAAATAC
1 GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATAC
*
2825 CCAAATGATTGCAAAAAA
66 CCAAATGAGTGCAAAAAA
2843 GAAAAAACAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
89 52 0.74
90 8 0.11
91 10 0.14
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (91 bp):
GGCTTAATTGCTTTTTTTGAAAAAAATTTGAGAGTCTTTTTGATACATTTTAAAAATTCAAATAC
CCAAATGAGTGCAAAAAAAAAGTATA
Found at i:6997 original size:11 final size:11
Alignment explanation
Indices: 6981--7006 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6971 AACCAACACC
6981 AAAAAATTAAA
1 AAAAAATTAAA
6992 AAAAAATTAAA
1 AAAAAATTAAA
7003 AAAA
1 AAAA
7007 TTACTCGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:22175 original size:191 final size:195
Alignment explanation
Indices: 21843--22231 Score: 642
Period size: 191 Copynumber: 2.0 Consensus size: 195
21833 TATTTAGATT
*
21843 ATAAAAGTTATTTAATTCTAGCATTTGAGTACACCAAAACTTGCATACTAGTTAAATGATTACTT
1 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTG---ACTAG-TAAATGATTACTT
* * *
21908 AAATGGTAGTGTCTTGAGAAGGGCATGTTGGTTCTTTTACAGAAGCAACTTCACTTACTGTTTCT
62 AAATGGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCT
21973 TAAGCAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTC
127 TAAGCAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTC
22038 AGGA
192 AGGA
*
22042 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTG-C-A-T-AATGCTTACTTAAAT
1 ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTGACTAGTAAATGATTACTTAAAT
* *
22103 GGTGGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTGCCGGTTCTTAAG
66 GGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCTTAAG
*
22168 CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAATTCCAGATGGCCAATTTCAGG
131 CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTCAGG
22232 GATTCCATTT
Statistics
Matches: 182, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
191 137 0.75
192 1 0.01
194 1 0.01
195 1 0.01
199 42 0.23
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (195 bp):
ATAAAAGCTATTTAATTCTAGCATTTGAGTACACCAAAACTTGACTAGTAAATGATTACTTAAAT
GGTAGTGTCTTGAGAAGGACATGTTGGTTCTTTTACAGAAGCAACTTCACTTACCGGTTCTTAAG
CAGCTCCTGACCCTGAGCATTAAGTGCACTTGGGTGTTTAAAACTCCAGATGGCCAATTTCAGGA
Found at i:23720 original size:28 final size:28
Alignment explanation
Indices: 23680--23737 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
23670 ATGTAGGGGG
23680 TTAAAATGTTTTTACATGAAATCCTTTC
1 TTAAAATGTTTTTACATGAAATCCTTTC
23708 TTAAAATGTTTTTACATGAAATCCTTTC
1 TTAAAATGTTTTTACATGAAATCCTTTC
23736 TT
1 TT
23738 TCCTCTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (28 bp):
TTAAAATGTTTTTACATGAAATCCTTTC
Found at i:28742 original size:115 final size:113
Alignment explanation
Indices: 28578--28787 Score: 269
Period size: 115 Copynumber: 1.8 Consensus size: 113
28568 GCACCAGAGG
* * ** * *
28578 CATTTAAAATTTTTTTTTTGGATGCTGGCCAATAGATGGCCGGTACCAAGTACATTTTTCGGCTC
1 CATTTAAAATTTTTTTCTTGGATGCTGGCCAATAAATGGCCGACACCAAGTACATCTTTCAGCTC
*
28643 CCAAGAAACTTTTTTTTTTTACTTTGGGACACTAACGGCCTGCACTAGTGT
66 CCAAG--AC-ATTTTTTTTTACTTTGGGACACTAACGGCCTGCACTAGTGT
* * *
28694 CATTTAAAATTTTTTTCTTGG-TGCTGGCCAGTAAATGGTCGACACCAAGTCCATCTTTCAGCTC
1 CATTTAAAATTTTTTTCTTGGATGCTGGCCAATAAATGGCCGACACCAAGTACATCTTTCAGCTC
** *
28758 TTAAGGCATTTTTTTTTACTTTGGGACACT
66 CCAAGACATTTTTTTTTACTTTGGGACACT
28788 GATGGCCCGC
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
112 22 0.27
113 1 0.01
115 38 0.47
116 20 0.25
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (113 bp):
CATTTAAAATTTTTTTCTTGGATGCTGGCCAATAAATGGCCGACACCAAGTACATCTTTCAGCTC
CCAAGACATTTTTTTTTACTTTGGGACACTAACGGCCTGCACTAGTGT
Found at i:28896 original size:58 final size:58
Alignment explanation
Indices: 28764--28902 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 58
28754 GCTCTTAAGG
* * * * * * *
28764 CATTTTTTTTTACTTTGGGACACTGATGGCCCGCACCACCTTTTTCGGGTCCCAAAAA
1 CATTTTTTTTTATTTTGGGACACCGATGGCCCGCACCAACTTTATCAGATCCAAAAAA
* ** * *
28822 TATTTTTTTTGGTTTTGGGACACCGATGGCCGGCACCAACTTTATCAGAT-TAAAAAA
1 CATTTTTTTTTATTTTGGGACACCGATGGCCCGCACCAACTTTATCAGATCCAAAAAA
*
28879 CATTTTTTTCTTATTTTGGAACAC
1 CATTTTTTT-TTATTTTGGGACAC
28903 TAATAGCCGA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
57 13 0.20
58 51 0.80
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (58 bp):
CATTTTTTTTTATTTTGGGACACCGATGGCCCGCACCAACTTTATCAGATCCAAAAAA
Found at i:32235 original size:15 final size:16
Alignment explanation
Indices: 32202--32241 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
32192 AAGATAATTT
*
32202 AAATGAAATGAGAAAA
1 AAATTAAATGAGAAAA
32218 AAATTAAATGAGAAAA
1 AAATTAAATGAGAAAA
32234 AAA-TAAAT
1 AAATTAAAT
32242 TTAAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (16 bp):
AAATTAAATGAGAAAA
Found at i:32245 original size:21 final size:21
Alignment explanation
Indices: 32150--32270 Score: 83
Period size: 21 Copynumber: 5.7 Consensus size: 21
32140 GATGAAATAT
32150 ATAAA-TTAATATG-GAAAAAA
1 ATAAATTTAA-ATGAGAAAAAA
* *
32170 CATAAATTAAAATGGAAAAAAAA
1 -ATAAATTTAAAT-GAGAAAAAA
*
32193 AGATAATTTAAATGA-AATGAGAAA
1 ATA-AATTTAAATGAGAA--A-AAA
32217 A-AAA-TTAAATGAGAAAAAA
1 ATAAATTTAAATGAGAAAAAA
32236 ATAAATTTAAAT-AGAAAAAA
1 ATAAATTTAAATGAGAAAAAA
* *
32256 AGATAATTTAGATGA
1 ATA-AATTTAAATGA
32271 AATGGAAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
19 4 0.05
20 14 0.17
21 31 0.38
22 13 0.16
23 16 0.20
24 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.12, T:0.23
Consensus pattern (21 bp):
ATAAATTTAAATGAGAAAAAA
Found at i:32263 original size:63 final size:65
Alignment explanation
Indices: 32152--32284 Score: 184
Period size: 63 Copynumber: 2.1 Consensus size: 65
32142 TGAAATATAT
32152 AAATTAATATGGAAAAAACATAAATTAAAATGGAAAAAAAAAGATAATTTAAATGAAATGAGAAA
1 AAATTAATATGGAAAAAACATAAATTAAAAT-GAAAAAAAAAGATAATTTAAATGAAATG-GAAA
32217 -A
64 TA
* * *
32218 AAATTAA-ATGAGAAAAAA-ATAAATTTAAAT-AGAAAAAAAGATAATTTAGATGAAATGGAAAT
1 AAATTAATATG-GAAAAAACATAAATTAAAATGAAAAAAAAAGATAATTTAAATGAAATGGAAAT
32280 A
65 A
32281 AAAT
1 AAAT
32285 GAAAAAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
62 4 0.06
63 30 0.48
65 14 0.23
66 14 0.23
ACGTcount: A:0.65, C:0.01, G:0.12, T:0.23
Consensus pattern (65 bp):
AAATTAATATGGAAAAAACATAAATTAAAATGAAAAAAAAAGATAATTTAAATGAAATGGAAATA
Found at i:32684 original size:5 final size:5
Alignment explanation
Indices: 32674--32773 Score: 74
Period size: 5 Copynumber: 18.4 Consensus size: 5
32664 AAAAAAAATT
* *
32674 AATGA AATGA AATGTTA AATGA ATATGA AATGA AATGTA ATTTGT AATGA
1 AATGA AATGA AATG--A AATGA A-ATGA AATGA AATG-A A-ATGA AATGA
* * * *
32724 ATATGA AATGA AATGA AATGA ATTTGT AATGA TTATGA AATGG AATGA
1 A-ATGA AATGA AATGA AATGA A-ATGA AATGA -AATGA AATGA AATGA
32772 AA
1 AA
32774 GTTTAAAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
5 48 0.64
6 20 0.27
7 7 0.09
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (5 bp):
AATGA
Found at i:32706 original size:11 final size:10
Alignment explanation
Indices: 32674--32773 Score: 74
Period size: 11 Copynumber: 9.2 Consensus size: 10
32664 AAAAAAAATT
32674 AATGAAATGA
1 AATGAAATGA
32684 AATGTTAAATGA
1 AATG--AAATGA
32696 ATATGAAATGA
1 A-ATGAAATGA
* *
32707 AATGTAATTTGT
1 AATG-AA-ATGA
32719 AATGAATATGA
1 AATGAA-ATGA
32730 AATGAAATGA
1 AATGAAATGA
* *
32740 AATGAATTTGT
1 AATGAA-ATGA
*
32751 AATGATTATGA
1 AATGA-AATGA
*
32762 AATGGAATGA
1 AATGAAATGA
32772 AA
1 AA
32774 GTTTAAAAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
10 23 0.32
11 33 0.46
12 13 0.18
13 3 0.04
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (10 bp):
AATGAAATGA
Found at i:32706 original size:28 final size:29
Alignment explanation
Indices: 32674--32773 Score: 114
Period size: 28 Copynumber: 3.4 Consensus size: 29
32664 AAAAAAAATT
32674 AATGAAATGAAATGTT-AAATGAATATGA
1 AATGAAATGAAATGTTGAAATGAATATGA
* *
32702 AATGAAATGTAAT-TTGTAATGAATATGA
1 AATGAAATGAAATGTTGAAATGAATATGA
* *
32730 AATGAAATGAAATGAATTTGTAATGATTATGA
1 AATGAAATGAAATG---TTGAAATGAATATGA
*
32762 AATGGAATGAAA
1 AATGAAATGAAA
32774 GTTTAAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 2 0.03
28 35 0.56
32 25 0.40
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (29 bp):
AATGAAATGAAATGTTGAAATGAATATGA
Found at i:32753 original size:32 final size:33
Alignment explanation
Indices: 32692--32773 Score: 130
Period size: 32 Copynumber: 2.5 Consensus size: 33
32682 GAAATGTTAA
32692 ATGAATATGAAATGAAATGTAATTTGTAATGAAT
1 ATGAA-ATGAAATGAAATGTAATTTGTAATGAAT
*
32726 ATGAAATGAAATGAAATG-AATTTGTAATGATT
1 ATGAAATGAAATGAAATGTAATTTGTAATGAAT
*
32758 ATGAAATGGAATGAAA
1 ATGAAATGAAATGAAA
32774 GTTTAAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 28 0.61
33 13 0.28
34 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (33 bp):
ATGAAATGAAATGAAATGTAATTTGTAATGAAT
Found at i:32820 original size:18 final size:17
Alignment explanation
Indices: 32799--32832 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
32789 AATTATAAAT
32799 TGAAATGAAAACAAAAAC
1 TGAAATGAAAA-AAAAAC
32817 TGAAATGAAAAAAAAA
1 TGAAATGAAAAAAAAA
32833 TTAATATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (17 bp):
TGAAATGAAAAAAAAAC
Found at i:32891 original size:21 final size:20
Alignment explanation
Indices: 32866--32904 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
32856 AATATGAAAA
32866 AAATTGAAATGAGAAAAAATT
1 AAATTGAAATG-GAAAAAATT
*
32887 AAATTTAAATGGAAAAAA
1 AAATTGAAATGGAAAAAA
32905 AGATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (20 bp):
AAATTGAAATGGAAAAAATT
Found at i:32905 original size:21 final size:21
Alignment explanation
Indices: 32862--32918 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
32852 TATTAATATG
*
32862 AAAA-AAATTGAAAT-GAGAA
1 AAAAGAAATTTAAATGGAGAA
*
32881 AAAATTAAATTTAAATGGA-AA
1 AAAA-GAAATTTAAATGGAGAA
32902 AAAAGATAATTTAAATG
1 AAAAGA-AATTTAAATG
32919 AAATGGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 4 0.12
20 1 0.03
21 25 0.78
22 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAAGAAATTTAAATGGAGAA
Found at i:33356 original size:6 final size:6
Alignment explanation
Indices: 33345--33376 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
33335 CACTCGATGG
*
33345 ATCCTA ATCCTA ATTCTA ATCCTA ATCCTA AT
1 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA AT
33377 ATTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (6 bp):
ATCCTA
Found at i:35710 original size:89 final size:90
Alignment explanation
Indices: 35616--35825 Score: 262
Period size: 90 Copynumber: 2.3 Consensus size: 90
35606 ATTCTTGAAT
* * * * *
35616 ATTAATATACAAAAATATAAAATTTAAAC-AAAAATAATATG-CATTAAATTAAATTTAAACACC
1 ATTAATACACAAAAATATAAAATTCAAACTAAAAATAACA-GAAACTAAATTAAATTTAAACACC
*
35679 CAAAAAACTATAAACAGATGGGTAAA
65 CAAAAAACTAAAAACAGATGGGTAAA
* * * * *
35705 TTTAATACACAAAAATTTTAAATTCAAACTACATATAACAGAAACTAAATTAAATTTAAACACCC
1 ATTAATACACAAAAATATAAAATTCAAACTAAAAATAACAGAAACTAAATTAAATTTAAACACCC
*
35770 AACAAACTAAAAACAGATGGGTAAA
66 AAAAAACTAAAAACAGATGGGTAAA
* * *
35795 ATTAATACACGAAAATTTTAAATTCAAACTA
1 ATTAATACACAAAAATATAAAATTCAAACTA
35826 CATATAATAC
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
89 25 0.24
90 80 0.76
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (90 bp):
ATTAATACACAAAAATATAAAATTCAAACTAAAAATAACAGAAACTAAATTAAATTTAAACACCC
AAAAAACTAAAAACAGATGGGTAAA
Found at i:35768 original size:90 final size:90
Alignment explanation
Indices: 35660--35832 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 90
35650 TAATATGCAT
* *
35660 TAAATTAAATTTAAACACCCAAAAAACTATAAACAGATGGGTAAATTTAATACACAAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
35725 AATTCAAACTACATATAACAGAAAC
66 AATTCAAACTACATATAACAGAAAC
* *
35750 TAAATTAAATTTAAACACCCAACAAACTAAAAACAGATGGGTAAAATTAATACACGAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
35815 AATTCAAACTACATATAA
66 AATTCAAACTACATATAA
35833 TACCGGCTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.25
Consensus pattern (90 bp):
TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
AATTCAAACTACATATAACAGAAAC
Found at i:35874 original size:90 final size:90
Alignment explanation
Indices: 35660--35852 Score: 305
Period size: 90 Copynumber: 2.1 Consensus size: 90
35650 TAATATGCAT
* *
35660 TAAATTAAATTTAAACACCCAAAAAACTATAAACAGATGGGTAAATTTAATACACAAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
*
35725 AATTCAAACTACATATAACAGAAAC
66 AATTCAAACTACATATAACACAAAC
* *
35750 TAAATTAAATTTAAACACCCAACAAACTAAAAACAGATGGGTAAAATTAATACACGAAAATTTTA
1 TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
* ***
35815 AATTCAAACTACATATAATACCGGC
66 AATTCAAACTACATATAACACAAAC
35840 TAAATTAAATTTA
1 TAAATTAAATTTA
35853 CAGATACAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 94 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (90 bp):
TAAATTAAATTTAAACACCCAAAAAACTAAAAACAGATGGGTAAAATTAATACACAAAAATTTTA
AATTCAAACTACATATAACACAAAC
Found at i:36878 original size:111 final size:111
Alignment explanation
Indices: 36567--36894 Score: 453
Period size: 111 Copynumber: 2.9 Consensus size: 111
36557 CCAAAAAAGG
* * *
36567 TGGTGCCGGACATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTAGGAGCCGAAAAATGTACTTGG
1 TGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTGGGAGCCGGAAAATGTACTTGG
* * *
36632 TGCCGGCTAGCTGCTGGCC-GACACCCAAAATATTTCTTTAAATGACAC
66 TGCCGGCCATCTACTGGCCAG-CACCCAAAAT-TTT-TTTAAATGACAC
* *
36680 TGGTGTCGGCCATCAGTGTACCAAAGTAAAAAAAAAAGTGCCTTGGGAGCC-GAAACATGTACTT
1 TGGTGCCGGCCATCAGTGTCCCAAAGT-AAAAAAAAAGTGCCTTGGGAGCCGGAAA-ATGTACTT
*
36744 GGTGCCGACCATCTACTGGCCAGCACCCAAAATTTTTTTAAATGACAC
64 GGTGCCGGCCATCTACTGGCCAGCACCCAAAATTTTTTTAAATGACAC
* * *
36792 TGGTGCCGGCCATCAGTGTCCCAAAGTAAAATAAAAGTTCATTGGGAGCCGGAAAATGTACTTGG
1 TGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTGGGAGCCGGAAAATGTACTTGG
* * *
36857 TGCTGGCCATCTATTGACCAGCACCCAAAATTATTTTT
66 TGCCGGCCATCTACTGGCCAGCACCCAAAATT-TTTTT
36895 TTAAAATGCC
Statistics
Matches: 192, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
111 58 0.30
112 46 0.24
113 30 0.16
114 57 0.30
115 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (111 bp):
TGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAGTGCCTTGGGAGCCGGAAAATGTACTTGG
TGCCGGCCATCTACTGGCCAGCACCCAAAATTTTTTTAAATGACAC
Found at i:40334 original size:17 final size:17
Alignment explanation
Indices: 40312--40351 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
40302 GCTTATAGAC
40312 CCAAAAGAATTTGGGTA
1 CCAAAAGAATTTGGGTA
40329 CCAAAAGAATTTGGGTA
1 CCAAAAGAATTTGGGTA
40346 CCAAAA
1 CCAAAA
40352 ATCAAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (17 bp):
CCAAAAGAATTTGGGTA
Found at i:42406 original size:26 final size:26
Alignment explanation
Indices: 42357--42406 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
42347 AAGTTTAATT
* **
42357 AATTTTATATTTAAATAATTTAATAA
1 AATTATATATTTAAATAAGATAATAA
42383 AATTATATATTTAAATAAGATAAT
1 AATTATATATTTAAATAAGATAAT
42407 TGATCAGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTATATATTTAAATAAGATAATAA
Found at i:42406 original size:31 final size:30
Alignment explanation
Indices: 42319--42407 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 30
42309 TTTAATTTAA
*
42319 TTAATAAAATTACATACTTAAATGAAGA-AAGT
1 TTAATAAAATTATATA-TTAAAT-AAGATAA-T
* *
42351 TTAAT-TAATTTTATATT---TAA-ATAAT
1 TTAATAAAATTATATATTAAATAAGATAAT
42376 TTAATAAAATTATATATTTAAATAAGATAAT
1 TTAATAAAATTATATA-TTAAATAAGATAAT
42407 T
1 T
42408 GATCAGCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
25 7 0.16
26 12 0.27
27 3 0.07
30 5 0.11
31 13 0.29
32 5 0.11
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (30 bp):
TTAATAAAATTATATATTAAATAAGATAAT
Found at i:45647 original size:5 final size:5
Alignment explanation
Indices: 45637--45669 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
45627 GAAAATTTTT
45637 GATTC GATTC GATTC GATTC GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GATTC GAT
45670 CGAATGCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:53551 original size:19 final size:20
Alignment explanation
Indices: 53524--53562 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
53514 TATGTGCTAT
*
53524 AAATTACATAATAT-ATATA
1 AAATAACATAATATAATATA
53543 AAATAACATAATATAATATA
1 AAATAACATAATATAATATA
53563 TTATACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAACATAATATAATATA
Found at i:56608 original size:16 final size:16
Alignment explanation
Indices: 56589--56621 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56579 TCCCAAAATT
56589 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
*
56605 AAAAGAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
56621 A
1 A
56622 GTAAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:68009 original size:18 final size:19
Alignment explanation
Indices: 67974--68011 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
67964 AAAATAATAA
*
67974 TATTATTTTGATATTATTT
1 TATTATTTTGATAATATTT
*
67993 TATTTTTTTG-TAATATTT
1 TATTATTTTGATAATATTT
68011 T
1 T
68012 TATAAAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TATTATTTTGATAATATTT
Found at i:69636 original size:22 final size:20
Alignment explanation
Indices: 69597--69647 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
69587 AATAAAAAAA
*
69597 TGCTATTTTTTTTGTTTTCT
1 TGCTATTTTTTTTATTTTCT
*
69617 TGCTATTTTTTTTAAATTTTGT
1 TGCTATTTTTTTT--ATTTTCT
69639 TGCTATTTT
1 TGCTATTTT
69648 CTTCTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.71
Consensus pattern (20 bp):
TGCTATTTTTTTTATTTTCT
Found at i:71262 original size:40 final size:41
Alignment explanation
Indices: 71216--71298 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
71206 AATTCATTAC
* * *
71216 TTTAGTAATTTCACAGTTCAATGCAGTACACA-TAACAATA
1 TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
* *
71256 TTTAGTAACTTCACAATTCAATTCAGTACTCAGAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
71297 TT
1 TT
71299 CAGTTCAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 28 0.76
41 9 0.24
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (41 bp):
TTTAGTAACTTCACAATTCAATGCAGTACACAGAAACAATA
Found at i:73614 original size:12 final size:12
Alignment explanation
Indices: 73597--73644 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 12
73587 AATTAAAGTA
73597 AAATAATATTTT
1 AAATAATATTTT
*
73609 AAATAAT-TATT
1 AAATAATATTTT
*
73620 -AATAATATTAT
1 AAATAATATTTT
73631 AAA-AATA-TTT
1 AAATAATATTTT
73641 AAAT
1 AAAT
73645 GTTCTTGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
10 11 0.38
11 9 0.31
12 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:75031 original size:31 final size:30
Alignment explanation
Indices: 74976--75034 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
74966 GTAAATACTC
***
74976 AAAATTTGAAGGGTTAAAGTGTAAATATAA
1 AAAATTTGAAGGACCAAAGTGTAAATATAA
75006 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAA-AGTGTAAATAT
75035 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAATTTGAAGGACCAAAGTGTAAATATAA
Found at i:76223 original size:21 final size:21
Alignment explanation
Indices: 76197--76290 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 21
76187 TTTTACTTTT
**
76197 TGTTTAGCTTTTACGAGCTTC
1 TGTTTAGCTCATACGAGCTTC
* * *
76218 TGTTTAACTCATATGAGTTTC
1 TGTTTAGCTCATACGAGCTTC
* * ** **
76239 CGTTCAGCTTTTTTGAGCTTC
1 TGTTTAGCTCATACGAGCTTC
* *
76260 TGTTTACCTCATACGAGTTTC
1 TGTTTAGCTCATACGAGCTTC
*
76281 CGTTTAGCTC
1 TGTTTAGCTC
76291 CTTTGAGCTT
Statistics
Matches: 51, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
TGTTTAGCTCATACGAGCTTC
Found at i:76249 original size:42 final size:42
Alignment explanation
Indices: 76198--76389 Score: 190
Period size: 42 Copynumber: 4.6 Consensus size: 42
76188 TTTACTTTTT
*
76198 GTTTAGCTTTTACGAGCTTCTGTTTAACTCATATGAGTTTCC
1 GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
* * * *
76240 GTTCAGCTTTTTTGAGCTTCTGTTTACCTCATACGAGTTTCC
1 GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
* * * * *
76282 GTTTAGCTCCTT-TGAGCTTCTATTTAAACT-TTATGGGTTTTC
1 GTTTAGCT-TTTATGAGCTTCTGTTT-AACTCATATGAGTTTCC
* * * * * * *
76324 GTTAAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCT
1 GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
*
76366 GTTTAGCTTTCATGAGCTTCTGTT
1 GTTTAGCTTTTATGAGCTTCTGTT
76390 CAGCCTCCGG
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 6 0.05
42 113 0.91
43 5 0.04
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
GTTTAGCTTTTATGAGCTTCTGTTTAACTCATATGAGTTTCC
Found at i:76356 original size:21 final size:21
Alignment explanation
Indices: 76332--76391 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
76322 TCGTTAAGCT
76332 CTTATGAGCTTCTGTTCAACC
1 CTTATGAGCTTCTGTTCAACC
* * * *
76353 CTTATGGGTTTCTGTT-TAGC
1 CTTATGAGCTTCTGTTCAACC
*
76373 TTTCATGAGCTTCTGTTCA
1 CTT-ATGAGCTTCTGTTCA
76392 GCCTCCGGGC
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (21 bp):
CTTATGAGCTTCTGTTCAACC
Found at i:76524 original size:2 final size:2
Alignment explanation
Indices: 76517--76544 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76507 ATGTATTATG
76517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76545 CAATATCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78261 original size:41 final size:39
Alignment explanation
Indices: 78142--78277 Score: 114
Period size: 41 Copynumber: 3.5 Consensus size: 39
78132 ACCAGTTTGG
* ** * *
78142 CACCCAGTGCCTTATCGAATAATTTGAAGCAATAATTTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAG-AGTAAATTGA
* * ** *
78182 CACTCAGTGTCTCATCGGCTAAACCG-A-AGTAAATTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGAGTAAATTGA
78219 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAG-AGTAAATTGA
* * *
78260 CATCTAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
78278 CTCAAAGTCA
Statistics
Matches: 74, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 23 0.31
38 6 0.08
39 2 0.03
40 18 0.24
41 25 0.34
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGAGTAAATTGA
Found at i:78470 original size:24 final size:24
Alignment explanation
Indices: 78433--78479 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
78423 TATATATACC
78433 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
78457 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
78480 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:79217 original size:21 final size:20
Alignment explanation
Indices: 79180--79220 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
79170 TTTCGTTTGG
79180 CTTTCTCTATTTC-TTTCTTT
1 CTTT-TCTATTTCTTTTCTTT
79200 CTTTTCTATTTCTATTTCTTT
1 CTTTTCTATTTCT-TTTCTTT
79221 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
CTTTTCTATTTCTTTTCTTT
Found at i:87538 original size:7 final size:7
Alignment explanation
Indices: 87528--87615 Score: 85
Period size: 7 Copynumber: 12.4 Consensus size: 7
87518 AAAAATTCAA
87528 AAAAATC
1 AAAAATC
87535 AAAAATC
1 AAAAATC
87542 AAAAATC
1 AAAAATC
87549 AAAAATC
1 AAAAATC
87556 AAAAAATC
1 -AAAAATC
87564 AAAAAAAATC
1 ---AAAAATC
87574 AAAAAATC
1 -AAAAATC
*
87582 -AAAA-G
1 AAAAATC
87587 AAAAA-C
1 AAAAATC
87593 AAAAAT-
1 AAAAATC
*
87599 AAAAATA
1 AAAAATC
87606 AAAAATC
1 AAAAATC
87613 AAA
1 AAA
87616 TTCAAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
6 19 0.26
7 30 0.42
8 15 0.21
10 8 0.11
ACGTcount: A:0.77, C:0.10, G:0.01, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:87598 original size:18 final size:19
Alignment explanation
Indices: 87526--87615 Score: 89
Period size: 18 Copynumber: 4.6 Consensus size: 19
87516 AAAAAAATTC
87526 AAAAAAATC-AAAAATCAAA
1 AAAAAAATCAAAAAATC-AA
87545 AATCAAAAATCAAAAAATC-A
1 AA--AAAAATCAAAAAATCAA
87565 AAAAAAATCAAAAAATCAA
1 AAAAAAATCAAAAAATCAA
*
87584 AAGAAAAA-C-AAAAATAAAA
1 AA-AAAAATCAAAAAAT-CAA
87603 ATAAAAAATCAAA
1 A-AAAAAATCAAA
87616 TTCAAAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
18 21 0.34
19 14 0.23
20 10 0.16
21 9 0.15
22 7 0.11
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (19 bp):
AAAAAAATCAAAAAATCAA
Found at i:87602 original size:5 final size:6
Alignment explanation
Indices: 87528--87609 Score: 51
Period size: 6 Copynumber: 12.8 Consensus size: 6
87518 AAAAATTCAA
*
87528 AAAAAT CAAAAAT CAAAAAT CAAAAAT CAAAAA- ATCAAA- AAAAAT CAAAAAAT
1 AAAAAT -AAAAAT -AAAAAT -AAAAAT -AAAAAT A-AAAAT AAAAAT --AAAAAT
* * *
87581 CAAAAG AAAAAC AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
87610 ATCAAATTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
5 4 0.06
6 28 0.44
7 26 0.41
8 6 0.09
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (6 bp):
AAAAAT
Found at i:87609 original size:39 final size:40
Alignment explanation
Indices: 87526--87615 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
87516 AAAAAAATTC
**
87526 AAAAAAATC-AAAAATCAAAAATCAAAAATCAAAAAATCA
1 AAAAAAATCAAAAAATCAAAAATCAAAAATCAAAAAAAAA
*
87565 AAAAAAATCAAAAAATC-AAAA-GAAAAA-CAAAAATAAAA
1 AAAAAAATCAAAAAATCAAAAATCAAAAATCAAAAA-AAAA
87603 ATAAAAAATCAAA
1 A-AAAAAATCAAA
87616 TTCAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
37 6 0.13
38 8 0.18
39 24 0.53
40 7 0.16
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (40 bp):
AAAAAAATCAAAAAATCAAAAATCAAAAATCAAAAAAAAA
Found at i:88493 original size:15 final size:14
Alignment explanation
Indices: 88475--88511 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
88465 AAAATGATGA
88475 AAAAAATGAAAAATG
1 AAAAAATGAAAAA-G
88490 AAAAAATGAAAAAG
1 AAAAAATGAAAAAG
*
88504 TAAAAATG
1 AAAAAATG
88512 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAATGAAAAAG
Found at i:93298 original size:86 final size:85
Alignment explanation
Indices: 93119--93420 Score: 345
Period size: 86 Copynumber: 3.5 Consensus size: 85
93109 CAATAAAGTT
* * * * * *
93119 GCAGATCTTGCCTTACTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGG
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAACTTGCCT-TCATTGG
** *
93183 TTGTGATGGAGCTAGTTAAAGAA
63 TTGCAATGGAGCTGGTTAAAGAA
* *
93206 GCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGTTCGAAAACAAAGACTTGCCTTCATTGGTT
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAA-ACTTGCCTTCATTGGTT
93271 GCAATGGAGCTGGTTAAAGAA
65 GCAATGGAGCTGGTTAAAGAA
* * * *
93292 GTAGATCTTGTCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAAACCTTACCTTCATTGGTT
1 GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAA-CTTGCCTTCATTGGTT
*
93357 GCAATGGAACTGGTTAAAGATA
65 GCAATGGAGCTGGTTAAAGA-A
* * * **
93379 GCAGATCATGCCTTCCTGTACTGGCAAGCGAAGCAGATCGAA
1 GCAGATCTTGCCTTCCTGCATTAAC-AGCGAAGCAGATCGAA
93421 GACACAAGCC
Statistics
Matches: 185, Mismatches: 25, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
85 8 0.04
86 107 0.58
87 55 0.30
88 15 0.08
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (85 bp):
GCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAACTTGCCTTCATTGGTTG
CAATGGAGCTGGTTAAAGAA
Found at i:93479 original size:90 final size:89
Alignment explanation
Indices: 93376--93538 Score: 254
Period size: 89 Copynumber: 1.8 Consensus size: 89
93366 CTGGTTAAAG
* * **
93376 ATAGCAGATCATGCCTTCCTGTACTGGCAAGCGAAGCAGATCGAAGACACAAGCCTTGCCTTTCT
1 ATAGCAGATCATGCATTCCTATACTGGC-AGCGAAGCAGATCGAAGACACAAGCCTTGCCTGCCT
93441 GTACTGACAGTGAAGTAGATTGAAA
65 GTACTGACAGTGAAGTAGATTGAAA
* * *
93466 ATAGCAGATCATGCATTCCTATGCTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTGCCTG
1 ATAGCAGATCATGCATTCCTATACTGGCAGCGAAGCAGATCGAAGACACAAGCCTTGCCTGCCTG
93531 TACTGACA
66 TACTGACA
93539 ACGAAGCAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
89 41 0.62
90 25 0.38
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (89 bp):
ATAGCAGATCATGCATTCCTATACTGGCAGCGAAGCAGATCGAAGACACAAGCCTTGCCTGCCTG
TACTGACAGTGAAGTAGATTGAAA
Found at i:93642 original size:50 final size:49
Alignment explanation
Indices: 93565--94141 Score: 393
Period size: 50 Copynumber: 11.8 Consensus size: 49
93555 AAACCATAGT
* *
93565 TTGCAATTTAAAATATTGAAG-TCACAACAGCAGATCTTACTTCCCTGACA
1 TTGCAA-TTAAAAGATTGAAGCT-ACAACAGCGGATCTTACTTCCCTGACA
* * * **
93615 TTGTAATTAAGAAGATTAAAGCTACAACAGCGGATCTTACTTTCCT-AGTG
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * *
93665 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * *
93715 TTGTAATTAAGAAGATTGAAGCTACAATAGCGGATCTTACTTTCCT-AGCG
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * *
93765 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * **
93815 TTGCAATTAAAAAGATTGAAGTTACAACAGCGGATCTTACTTTCCT-AGTG
1 TTGCAATT-AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * ** *
93865 TTGCAGTGGAACGGATTGAAGCTACAATAGCGGAT-TGT--TTCCC---C-
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCT-TACTTCCCTGACA
* * * **
93909 -GGCAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGTG
1 TTGCAATT-AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * * *
93958 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTATTTCCC---C-
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * ** * * *
94004 -GGCAGTTAAAAGGATT-AAGGCTACAACAATGGATCTTATTTTCCT-AGCG
1 TTGCAATTAAAA-GATTGAA-GCTACAACAGCGGATCTTACTTCCCTGA-CA
* * *
94053 TTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * *
94103 TTGCATTTAAAAATATTGAAGCTACATCAGCGAATCTTA
1 TTGCAATT-AAAAGATTGAAGCTACAACAGCGGATCTTA
94142 TCTCCCAGGC
Statistics
Matches: 416, Mismatches: 77, Indels: 68
0.74 0.14 0.12
Matches are distributed among these distances:
43 29 0.07
44 6 0.01
45 35 0.08
48 5 0.01
49 10 0.02
50 318 0.76
51 13 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (49 bp):
TTGCAATTAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:93738 original size:100 final size:100
Alignment explanation
Indices: 93579--94244 Score: 770
Period size: 100 Copynumber: 6.8 Consensus size: 100
93569 AATTTAAAAT
* * *
93579 ATTGAAG-TCACAACAGCAGATCTTACTTCCCTGACATTGTAATTAAGAAGATTAAAGCTACAAC
1 ATTGAAGCT-ACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAAC
93643 AGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
65 AGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
* *
93679 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAGAAGATTGAAGCTACAATA
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAACA
*
93744 GCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAG
66 GCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
* *
93779 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGTTACAACA
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAACA
*
93844 GCGGATCTTACTTTCCTAGTGTTGCAGTGGAACGG
66 GCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
* * *
93879 ATTGAAGCTACAATAGCGGAT-TGT--TTCCCCGGCA--G---TTAAAAAGATTGAAGCTACAAC
1 ATTGAAGCTACAACAGCGGATCT-TACTTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAAC
93936 AGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
65 AGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
* * * *
93972 ATTGAAGCTACAACAGCGGATCTTATTTCCCCGGCA--G---TTAAAAGGATT-AAGGCTACAAC
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAAAGATTGAA-GCTACAAC
** * *
94031 AATGGATCTTATTTTCCTAGCGTTGCAGTGGAACAG
65 AGCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
* * * *
94067 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAATATTGAAGCTACATCA
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAACA
* * * * * *
94132 GCGAATCTTA-TCTCCCAGGCGGTGCAGTGGAATAG
66 GCGGATCTTACTTTCCTA-GTGTTGCAGTGGAACAG
* * * * * * * * *** * *
94167 ATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACATTGCGGTTAAAAAAAGATTAAAGCTACAG
1 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATT--AAAAAGATTGAAGCTACAA
*
94232 CAGCGAATCTTAC
64 CAGCGGATCTTAC
94245 CTCCCAGGCG
Statistics
Matches: 503, Mismatches: 47, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
93 77 0.15
94 3 0.01
95 94 0.19
96 1 0.00
97 1 0.00
98 8 0.02
99 6 0.01
100 282 0.56
101 3 0.01
102 28 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (100 bp):
ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAACA
GCGGATCTTACTTTCCTAGTGTTGCAGTGGAACAG
Found at i:94287 original size:102 final size:100
Alignment explanation
Indices: 94095--94326 Score: 304
Period size: 102 Copynumber: 2.3 Consensus size: 100
94085 GATCTTACTT
* * * * *
94095 CCCTGACATTGCATTTAAAAATATTGAAGCTACATCAGCGAATCTTATCTCCCAGGCGGTGCAGT
1 CCCT-ACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGCAGT
* * *
94160 GGAATAGATTAAAGCCACAACGGTGAATCTTGCCT-
65 GAAACAGATTAAAACCACAACGGTGAATCTTGCCTC
* * *
94195 CTCTGACATTGCGGTTAAAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGTA
1 CCCT-ACATTGCAGTT--AAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGCA
* *
94260 GTGAAACAGATTAAAACCACATCGGTGAATCTTGCTTC
63 GTGAAACAGATTAAAACCACAACGGTGAATCTTGCCTC
94298 CCCTACATTGCAGTTAAAAAGATTAAAGC
1 CCCTACATTGCAGTTAAAAAGATTAAAGC
94327 CACATCGGTG
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
100 27 0.24
102 84 0.74
103 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (100 bp):
CCCTACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGCAGTG
AAACAGATTAAAACCACAACGGTGAATCTTGCCTC
Found at i:94290 original size:50 final size:50
Alignment explanation
Indices: 94111--94342 Score: 158
Period size: 50 Copynumber: 4.6 Consensus size: 50
94101 CATTGCATTT
* * * * * *
94111 AAAAATATTGAAGCTACATCAGCGAATCTTATCTCCCAGGCGGTGCAGTG
1 AAAAAGATTAAAGCCACATCGGTGAATCTTACCTCCCAGGCGGTGCAGTG
* * * * * * * ** * *
94161 GAATAGATTAAAGCCACAACGGTGAATCTTGCCTCTCTGACATTGCGGTTAA
1 AAAAAGATTAAAGCCACATCGGTGAATCTTACCTCCCAGGCGGTGCAG-T-G
* * * * *
94213 AAAAAGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGTAGTG
1 AAAAAGATTAAAGCCACATCGGTGAATCTTACCTCCCAGGCGGTGCAGTG
* * * * *** ** *
94263 AAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCTACATTGCAGTT
1 AAAAAGATTAAAGCCACATCGGTGAATCTTACCTCCCAGGCGGTGCAGTG
94313 AAAAAGATTAAAGCCACATCGGTGAATCTT
1 AAAAAGATTAAAGCCACATCGGTGAATCTT
94343 GATTAAAGCT
Statistics
Matches: 131, Mismatches: 49, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
50 95 0.73
51 2 0.02
52 34 0.26
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (50 bp):
AAAAAGATTAAAGCCACATCGGTGAATCTTACCTCCCAGGCGGTGCAGTG
Found at i:94343 original size:50 final size:50
Alignment explanation
Indices: 94165--94343 Score: 162
Period size: 50 Copynumber: 3.5 Consensus size: 50
94155 GCAGTGGAAT
* * *
94165 AGATTAAAGCCACAACGGTGAATCTTGCCT-CTCTGACATTGCGGTTAAAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCCTCCCCT-ACATTGCAGTT--AAAA
* * * * * *** ** * * *
94217 AGATTAAAGCTACAGCAGCGAATCTTACCTCCCAGGCGGTGTAGTGAAAC
1 AGATTAAAGCCACATCGGTGAATCTTGCCTCCCCTACATTGCAGTTAAAA
* *
94267 AGATTAAAACCACATCGGTGAATCTTGCTTCCCCTACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCCTCCCCTACATTGCAGTTAAAA
94317 AGATTAAAGCCACATCGGTGAATCTTG
1 AGATTAAAGCCACATCGGTGAATCTTG
94344 ATTAAAGCTA
Statistics
Matches: 95, Mismatches: 31, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
50 64 0.67
52 30 0.32
53 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGTGAATCTTGCCTCCCCTACATTGCAGTTAAAA
Found at i:94364 original size:25 final size:25
Alignment explanation
Indices: 94318--94367 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
94308 CAGTTAAAAA
* * *
94318 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
94343 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
94368 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:94614 original size:25 final size:25
Alignment explanation
Indices: 94568--94617 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
94558 CAGTTAAAAA
* * *
94568 GATTAAAGCCACATCCGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
94593 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
94618 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:94717 original size:125 final size:125
Alignment explanation
Indices: 94218--94705 Score: 807
Period size: 125 Copynumber: 3.9 Consensus size: 125
94208 GTTAAAAAAA
* * * * *
94218 GATTAAAGCTACAGCAGCGAATCTTAC-CTCCCAGGCGGTGTAGTGAAACAGATTAAAACCACAT
1 GATTAAAGCTACAACAGCGAATCTTACGC-CCCAAGCGATGCAGTGGAACAGATTAAAACCACAT
94282 CGGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
65 CGGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
94343 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
*
94408 GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAATATTAAAGCCACATCGGTGAATCTT
66 GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
* * *
94468 GATTAAAGCTACAACAACGAATCTTACGCCTCAAGCGATGCAGTAGAACAGATTAAAACCACATC
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
*
94533 GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCCGTGAATCTT
66 GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
* * *
94593 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAGCCAAATT
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
* * * *
94658 GGTGAATCTTGTTTCTCCGATATTGCAGTTAAAAAGATTAAAGCCACA
66 GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACA
94706 ATGATGAATC
Statistics
Matches: 341, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
125 340 1.00
126 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (125 bp):
GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
Found at i:94867 original size:44 final size:43
Alignment explanation
Indices: 94738--94996 Score: 146
Period size: 44 Copynumber: 5.9 Consensus size: 43
94728 AGTTACGAGT
* * ** * *
94738 TACAAATCCTATCTCCCTGATA-TTACAGTGGAGTGGATCGAAC
1 TACAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTGAAG
* * * * *
94781 AACCAAAGTCTTATCCCCCTGAAGATGCAGTGGGGCAAATTGAAG
1 TA-CAAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
* *
94826 ATACAAATCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAG
1 -TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
* * * * *
94870 -CCGATAATCCTATCTCCCT-AAGGTTGCAGAGGAGCGGATTAAAG
1 TAC-A-AATCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTGAAG
* * * * * * *
94914 TAGTAGATCTTATCTCCCTAAAGTTGCAGTGGAGCGGGTTAAAA
1 TA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
*** * *
94958 TGATTGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 T-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
94997 CGCATCAGAC
Statistics
Matches: 167, Mismatches: 38, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 129 0.77
45 33 0.20
46 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
Found at i:100468 original size:7 final size:7
Alignment explanation
Indices: 100456--100482 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
100446 CTAGTAGTTC
100456 TTTGATA
1 TTTGATA
100463 TTTGATA
1 TTTGATA
100470 TTTGATA
1 TTTGATA
100477 TTTGAT
1 TTTGAT
100483 TAAGTTCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
TTTGATA
Found at i:102144 original size:9 final size:9
Alignment explanation
Indices: 102127--102157 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
102117 TCGAGTTGAT
102127 TCGAATAAC
1 TCGAATAAC
*
102136 TCGATTAAC
1 TCGAATAAC
102145 TCGAATAAC
1 TCGAATAAC
102154 TCGA
1 TCGA
102158 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:106090 original size:41 final size:41
Alignment explanation
Indices: 106034--106137 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
106024 ATGTAAACAT
* * *
106034 GGCACATATGTGCAATTCAGGGGTACCAAAGTATAATCAGG
1 GGCACATATGTGCAATTTAGGGGTACCAAAGTACAAACAGG
** ** **
106075 GGCATGTATGTGCAATTTAAAGGTACTGAAGTACAAACAGG
1 GGCACATATGTGCAATTTAGGGGTACCAAAGTACAAACAGG
106116 GGCACATATGTGCAATTTAGGG
1 GGCACATATGTGCAATTTAGGG
106138 AATAATTAAC
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (41 bp):
GGCACATATGTGCAATTTAGGGGTACCAAAGTACAAACAGG
Found at i:109936 original size:16 final size:16
Alignment explanation
Indices: 109915--109947 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
109905 AGGATCAAGT
109915 TATAGG-TTGAAAAAAA
1 TATAGGATT-AAAAAAA
109931 TATAGGATTAAAAAAA
1 TATAGGATTAAAAAAA
109947 T
1 T
109948 TTTAGTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (16 bp):
TATAGGATTAAAAAAA
Found at i:120484 original size:18 final size:18
Alignment explanation
Indices: 120449--120493 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
120439 GCAATAAGTG
**
120449 ACGTTTTGAAACTTAATA
1 ACGTTTTGAAACAGAATA
*
120467 ACGTTTTGAAAGAGAATA
1 ACGTTTTGAAACAGAATA
120485 AC-TTTTGAA
1 ACGTTTTGAA
120494 TACAAATCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAACAGAATA
Found at i:121148 original size:19 final size:19
Alignment explanation
Indices: 121126--121162 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
121116 AATTACAGAC
121126 TTTT-GAACTTTTAATTTTT
1 TTTTAGAAC-TTTAATTTTT
121145 TTTTAGAACTTTAATTTT
1 TTTTAGAACTTTAATTTT
121163 GATTTTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTAGAACTTTAATTTTT
Found at i:121168 original size:20 final size:19
Alignment explanation
Indices: 121126--121169 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
121116 AATTACAGAC
*
121126 TTTTGAACTTTTAATTTTT
1 TTTTGAACTTTTAATTTTA
121145 TTTTAGAAC-TTTAATTTTGA
1 TTTT-GAACTTTTAATTTT-A
121165 TTTTG
1 TTTTG
121170 GTATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTTGAACTTTTAATTTTA
Found at i:123586 original size:224 final size:221
Alignment explanation
Indices: 123176--123622 Score: 691
Period size: 224 Copynumber: 2.0 Consensus size: 221
123166 CTCTGCAGCG
* * *
123176 ATCAACGAGCAAACATTTTTTTTCTATTACTAGAACGCCAAAAAATATAGAAAGGAAAAAAATAA
1 ATCAACGAACAAACATTTTTTTTCTATTACCAAAACGCCAAAAAATATAGAAAGGAAAAAAATAA
*
123241 TTTTGAGAGTAAAATAAATTCTGTGTGAGAAAGTATGATGTAGAAAAATTCTTCAAAATTCATAG
66 TTTTGAGAGGAAAATAAATTCTGTGTGAGAAAGTATGATGTAGAAAAATTCTTCAAAATTCATAG
* * * * *
123306 CCTTTTATAGGCATTCAGTATGGTGAAATTTTTGAAATTTCCAAAAAAATTACCTTTAATGGAGC
131 CCTTTTATAGCCATTCAGCATGGTGAAATTTTGGAAATTTCCAAAAAAAATACCTTTAAAGGAGC
123371 CAATAAATCAATTTGATTAAAATTAA
196 CAATAAATCAATTTGATTAAAATTAA
* *** *
123397 ATCAACGAACAGACATTTCCTTTTTCTATTACCAAAACGTTGAAAAATATAGAAAGGAAAAGAAT
1 ATCAACGAACAAACATTT--TTTTTCTATTACCAAAACGCCAAAAAATATAGAAAGGAAAAAAAT
*
123462 AATTTTGAGAGGAAAATAAATT-TGGTGTGA-AAGAGTATGAGTGTAGAAAAATTCTTCAGAATT
64 AATTTTGAGAGGAAAATAAATTCT-GTGTGAGAA-AGTATGA-TGTAGAAAAATTCTTCAAAATT
123525 CATAGCCTTTTATAGCCATTCAGCATGGTGAAATTTTGGAAATTTCCAAAAAAAATACCTTTAAA
126 CATAGCCTTTTATAGCCATTCAGCATGGTGAAATTTTGGAAATTTCCAAAAAAAATACCTTTAAA
*
123590 GGAGTCAATAAATCAATTTGATTAAAATTAA
191 GGAGCCAATAAATCAATTTGATTAAAATTAA
123621 AT
1 AT
123623 TAAATTGATT
Statistics
Matches: 205, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
221 16 0.08
222 3 0.01
223 73 0.36
224 113 0.55
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (221 bp):
ATCAACGAACAAACATTTTTTTTCTATTACCAAAACGCCAAAAAATATAGAAAGGAAAAAAATAA
TTTTGAGAGGAAAATAAATTCTGTGTGAGAAAGTATGATGTAGAAAAATTCTTCAAAATTCATAG
CCTTTTATAGCCATTCAGCATGGTGAAATTTTGGAAATTTCCAAAAAAAATACCTTTAAAGGAGC
CAATAAATCAATTTGATTAAAATTAA
Found at i:135979 original size:152 final size:152
Alignment explanation
Indices: 135703--136375 Score: 1301
Period size: 152 Copynumber: 4.4 Consensus size: 152
135693 NNNNNNNNNN
135703 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
1 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
135768 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
66 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
135833 TTAAAATATTTATTATTGATAA
131 TTAAAATATTTATTATTGATAA
135855 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
1 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
135920 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
66 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
135985 TTAAAATATTTATTATTGATAA
131 TTAAAATATTTATTATTGATAA
136007 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
1 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
136072 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
66 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
136137 TTAAAATATTTATTATTGATAA
131 TTAAAATATTTATTATTGATAA
136159 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
1 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
136224 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
66 TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
136289 TTAAAATATTTATTATTGATAA
131 TTAAAATATTTATTATTGATAA
*
136311 TAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAAATTTATGCTAA
1 TAATAATCTTATTAAAATTTAAATAACAATAACAAT-A--A-TTACCAAAACAAATTTCTGCTAA
136376 GGGTATTCTA
Statistics
Matches: 516, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
152 492 0.95
153 1 0.00
155 1 0.00
156 22 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (152 bp):
TAATAATCTTATTAAAATTTAAATAACAATAACAATAATTACCAAAACAAATTTCTGCTAATTAT
TAAGAATTTTATGAAATTATATATTTTATTAAAATGGGTTTAATAATAGTTATGTTTAAATATGA
TTAAAATATTTATTATTGATAA
Found at i:136506 original size:45 final size:43
Alignment explanation
Indices: 136408--136517 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
136398 TTTTCCATTA
136408 TGCTATTACACCTCTATT-C-T--ATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* ***
136447 TACTATTACACCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
*
136492 TGCTATTACACCTCTAATCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
136518 CCTTTAATCT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
39 17 0.29
40 1 0.02
42 1 0.02
44 15 0.26
45 23 0.40
46 1 0.02
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:136519 original size:16 final size:16
Alignment explanation
Indices: 136498--136533 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
136488 GATTTGCTAT
136498 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
* *
136514 TACACCTTTAATCTAA
1 TACACCTCTAATCCAA
136530 TACA
1 TACA
136534 GCGAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:139348 original size:20 final size:19
Alignment explanation
Indices: 139323--139362 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
139313 ATTACAAAAT
139323 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
139343 AATTCAAAATAATTTTAAA
1 AATTCAAAATAATTTTAAA
139362 A
1 A
139363 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:139632 original size:22 final size:22
Alignment explanation
Indices: 139590--139634 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
139580 AATAACGGAA
**
139590 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
139612 TTTTAATTTAAC-TCGAATAATT
1 TTTTAATTTAACAT-GAATAATT
139634 T
1 T
139635 CACGTTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:158589 original size:30 final size:30
Alignment explanation
Indices: 158549--158607 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
158539 TGGGTTGTCA
*
158549 CACGGCCGTGTGAGACATACAGCCTGGTGG
1 CACGGCCGTGTGAGACACACAGCCTGGTGG
*
158579 CACGGTCGTGTGAGACACACAGCCTGGTG
1 CACGGCCGTGTGAGACACACAGCCTGGTG
158608 ACATGGCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.27, G:0.36, T:0.17
Consensus pattern (30 bp):
CACGGCCGTGTGAGACACACAGCCTGGTGG
Found at i:158768 original size:33 final size:32
Alignment explanation
Indices: 158723--158795 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 32
158713 ACCGGTGAGG
158723 ACACGGGCTGGGGTGATTCCAAACGACCTGGCC
1 ACAC-GGCTGGGGTGATTCCAAACGACCTGGCC
*
158756 ACACGGCTTGGGGTGATTCCAAACGGCCTGGCC
1 ACACGGC-TGGGGTGATTCCAAACGACCTGGCC
158789 ACACGGC
1 ACACGGC
158796 CGTGTGACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.21, C:0.32, G:0.33, T:0.15
Consensus pattern (32 bp):
ACACGGCTGGGGTGATTCCAAACGACCTGGCC
Found at i:160060 original size:15 final size:15
Alignment explanation
Indices: 160040--160094 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
160030 AAAGTAACTT
*
160040 TAATAATAATGATAA
1 TAATAATAAAGATAA
160055 TAATAATAAAGATAA
1 TAATAATAAAGATAA
*
160070 TAA-AATGAAAACATAA
1 TAATAAT--AAAGATAA
160086 TAA-AATAAA
1 TAATAATAAA
160095 TGAAAGAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 6 0.17
15 17 0.47
16 13 0.36
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (15 bp):
TAATAATAAAGATAA
Found at i:160892 original size:25 final size:25
Alignment explanation
Indices: 160844--160892 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
160834 CATAATTGAA
* * *
160844 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
160869 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
160893 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:161345 original size:15 final size:15
Alignment explanation
Indices: 161288--161349 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
161278 TATGTGATTG
161288 ATATTGAAATGGAAA
1 ATATTGAAATGGAAA
* *
161303 AGATGAGAAAT-G--A
1 ATAT-TGAAATGGAAA
*
161316 ATA-TGAGATGAGAAA
1 ATATTGAAATG-GAAA
161331 ATATTGAAATGGAAA
1 ATATTGAAATGGAAA
161346 ATAT
1 ATAT
161350 GATAAATGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
11 4 0.11
13 4 0.11
15 16 0.46
16 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.24
Consensus pattern (15 bp):
ATATTGAAATGGAAA
Found at i:161928 original size:22 final size:23
Alignment explanation
Indices: 161902--161944 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
161892 TATGTTAGCC
* *
161902 TAGTTTATATTTTGGT-GTGTGA
1 TAGTTTAAAGTTTGGTAGTGTGA
161924 TAGTTTAAAGTTTGGTAGTGT
1 TAGTTTAAAGTTTGGTAGTGT
161945 AGCATAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (23 bp):
TAGTTTAAAGTTTGGTAGTGTGA
Found at i:162890 original size:15 final size:15
Alignment explanation
Indices: 162865--162899 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
162855 GACTCTATTT
*
162865 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
162879 TAATTAATATTAAGA
1 TAATTAATATTAAGA
162894 TAATTA
1 TAATTA
162900 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:164424 original size:24 final size:24
Alignment explanation
Indices: 164392--164442 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
164382 CCCACAAGCA
164392 TCTGAAAGAGCTTCATATGGTTTG
1 TCTGAAAGAGCTTCATATGGTTTG
164416 TCTGAAAGAGCTTCATATGGTTTG
1 TCTGAAAGAGCTTCATATGGTTTG
164440 TCT
1 TCT
164443 TAGCATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (24 bp):
TCTGAAAGAGCTTCATATGGTTTG
Found at i:166822 original size:14 final size:15
Alignment explanation
Indices: 166803--166878 Score: 66
Period size: 15 Copynumber: 4.9 Consensus size: 15
166793 GGCAACCCAA
166803 TTTTTATTT-TTATT
1 TTTTTATTTATTATT
166817 TTTTTATTTATTATT
1 TTTTTATTTATTATT
*
166832 TTTTTCTTTACTT-TAT
1 TTTTTATTTA-TTAT-T
*
166848 TTATTACTTTATTTTATT
1 TTTTTA-TTTA--TTATT
*
166866 TTATTATTTATTA
1 TTTTTATTTATTA
166879 CTTATTTGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.17
15 18 0.35
16 7 0.13
17 8 0.15
18 9 0.17
19 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTTATTATT
Found at i:166828 original size:4 final size:4
Alignment explanation
Indices: 166811--166877 Score: 50
Period size: 4 Copynumber: 16.5 Consensus size: 4
166801 AATTTTTATT
* * *
166811 TTTA TTTT TTTA TTTA -TTA TTTT TTTC TTTA CTTTA TTTA -TTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA
166859 TTTTA TTT- TATTA TTTA TT
1 -TTTA TTTA T-TTA TTTA TT
166878 ACTTATTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
3 7 0.14
4 32 0.63
5 12 0.24
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:166847 original size:17 final size:16
Alignment explanation
Indices: 166811--166877 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
166801 AATTTTTATT
*
166811 TTTATTTTTTTATTTA
1 TTTATTTTTTTCTTTA
166827 -TTATTTTTTTCTTTA
1 TTTATTTTTTTCTTTA
* *
166842 CTTTATTTATTACTTTA
1 -TTTATTTTTTTCTTTA
* *
166859 TTTTATTTTATTATTTA
1 -TTTATTTTTTTCTTTA
166876 TT
1 TT
166878 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 14 0.34
16 2 0.05
17 25 0.61
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTTTTCTTTA
Found at i:167910 original size:101 final size:101
Alignment explanation
Indices: 167717--167908 Score: 260
Period size: 101 Copynumber: 1.9 Consensus size: 101
167707 TTTAAGAACA
* * * *
167717 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGTGTCAAAAGGTTCGAT
1 TGTTGGGCTAAGTAACCGGGGTGGGGTGCATGACTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
* * *
167782 GTGTTCTTAAGAAAAAAATATAATAAATTAGGAGTC
66 ATGTCCTAAAGAAAAAAATATAATAAATTAGGAGTC
* *
167818 TGTTGGGTTAAGTAACCGGGGTGGGGTGCATGACTGTCATCTCTCTTTGCGTCAAAAGGTTCAGT
1 TGTTGGGCTAAGTAACCGGGGTGGGGTGCATGACTGTCATCTCTCTTCGCGTCAAAAGGTTC-G-
167883 ATAT-TCCTAAAGCATAAAAAATATAA
64 ATATGTCCTAAAG-A-AAAAAATATAA
167909 ATAATAAATC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
101 56 0.72
102 7 0.09
103 4 0.05
104 11 0.14
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (101 bp):
TGTTGGGCTAAGTAACCGGGGTGGGGTGCATGACTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
ATGTCCTAAAGAAAAAAATATAATAAATTAGGAGTC
Found at i:168026 original size:77 final size:77
Alignment explanation
Indices: 167930--168073 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 77
167920 AAATCAAAAT
* *
167930 AAATAAATAAAAAGAAAAAATATATAATTTGGGGACTAAAGGAGGAAACAGAA-AGGGTGTCTTG
1 AAATAAATAAAAAGAAAAAAAATATAATTTGGGGACTAAAGGAGGAAACA-AATAGAGTGTCTTG
167994 GTATTAAAAATTA
65 GTATTAAAAATTA
168007 AAATAAATAAAAA-AGAAAAAAATATAATTTGGGGACTAAAGGAGGAAACAAATAGAGTGTCTTG
1 AAATAAATAAAAAGA-AAAAAAATATAATTTGGGGACTAAAGGAGGAAACAAATAGAGTGTCTTG
168071 GTA
65 GTA
168074 GGTTTGGTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
76 3 0.05
77 60 0.95
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.22
Consensus pattern (77 bp):
AAATAAATAAAAAGAAAAAAAATATAATTTGGGGACTAAAGGAGGAAACAAATAGAGTGTCTTGG
TATTAAAAATTA
Found at i:168607 original size:15 final size:15
Alignment explanation
Indices: 168582--168616 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
168572 GACTCTATTT
*
168582 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
168596 TAATTAATATTAAGA
1 TAATTAATATTAAGA
168611 TAATTA
1 TAATTA
168617 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:170226 original size:18 final size:18
Alignment explanation
Indices: 170200--170239 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
170190 GTACACTAAT
170200 AAAAAATAAAAAAAT-AA
1 AAAAAATAAAAAAATGAA
*
170217 AAAAAGATAAAGAAATGAA
1 AAAAA-ATAAAAAAATGAA
170236 AAAA
1 AAAA
170240 CAAATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAAAATAAAAAAATGAA
Found at i:170338 original size:6 final size:6
Alignment explanation
Indices: 170323--170393 Score: 71
Period size: 6 Copynumber: 12.5 Consensus size: 6
170313 TATAAATTTG
* *
170323 AAAAAT -AAAAT AAAAAT --AAAT AACAAT AAAAAT AAAAGT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
170368 AAAAAT --AAAT AAAACAT AAAACT AAA
1 AAAAAT AAAAAT AAAA-AT AAAAAT AAA
170394 TGAAATCACT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
4 8 0.15
5 5 0.09
6 35 0.65
7 6 0.11
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:170354 original size:28 final size:28
Alignment explanation
Indices: 170323--170393 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
170313 TATAAATTTG
*
170323 AAAAATAAAA-TAAAAATAAATAA-CAAT
1 AAAAATAAAACTAAAAATAAA-AATAAAT
*
170350 AAAAATAAAAGTAAAAATAAAAATAAAT
1 AAAAATAAAACTAAAAATAAAAATAAAT
170378 AAAACATAAAACTAAA
1 AAAA-ATAAAACTAAA
170394 TGAAATCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 12 0.31
28 17 0.44
29 10 0.26
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.17
Consensus pattern (28 bp):
AAAAATAAAACTAAAAATAAAAATAAAT
Found at i:173655 original size:20 final size:20
Alignment explanation
Indices: 173632--173673 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
173622 ATTAGAATGT
* *
173632 AAAAATTAAATTAAAAACAA
1 AAAAATAAAAATAAAAACAA
*
173652 AAAAATAAAAATAAAAATAA
1 AAAAATAAAAATAAAAACAA
173672 AA
1 AA
173674 TGGCTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAATAAAAATAAAAACAA
Found at i:175746 original size:14 final size:14
Alignment explanation
Indices: 175727--175754 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
175717 ACCGTGTGTC
175727 ATTAAACGACTATG
1 ATTAAACGACTATG
175741 ATTAAACGACTATG
1 ATTAAACGACTATG
175755 TTCACGTCAT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATTAAACGACTATG
Found at i:178570 original size:35 final size:35
Alignment explanation
Indices: 178389--178561 Score: 328
Period size: 35 Copynumber: 4.9 Consensus size: 35
178379 TCCTCTCTTT
178389 TTTTAACAATTAAATCCTATTTAATTAATATTTTTG
1 TTTT-ACAATTAAATCCTATTTAATTAATATTTTTG
178425 TTTTACAATTAAATCCTATTTAATTAATATTTTTG
1 TTTTACAATTAAATCCTATTTAATTAATATTTTTG
178460 TTTTACAATTAAATCCTATTTAATTAATATTTTTG
1 TTTTACAATTAAATCCTATTTAATTAATATTTTTG
178495 TTTTACAATTAAATCCTATTTAATTAATATTTTTG
1 TTTTACAATTAAATCCTATTTAATTAATATTTTTG
*
178530 TTTTACAATTAAATTCTATTTAATTAATATTT
1 TTTTACAATTAAATCCTATTTAATTAATATTT
178562 AAATTTTACT
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
35 132 0.97
36 4 0.03
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTTACAATTAAATCCTATTTAATTAATATTTTTG
Found at i:181116 original size:20 final size:19
Alignment explanation
Indices: 181077--181113 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
181067 TACTGTCACC
181077 CACCGTAATCAAATTTTTG
1 CACCGTAATCAAATTTTTG
181096 CACCGTAATCAAATTTTT
1 CACCGTAATCAAATTTTT
181114 TGCTGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (19 bp):
CACCGTAATCAAATTTTTG
Found at i:182240 original size:82 final size:84
Alignment explanation
Indices: 182125--182289 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 84
182115 TGAAATTGTA
* * *
182125 TTTTGTTTGTAAACAGAAATCAACTGAACAATTCT-GTTTCAGGATT-TTGTTCCTACTGTTTAA
1 TTTTGTTTGCAAACAAAAATCAACTGAACAATTCTAGTTTC-GGATTCTT-TTCCTACTGTTCAA
* *
182188 AAG-GATTTGTTCGATTTCTT
64 AAGAAATTTATTCGATTTCTT
* * * * *
182208 TTTTGTTT-CAAACAAAAATCAATTGAATAATTCTATTTTCGGATTCTTTTCCTATTGTTCAACA
1 TTTTGTTTGCAAACAAAAATCAACTGAACAATTCTAGTTTCGGATTCTTTTCCTACTGTTCAAAA
182272 GAAATTTATTCGATTTCT
66 GAAATTTATTCGATTTCT
182290 GTTGTTAACA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 41 0.59
83 28 0.41
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (84 bp):
TTTTGTTTGCAAACAAAAATCAACTGAACAATTCTAGTTTCGGATTCTTTTCCTACTGTTCAAAA
GAAATTTATTCGATTTCTT
Found at i:187449 original size:26 final size:25
Alignment explanation
Indices: 187413--187493 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
187403 TAAAAATTTG
* *
187413 AAATATATAT-ACATAAGTTTATAAT
1 AAATATATATAAAATAAATTTA-AAT
187438 AAATAATATATAAAATAAATTTAAAT
1 AAAT-ATATATAAAATAAATTTAAAT
*
187464 AAAT-TATATGTAAA-AAATTTCAAAT
1 AAATATATAT-AAAATAAATTT-AAAT
187489 AAATA
1 AAATA
187494 ATAAATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
24 11 0.23
25 15 0.31
26 13 0.27
27 9 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATATATATAAAATAAATTTAAAT
Found at i:187505 original size:25 final size:24
Alignment explanation
Indices: 187413--187518 Score: 88
Period size: 26 Copynumber: 4.2 Consensus size: 24
187403 TAAAAATTTG
* *
187413 AAAT-ATATATACATAAGTTTATAAT
1 AAATAATATATA-AAAAATTTA-AAT
187438 AAATAATATATAAAATAAATTTAAAT
1 AAATAATATAT-AAA-AAATTTAAAT
* *
187464 AAATTATATGTAAAAAATTTCAAAT
1 AAATAATATATAAAAAATTT-AAAT
* *
187489 AAATAATAAATATAAAAACTTAAAAT
1 AAATAAT--ATATAAAAAATTTAAAT
187515 AAAT
1 AAAT
187519 GATGATAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
24 6 0.09
25 17 0.25
26 27 0.40
27 17 0.25
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATAATATATAAAAAATTTAAAT
Found at i:191149 original size:141 final size:143
Alignment explanation
Indices: 190741--191338 Score: 718
Period size: 143 Copynumber: 4.2 Consensus size: 143
190731 AGTAGTAGGA
* * * * *
190741 AAATAAGATTCGCTGTCTTCAATCTGGTTCGCTGCAACTTCAGGGAAATAAGGCTGATGGCTTCA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCA
* ** * **
190806 ATCTGCTCCACTGCAACTTCAGGAAGATAATATCCGTTATATTTTGTAATTTTAATCTATTCCAC
66 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCAC
*
190871 TATAACGCCAGGG
131 TACAACGCCAGGG
* * * * * * *
190884 AAATAAGATTCGCTATTTTTAGTCTACTCCGCTGCAACTTCAGGGAGAGAAGGCTGGGGGCTTTA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCA
* * * * * *
190949 ATATGCTCCACTGTAACTTCAAGAAGATAAGATCCGCTATAATTTGTAGCATTAATCTGTTCCAC
66 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCAC
* *
191014 TGCAATGCCAGGG
131 TACAACGCCAGGG
* * * * *
191027 AAATAAAATTCGTTGTCTTCAGTCTGCTCCACTGCAACTTAAAGGAGATAAGGCT-G-GGCTTCA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCA
* * *
191090 ATTTGCTCCACTGCAACTTCAGGAAGATAAGTTCCGCCATAATTTGTAGCTTTAATCTGTTCCAC
66 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCAC
** *
191155 TGTAACACCAGGG
131 TACAACGCCAGGG
* * * * *
191168 AAATAAGATTTGCTGTCTTCAGTCTACTCCGCTGCGACTTCGGGGAGATAAGGCTAGTGGCTTCA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCA
* * * * *
191233 ATCTGCTCTACTGCAACTTTAGGAAGATAAGATCCACCATAATTTGTAGATTTAACCTATT-C-C
66 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCAC
*
191296 TACAACGCTAGGG
131 TACAACGCCAGGG
*
191309 AAATAAGATTCACTGTCTTCAGTCTGCTCC
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCC
191339 ACAGCATCTT
Statistics
Matches: 384, Mismatches: 69, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
141 158 0.41
142 3 0.01
143 223 0.58
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (143 bp):
AAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCA
ATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCAC
TACAACGCCAGGG
Found at i:191261 original size:284 final size:283
Alignment explanation
Indices: 190741--191359 Score: 776
Period size: 284 Copynumber: 2.2 Consensus size: 283
190731 AGTAGTAGGA
* * * * * *
190741 AAATAAGATTCGCTGTCTTCAATCTGGTTCGCTGCAACTTCAGGGAAATAAGGCTGATGGCTTCA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGA-GGCTTCA
** * *
190806 ATCTGCTCCACTGCAACTTCAGGAAGATAATATCCGTTATATTTTGTAATTTTAATCTATTCCAC
65 ATCTGCTCCACTGCAACTTCAGGAAGATAATATCCGCCATAATTTGTAACTTTAATCTATTCCAC
* * *
190871 TATAACGCCAGGGAAATAAGATTCGCTATTTTTAGTCTACTCCGCTGCAACTTCAGGGAGAGAAG
130 TATAACACCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCGCTGCAACTTCAGGGAGAGAAG
* * * * *
190936 GCTGGGGGCTTTAATATGCTCCACTGTAACTTCAAGAAGATAAGATCCGCTATAATTTGTAGCA-
195 GCTAGGGGCTTCAATATGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTGTAG-AT
* * * *
191000 TTAATCTGTTCCACTGCAATGCCAGGG
259 TTAACCTATT-C-CTACAACGCCAGGG
* * *
191027 AAATAAAATTCGTTGTCTTCAGTCTGCTCCACTGCAACTTAAAGGAGATAAGGCTG-GGCTTCAA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGAGGCTTCAA
* * *
191091 TTTGCTCCACTGCAACTTCAGGAAGATAAGT-TCCGCCATAATTTGTAGCTTTAATCTGTTCCAC
66 TCTGCTCCACTGCAACTTCAGGAAGATAA-TATCCGCCATAATTTGTAACTTTAATCTATTCCAC
* * * * * *
191155 TGTAACACCAGGGAAATAAGATTTGCTGTCTTCAGTCTACTCCGCTGCGACTTCGGGGAGATAAG
130 TATAACACCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCGCTGCAACTTCAGGGAGAGAAG
* * * * *
191220 GCTAGTGGCTTCAATCTGCTCTACTGCAACTTTAGGAAGATAAGATCCACCATAATTTGTAGATT
195 GCTAGGGGCTTCAATATGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTGTAGATT
*
191285 TAACCTATTCCTACAACGCTAGGG
260 TAACCTATTCCTACAACGCCAGGG
* * * *
191309 AAATAAGATTCACTGTCTTCAGTCTGCTCCACAGCATCTTCAATGAGATAA
1 AAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAA
191360 AACTTGTAAC
Statistics
Matches: 284, Mismatches: 47, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
282 55 0.19
283 2 0.01
284 179 0.63
285 1 0.00
286 47 0.17
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (283 bp):
AAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGGCTGAGGCTTCAA
TCTGCTCCACTGCAACTTCAGGAAGATAATATCCGCCATAATTTGTAACTTTAATCTATTCCACT
ATAACACCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCGCTGCAACTTCAGGGAGAGAAGG
CTAGGGGCTTCAATATGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTGTAGATTT
AACCTATTCCTACAACGCCAGGG
Found at i:192935 original size:6 final size:6
Alignment explanation
Indices: 192924--192991 Score: 52
Period size: 6 Copynumber: 10.8 Consensus size: 6
192914 CGCAGTAGAG
*
192924 GTTTTT GTTTTTT GTTTTT GCTCTTTT -ATTTT GCTTATTT GTTTTT GTTTGTT
1 GTTTTT G-TTTTT GTTTTT G-T-TTTT GTTTTT G-TT-TTT GTTTTT GTTT-TT
192977 -TTTTT GTTTTT -TTTT
1 GTTTTT GTTTTT GTTTT
192992 GCCTCTCCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
5 10 0.19
6 22 0.42
7 12 0.23
8 8 0.15
ACGTcount: A:0.03, C:0.04, G:0.13, T:0.79
Consensus pattern (6 bp):
GTTTTT
Found at i:192942 original size:13 final size:13
Alignment explanation
Indices: 192924--192988 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
192914 CGCAGTAGAG
192924 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
*
192937 GTTTTTGCTCTTTT
1 GTTTTTG-TTTTTT
* *
192951 -ATTTTGCTTATTT
1 GTTTTTG-TTTTTT
*
192964 GTTTTTGTTTGTT
1 GTTTTTGTTTTTT
192977 -TTTTTGTTTTTT
1 GTTTTTGTTTTTT
192989 TTTGCCTCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 11 0.26
13 21 0.50
14 10 0.24
ACGTcount: A:0.03, C:0.05, G:0.14, T:0.78
Consensus pattern (13 bp):
GTTTTTGTTTTTT
Found at i:197266 original size:26 final size:25
Alignment explanation
Indices: 197226--197318 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
197216 AATAAAACAT
197226 AAATTTACAATAAATAATATATAAAA
1 AAATTTA-AATAAATAATATATAAAA
* *
197252 GAAATTTAAATAAATTATATGTAAAA
1 -AAATTTAAATAAATAATATATAAAA
** * *
197278 TAGTTTTAAATTAATAATAAATATAAA
1 -AAATTTAAATAAATAATATATA-AAA
* *
197305 AACTTAAAATAAAT
1 AAATTTAAATAAAT
197319 GATGGTAAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
26 42 0.81
27 10 0.19
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (25 bp):
AAATTTAAATAAATAATATATAAAA
Found at i:202174 original size:28 final size:27
Alignment explanation
Indices: 202105--202179 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
202095 ATCGAAATTT
* * *
202105 ATATAAGATAAAATTTTATAATAATAA
1 ATATAATATAAAACTTAATAATAATAA
*
202132 ATATCATATATAAACTTAATAATAATAA
1 ATATAATATA-AAACTTAATAATAATAA
202160 ATACCTAAT-TAAAACTTAAT
1 ATA--TAATATAAAACTTAAT
202180 TTAAATTACA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 8 0.20
28 27 0.68
29 2 0.05
30 3 0.08
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (27 bp):
ATATAATATAAAACTTAATAATAATAA
Found at i:202917 original size:31 final size:31
Alignment explanation
Indices: 202882--202943 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
202872 ACAACCCAAC
*
202882 GACTTAAATAAAAACTTTTAAATAGTTTAGT
1 GACTTAAATAAAAACTTTCAAATAGTTTAGT
* * *
202913 GACTTCAATGAACACTTTCAAATAGTTTAGT
1 GACTTAAATAAAAACTTTCAAATAGTTTAGT
202944 AACCATTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (31 bp):
GACTTAAATAAAAACTTTCAAATAGTTTAGT
Found at i:212654 original size:3 final size:3
Alignment explanation
Indices: 212646--212673 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
212636 TGAGGCAATT
212646 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
212674 GCGGCTCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:219460 original size:40 final size:41
Alignment explanation
Indices: 219324--219469 Score: 231
Period size: 41 Copynumber: 3.6 Consensus size: 41
219314 TTTAATAAAC
* * *
219324 AAAGTCTGAAATGTTTCACCAGCGTCAAGCCTGTTAGACGT
1 AAAGTCTGAAATGTTTCACCGGCATCAAGCCTGCTAGACGT
* *
219365 AAAGCCTGAAATGTTTCACCGGCATCAAGCCTGCTAGACAT
1 AAAGTCTGAAATGTTTCACCGGCATCAAGCCTGCTAGACGT
219406 AAAGTCTGAAATGTTTCACCGGCATCAAGCCTGCT-GACGT
1 AAAGTCTGAAATGTTTCACCGGCATCAAGCCTGCTAGACGT
*
219446 AAAGTCTGAAATGTTTCACTGGCA
1 AAAGTCTGAAATGTTTCACCGGCA
219470 ATAAACCTGA
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
40 27 0.28
41 70 0.72
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (41 bp):
AAAGTCTGAAATGTTTCACCGGCATCAAGCCTGCTAGACGT
Found at i:222024 original size:36 final size:36
Alignment explanation
Indices: 221984--222054 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
221974 TAATACAATG
221984 GTGTACGACATTTACGACTGTACAAAGCCTCGTAAT
1 GTGTACGACATTTACGACTGTACAAAGCCTCGTAAT
222020 GTGTACGACATTTACGACTGTACAAAGCCTCGTAA
1 GTGTACGACATTTACGACTGTACAAAGCCTCGTAA
222055 GGTGCCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (36 bp):
GTGTACGACATTTACGACTGTACAAAGCCTCGTAAT
Found at i:227136 original size:41 final size:41
Alignment explanation
Indices: 227091--227210 Score: 195
Period size: 41 Copynumber: 2.9 Consensus size: 41
227081 ACTGGCACTT
*
227091 AGCCTGCTAGACATAAAGTCTGCAATGTTTCACCAGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
* * *
227132 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCATCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
*
227173 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACTAGCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCA
227211 ATAAACCTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCAGCATCA
Found at i:232685 original size:16 final size:16
Alignment explanation
Indices: 232664--232716 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
232654 TTGGTTCGCT
232664 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
232680 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
232696 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
232712 GTAAT
1 GTAAT
232717 AGCAATTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.04, G:0.36, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:237532 original size:3 final size:3
Alignment explanation
Indices: 237515--237579 Score: 50
Period size: 3 Copynumber: 23.3 Consensus size: 3
237505 AGGTTTTTGG
* * *
237515 TGT TGT T-T TGG TGT TGT TGT TGG TGT TGT T-T T-T TG- TGT TGT TTT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* *
237559 TGG TGT TGT T-T TAT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT T
237580 TCACAGTTGT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
2 10 0.20
3 39 0.80
ACGTcount: A:0.02, C:0.00, G:0.31, T:0.68
Consensus pattern (3 bp):
TGT
Found at i:237537 original size:12 final size:12
Alignment explanation
Indices: 237507--237570 Score: 103
Period size: 12 Copynumber: 5.4 Consensus size: 12
237497 CATCTTGCAG
237507 GTTTTTGGTGTT
1 GTTTTTGGTGTT
237519 G-TTTTGGTGTT
1 GTTTTTGGTGTT
*
237530 GTTGTTGGTGTT
1 GTTTTTGGTGTT
*
237542 GTTTTTTGTGTT
1 GTTTTTGGTGTT
237554 GTTTTTGGTGTT
1 GTTTTTGGTGTT
237566 GTTTT
1 GTTTT
237571 ATTGTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
11 11 0.23
12 36 0.77
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (12 bp):
GTTTTTGGTGTT
Found at i:237631 original size:23 final size:23
Alignment explanation
Indices: 237605--237650 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
237595 ATGTTGTTCC
*
237605 GTTGTCGTTTTTAATATTATTTG
1 GTTGTCATTTTTAATATTATTTG
*
237628 GTTGTCATTTTTAATATTTTTTG
1 GTTGTCATTTTTAATATTATTTG
237651 TATATTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.63
Consensus pattern (23 bp):
GTTGTCATTTTTAATATTATTTG
Found at i:245672 original size:6 final size:6
Alignment explanation
Indices: 245608--245657 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
245598 GGAGGGATTG
*
245608 AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAAGTA
1 AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA
245656 AA
1 AA
245658 TTTAAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (6 bp):
AAACTA
Found at i:253862 original size:12 final size:12
Alignment explanation
Indices: 253845--253908 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
253835 AAACAACAAT
253845 AAAACAACACCA
1 AAAACAACACCA
*
253857 AAAACAACACAA
1 AAAACAACACCA
*
253869 AGAAATAACACCA
1 A-AAACAACACCA
*
253882 ACAACAACA-C-
1 AAAACAACACCA
*
253892 AAAACAGCACCA
1 AAAACAACACCA
253904 AAAAC
1 AAAAC
253909 CTGCAAGATG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
12 23 0.55
13 10 0.24
ACGTcount: A:0.66, C:0.30, G:0.03, T:0.02
Consensus pattern (12 bp):
AAAACAACACCA
Found at i:253878 original size:25 final size:24
Alignment explanation
Indices: 253834--253908 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 24
253824 AAAGACCTGC
*
253834 AAAACAACA-ATAAAACAACACCA
1 AAAACAACACAAAAAACAACACCA
*
253857 AAAACAACACAAAGAAATAACACCA
1 AAAACAACACAAA-AAACAACACCA
* *
253882 ACAACAACAC--AAAACAGCACCA
1 AAAACAACACAAAAAACAACACCA
253904 AAAAC
1 AAAAC
253909 CTGCAAGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 13 0.30
23 10 0.23
24 2 0.05
25 19 0.43
ACGTcount: A:0.67, C:0.28, G:0.03, T:0.03
Consensus pattern (24 bp):
AAAACAACACAAAAAACAACACCA
Found at i:257265 original size:138 final size:136
Alignment explanation
Indices: 257024--257313 Score: 357
Period size: 138 Copynumber: 2.1 Consensus size: 136
257014 CACTTTTACG
* * * * *
257024 GAAATTGCCATAAATGCACTTCTTTAGATTGCGCCAAAAAAGTGTCTTCTTATAGATTACCATAA
1 GAAATTACCACAAAAGCACTTCTTTAGATTGCGCCAAAAAAGTGTCTCCTTACAGATTACCATAA
* * * * *
257089 ATGTATTCCTTACAATAAATTTTCCACAAAGGCATTCCTTTAACATAAACAACCACAACGACTCA
66 AGGTAATCCTTACAAT-AATTTACCACAAAGGCATTCCTTTAACACAAACAACCACAAAGACTCA
*
257154 CTTGTAT
130 CTTATAT
* * *
257161 AGAAATTACCACAAAAGCACTTCTTTAGATTGCGCCACAAAGGTGTCTCCTTACAGATTACTATA
1 -GAAATTACCACAAAAGCACTTCTTTAGATTGCGCCAAAAAAGTGTCTCCTTACAGATTACCATA
* * * *
257226 AAGGTAATCCTTATCAGAT-ATTTAGCACAAAGGCTTTCCTTTAATACAAACAACCACAAAGGCT
65 AAGGTAATCCTTA-CA-ATAATTTACCACAAAGGCATTCCTTTAACACAAACAACCACAAAGACT
257290 CACTTATAT
128 CACTTATAT
*
257299 GAAAATTTCCACAAA
1 G-AAATTACCACAAA
257314 GGCGTCTCCT
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
137 1 0.01
138 125 0.96
139 2 0.02
140 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (136 bp):
GAAATTACCACAAAAGCACTTCTTTAGATTGCGCCAAAAAAGTGTCTCCTTACAGATTACCATAA
AGGTAATCCTTACAATAATTTACCACAAAGGCATTCCTTTAACACAAACAACCACAAAGACTCAC
TTATAT
Found at i:257387 original size:110 final size:112
Alignment explanation
Indices: 257195--257396 Score: 284
Period size: 110 Copynumber: 1.8 Consensus size: 112
257185 TTAGATTGCG
* * * *
257195 CCACAAAGGTGTCTCCTTACAGATTACTATAAAGGTAATCCTTATCAGATATTTAGCACAAAGGC
1 CCACAAAGGCGTCTCCTTACAGATTACCATAAAGGTAATCCTTATCAGAGATTTACCACAAAGGC
* *
257260 TTTCCTTTAATACAAACAACCACAAAGGCTCACTTATATGAAAATTT
66 TTTCCTTTAACACAAACAACCAAAAAGGCTCACTTATATGAAAATTT
* * *
257307 CCACAAAGGCGTCTCCTTACAGATTACCATAAA-GT-TTCCTTATTAGAGATTTTCCACAAAGG-
1 CCACAAAGGCGTCTCCTTACAGATTACCATAAAGGTAATCCTTATCAGAGATTTACCACAAAGGC
*
257369 TATTCCTTTAACAGAAACAACCAAAAAG
66 T-TTCCTTTAACACAAACAACCAAAAAG
257397 ACGTACTTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 1 0.01
110 45 0.57
111 2 0.03
112 31 0.39
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (112 bp):
CCACAAAGGCGTCTCCTTACAGATTACCATAAAGGTAATCCTTATCAGAGATTTACCACAAAGGC
TTTCCTTTAACACAAACAACCAAAAAGGCTCACTTATATGAAAATTT
Found at i:263865 original size:20 final size:20
Alignment explanation
Indices: 263842--263881 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
263832 ACATTATACG
263842 AACTTACTAAGCATTTATGC
1 AACTTACTAAGCATTTATGC
263862 AACTTACTAAGCATTTATGC
1 AACTTACTAAGCATTTATGC
263882 TTACTCTGTG
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:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
AACTTACTAAGCATTTATGC
Found at i:263886 original size:17 final size:18
Alignment explanation
Indices: 263843--263886 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
263833 CATTATACGA
263843 ACTTACTAAGCATTTATG
1 ACTTACTAAGCATTTATG
263861 CAACTTACTAAGCATTTATG
1 --ACTTACTAAGCATTTATG
263881 -CTTACT
1 ACTTACT
263887 CTGTGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
20 18 0.75
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (18 bp):
ACTTACTAAGCATTTATG
Found at i:263940 original size:17 final size:17
Alignment explanation
Indices: 263918--263951 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
263908 ATAGTGAATC
*
263918 GGAAGCTTGTTCGAGTT
1 GGAAGCTTGTTAGAGTT
263935 GGAAGCTTGTTAGAGTT
1 GGAAGCTTGTTAGAGTT
263952 ATATCACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.35, T:0.35
Consensus pattern (17 bp):
GGAAGCTTGTTAGAGTT
Found at i:265657 original size:26 final size:26
Alignment explanation
Indices: 265627--265689 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
265617 TATCATCACT
**
265627 ATTTTGCCTGTAGAAAAATTTTGACA
1 ATTTTGCCCCTAGAAAAATTTTGACA
* * *
265653 ATTTTACCCCTAGTAAAATTTTGACG
1 ATTTTGCCCCTAGAAAAATTTTGACA
265679 ATTTTGCCCCT
1 ATTTTGCCCCT
265690 GGTAAAACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (26 bp):
ATTTTGCCCCTAGAAAAATTTTGACA
Found at i:265694 original size:26 final size:26
Alignment explanation
Indices: 265641--265696 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
265631 TGCCTGTAGA
265641 AAAATTTTGACAATTTTACCCCTAGT
1 AAAATTTTGACAATTTTACCCCTAGT
* * *
265667 AAAATTTTGACGATTTTGCCCCTGGT
1 AAAATTTTGACAATTTTACCCCTAGT
265693 AAAA
1 AAAA
265697 CTTCGGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCCTAGT
Done.