Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015325.1 Kokia drynarioides strain JFW-HI SEQ_130371, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 591955
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 531 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1160 original size:15 final size:15
Alignment explanation
Indices: 1137--1184 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1127 CACTTTATAA
*
1137 TTGGACCATTTGTAT
1 TTGGGCCATTTGTAT
* *
1152 TTGGGCCATCTGTAA
1 TTGGGCCATTTGTAT
*
1167 CTGGGCCATTTGT-T
1 TTGGGCCATTTGTAT
1181 TTGG
1 TTGG
1185 ATTTTTTTGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.42
Consensus pattern (15 bp):
TTGGGCCATTTGTAT
Found at i:1268 original size:17 final size:17
Alignment explanation
Indices: 1207--1270 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
1197 TCGGACTTTT
* *
1207 ATAAATTTAATTTTATA
1 ATAAATTTAAATTTAAA
*
1224 ATAAATTTAAATTTCAA
1 ATAAATTTAAATTTAAA
1241 ATAAATTTAAATTTAAA
1 ATAAATTTAAATTTAAA
*
1258 ATAAACTTAAATT
1 ATAAATTTAAATT
1271 CAATTTCCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATTTAAATTTAAA
Found at i:2436 original size:47 final size:47
Alignment explanation
Indices: 2374--2468 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
2364 GTGTAAACCC
*
2374 TATTTAAATTTAAGTTTGAATATATTTTATTATTAATTTATTGTATT
1 TATTTAAATTTAAGTTTAAATATATTTTATTATTAATTTATTGTATT
* *
2421 TATTTAGATTTAAGTTTAAATATGTTTTATTATTAATTTATTGTATT
1 TATTTAAATTTAAGTTTAAATATATTTTATTATTAATTTATTGTATT
2468 T
1 T
2469 TATAATACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (47 bp):
TATTTAAATTTAAGTTTAAATATATTTTATTATTAATTTATTGTATT
Found at i:4703 original size:21 final size:22
Alignment explanation
Indices: 4662--4703 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4652 AAATAAAAAT
*
4662 AAGATTGGCATTTTTTTAATAA
1 AAGATTGGCATTTTTTAAATAA
4684 AAGATTGGCA-TTTTTAAATA
1 AAGATTGGCATTTTTTAAATA
4704 TGATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
AAGATTGGCATTTTTTAAATAA
Found at i:11534 original size:16 final size:16
Alignment explanation
Indices: 11498--11528 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11488 CATTAAAATT
*
11498 GAATAGGATTGTAATA
1 GAATAGAATTGTAATA
11514 GAATAGAATTGTAAT
1 GAATAGAATTGTAAT
11529 GAAATAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (16 bp):
GAATAGAATTGTAATA
Found at i:15858 original size:5 final size:5
Alignment explanation
Indices: 15850--15875 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15840 GAGATAGAAT
15850 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
15876 ATATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:16471 original size:42 final size:42
Alignment explanation
Indices: 16424--16507 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
16414 AAAAGGAGTT
* *
16424 GTTTATGAGT-GTTATTTAGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTGGTT-TTGAAGAATAAAATTATATTTGGGTTTA
* *
16466 GTTTATGAGTGGTTTTGAATAATAAAATTATATTTTGGTTTA
1 GTTTATGAGTGGTTTTGAAGAATAAAATTATATTTGGGTTTA
16508 AAAATATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 34 0.92
43 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (42 bp):
GTTTATGAGTGGTTTTGAAGAATAAAATTATATTTGGGTTTA
Found at i:21191 original size:17 final size:17
Alignment explanation
Indices: 21169--21214 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
21159 CCCTTGACTT
21169 TTAACCTTTCATCTTCC
1 TTAACCTTTCATCTTCC
*
21186 TTAACCTTCCATCTTCC
1 TTAACCTTTCATCTTCC
21203 TTAACCTTTCAT
1 TTAACCTTTCAT
21215 ATTCTTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAACCTTTCATCTTCC
Found at i:22383 original size:9 final size:9
Alignment explanation
Indices: 22371--22451 Score: 69
Period size: 9 Copynumber: 8.9 Consensus size: 9
22361 TTTATGATTT
22371 TTTTTATAA
1 TTTTTATAA
22380 TTTTTATAA
1 TTTTTATAA
*
22389 GTTTATATCAA
1 -TTTTTAT-AA
*
22400 TTTTAAT-A
1 TTTTTATAA
*
22408 TTTTTAATAC
1 TTTTT-ATAA
22418 TTTTTATAA
1 TTTTTATAA
22427 TATTTTAT--
1 T-TTTTATAA
*
22435 TTTTTATGA
1 TTTTTATAA
22444 TTTTTATA
1 TTTTTATA
22452 GAATTTTAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
7 6 0.10
8 6 0.10
9 22 0.38
10 22 0.38
11 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:22448 original size:16 final size:17
Alignment explanation
Indices: 22418--22450 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22408 TTTTTAATAC
22418 TTTTTATAATATTTTAT
1 TTTTTATAATATTTTAT
*
22435 TTTTTATGAT-TTTTAT
1 TTTTTATAATATTTTAT
22451 AGAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTTATAATATTTTAT
Found at i:22595 original size:19 final size:19
Alignment explanation
Indices: 22573--22618 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
22563 TTAATATTTA
*
22573 ATAATTTTCAATTTTTTTT
1 ATAATTTTCAATATTTTTT
***
22592 ATAATTTTTTCTATTTTTT
1 ATAATTTTCAATATTTTTT
22611 ATAATTTT
1 ATAATTTT
22619 TATGATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
ATAATTTTCAATATTTTTT
Found at i:22598 original size:27 final size:28
Alignment explanation
Indices: 22531--22598 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 28
22521 AGAAAAAATA
22531 TTTTTTATAAGTTTATATGAATTTTCATT
1 TTTTTTATAA-TTTATATGAATTTTCATT
*
22560 TTTTTAAT-ATTTA-AT-AATTTTCAATT
1 TTTTTTATAATTTATATGAATTTTC-ATT
22586 TTTTTTATAATTT
1 TTTTTTATAATTT
22599 TTTCTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.20
26 12 0.34
27 8 0.23
28 1 0.03
29 7 0.20
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTTTATAATTTATATGAATTTTCATT
Found at i:22599 original size:9 final size:9
Alignment explanation
Indices: 22587--22638 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
22577 TTTTCAATTT
22587 TTTTTATAA
1 TTTTTATAA
* *
22596 TTTTTTCTAT
1 -TTTTTATAA
22606 TTTTTATAA
1 TTTTTATAA
*
22615 TTTTTATGA
1 TTTTTATAA
* *
22624 TTTTTCTGA
1 TTTTTATAA
22633 TTTTTA
1 TTTTTA
22639 AAAGAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
9 28 0.80
10 7 0.20
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (9 bp):
TTTTTATAA
Found at i:22626 original size:19 final size:19
Alignment explanation
Indices: 22586--22628 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
22576 ATTTTCAATT
*
22586 TTTTTTATAATTTTTTCTA
1 TTTTTTATAATTTTTTCGA
22605 TTTTTTATAATTTTTAT-GA
1 TTTTTTATAATTTTT-TCGA
22624 TTTTT
1 TTTTT
22629 CTGATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTATAATTTTTTCGA
Found at i:24006 original size:59 final size:60
Alignment explanation
Indices: 23914--24043 Score: 208
Period size: 59 Copynumber: 2.2 Consensus size: 60
23904 GATGGCACTA
* *
23914 ATATTATTTTTTATTTTTTCCCTGTGATGCAGCCATTTGATAACCCTCCATTAATATAA-T
1 ATATT-TTTTTTATTTTTTCCCTGTAATACAGCCATTTGATAACCCTCCATTAATATAATT
*
23974 ATATTTTTTTTATTTTTTCCCTGTAATACAGCCATTTGATAACCCTTCATTAATATAATT
1 ATATTTTTTTTATTTTTTCCCTGTAATACAGCCATTTGATAACCCTCCATTAATATAATT
*
24034 TTATTTTTTT
1 ATATTTTTTT
24044 AATATAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
59 50 0.77
60 15 0.23
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (60 bp):
ATATTTTTTTTATTTTTTCCCTGTAATACAGCCATTTGATAACCCTCCATTAATATAATT
Found at i:30135 original size:26 final size:26
Alignment explanation
Indices: 30077--30135 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
30067 AATTTTCATC
* * * *
30077 AAGAAAATGAGAATTTTTTTAAATAA
1 AAGAAAGTGAGAATTATGTTAAAAAA
30103 AAGAAAGTGAGAATTATGTTAAAAAA
1 AAGAAAGTGAGAATTATGTTAAAAAA
30129 AAGAAAG
1 AAGAAAG
30136 ATAGTGAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (26 bp):
AAGAAAGTGAGAATTATGTTAAAAAA
Found at i:32122 original size:13 final size:13
Alignment explanation
Indices: 32104--32128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32094 CTTCAACCTT
32104 TTATTATTTTTTA
1 TTATTATTTTTTA
32117 TTATTATTTTTT
1 TTATTATTTTTT
32129 CGTTTGTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTATTTTTTA
Found at i:39826 original size:2 final size:2
Alignment explanation
Indices: 39819--39844 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39809 GTGGTACTTA
39819 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
39845 GAATTTGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43139 original size:44 final size:46
Alignment explanation
Indices: 43088--43177 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
43078 TGCTAAAAAC
* *
43088 GATGATTAA-C-CTAAGTTAGAGGGTGATTGAATATAATGTAAGCT
1 GATGATTAACCTCTAAATTAGAAGGTGATTGAATATAATGTAAGCT
* * *
43132 GATGATTAACCTCTAAATTAGAAGGTGTTTGAGTATAGTGTAAGCT
1 GATGATTAACCTCTAAATTAGAAGGTGATTGAATATAATGTAAGCT
43178 ATATATCTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 9 0.23
45 1 0.03
46 29 0.74
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.33
Consensus pattern (46 bp):
GATGATTAACCTCTAAATTAGAAGGTGATTGAATATAATGTAAGCT
Found at i:44785 original size:16 final size:15
Alignment explanation
Indices: 44764--44797 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
44754 AAGAATTATT
44764 TTTTAAATTCATAAAA
1 TTTTAAATTCA-AAAA
*
44780 TTTTAAATTTAAAAA
1 TTTTAAATTCAAAAA
44795 TTT
1 TTT
44798 AATAACCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAAATTCAAAAA
Found at i:46916 original size:31 final size:31
Alignment explanation
Indices: 46857--46923 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
46847 AATTAATAAA
*
46857 AATAAAATTATACTTTGAATTTCTTAAAAAT
1 AATAAAATTATACTTTGAATTTCGTAAAAAT
**
46888 AATAAAATTATA-TTTTTATTATCGTAAAAAT
1 AATAAAATTATACTTTGAATT-TCGTAAAAAT
*
46919 TATAA
1 AATAA
46924 TTTTTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (31 bp):
AATAAAATTATACTTTGAATTTCGTAAAAAT
Found at i:67676 original size:4 final size:4
Alignment explanation
Indices: 67667--67718 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
67657 AAATAAACGG
* * *
67667 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
67717 GA
1 GA
67719 TAATATGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:67686 original size:13 final size:13
Alignment explanation
Indices: 67668--67718 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
67658 AATAAACGGG
67668 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
67681 AAAGAAAGAAAG-
1 AAAGAAAGAAAGA
* *
67693 AAAGGAAGAAGGA
1 AAAGAAAGAAAGA
* *
67706 GAGGAAAGAAAGA
1 AAAGAAAGAAAGA
67719 TAATATGTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:67696 original size:25 final size:25
Alignment explanation
Indices: 67667--67718 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
67657 AAATAAACGG
67667 GAAAGAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
* * * *
67692 GAAAGGAAGAAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
67717 GA
1 GA
67719 TAATATGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAGAAAGAAA
Found at i:67712 original size:21 final size:21
Alignment explanation
Indices: 67666--67718 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
67656 CAAATAAACG
67666 GGAAAGAAAGAAAGAAAAGAA
1 GGAAAGAAAGAAAGAAAAGAA
* * *
67687 AGAAAGAAAGGAAG-AAGGAGA
1 GGAAAGAAAGAAAGAAAAGA-A
67708 GGAAAGAAAGA
1 GGAAAGAAAGA
67719 TAATATGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
GGAAAGAAAGAAAGAAAAGAA
Found at i:67792 original size:20 final size:19
Alignment explanation
Indices: 67755--67802 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
67745 CAGTATGATA
67755 TATTTTTAAAATCATATTT
1 TATTTTTAAAATCATATTT
**
67774 TATTTATTAAAATTTTATTT
1 TATTT-TTAAAATCATATTT
*
67794 AATTTTTAA
1 TATTTTTAA
67803 CAGATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTTAAAATCATATTT
Found at i:70386 original size:14 final size:14
Alignment explanation
Indices: 70343--70393 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
70333 TTAATCAATC
*
70343 TAGTGTTTACGATT
1 TAGTGTTTATGATT
* *
70357 TAGAGTTT-TAAGTT
1 TAGTGTTTATGA-TT
70371 TAGTGTTTATGATT
1 TAGTGTTTATGATT
*
70385 TAGGGTTTA
1 TAGTGTTTA
70394 CAATTTAGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 1 0.03
14 26 0.90
15 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.51
Consensus pattern (14 bp):
TAGTGTTTATGATT
Found at i:70400 original size:28 final size:29
Alignment explanation
Indices: 70338--70405 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
70328 CATCCTTAAT
* *
70338 CAATCTAGTGTTTACGATTTAGAGTTTTA
1 CAATTTAGTGTTTACGATTTAGAGGTTTA
* *
70367 -AGTTTAGTGTTTATGATTTAG-GGTTTA
1 CAATTTAGTGTTTACGATTTAGAGGTTTA
70394 CAATTTAG-GTTT
1 CAATTTAGTGTTT
70406 TAGAGTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.49
Consensus pattern (29 bp):
CAATTTAGTGTTTACGATTTAGAGGTTTA
Found at i:70802 original size:45 final size:45
Alignment explanation
Indices: 70672--70808 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
70662 GGGAGGAATA
* * * **
70672 GAGTATCGCGGTGGCTCGTCAAACTCAGCCTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
* *
70717 GAGTATTACGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
*
70762 GAGTATTGTGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
70807 GA
1 GA
70809 TAAGCTATGC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Found at i:72788 original size:16 final size:16
Alignment explanation
Indices: 72767--72816 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
72757 TGATGGGGAT
72767 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
72783 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
72798 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
72813 ATTA
1 ATTA
72817 ACTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:73291 original size:12 final size:12
Alignment explanation
Indices: 73276--73300 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73266 AAATTAAAAT
73276 ATTTTAAAATTA
1 ATTTTAAAATTA
73288 ATTTTAAAATTA
1 ATTTTAAAATTA
73300 A
1 A
73301 CCATACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:74409 original size:15 final size:15
Alignment explanation
Indices: 74391--74419 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
74381 ACTCCCACCT
74391 CAAAGCAAAGCAAAA
1 CAAAGCAAAGCAAAA
74406 CAAAGCAAAGCAAA
1 CAAAGCAAAGCAAA
74420 CGAAACTCCT
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:0.66, C:0.21, G:0.14, T:0.00
Consensus pattern (15 bp):
CAAAGCAAAGCAAAA
Found at i:79081 original size:3 final size:3
Alignment explanation
Indices: 79073--79098 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
79063 GATTAAAGCA
79073 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
79099 TCTTCAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:85756 original size:27 final size:27
Alignment explanation
Indices: 85725--85780 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
85715 ATGTTGGAGT
85725 TAGCATTTGCGGATAGTTTGGACTTTG
1 TAGCATTTGCGGATAGTTTGGACTTTG
85752 TAGCATTTGCGGATAGTTTGGACTTTG
1 TAGCATTTGCGGATAGTTTGGACTTTG
85779 TA
1 TA
85781 ATGACAGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (27 bp):
TAGCATTTGCGGATAGTTTGGACTTTG
Found at i:91451 original size:19 final size:20
Alignment explanation
Indices: 91429--91471 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
91419 TATATATATA
* *
91429 TATTTGGAATTTTTAT-AAT
1 TATTTGAAATATTTATAAAT
91448 TATTTGAAATATTTATAAAT
1 TATTTGAAATATTTATAAAT
91468 TATT
1 TATT
91472 AATAATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TATTTGAAATATTTATAAAT
Found at i:91540 original size:42 final size:42
Alignment explanation
Indices: 91460--91541 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 42
91450 TTTGAAATAT
91460 TTATAAATTATTAATAATCTTTTTTTTTTTTTGAATTTATACA
1 TTATAAATTATTAATAATCTTTTTTTTTTTTT-AATTTATACA
*
91503 TTATAAATT-TTTATAAT-TTTTAGTTTTTTATTT-ATTTAT
1 TTATAAATTATTAATAATCTTTT--TTTTTT-TTTAATTTAT
91542 TTATAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
41 4 0.11
42 13 0.37
43 15 0.43
44 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (42 bp):
TTATAAATTATTAATAATCTTTTTTTTTTTTTAATTTATACA
Found at i:95647 original size:5 final size:5
Alignment explanation
Indices: 95630--95667 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
95620 AAGATATCGT
* *
95630 AAAAT AAAAG AAATG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
95668 TTTTAGCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:96692 original size:15 final size:15
Alignment explanation
Indices: 96645--96702 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
96635 AATTCGATTT
96645 TAATATAAATATTCAA
1 TAATATAAA-ATTCAA
96661 T-ATAATTAAACAATTCAA
1 TAAT-A-T-AA-AATTCAA
96679 TAATATAAAATTCAA
1 TAATATAAAATTCAA
*
96694 GAATATAAA
1 TAATATAAA
96703 TAGTAGATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
15 17 0.47
16 4 0.11
17 2 0.06
18 10 0.28
19 3 0.08
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (15 bp):
TAATATAAAATTCAA
Found at i:97296 original size:18 final size:18
Alignment explanation
Indices: 97273--97308 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
97263 TTCGAGTTGT
*
97273 CTCGAATAACTTAATTAA
1 CTCGAATAACTCAATTAA
97291 CTCGAATAACTCAATTAA
1 CTCGAATAACTCAATTAA
97309 TTTAACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (18 bp):
CTCGAATAACTCAATTAA
Found at i:100913 original size:30 final size:31
Alignment explanation
Indices: 100849--100918 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
100839 ACAACAAGAG
* * * *
100849 GACTATTTTGTCACTTTTTGATAACTTTAGT
1 GACTGTTTTGTCACATTTTCATAACTTGAGT
*
100880 GACTGTTTTGTCACATTTTCA-AAGTTGAGT
1 GACTGTTTTGTCACATTTTCATAACTTGAGT
100910 GACTGTTTT
1 GACTGTTTT
100919 ATTAAATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (31 bp):
GACTGTTTTGTCACATTTTCATAACTTGAGT
Found at i:106041 original size:23 final size:23
Alignment explanation
Indices: 106019--106156 Score: 172
Period size: 23 Copynumber: 6.0 Consensus size: 23
106009 CAGAGAATAC
* *
106019 CAAAGTACTAA-CAGAGAGCATA
1 CAAAGTGCTAATCAGAGAGCACA
*
106041 CACAGTGCTAAAT-AGAGAGCACA
1 CAAAGTGCT-AATCAGAGAGCACA
*
106064 CAAAGTACTAATCAGAGAGCACA
1 CAAAGTGCTAATCAGAGAGCACA
106087 CAAAGTGCTAATCAGAGAGCACA
1 CAAAGTGCTAATCAGAGAGCACA
*
106110 CACAGTGCTAATCAGAGAGCACA
1 CAAAGTGCTAATCAGAGAGCACA
* *
106133 CATATTGCTAATAACAGAGAGCAC
1 CAAAGTGCTAAT--CAGAGAGCAC
106157 GAGACGTGCT
Statistics
Matches: 102, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
22 10 0.10
23 82 0.80
25 10 0.10
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (23 bp):
CAAAGTGCTAATCAGAGAGCACA
Found at i:106144 original size:69 final size:69
Alignment explanation
Indices: 106019--106156 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
106009 CAGAGAATAC
*
106019 CAAAGTACTAACAGAGAGCATACACAGTGCTAAATAGAGAGCACACAAAGTACTAAT-CAGAGAG
1 CAAAGTACTAACAGAGAGCACACACAGTGCTAAATAGAGAGCACACAAAGTACTAATACAGAGAG
106083 CACA
66 CACA
* * * *
106087 CAAAGTGCTAATCAGAGAGCACACACAGTGCT-AATCAGAGAGCACACATATTGCTAATAACAGA
1 CAAAGTACTAA-CAGAGAGCACACACAGTGCTAAAT-AGAGAGCACACAAAGTACTAAT-ACAGA
106151 GAGCAC
63 GAGCAC
106157 GAGACGTGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
68 13 0.21
69 38 0.62
71 10 0.16
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (69 bp):
CAAAGTACTAACAGAGAGCACACACAGTGCTAAATAGAGAGCACACAAAGTACTAATACAGAGAG
CACA
Found at i:106171 original size:23 final size:22
Alignment explanation
Indices: 106028--106177 Score: 120
Period size: 23 Copynumber: 6.5 Consensus size: 22
106018 CCAAAGTACT
*
106028 AACAGAGAGCATACACAGTGCTA
1 AACAGAGAGCACACAC-GTGCTA
* * *
106051 AATAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACAC-ACGTGCTA
* *
106074 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACAC-ACGTGCTA
*
106097 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAC-GTGCTA
* **
106120 ATCAGAGAGCACACATATTGCTAA
1 AACAGAGAGCACACA-CGTGCT-A
*
106144 TAACAGAGAGCACGAGACGTGCTA
1 -AACAGAGAGCAC-ACACGTGCTA
*
106168 AACAAAGAGC
1 AACAGAGAGC
106178 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.01
23 85 0.80
24 3 0.03
25 15 0.14
26 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (22 bp):
AACAGAGAGCACACACGTGCTA
Found at i:106177 original size:48 final size:46
Alignment explanation
Indices: 106028--106177 Score: 142
Period size: 46 Copynumber: 3.2 Consensus size: 46
106018 CCAAAGTACT
* * * * *
106028 AACAGAGAGCATACACAGTGCTAAAT-AGAGAGCACACAAAGTACTA
1 AACAAAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTGCTA
* *
106074 ATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTA
1 AACAAAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTA
* * * * *
106120 ATCAGAGAGCACACATATTGCTAATAACAGAGAGCACGAGAC-GTGCTA
1 AACAAAGAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACACAGTGCTA
106168 AACAAAGAGC
1 AACAAAGAGC
106178 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
45 3 0.03
46 60 0.67
48 24 0.27
49 3 0.03
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (46 bp):
AACAAAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTA
Found at i:119893 original size:14 final size:14
Alignment explanation
Indices: 119874--119903 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
119864 TGGTTTCTTT
*
119874 TTCTTTTCTGTTTG
1 TTCTTTTCTATTTG
119888 TTCTTTTCTATTTG
1 TTCTTTTCTATTTG
119902 TT
1 TT
119904 TGTCATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.10, T:0.73
Consensus pattern (14 bp):
TTCTTTTCTATTTG
Found at i:122781 original size:18 final size:17
Alignment explanation
Indices: 122758--122792 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
122748 GAATAAATGT
122758 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
122776 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
122793 ACCCTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:126373 original size:24 final size:24
Alignment explanation
Indices: 126342--126390 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
126332 GAGTAAACTT
126342 AAAAAAGATAACATTTAATATAAA
1 AAAAAAGATAACATTTAATATAAA
126366 AAAAAAGATAACATTTAATATAAA
1 AAAAAAGATAACATTTAATATAAA
126390 A
1 A
126391 TGTTCTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAAAAGATAACATTTAATATAAA
Found at i:129512 original size:3 final size:3
Alignment explanation
Indices: 129506--129536 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
129496 CGCAACATCA
129506 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
129537 TATCTGAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:133200 original size:23 final size:23
Alignment explanation
Indices: 133148--133200 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
133138 ACGGTTAAAA
* *
133148 ATATAAAAAAATTATTAATAATT
1 ATATAAAAAAACTATAAATAATT
* *
133171 ATTTAAAAAAACTCTAAAT-ATAT
1 ATATAAAAAAACTATAAATAAT-T
133194 ATATAAA
1 ATATAAA
133201 TTTCAAATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATAAAAAAACTATAAATAATT
Found at i:133240 original size:6 final size:7
Alignment explanation
Indices: 133221--133250 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
133211 GCAAAAAACT
133221 TTAAAAA
1 TTAAAAA
133228 TTAAAAA
1 TTAAAAA
133235 TTAAAAA
1 TTAAAAA
133242 TTAAAAA
1 TTAAAAA
133249 TT
1 TT
133251 TTATGTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TTAAAAA
Found at i:138567 original size:6 final size:6
Alignment explanation
Indices: 138556--138637 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
138546 CCAGGCCCAA
* *
138556 TAAATT TAAATT T-ATTT TAAAAT TAAATT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
*
138602 T--ATT TAAATT T--ATT ATAAATT TGAATT TAAAATT TA
1 TAAATT TAAATT TAAATT -TAAATT TAAATT T-AAATT TA
138638 TTTAAATAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
4 10 0.17
5 6 0.10
6 33 0.55
7 11 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:138608 original size:10 final size:10
Alignment explanation
Indices: 138593--138644 Score: 68
Period size: 10 Copynumber: 4.8 Consensus size: 10
138583 TTTATTCTAA
138593 ATTTAAATTT
1 ATTTAAATTT
138603 ATTTAAATTT
1 ATTTAAATTT
138613 ATTATAAATTT
1 ATT-TAAATTT
138624 GAATTTAAAATTT
1 --ATTT-AAATTT
138637 ATTTAAAT
1 ATTTAAAT
138645 AATGTCAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 17 0.45
11 11 0.29
12 1 0.03
13 9 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:138612 original size:27 final size:25
Alignment explanation
Indices: 138577--138644 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 25
138567 TTATTTTAAA
138577 ATTAAATTTATTCTAAATTTAAATTT
1 ATTAAATTTATT-TAAATTTAAATTT
*
138603 ATTTAAATTTATTATAAATTTGAATTT
1 A-TTAAATTTATT-TAAATTTAAATTT
138630 A--AAATTTATTTAAAT
1 ATTAAATTTATTTAAAT
138645 AATGTCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.13
24 9 0.23
26 1 0.03
27 24 0.62
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
ATTAAATTTATTTAAATTTAAATTT
Found at i:138623 original size:17 final size:16
Alignment explanation
Indices: 138556--138644 Score: 97
Period size: 17 Copynumber: 5.3 Consensus size: 16
138546 CCAGGCCCAA
138556 TAAATTTAAATTTATTT
1 TAAATTTAAATTTA-TT
*
138573 TAAAATTAAATTTATT
1 TAAATTTAAATTTATT
138589 CTAAATTTAAATTTATT
1 -TAAATTTAAATTTATT
* **
138606 TAAATTTATTATAAATT
1 TAAATTTA-AATTTATT
*
138623 TGAATTTAAAATTTATT
1 TAAATTT-AAATTTATT
138640 TAAAT
1 TAAAT
138645 AATGTCAAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
16 10 0.17
17 48 0.81
18 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
TAAATTTAAATTTATT
Found at i:139293 original size:19 final size:20
Alignment explanation
Indices: 139265--139306 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
139255 ACATTAAATG
139265 AAATTTATTATT-ATTAA-A
1 AAATTTATTATTAATTAATA
139283 AAATATTATTATTAATTAATA
1 AAAT-TTATTATTAATTAATA
139304 AAA
1 AAA
139307 AAAACGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 5 0.24
21 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTATTATTAATTAATA
Found at i:140458 original size:59 final size:59
Alignment explanation
Indices: 140366--140764 Score: 546
Period size: 59 Copynumber: 6.8 Consensus size: 59
140356 CCTAAACTAT
* * *
140366 CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAACATTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
** ** *
140425 CAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCTAATTTTTGACCCCAAACCTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
* * *
140484 CAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCTCATTTTTAACCCCGAACCTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
* * * * *
140543 TAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCAAACCTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
* * * *
140602 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCTCGAACCTTT
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
* * * *
140661 CAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCTCATTTTTGACCCCGAACCTTC
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
* * **
140720 TAGAAATTACCATTTTACCCCCGGACTTCCAAAAATCCCATTTTT
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
140765 TGTCCTTCGA
Statistics
Matches: 299, Mismatches: 41, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 299 1.00
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAACCTTC
Found at i:140574 original size:118 final size:118
Alignment explanation
Indices: 140366--140787 Score: 603
Period size: 118 Copynumber: 3.6 Consensus size: 118
140356 CCTAAACTAT
* * * *
140366 CAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAACATTCCAAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAA
* *
140431 TTACCATTTTACCCTTAAACTTCCAAAAATCTAATTTTTGACCCCAAACCTTC
66 TTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTC
* * *
140484 CAAAAATTACCATTTTACCCCCAAACTTCTAAAAATCTCATTTTTAACCCCGAACCTTCTAAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAA
* * *
140549 TTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCAAACCTTC
66 TTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTC
*
140602 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCTCGAACCTT-TCAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCT-AAAA
* * *
140666 ATTACCATTTTACCCCCAAACTTCTAAAAATCTCATTTTTGACCCCGAACCTTC
65 ATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTC
* * ** ** *
140720 TAGAAATTACCATTTTACCCCCGGACTTCCAAAAATCCCATTTTTTGTCCTTCGAACCTTTTAAA
1 CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTTAACC-TCGAACCTTCTAAA
140785 AAT
64 AAT
140788 CTCATTTTTG
Statistics
Matches: 271, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
117 1 0.00
118 247 0.91
119 7 0.03
120 15 0.06
121 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAA
TTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTC
Found at i:140605 original size:177 final size:176
Alignment explanation
Indices: 140367--140764 Score: 629
Period size: 177 Copynumber: 2.2 Consensus size: 176
140357 CTAAACTATC
*
140367 AAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCAAACATTCCAAAAAT
1 AAAAATTACCATTTTACCCC-GAACTTCCAAAAATCCCATTTTTAACCTCAAACATTCCAAAAAT
** *
140432 TACCATTTTACCCTTAAACTTCCAAAAAT-CTAATTTTTGACCCCAAACCTTCCAAAAATTACCA
65 TACCATTTTACCCCCAAACTTCCAAAAATCCT-ATTTTTAACCCCAAACCTTCCAAAAATTACCA
140496 TTTTACCCCCAAACTTCTAAAAATCTCATTTTTAACCCCGAACCTTCT
129 TTTTACCCCCAAACTTCTAAAAATCTCATTTTTAACCCCGAACCTTCT
* *
140544 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACAC-CAAACCTTCCAAAAA
1 AAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTAAC-CTCAAACATTCCAAAAA
* * *
140608 TTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCTCGAACCTTTCAAAAATTACCA
64 TTACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCCCAAACCTTCCAAAAATTACCA
*
140673 TTTTACCCCCAAACTTCTAAAAATCTCATTTTTGACCCCGAACCTTCT
129 TTTTACCCCCAAACTTCTAAAAATCTCATTTTTAACCCCGAACCTTCT
* *
140721 AGAAATTACCATTTTACCCCCGGACTTCCAAAAATCCCATTTTT
1 AAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTT
140765 TGTCCTTCGA
Statistics
Matches: 205, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
177 198 0.97
178 7 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (176 bp):
AAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTAACCTCAAACATTCCAAAAATT
ACCATTTTACCCCCAAACTTCCAAAAATCCTATTTTTAACCCCAAACCTTCCAAAAATTACCATT
TTACCCCCAAACTTCTAAAAATCTCATTTTTAACCCCGAACCTTCT
Found at i:142816 original size:16 final size:16
Alignment explanation
Indices: 142785--142834 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
142775 TTTATGAACT
142785 TTTTATATTTTA--TAA
1 TTTTA-ATTTTATTTAA
142800 TTTTAATTTTATTTAA
1 TTTTAATTTTATTTAA
*
142816 -TTTAATTTTTATTTTA
1 TTTTAA-TTTTATTTAA
142832 TTT
1 TTT
142835 GAATAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.20
15 10 0.33
16 12 0.40
17 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAATTTTATTTAA
Found at i:144893 original size:17 final size:17
Alignment explanation
Indices: 144856--144892 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
144846 TTATTTACTC
*
144856 AAAATAAGAAAAAAATA
1 AAAATAACAAAAAAATA
144873 AAAATAAC-AAAAAATA
1 AAAATAACAAAAAAATA
144889 AAAA
1 AAAA
144893 AGTCACTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAATAACAAAAAAATA
Found at i:145248 original size:20 final size:18
Alignment explanation
Indices: 145224--145275 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
145214 AATAGTATTT
145224 TATTAATCTAATATTAAA
1 TATTAATCTAATATTAAA
145242 GTGATT-ATCTTAATATTAAA
1 -T-ATTAATC-TAATATTAAA
145262 T-TTAATCTAATATT
1 TATTAATCTAATATT
145276 TATCAAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.30
18 3 0.10
19 5 0.17
20 13 0.43
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (18 bp):
TATTAATCTAATATTAAA
Found at i:153603 original size:22 final size:22
Alignment explanation
Indices: 153541--153619 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
153531 GCATAGATGT
* *
153541 GAACCCTATATGTTTTATACATGC
1 GAACCCTATA-GATTTA-ATATGC
* * * *
153565 GAACTCTACAAGCTTTAATATGT
1 GAACCCTA-TAGATTTAATATGC
*
153588 GAATCCTATAGATTTAATATGC
1 GAACCCTATAGATTTAATATGC
153610 GAACCCTATA
1 GAACCCTATA
153620 TATCGTATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
22 20 0.47
23 10 0.23
24 12 0.28
25 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (22 bp):
GAACCCTATAGATTTAATATGC
Found at i:161015 original size:19 final size:19
Alignment explanation
Indices: 160995--161031 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
160985 ATTTATATAT
160995 TTTTA-AATCTTTTTAAAA
1 TTTTATAATCTTTTTAAAA
*
161013 TTTTATAATTTTTTTAAAA
1 TTTTATAATCTTTTTAAAA
161032 AATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATAATCTTTTTAAAA
Found at i:163867 original size:6 final size:6
Alignment explanation
Indices: 163853--163892 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
163843 CTTCATAAAT
*
163853 GATGGA GATGTA GATGTA GATGTA GATGTA GATGTA GATG
1 GATGTA GATGTA GATGTA GATGTA GATGTA GATGTA GATG
163893 ATGAAGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.30
Consensus pattern (6 bp):
GATGTA
Found at i:172415 original size:6 final size:6
Alignment explanation
Indices: 172406--172442 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
172396 TAGTATTAGA
172406 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG A
1 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG A
172443 GCTGGGCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
AATAGG
Found at i:172416 original size:18 final size:18
Alignment explanation
Indices: 172402--172440 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
172392 GCGATAGTAT
172402 TAGAAATAGGAATAGGAA
1 TAGAAATAGGAATAGGAA
*
172420 TAGGAATAGGAATAGGAA
1 TAGAAATAGGAATAGGAA
172438 TAG
1 TAG
172441 GAGCTGGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (18 bp):
TAGAAATAGGAATAGGAA
Found at i:175029 original size:20 final size:22
Alignment explanation
Indices: 174994--175041 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
174984 CAAAATAATT
174994 AAATATAACGAAAATT-ATTATA
1 AAATATAAC-AAAATTAATTATA
*
175016 AAATATAA-AAAATTAATTCTA
1 AAATATAACAAAATTAATTATA
175037 AAATA
1 AAATA
175042 AAATGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 10 0.42
22 8 0.33
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATAACAAAATTAATTATA
Found at i:175040 original size:21 final size:21
Alignment explanation
Indices: 174994--175059 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
174984 CAAAATAATT
174994 AAATATAACGAAAATTATTATA
1 AAATATAAC-AAAATTATTATA
*
175016 AAATATAA-AAAATTAATTCTA
1 AAATATAACAAAATT-ATTATA
* *
175037 AAATAAAATGAAATATTATTATA
1 AAATATAA-CAAA-ATTATTATA
175060 GAAGATCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.16
21 12 0.32
22 8 0.22
23 8 0.22
24 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATATAACAAAATTATTATA
Found at i:176253 original size:16 final size:16
Alignment explanation
Indices: 176229--176260 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
176219 TAAAGTGTGC
*
176229 GTAATAAAATTAAAAT
1 GTAAAAAAATTAAAAT
176245 GTAAAAAAATTAAAAT
1 GTAAAAAAATTAAAAT
176261 AAATTATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
GTAAAAAAATTAAAAT
Found at i:176587 original size:6 final size:6
Alignment explanation
Indices: 176549--176640 Score: 57
Period size: 6 Copynumber: 15.8 Consensus size: 6
176539 TATTTTGAGG
* * * * **
176549 TTAAAT TT-ATT TTGAAT ATAAAT TT-ATT TTAAAT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
176594 TTAAAAT TTAAAT TT-AAT ATAAAT TTAGAT TTATAT GTAAAT TTAAA
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
176641 ACTTATTATA
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
5 15 0.24
6 45 0.71
7 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:176602 original size:18 final size:17
Alignment explanation
Indices: 176534--176640 Score: 106
Period size: 17 Copynumber: 6.2 Consensus size: 17
176524 ACTCATTCTA
* **
176534 AAATTTATTTTGAGGTT
1 AAATTTATTTTAAATTT
* *
176551 AAATTTATTTTGAATAT
1 AAATTTATTTTAAATTT
176568 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
176585 AAATTTGTTTTAAAATTT
1 AAATTTATTTT-AAATTT
* *
176603 AAATTTAATATAAATTT
1 AAATTTATTTTAAATTT
* *
176620 AGATTTATATGTAAATTT
1 AAATTTAT-TTTAAATTT
176638 AAA
1 AAA
176641 ACTTATTATA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
17 51 0.68
18 24 0.32
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:176617 original size:35 final size:34
Alignment explanation
Indices: 176549--176627 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
176539 TATTTTGAGG
* * *
176549 TTAAATTTATTTTGAATATAAATTTATTTTAAAT
1 TTAAATTTATTTTAAATATAAATTTAATATAAAT
* *
176583 TTAAATTTGTTTTAAAATTTAAATTTAATATAAAT
1 TTAAATTTATTTT-AAATATAAATTTAATATAAAT
*
176618 TTAGATTTAT
1 TTAAATTTAT
176628 ATGTAAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 12 0.32
35 25 0.68
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTATTTTAAATATAAATTTAATATAAAT
Found at i:176710 original size:21 final size:22
Alignment explanation
Indices: 176684--176729 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
176674 AGGCCCAAAC
*
176684 AATGTCCAAAT-TAAAAGTCCA
1 AATGTCCAAATACAAAAGTCCA
*
176705 AATGTCCAGATACAAAAGTCCA
1 AATGTCCAAATACAAAAGTCCA
176727 AAT
1 AAT
176730 TGGGGCCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.22
Consensus pattern (22 bp):
AATGTCCAAATACAAAAGTCCA
Found at i:178434 original size:30 final size:30
Alignment explanation
Indices: 178390--178756 Score: 123
Period size: 30 Copynumber: 12.4 Consensus size: 30
178380 AAAGGTCCCT
*
178390 AAACTATCT-AAAAATTATATTTTGACCCCC
1 AAACT-TCTCAAAAATTATATTTTAACCCCC
* *
178420 AAACTTCTCTAAAATT-TCACTTTTAACCCCG
1 AAACTTCTCAAAAATTAT-A-TTTTAACCCCC
* * *
178451 AAGCTTC-CAAAAATTACATTTTTA-CCCC
1 AAACTTCTCAAAAATTATATTTTAACCCCC
* * * *
178479 AAACTT-TCGAAAATTCTAATTTTAACCTCA
1 AAACTTCTCAAAAATTAT-ATTTTAACCCCC
**
178509 AAACTTC-CAAAAATCCTA-ATTTTAACCCTA
1 AAACTTCTCAAAAAT--TATATTTTAACCCCC
* *
178539 AAACTTCT-AAAAAATACCATTTT-ACCCCC
1 AAACTTCTCAAAAATTA-TATTTTAACCCCC
* * ***
178568 GAACTTCT-AAAAACCTT-GATTTT-ACCTTA
1 AAACTTCTCAAAAA--TTATATTTTAACCCCC
* *
178597 AAACTTCT-AAAAATTACCATTTT-ACCCTC
1 AAACTTCTCAAAAATTA-TATTTTAACCCCC
* * * **
178626 GAACTTC-CAAAAAATCCCA-ATTTTGACCCTA
1 AAACTTCTC-AAAAAT--TATATTTTAACCCCC
*
178657 AAACTTC-CAAAAATTATCATTTT-ACCACC
1 AAACTTCTCAAAAATTAT-ATTTTAACCCCC
* * **
178686 GAACATC-CAAAAATTCCAT-TTTTAACCCTG
1 AAACTTCTCAAAAATT--ATATTTTAACCCCC
* *
178716 AAAC-TCTCCAAAATTACTATTTT-ACCCCT
1 AAACTTCTCAAAAATTA-TATTTTAACCCCC
178745 AAACTTC-CAAAA
1 AAACTTCTCAAAA
178757 TTCCATTTTT
Statistics
Matches: 256, Mismatches: 50, Indels: 63
0.69 0.14 0.17
Matches are distributed among these distances:
27 2 0.01
28 19 0.07
29 101 0.39
30 102 0.40
31 30 0.12
32 2 0.01
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.32
Consensus pattern (30 bp):
AAACTTCTCAAAAATTATATTTTAACCCCC
Found at i:178472 original size:29 final size:29
Alignment explanation
Indices: 178390--178784 Score: 195
Period size: 29 Copynumber: 13.4 Consensus size: 29
178380 AAAGGTCCCT
* * * *
178390 AAACTATCTAAAAATTATATTTTGACCCCC
1 AAACT-TCCAAAAATTACATTTTAACCCCG
* *
178420 AAACTTCTCTAAAATTTCACTTTTAACCCCG
1 AAACTTC-CAAAAATTACA-TTTTAACCCCG
* *
178451 AAGCTTCCAAAAATTACATTTTTACCCC-
1 AAACTTCCAAAAATTACATTTTAACCCCG
* * * *
178479 AAACTTTCGAAAATT-CTAATTTTAACCTCA
1 AAACTTCCAAAAATTAC--ATTTTAACCCCG
**
178509 AAACTTCCAAAAATCCTA-ATTTTAACCCTA
1 AAACTTCCAAAAAT--TACATTTTAACCCCG
* * *
178539 AAACTTCTAAAAAATACCATTTTACCCCCG
1 AAACTTCCAAAAATTA-CATTTTAACCCCG
* * ***
178569 -AACTTCTAAAAACCTT-GATTTT-ACCTTA
1 AAACTTCCAAAAA--TTACATTTTAACCCCG
*
178597 AAACTTCTAAAAATTACCATTTT-ACCCTCG
1 AAACTTCCAAAAATTA-CATTTTAACCC-CG
** * **
178627 -AACTTCCAAAAAATCCCAATTTTGACCCTA
1 AAACTTCC-AAAAATTAC-ATTTTAACCCCG
178657 AAACTTCCAAAAATTATCATTTT-ACCACCG
1 AAACTTCCAAAAATTA-CATTTTAACC-CCG
* * *
178687 -AACATCCAAAAATTCCATTTTTAACCCTG
1 AAACTTCCAAAAATTACA-TTTTAACCCCG
*
178716 AAACTCTCC-AAAATTACTATTTT-ACCCCT
1 AAACT-TCCAAAAATTAC-ATTTTAACCCCG
* * *
178745 AAACTTCC-AAAATTCCATTTTTGACCCAG
1 AAACTTCCAAAAATTACA-TTTTAACCCCG
*
178774 AAACTTTCAAA
1 AAACTTCCAAA
178785 CGTTACCCTT
Statistics
Matches: 281, Mismatches: 54, Indels: 60
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.01
28 32 0.11
29 106 0.38
30 106 0.38
31 32 0.11
32 1 0.00
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAACCCCG
Found at i:178615 original size:58 final size:59
Alignment explanation
Indices: 178510--178756 Score: 277
Period size: 59 Copynumber: 4.2 Consensus size: 59
178500 TTAACCTCAA
*
178510 AACTTCCAAAAATCCTAATTTTAACCCTAAAACTTCTAAAAAATACCATTTTACCCCCG
1 AACTTCCAAAAATCCTAATTTTAACCCTAAAACTTCTAAAAATTACCATTTTACCCCCG
* * * *
178569 AACTTCTAAAAA-CCTTGATTTT-ACCTTAAAACTTCTAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATCC-TAATTTTAACCCTAAAACTTCTAAAAATTACCATTTTACCCCCG
* * * * *
178627 AACTTCCAAAAAATCCCAATTTTGACCCTAAAACTTCCAAAAATTATCATTTTACCACCG
1 AACTTCC-AAAAATCCTAATTTTAACCCTAAAACTTCTAAAAATTACCATTTTACCCCCG
* * * * * **
178687 AACATCCAAAAATTCC-ATTTTTAACCCTGAAAC-TCTCCAAAATTACTATTTTACCCCTA
1 AACTTCCAAAAA-TCCTAATTTTAACCCTAAAACTTCT-AAAAATTACCATTTTACCCCCG
178746 AACTTCCAAAA
1 AACTTCCAAAA
178757 TTCCATTTTT
Statistics
Matches: 157, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
58 43 0.27
59 72 0.46
60 42 0.27
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATCCTAATTTTAACCCTAAAACTTCTAAAAATTACCATTTTACCCCCG
Found at i:178709 original size:118 final size:117
Alignment explanation
Indices: 178408--178826 Score: 340
Period size: 118 Copynumber: 3.5 Consensus size: 117
178398 TAAAAATTAT
** * * *
178408 ATTTTGACCCCCAAACTTCTCTAAAATT-TCACTTTTAACCCCGAAGCTTCCAAAAATTACATTT
1 ATTTTGACCCTAAAACTTC-CAAAAATTACCA-TTTT-ACCCCGAA-CTTCCAAAAATTCCATTT
** * * *
178472 TTACCCCAAACTT-TCGAAAATT-CTAATTTTAACCTCAAAACTTCCAAAAATCCTA
62 TTACCTAAAACTTCTCAAAAATTAC-AATTTTACCCTCAAAACTTCCAAAAATCCCA
* * * * *
178527 ATTTTAACCCTAAAACTTCTAAAAAATACCATTTTACCCCCGAACTTCTAAAAA--CCTTGATTT
1 ATTTTGACCCTAAAACTTCCAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATTCCAT--TTT
* *
178590 TACCTTAAAACTTCT-AAAAATTACCATTTTACCCTC-GAACTTCCAAAAAATCCCA
63 TACC-TAAAACTTCTCAAAAATTACAATTTTACCCTCAAAACTTCC-AAAAATCCCA
* *
178645 ATTTTGACCCTAAAACTTCCAAAAATTATCATTTTACCACCGAACATCCAAAAATTCCATTTTTA
1 ATTTTGACCCTAAAACTTCCAAAAATTACCATTTTACC-CCGAACTTCCAAAAATTCCATTTTT-
* * * * *
178710 ACCCTGAAAC-TCTCCAAAATTACTATTTTACCC-CTAAACTTCC-AAAATTCCA
64 A-CCTAAAACTTCTCAAAAATTACAATTTTACCCTCAAAACTTCCAAAAATCCCA
* * ** * *
178762 TTTTTGACCC-AGAAACTTTCAAACGTTACCCTTTTACCCTCGGA-TGTCCAAAAATTCCATTTT
1 ATTTTGACCCTA-AAACTTCCAAAAATTACCATTTTACCC-CGAACT-TCCAAAAATTCCATTTT
178825 TA
63 TA
178827 ATCCCGATTT
Statistics
Matches: 245, Mismatches: 37, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
115 2 0.01
116 3 0.01
117 85 0.35
118 100 0.41
119 50 0.20
120 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (117 bp):
ATTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATTCCATTTTTAC
CTAAAACTTCTCAAAAATTACAATTTTACCCTCAAAACTTCCAAAAATCCCA
Found at i:180701 original size:21 final size:21
Alignment explanation
Indices: 180676--180724 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
180666 GATACTGGTT
* **
180676 TACTTTAAATATGGGTATTGA
1 TACTTTAAAGATGGGTACCGA
* *
180697 TACTTCAAAGGTGGGTACCGA
1 TACTTTAAAGATGGGTACCGA
180718 TACTTTA
1 TACTTTA
180725 CTATCTAGAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (21 bp):
TACTTTAAAGATGGGTACCGA
Found at i:181113 original size:26 final size:26
Alignment explanation
Indices: 181084--181138 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
181074 AAATATAGAG
181084 TCTGAATCAAAAGTTGT-AACAATCTC
1 TCTGAATCAAAAGTT-TCAACAATCTC
*
181110 TCTGAATCAAAAGTTTCAGCAATCTC
1 TCTGAATCAAAAGTTTCAACAATCTC
181136 TCT
1 TCT
181139 CTCAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (26 bp):
TCTGAATCAAAAGTTTCAACAATCTC
Found at i:184224 original size:14 final size:14
Alignment explanation
Indices: 184205--184378 Score: 65
Period size: 14 Copynumber: 12.4 Consensus size: 14
184195 TGAATTCAAC
184205 GAGTTTAAGGTTAT
1 GAGTTTAAGGTTAT
* *
184219 GAGTTTAGGGTTAC
1 GAGTTTAAGGTTAT
* * *
184233 AATTTTAGGGTTTAT
1 GAGTTTAAGG-TTAT
* *
184248 G-GTTATGAGTTTA-
1 GAGTT-TAAGGTTAT
* *
184261 GGGTTTAGAGTTTAT
1 GAGTTTA-AGGTTAT
184276 -AGTTTAAGGTTAT
1 GAGTTTAAGGTTAT
* *
184289 TAGTAT-AGGATT-T
1 GAGTTTAAGG-TTAT
* *
184302 GGGATTTAGAGTTTA-
1 GAG-TTTA-AGGTTAT
184317 GAGTTTAAGGTTAT
1 GAGTTTAAGGTTAT
* *
184331 TAGTTT-AGGATTAC
1 GAGTTTAAGG-TTAT
*
184345 GAGTTTGAGGTTAT
1 GAGTTTAAGGTTAT
* *
184359 AAGTTTAGGGTTAT
1 GAGTTTAAGGTTAT
*
184373 AAGTTT
1 GAGTTT
184379 GGGTTTAGGG
Statistics
Matches: 119, Mismatches: 27, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
13 21 0.18
14 84 0.71
15 12 0.10
16 2 0.02
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.44
Consensus pattern (14 bp):
GAGTTTAAGGTTAT
Found at i:184251 original size:21 final size:21
Alignment explanation
Indices: 184221--184268 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
184211 AAGGTTATGA
*
184221 GTTTAGGGTTACAATTTTAGG
1 GTTTAGGGTTACAAGTTTAGG
* **
184242 GTTTATGGTTATGAGTTTAGG
1 GTTTAGGGTTACAAGTTTAGG
184263 GTTTAG
1 GTTTAG
184269 AGTTTATAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (21 bp):
GTTTAGGGTTACAAGTTTAGG
Found at i:184315 original size:35 final size:35
Alignment explanation
Indices: 184205--184316 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
184195 TGAATTCAAC
* * * *
184205 GAGTTTAAGGTTATGAGTTTAGG-GTTACAATTTTA
1 GAGTTTAAGGTTATGAGTATAGGATTTA-GAGTTTA
* * * *
184240 GGGTTTATGGTTATGAGTTTAGGGTTTAGAGTTTA
1 GAGTTTAAGGTTATGAGTATAGGATTTAGAGTTTA
* * *
184275 TAGTTTAAGGTTATTAGTATAGGATTT-GGGATTTA
1 GAGTTTAAGGTTATGAGTATAGGATTTAGAG-TTTA
184310 GAGTTTA
1 GAGTTTA
184317 GAGTTTAAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
34 2 0.03
35 57 0.92
36 3 0.05
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (35 bp):
GAGTTTAAGGTTATGAGTATAGGATTTAGAGTTTA
Found at i:184364 original size:42 final size:41
Alignment explanation
Indices: 184263--184378 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 41
184253 TGAGTTTAGG
* * * *
184263 GTTTAGAGTTTAT-AGTTTAAGGTTATTAGTATAGGATTTGG
1 GTTT-GAGGTTATAAGTTTAAGGTTATTAGTTTAGGATTCGA
184304 GATTT-AGAGTT-TAGAGTTTAAGGTTATTAGTTTAGGATTACGA
1 G-TTTGAG-GTTATA-AGTTTAAGGTTATTAGTTTAGGATT-CGA
* *
184347 GTTTGAGGTTATAAGTTTAGGGTTATAAGTTT
1 GTTTGAGGTTATAAGTTTAAGGTTATTAGTTT
184379 GGGTTTAGGG
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
40 3 0.05
41 3 0.05
42 50 0.81
43 6 0.10
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (41 bp):
GTTTGAGGTTATAAGTTTAAGGTTATTAGTTTAGGATTCGA
Found at i:184377 original size:28 final size:28
Alignment explanation
Indices: 184317--184405 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 28
184307 TTAGAGTTTA
* * * *
184317 GAGTTTAAGGTTATTAGTTTAGGATTAC
1 GAGTTTGAGGTTATAAGTTTAGGGTTAT
184345 GAGTTTGAGGTTATAAGTTTAGGGTTAT
1 GAGTTTGAGGTTATAAGTTTAGGGTTAT
* * * *
184373 AAGTTTG-GGTT-TAGGGTCAGGGTTAT
1 GAGTTTGAGGTTATAAGTTTAGGGTTAT
184399 GAGTTTG
1 GAGTTTG
184406 GTTTAGGGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 18 0.35
27 4 0.08
28 30 0.58
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.42
Consensus pattern (28 bp):
GAGTTTGAGGTTATAAGTTTAGGGTTAT
Found at i:184414 original size:25 final size:26
Alignment explanation
Indices: 184365--184414 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
184355 TTATAAGTTT
184365 AGGGTTATAAGTTTGGGTTTAGGGTC
1 AGGGTTATAAGTTTGGGTTTAGGGTC
*
184391 AGGGTTATGAGTTT-GGTTTAGGGT
1 AGGGTTATAAGTTTGGGTTTAGGGT
184415 TTTTAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.18, C:0.02, G:0.40, T:0.40
Consensus pattern (26 bp):
AGGGTTATAAGTTTGGGTTTAGGGTC
Found at i:191573 original size:18 final size:18
Alignment explanation
Indices: 191550--191584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
191540 CATCAGCTTC
*
191550 GTTCTTCCCTCTCTTTCT
1 GTTCTTCCCTCCCTTTCT
*
191568 GTTCTTGCCTCCCTTTC
1 GTTCTTCCCTCCCTTTC
191585 CCTTGTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.09, T:0.51
Consensus pattern (18 bp):
GTTCTTCCCTCCCTTTCT
Found at i:192765 original size:19 final size:21
Alignment explanation
Indices: 192724--192765 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
192714 ATATAATTAA
192724 ATTAAATTTTACAAATAATTT
1 ATTAAATTTTACAAATAATTT
*
192745 ATTAATTTTTA-AAAT-ATTT
1 ATTAAATTTTACAAATAATTT
192764 AT
1 AT
192766 ATATAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 4 0.20
21 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAAATTTTACAAATAATTT
Found at i:199593 original size:16 final size:17
Alignment explanation
Indices: 199552--199595 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
199542 ACTTAAATTC
199552 AACACTTAATTTTTTAG
1 AACACTTAATTTTTTAG
*
199569 TA-AC-T-ATTTTTT-G
1 AACACTTAATTTTTTAG
199582 AACACTTAATTTTT
1 AACACTTAATTTTT
199596 CAATTTATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 7
0.71 0.06 0.23
Matches are distributed among these distances:
13 2 0.09
14 9 0.41
15 2 0.09
16 8 0.36
17 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (17 bp):
AACACTTAATTTTTTAG
Found at i:210241 original size:21 final size:22
Alignment explanation
Indices: 210211--210255 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
210201 ATATTGAGAT
210211 AATATTATTATATT-AAATATAA
1 AATATTATTAT-TTGAAATATAA
*
210233 AATA-TATTATTTGTAATATAA
1 AATATTATTATTTGAAATATAA
210254 AA
1 AA
210256 GATTTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 15 0.71
22 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATATTATTATTTGAAATATAA
Found at i:217292 original size:24 final size:24
Alignment explanation
Indices: 217265--217316 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
217255 GAAAGATGGA
*
217265 AAGAAAG-CGGAGAATTTGCAGAGG
1 AAGAAAGAC-GAGAATTTGCAGAGC
*
217289 AAGAAAGACGAGAATTTTCAGAGC
1 AAGAAAGACGAGAATTTGCAGAGC
217313 AAGA
1 AAGA
217317 GCAAGAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.10, G:0.31, T:0.13
Consensus pattern (24 bp):
AAGAAAGACGAGAATTTGCAGAGC
Found at i:221403 original size:16 final size:17
Alignment explanation
Indices: 221368--221405 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
221358 TAATTCTAAA
221368 AAAATAAATAATTAATT
1 AAAATAAATAATTAATT
* *
221385 AAAATAAA-ATTTTATT
1 AAAATAAATAATTAATT
221401 AAAAT
1 AAAAT
221406 TAAGTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAAATAATTAATT
Found at i:222277 original size:23 final size:24
Alignment explanation
Indices: 222251--222316 Score: 62
Period size: 29 Copynumber: 2.6 Consensus size: 24
222241 TAAATGTCTT
*
222251 TAAAATAATAGCAAA-ATTAACAA
1 TAAAATAATAGCAAACAATAACAA
222274 TAAAATGAGAGTTATGCAAACAATAACAA
1 TAAAAT-A-A--TA-GCAAACAATAACAA
*
222303 CAAAATAATAGCAA
1 TAAAATAATAGCAA
222317 TATAATAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
23 6 0.17
24 5 0.14
25 3 0.09
27 3 0.09
28 6 0.17
29 12 0.34
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.20
Consensus pattern (24 bp):
TAAAATAATAGCAAACAATAACAA
Found at i:222321 original size:11 final size:11
Alignment explanation
Indices: 222303--222340 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
222293 ACAATAACAA
222303 CAAAATAATAG
1 CAAAATAATAG
*
222314 CAATATAATAG
1 CAAAATAATAG
*
222325 CAAAATGATAG
1 CAAAATAATAG
222336 CAAAA
1 CAAAA
222341 CAACAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:222350 original size:22 final size:22
Alignment explanation
Indices: 222298--222362 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
222288 TGCAAACAAT
* *
222298 AACAACAAAATAATAGCAATAT
1 AACAACAAAATAATAGCAAAAC
* * *
222320 AATAGCAAAATGATAGCAAAAC
1 AACAACAAAATAATAGCAAAAC
* *
222342 AACAACAAAACAACAGCAAAA
1 AACAACAAAATAATAGCAAAA
222363 AATATGTAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.11
Consensus pattern (22 bp):
AACAACAAAATAATAGCAAAAC
Found at i:225397 original size:30 final size:30
Alignment explanation
Indices: 225346--225403 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
225336 TTTAATAATA
**
225346 TGTAATTTTATACATGTAATTTTGATTTTT
1 TGTAATTTTATACATAAAATTTTGATTTTT
* *
225376 TGTATTTTTATACATAAAATTTTTATTT
1 TGTAATTTTATACATAAAATTTTGATTT
225404 GATCCAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.60
Consensus pattern (30 bp):
TGTAATTTTATACATAAAATTTTGATTTTT
Found at i:225563 original size:31 final size:30
Alignment explanation
Indices: 225528--225624 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
225518 ATTTTTTAAA
*
225528 ATATATATTATTGAATCAAAATTAAAATTTT
1 ATATATATAATT-AATCAAAATTAAAATTTT
* * * * *
225559 ATATATACATTTAAACTATAATCAAAATTTT
1 ATATATATAATTAATC-AAAATTAAAATTTT
*
225590 ATGTATATAATTACATC-AAATTAAAA-TTT
1 ATATATATAATTA-ATCAAAATTAAAATTTT
225619 ATATAT
1 ATATAT
225625 TAAATCAACA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 8 0.16
30 10 0.20
31 31 0.61
32 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (30 bp):
ATATATATAATTAATCAAAATTAAAATTTT
Found at i:227573 original size:15 final size:16
Alignment explanation
Indices: 227553--227585 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
227543 TATCATTATA
227553 ATTTAGATGTA-TTTT
1 ATTTAGATGTACTTTT
*
227568 ATTTAGATTTACTTTT
1 ATTTAGATGTACTTTT
227584 AT
1 AT
227586 ACTTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (16 bp):
ATTTAGATGTACTTTT
Found at i:228085 original size:20 final size:18
Alignment explanation
Indices: 228041--228087 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
228031 TAGTTTTTTT
228041 ATTT-AAAATAAGATAAA
1 ATTTAAAAATAAGATAAA
228058 ATAGTTAAAAATTAAGAATAAA
1 AT--TTAAAAA-TAAG-ATAAA
228080 ATTTAAAA
1 ATTTAAAA
228088 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.08
19 2 0.08
20 10 0.40
21 4 0.16
22 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
ATTTAAAAATAAGATAAA
Found at i:228089 original size:19 final size:18
Alignment explanation
Indices: 228041--228089 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
228031 TAGTTTTTTT
228041 ATTTAAAA-TAAGATAAA
1 ATTTAAAATTAAGATAAA
228058 ATAGTTAAAAATTAAGAATAAA
1 AT--TT-AAAATTAAG-ATAAA
228080 ATTTAAAATT
1 ATTTAAAATT
228090 TTTTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.07
19 8 0.30
20 6 0.22
21 4 0.15
22 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
ATTTAAAATTAAGATAAA
Found at i:231207 original size:29 final size:29
Alignment explanation
Indices: 231166--231373 Score: 276
Period size: 29 Copynumber: 7.1 Consensus size: 29
231156 AAACTGTCTG
* *
231166 AAAATTCCATTTTTAGCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCCA
*
231195 AAAATTCCATTTTTGA-CCTCAAAACTTTCA
1 AAAATTCCATTTTT-ACCCTC-AAACTTCCA
231225 AAAATTCCATTTTTACCC-CTAAACTTCCA
1 AAAATTCCATTTTTACCCTC-AAACTTCCA
*
231254 AAAATTCCATTTTTACCCTTAAACTTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCCA
*
231283 AAAATTCCATTTTTACCCTTAAACTTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCCA
* * *
231312 AAAATTCCATTTTTGACCTTGAAACTTCTA
1 AAAATTCCATTTTT-ACCCTCAAACTTCCA
* *
231342 AAAATTCCATTTTTACCCTCGAACCTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCCA
231371 AAA
1 AAA
231374 TCTACATTCT
Statistics
Matches: 161, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
29 111 0.69
30 50 0.31
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCAAACTTCCA
Found at i:231258 original size:59 final size:59
Alignment explanation
Indices: 231166--231403 Score: 288
Period size: 59 Copynumber: 4.1 Consensus size: 59
231156 AAACTGTCTG
* *
231166 AAAATTCCATTTTTAGCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTCA
1 AAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTCA
* *
231225 AAAATTCCATTTTTACCC-CTAAACTTCCAAAAATTCCATTTTT-ACC-CTTAAACTTCCA
1 AAAATTCCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGACCTC-AAAACTTTCA
* **
231283 AAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCTTGAAAC-TTCTA
1 AAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTC-A
* * * * * *
231342 AAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTACATTCTCGACCTCAAAACTCTCA
1 AAAATTCCATTTTTACCCTCAAACTTCCAAAAAT-TCCATTTTTGACCTCAAAACTTTCA
231401 AAA
1 AAA
231404 TTACTCTTTT
Statistics
Matches: 154, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
57 1 0.01
58 60 0.39
59 91 0.59
60 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTCA
Found at i:231405 original size:88 final size:86
Alignment explanation
Indices: 231152--231403 Score: 294
Period size: 88 Copynumber: 2.8 Consensus size: 86
231142 CCCTGGAGAT
* *
231152 CCCTAAACTGTCTGAAAATTCCATTTTTAGCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAA
1 CCCTAAACT-TCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCTCAA
231217 AACTTTCAAAAATTCCATTTTTAC
64 AAC-TTCAAAAATTCCATTTTTAC
* ** * *
231241 CCCTAAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACC-CTTAA
1 CCCTAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCTC-AAA
231305 ACTTCCAAAAATTCCATTTTTGA-
65 ACTT-CAAAAATTCCATTTTT-AC
* * * *
231328 CCTTGAAACTTCTAAAAATTCCATTTTTACCCTCGAACCTCC-AAAATCTACATTCTCGACCTCA
1 CCCT-AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAT-TCCATT-TTGACCTCA
231392 AAACTCTCAAAA
63 AAACT-TCAAAA
231404 TTACTCTTTT
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
86 3 0.02
87 35 0.25
88 76 0.55
89 23 0.17
90 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (86 bp):
CCCTAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCTCAAAA
CTTCAAAAATTCCATTTTTAC
Found at i:232438 original size:47 final size:47
Alignment explanation
Indices: 232369--232464 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
232359 ACATCAACTA
*
232369 CAAATATTTTGAGTTAAAATTATTTAATCTTATTAGATTGGTACATG
1 CAAATATTTCGAGTTAAAATTATTTAATCTTATTAGATTGGTACATG
*
232416 CAAATATTTCGAGTTAAAATTATTTAATCTTATTAGATTGGTGCATG
1 CAAATATTTCGAGTTAAAATTATTTAATCTTATTAGATTGGTACATG
232463 CA
1 CA
232465 TCAGGCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (47 bp):
CAAATATTTCGAGTTAAAATTATTTAATCTTATTAGATTGGTACATG
Found at i:233232 original size:25 final size:25
Alignment explanation
Indices: 233193--233253 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
233183 AAGCTTTTTT
* *
233193 TTTAATT-TATTAAATAGCATAGTC
1 TTTAATTATATGAAATAACATAGTC
** *
233217 TTTTTTTATATGAAATAACATTGTC
1 TTTAATTATATGAAATAACATAGTC
233242 TTTAATTATATG
1 TTTAATTATATG
233254 TCTTATTGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (25 bp):
TTTAATTATATGAAATAACATAGTC
Found at i:233455 original size:13 final size:13
Alignment explanation
Indices: 233437--233461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233427 TCTTAAAATC
233437 CTATCATGTGTGA
1 CTATCATGTGTGA
233450 CTATCATGTGTG
1 CTATCATGTGTG
233462 GGTTTAGTCT
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (13 bp):
CTATCATGTGTGA
Found at i:235837 original size:30 final size:29
Alignment explanation
Indices: 235801--235872 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 29
235791 AGTTTCAATT
235801 TAATCACTCAACTTTA-AAAAAATGACAAAA
1 TAATCACT-AA-TTTACAAAAAATGACAAAA
235831 TAATCACTAATTTATCAAAAAATGACAAAA
1 TAATCACTAATTTA-CAAAAAATGACAAAA
*
235861 CAATCACTAATT
1 TAATCACTAATT
235873 AACAGTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 4 0.10
29 2 0.05
30 33 0.85
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (29 bp):
TAATCACTAATTTACAAAAAATGACAAAA
Found at i:236472 original size:3 final size:3
Alignment explanation
Indices: 236464--236505 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
236454 TCTCTTCTCT
* *
236464 TTC TTC TTC TTC TTT TTC TTC TT- TTC TTC TTT TTC -TC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
236506 AAACCCTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:236794 original size:13 final size:13
Alignment explanation
Indices: 236776--236800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
236766 TCAAATATAA
236776 AATATTTAAAAAT
1 AATATTTAAAAAT
236789 AATATTTAAAAA
1 AATATTTAAAAA
236801 AATTAAAAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTTAAAAAT
Found at i:237021 original size:15 final size:14
Alignment explanation
Indices: 236984--237022 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
236974 TTAAAAGCTT
**
236984 AAAATTTTAAAATA
1 AAAATTTTATTATA
236998 AAAATTTTATTATA
1 AAAATTTTATTATA
237012 AAAATATTTAT
1 AAAAT-TTTAT
237023 GAATTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTTATTATA
Found at i:241126 original size:18 final size:19
Alignment explanation
Indices: 241092--241129 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
241082 ATGTTTACTC
241092 AATTATAAAATATTTAAAA
1 AATTATAAAATATTTAAAA
241111 AATTA-AAAAT-TATTAAAA
1 AATTATAAAATAT-TTAAAA
241129 A
1 A
241130 CTAAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 12 0.67
19 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTATAAAATATTTAAAA
Found at i:241128 original size:17 final size:16
Alignment explanation
Indices: 241092--241157 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
241082 ATGTTTACTC
241092 AATTATAAAATATTTAAAA
1 AATTA-AAAAT-TTT-AAA
241111 AATTAAAAATTATTAAA
1 AATTAAAAATT-TTAAA
* *
241128 AACTAAAAGTTTTAAA
1 AATTAAAAATTTTAAA
241144 AA-TAACAAATTTTA
1 AATTAA-AAATTTTA
241158 TTATAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.07
16 14 0.33
17 13 0.31
18 7 0.17
19 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (16 bp):
AATTAAAAATTTTAAA
Found at i:241156 original size:16 final size:16
Alignment explanation
Indices: 241097--241157 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
241087 TACTCAATTA
* *
241097 TAAAATATTTAAAAAAT
1 TAAAA-ATTTTAAAAAC
241114 TAAAAATTATTAAAAAC
1 TAAAAATT-TTAAAAAC
*
241131 TAAAAGTTTTAAAAA-
1 TAAAAATTTTAAAAAC
241146 TAACAAATTTTA
1 TAA-AAATTTTA
241158 TTATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
15 3 0.08
16 17 0.45
17 18 0.47
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (16 bp):
TAAAAATTTTAAAAAC
Found at i:241655 original size:8 final size:9
Alignment explanation
Indices: 241628--241657 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
241618 GATTTGTTTC
241628 AATTCGAAA
1 AATTCGAAA
241637 AATTCGAAA
1 AATTCGAAA
241646 AATTCGAAA
1 AATTCGAAA
241655 AAT
1 AAT
241658 AATTCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTCGAAA
Found at i:241980 original size:28 final size:28
Alignment explanation
Indices: 241940--242008 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
241930 ATTGTTTATG
241940 TAGTTAAATAATCTTCTGCTTCGTCTAC
1 TAGTTAAATAATCTTCTGCTTCGTCTAC
241968 TAGTTAAATAATCTTCTGCTTCGTCTAC
1 TAGTTAAATAATCTTCTGCTTCGTCTAC
241996 TAGTTAAATAATC
1 TAGTTAAATAATC
242009 GGTCCATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (28 bp):
TAGTTAAATAATCTTCTGCTTCGTCTAC
Found at i:245639 original size:4 final size:4
Alignment explanation
Indices: 245630--245673 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
245620 TCTTCCTACC
*
245630 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
245674 CTTTGTTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:249715 original size:3 final size:3
Alignment explanation
Indices: 249707--249756 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
249697 AGTCATGTCA
* * *
249707 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT CAT AGT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
249754 AAT
1 AAT
249757 TATTATTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:249888 original size:24 final size:25
Alignment explanation
Indices: 249841--249897 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
249831 TAATAAATGT
*
249841 ATATAAAA-TATTTATAAATATTAA
1 ATATAAAATTATATATAAATATTAA
249865 ATAATAAAATTATATA-AAAT-TTAA
1 AT-ATAAAATTATATATAAATATTAA
249889 ATATAAAAT
1 ATATAAAAT
249898 ATTATTTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.23
24 8 0.27
25 10 0.33
26 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATAAAATTATATATAAATATTAA
Found at i:250624 original size:12 final size:12
Alignment explanation
Indices: 250607--250656 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
250597 TTGTAATAAG
250607 ATAATAATAAAA
1 ATAATAATAAAA
*
250619 ATAATATTAAAA
1 ATAATAATAAAA
* *
250631 ATACTTATTAAAA
1 ATA-ATAATAAAA
*
250644 ATAAAAATAAAA
1 ATAATAATAAAA
250656 A
1 A
250657 CACTAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAATAAAA
Found at i:250642 original size:25 final size:25
Alignment explanation
Indices: 250614--250674 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
250604 AAGATAATAA
* * * *
250614 TAAAAATAATATTAAAAATACTTAT
1 TAAAAATAAAAATAAAAACACTAAT
250639 TAAAAATAAAAATAAAAACACTAAT
1 TAAAAATAAAAATAAAAACACTAAT
*
250664 TCAAAATAAAA
1 TAAAAATAAAA
250675 TATATTTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (25 bp):
TAAAAATAAAAATAAAAACACTAAT
Found at i:255515 original size:21 final size:21
Alignment explanation
Indices: 255481--255534 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
255471 AAATTTTGAA
* *
255481 TTTAAATTTTAAAATTTGAA-G
1 TTTAAAGTTCAAAATTT-AAGG
*
255502 TTTGAAGTTCAAAATTTAAGG
1 TTTAAAGTTCAAAATTTAAGG
255523 TTTAAAGTTCAA
1 TTTAAAGTTCAA
255535 GTTTAAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.43
Consensus pattern (21 bp):
TTTAAAGTTCAAAATTTAAGG
Done.