Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 15 of 26
Found at i:2490299 original size:18 final size:18
Alignment explanation
Indices: 2490274--2490310 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
2490264 ATATAATTTG
2490274 ATATAAAAATA-ATTAAA
1 ATATAAAAATATATTAAA
2490291 ATATAAAAATATATTAAA
1 ATATAAAAATATATTAAA
2490309 AT
1 AT
2490311 TTATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATAAAAATATATTAAA
Found at i:2490673 original size:18 final size:17
Alignment explanation
Indices: 2490646--2490691 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2490636 AAATTTATTT
2490646 TATT-AATATATTTAAA
1 TATTAAATATATTTAAA
2490662 TATATAAATATA-TTAAA
1 TAT-TAAATATATTTAAA
*
2490679 TATTAAAAATATT
1 TATTAAATATATT
2490692 CAGGTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 10 0.38
18 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAATATATTTAAA
Found at i:2491319 original size:2 final size:2
Alignment explanation
Indices: 2491312--2491353 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2491302 ATTCTTTTAC
* *
2491312 AT AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT -T AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2491352 AT
1 AT
2491354 TGACAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2491954 original size:23 final size:23
Alignment explanation
Indices: 2491917--2492007 Score: 62
Period size: 23 Copynumber: 3.9 Consensus size: 23
2491907 ATTTAATAAT
**
2491917 TTATATTATTTTTATATATTTTA
1 TTATATTATAATTATATATTTTA
**
2491940 TTATATTATAATTATAT-TTAAAA
1 TTATATTATAATTATATATT-TTA
*
2491963 TT-TATATATATATATATAAATTTTA
1 TTATAT-TATA-AT-TATATATTTTA
*
2491988 ATATATTAATAATT-TATATT
1 TTATATT-ATAATTATATATT
2492008 AAATAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
22 5 0.10
23 27 0.52
24 3 0.06
25 9 0.17
26 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATTATAATTATATATTTTA
Found at i:2491960 original size:48 final size:51
Alignment explanation
Indices: 2491898--2492029 Score: 141
Period size: 48 Copynumber: 2.6 Consensus size: 51
2491888 ATTTTAATTA
* * * *
2491898 AATTTAATAATTTAATAATTTATAT-TATTTTTATATATTTTATTATATT-AT
1 AATTT-AT-ATTTAATAATTTATATATATATATATAAATTTTAATATATTAAT
2491949 AA-TTATATTTAA-AATTTATATATATATATATAAATTTTAATATATTAAT
1 AATTTATATTTAATAATTTATATATATATATATAAATTTTAATATATTAAT
* *
2491998 AATTTATATTAAATAAATTT-TA-AAATATATAT
1 AATTTATATTTAAT-AATTTATATATATATATAT
2492030 TCGTATTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
47 9 0.13
48 26 0.37
49 6 0.09
50 20 0.29
51 4 0.06
52 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (51 bp):
AATTTATATTTAATAATTTATATATATATATATAAATTTTAATATATTAAT
Found at i:2491970 original size:21 final size:23
Alignment explanation
Indices: 2491946--2491992 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
2491936 TTTATTATAT
*
2491946 TATAAT-TATATTTAAAATTT-A
1 TATAATATATATATAAAATTTAA
*
2491967 TAT-ATATATATATAAATTTTAA
1 TATAATATATATATAAAATTTAA
2491989 TATA
1 TATA
2491993 TTAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 2 0.10
21 15 0.71
22 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAATATATATATAAAATTTAA
Found at i:2491993 original size:16 final size:16
Alignment explanation
Indices: 2491972--2492028 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2491962 ATTTATATAT
2491972 ATATATATAAATTTTA
1 ATATATATAAATTTTA
*
2491988 ATATAT-TAATAATTT-
1 ATATATATAA-ATTTTA
*
2492003 ATATTAAATAAATTTTA
1 ATA-TATATAAATTTTA
*
2492020 AAATATATA
1 ATATATATA
2492029 TTCGTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
15 6 0.19
16 21 0.66
17 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATATAAATTTTA
Found at i:2492005 original size:56 final size:54
Alignment explanation
Indices: 2491882--2492011 Score: 133
Period size: 56 Copynumber: 2.4 Consensus size: 54
2491872 AGATTTCGTC
* * *
2491882 ATTAA-AATTT-TAATTAAATTTAATAATTTAATAATTTATATTATTTTTATAT
1 ATTAATAATTTATAATTAAATTTAATAATTTAATAATATATATAATTTTAATAT
* * *
2491934 ATTTTATTATATTATAATTATATTTAA-AATTTATATATATATATATAAATTTTAATAT
1 A-TTAATAAT-TTATAATTAAATTTAATAATTTA-ATA-ATATATAT-AATTTTAATAT
2491992 ATTAATAATTTAT-ATTAAAT
1 ATTAATAATTTATAATTAAAT
2492012 AAATTTTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
52 1 0.02
53 3 0.05
54 2 0.03
55 14 0.23
56 19 0.31
57 13 0.21
58 10 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (54 bp):
ATTAATAATTTATAATTAAATTTAATAATTTAATAATATATATAATTTTAATAT
Found at i:2492613 original size:28 final size:29
Alignment explanation
Indices: 2492582--2492648 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
2492572 ATCGAATTCG
***
2492582 TTTATATAATTATTTTTAAAA-TATAATA
1 TTTATATAATTAAAATTAAAATTATAATA
*
2492610 TTTA-ATAAATTAAAATTAAAATTTTAATA
1 TTTATAT-AATTAAAATTAAAATTATAATA
2492639 TTTATA-AATT
1 TTTATATAATT
2492649 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.06
28 19 0.59
29 10 0.31
30 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTATATAATTAAAATTAAAATTATAATA
Found at i:2492622 original size:22 final size:22
Alignment explanation
Indices: 2492597--2492638 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2492587 ATAATTATTT
*
2492597 TTAAAA-TATAATATTTAATAAA
1 TTAAAATTAAAAT-TTTAATAAA
2492619 TTAAAATTAAAATTTTAATA
1 TTAAAATTAAAATTTTAATA
2492639 TTTATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAATTAAAATTTTAATAAA
Found at i:2494287 original size:2 final size:2
Alignment explanation
Indices: 2494234--2494272 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2494224 CTCTCCATCC
2494234 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2494273 CTCTTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2494798 original size:19 final size:18
Alignment explanation
Indices: 2494763--2494818 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
2494753 AATATGATGT
2494763 AAAATATAATATAATATA
1 AAAATATAATATAATATA
*
2494781 AAAATATAAATATTATATA
1 AAAATAT-AATATAATATA
* *
2494800 AATATATGATATTAATATA
1 AAAATATAATA-TAATATA
2494819 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATATAATATAATATA
Found at i:2494800 original size:11 final size:11
Alignment explanation
Indices: 2494784--2494837 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
2494774 TAATATAAAA
2494784 ATATAAATATT
1 ATATAAATATT
2494795 ATATAAATATAT
1 ATATAAATAT-T
*
2494807 GATATTAATA-T
1 -ATATAAATATT
*
2494818 AT-TAAATTTT
1 ATATAAATATT
2494828 ATATAAATAT
1 ATATAAATAT
2494838 ATTATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 17 0.49
12 1 0.03
13 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
ATATAAATATT
Found at i:2494844 original size:18 final size:18
Alignment explanation
Indices: 2494762--2494846 Score: 61
Period size: 18 Copynumber: 4.9 Consensus size: 18
2494752 AAATATGATG
* *
2494762 TAAA-ATATAATATAATA
1 TAAATATATAATTTTATA
* *
2494779 TAAAAATATAAATATTATA
1 TAAATATAT-AATTTTATA
* *
2494798 TAAATATATGATATTA-A
1 TAAATATATAATTTTATA
*
2494815 TATAT-TA-AATTTTATA
1 TAAATATATAATTTTATA
*
2494831 TAAATATATTATTTTA
1 TAAATATATAATTTTA
2494847 AATATAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
15 5 0.09
16 7 0.13
17 11 0.20
18 16 0.29
19 16 0.29
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (18 bp):
TAAATATATAATTTTATA
Found at i:2497849 original size:132 final size:132
Alignment explanation
Indices: 2497706--2497972 Score: 516
Period size: 132 Copynumber: 2.0 Consensus size: 132
2497696 TATTATATTT
*
2497706 TATATTTTTTATAATGTTAATTATATAAATATAAACACAACATAAATAATTAAAAATATAAAAAT
1 TATATTTTTTATAATGTTAATTATATAAATATAAACACAACATAAATAATTAAAAATATAAAAAA
2497771 TCTAAATATTGATATAATCCTTATATTAAATGTGTTTTATTATTAATATATTCATTGTATTTAAA
66 TCTAAATATTGATATAATCCTTATATTAAATGTGTTTTATTATTAATATATTCATTGTATTTAAA
2497836 TA
131 TA
2497838 TATATTTTTTATAATGTTAATTATATAAATATAAACACAACATAAATAATTAAAAATATAAAAAA
1 TATATTTTTTATAATGTTAATTATATAAATATAAACACAACATAAATAATTAAAAATATAAAAAA
*
2497903 TCTAAATATTGATATAATCCTTATATTAAATGTGTTTTATTATTAATATATTCATTGTATTTAGA
66 TCTAAATATTGATATAATCCTTATATTAAATGTGTTTTATTATTAATATATTCATTGTATTTAAA
2497968 TA
131 TA
2497970 TAT
1 TAT
2497973 TATGTTTAAT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (132 bp):
TATATTTTTTATAATGTTAATTATATAAATATAAACACAACATAAATAATTAAAAATATAAAAAA
TCTAAATATTGATATAATCCTTATATTAAATGTGTTTTATTATTAATATATTCATTGTATTTAAA
TA
Found at i:2499022 original size:6 final size:6
Alignment explanation
Indices: 2499011--2499036 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2499001 TTCTGGAATA
2499011 TTTTGG TTTTGG TTTTGG TTTTGG TT
1 TTTTGG TTTTGG TTTTGG TTTTGG TT
2499037 CATAAACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (6 bp):
TTTTGG
Found at i:2499692 original size:22 final size:21
Alignment explanation
Indices: 2499655--2499709 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2499645 TAATTTTTAT
2499655 AATT-TTTTAATT-AATAATA
1 AATTATTTTAATTAAATAATA
*
2499674 AATTAATTTTAATTAAATAATT
1 AATT-ATTTTAATTAAATAATA
*
2499696 AATTATTTAAATTA
1 AATTATTTTAATTA
2499710 TTTATTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.13
21 17 0.55
22 10 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTATTTTAATTAAATAATA
Found at i:2500279 original size:16 final size:16
Alignment explanation
Indices: 2500260--2500313 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 16
2500250 TTTTTTAATT
2500260 TATTTTTAAAAA--TA
1 TATTTTTAAAAATTTA
*
2500274 TATATTTAAAAATTTA
1 TATTTTTAAAAATTTA
2500290 -ATTTTTAAATAATTTAA
1 TATTTTTAAA-AATTT-A
2500307 TATTTTT
1 TATTTTT
2500314 TTATTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 11 0.33
15 8 0.24
16 7 0.21
17 1 0.03
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTTAAAAATTTA
Found at i:2500713 original size:27 final size:27
Alignment explanation
Indices: 2500657--2500719 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2500647 AATGAATTGA
* ***
2500657 AAACGAAAACTAAAAAAATAAACCTTT
1 AAACTAAAACTAAAAAAATAAACAAAT
2500684 AAACTAAAACTAAAAGAAATAAA-AAAT
1 AAACTAAAACTAAAA-AAATAAACAAAT
*
2500711 AAAATAAAA
1 AAACTAAAA
2500720 AACAAAACAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.71, C:0.10, G:0.03, T:0.16
Consensus pattern (27 bp):
AAACTAAAACTAAAAAAATAAACAAAT
Found at i:2511743 original size:22 final size:20
Alignment explanation
Indices: 2511704--2511746 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2511694 TTAATTAATT
*
2511704 TAATTTAAATAAATATAAAA
1 TAATTTAAATAAAAATAAAA
2511724 TAATATTAATATAAAAATAAAA
1 TAAT-TTAA-ATAAAAATAAAA
2511746 T
1 T
2511747 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATTTAAATAAAAATAAAA
Found at i:2511761 original size:54 final size:55
Alignment explanation
Indices: 2511692--2511800 Score: 136
Period size: 55 Copynumber: 2.0 Consensus size: 55
2511682 TTTTTATTTA
2511692 TTTTAATTAATTTAATTTAA-ATAAAT-ATAAAATAATATTAATATAAA-AATAAAAT
1 TTTTAATTAATTTAA-TTAATATAAATAATAAAATAA-A-TAATATAAACAATAAAAT
* *
2511747 TTTTAATT-TTTTAATTAATTATAAATAATAATATAAATAATATAAACAATAAAA
1 TTTTAATTAATTTAATTAA-TATAAATAATAAAATAAATAATATAAACAATAAAA
2511801 AAAATCTGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
53 4 0.08
54 14 0.29
55 22 0.46
56 8 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (55 bp):
TTTTAATTAATTTAATTAATATAAATAATAAAATAAATAATATAAACAATAAAAT
Found at i:2511805 original size:21 final size:21
Alignment explanation
Indices: 2511766--2511805 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2511756 TTTAATTAAT
* * *
2511766 TATAAATAATAATATAAATAA
1 TATAAACAATAAAAAAAATAA
2511787 TATAAACAATAAAAAAAAT
1 TATAAACAATAAAAAAAAT
2511806 CTGACAAAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
TATAAACAATAAAAAAAATAA
Found at i:2513436 original size:24 final size:24
Alignment explanation
Indices: 2513407--2513458 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2513397 GATTATTTGA
2513407 TTGTAATAAACTTAATTATTCCGT
1 TTGTAATAAACTTAATTATTCCGT
2513431 TTGTAATAAACTTAATTATTCCGT
1 TTGTAATAAACTTAATTATTCCGT
2513455 TTGT
1 TTGT
2513459 TTATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (24 bp):
TTGTAATAAACTTAATTATTCCGT
Found at i:2517465 original size:11 final size:11
Alignment explanation
Indices: 2517445--2517478 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2517435 TTCCTTGTGA
2517445 TCTCTGTTTTT
1 TCTCTGTTTTT
2517456 TCTCT-TTTTT
1 TCTCTGTTTTT
*
2517466 GCTCTGTTTTT
1 TCTCTGTTTTT
2517477 TC
1 TC
2517479 CCCATCGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.71
Consensus pattern (11 bp):
TCTCTGTTTTT
Found at i:2519551 original size:61 final size:61
Alignment explanation
Indices: 2519469--2519602 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 61
2519459 ACTATTTTCC
*
2519469 AAAT-TATAATTATGGGAATTAAACTAGTAATAATTTAATCAAGGATCAAAACTTCACTAAA
1 AAATCTATAA-TATGGGAATTAAACTAGTAATAATTAAATCAAGGATCAAAACTTCACTAAA
* ** **
2519530 AAATCTATAATATGGGAATTAAACTAGTAATAATTAAATGAAGGATCAAAACTTTGCTCCA
1 AAATCTATAATATGGGAATTAAACTAGTAATAATTAAATCAAGGATCAAAACTTCACTAAA
2519591 AAATCTATAATA
1 AAATCTATAATA
2519603 GCACTTAGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 61 0.92
62 5 0.08
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (61 bp):
AAATCTATAATATGGGAATTAAACTAGTAATAATTAAATCAAGGATCAAAACTTCACTAAA
Found at i:2520728 original size:23 final size:22
Alignment explanation
Indices: 2520702--2520750 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
2520692 CCAAATTTAA
*
2520702 ATTTTAATATTTAT-AATTTTTTT
1 ATTTTAA-A-TTATGAATTCTTTT
2520725 ATTTTTAAATTATGAATTCTTTT
1 A-TTTTAAATTATGAATTCTTTT
2520748 ATT
1 ATT
2520751 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 6 0.26
23 11 0.48
24 6 0.26
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTAAATTATGAATTCTTTT
Found at i:2522726 original size:16 final size:17
Alignment explanation
Indices: 2522697--2522729 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2522687 TATGTTAAGA
*
2522697 TTATAATTTTATTTTTT
1 TTATAATTTAATTTTTT
2522714 TTAT-ATTTAATTTTTT
1 TTATAATTTAATTTTTT
2522730 AAAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATAATTTAATTTTTT
Found at i:2523293 original size:27 final size:28
Alignment explanation
Indices: 2523263--2523320 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
2523253 TTTATTTAAT
2523263 TATTTAT-A-TATTCATATTATAACTATA
1 TATTTATAATTATT-ATATTATAACTATA
*
2523290 TATTTATAGATTATTATATTATAATTATA
1 TATTTATA-ATTATTATATTATAACTATA
2523319 TA
1 TA
2523321 AATTTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
29 16 0.59
30 4 0.15
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (28 bp):
TATTTATAATTATTATATTATAACTATA
Found at i:2523320 original size:23 final size:22
Alignment explanation
Indices: 2523277--2523337 Score: 52
Period size: 23 Copynumber: 2.6 Consensus size: 22
2523267 TATATATTCA
* *
2523277 TATTATAACTATATATTTATAGAT
1 TATTAT-ATTATA-ATTTATAAAT
2523301 TATTATATTATAATTATATAAAT
1 TATTATATTATAATT-TATAAAT
*
2523324 T-TTAATATTTTAAT
1 TATT-ATATTATAAT
2523338 AATTTATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 5 0.16
23 21 0.66
24 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTATATTATAATTTATAAAT
Found at i:2523850 original size:2 final size:2
Alignment explanation
Indices: 2523829--2523872 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2523819 TTTACTATGT
* *
2523829 TA TA TC TA TC TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2523870 TA T
1 TA T
2523873 TTTGGATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2525303 original size:2 final size:2
Alignment explanation
Indices: 2525296--2525321 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2525286 TCCAAGAAAT
2525296 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2525322 AAAGTTAAAG
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):
TA
Found at i:2526807 original size:3 final size:3
Alignment explanation
Indices: 2526792--2526824 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2526782 TTGAATTGAA
*
2526792 ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2526825 TTGTATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:2527228 original size:28 final size:29
Alignment explanation
Indices: 2527196--2527251 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2527186 GTTAATATCA
* * *
2527196 TAAAATAATTAAATATTAATTTA-ATTAT
1 TAAAATAATAAAAAATTAAATTATATTAT
2527224 TAAAATAATAAAAAATTAAATTATATTA
1 TAAAATAATAAAAAATTAAATTATATTA
2527252 ATAATTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAAATAATAAAAAATTAAATTATATTAT
Found at i:2528543 original size:3 final size:3
Alignment explanation
Indices: 2528535--2528562 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2528525 TACGAAGATC
2528535 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2528563 TTGCCTTGAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2529499 original size:2 final size:2
Alignment explanation
Indices: 2529478--2529533 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
2529468 TTTCAGACTC
2529478 TA TA T- TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2529517 TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA T
2529534 CTTAGCAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2529908 original size:19 final size:20
Alignment explanation
Indices: 2529878--2529916 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2529868 ATTTATTAAC
2529878 GATAAGTTTTAAATAAATAT
1 GATAAGTTTTAAATAAATAT
*
2529898 GATAA-TTTTAAATATATAT
1 GATAAGTTTTAAATAAATAT
2529917 CAAAATATAA
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:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
GATAAGTTTTAAATAAATAT
Found at i:2529931 original size:19 final size:19
Alignment explanation
Indices: 2529907--2529963 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
2529897 TGATAATTTT
2529907 AAATATAT-ATCAAAATATA
1 AAATATATGAT-AAAATATA
* *
2529926 ACATATTTGATAAAATATA
1 AAATATATGATAAAATATA
2529945 AAATATA--A-AAAATATA
1 AAATATATGATAAAATATA
2529961 AAA
1 AAA
2529964 GACACAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 11 0.33
17 1 0.03
19 19 0.58
20 2 0.06
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
AAATATATGATAAAATATA
Found at i:2531332 original size:25 final size:26
Alignment explanation
Indices: 2531273--2531332 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
2531263 TATGTACTAT
2531273 AATTTAATTTATAATTCAATATTTTA
1 AATTTAATTTATAATTCAATATTTTA
** *
2531299 AA-AAAATTTATAATTTAATA-TTTA
1 AATTTAATTTATAATTCAATATTTTA
*
2531323 AATTTTATTT
1 AATTTAATTT
2531333 TTTTATATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 6 0.22
25 19 0.70
26 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTTAATTTATAATTCAATATTTTA
Found at i:2532048 original size:33 final size:36
Alignment explanation
Indices: 2531980--2532051 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 36
2531970 TAATAAAATT
*
2531980 AAAATATTTATATATATTTATAATTAAATTTTAATA
1 AAAATATTTATATATATTAATAATTAAATTTTAATA
2532016 AAAATATTT-TA-ATATTAAATAA-T-AATTTTAATA
1 AAAATATTTATATATATT-AATAATTAAATTTTAATA
2532049 AAA
1 AAA
2532052 TTTATTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 13 0.38
34 6 0.18
35 6 0.18
36 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AAAATATTTATATATATTAATAATTAAATTTTAATA
Found at i:2532060 original size:33 final size:30
Alignment explanation
Indices: 2532000--2532075 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 30
2531990 TATATATTTA
*
2532000 TAATTAAATTTTAATAAAAATATTTTAATAT
1 TAATAAAATTTTAATAAAAATATTTTAA-AT
*
2532031 TAAATAATAATTTTAAT-AAAATTTATTTAAAT
1 T-AATAA-AATTTTAATAAAAATAT-TTTAAAT
*
2532063 TTATAAAATTTTA
1 TAATAAAATTTTA
2532076 TTCGAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 7 0.18
31 5 0.13
32 13 0.33
33 14 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAATAAAATTTTAATAAAAATATTTTAAAT
Found at i:2532359 original size:2 final size:2
Alignment explanation
Indices: 2532346--2532375 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2532336 CATTTTCATC
*
2532346 AT AT AC 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 AT
2532376 TTTTTACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2532613 original size:3 final size:3
Alignment explanation
Indices: 2532605--2532644 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
2532595 ACCATAGCAC
2532605 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
2532645 TTTAATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2532957 original size:25 final size:25
Alignment explanation
Indices: 2532925--2532982 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
2532915 TTGAATTCTT
* *
2532925 TTATTATTTATA-TTAAATGTAATTA
1 TTATTATTTAAATTTAAAT-TAAATA
2532950 TTATTATTTAAATTTAAATTAAATA
1 TTATTATTTAAATTTAAATTAAATA
*
2532975 ATATTATT
1 TTATTATT
2532983 CATCAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTATTATTTAAATTTAAATTAAATA
Found at i:2534016 original size:22 final size:22
Alignment explanation
Indices: 2533969--2534053 Score: 68
Period size: 22 Copynumber: 3.8 Consensus size: 22
2533959 CTCACTTCTC
* *
2533969 ATTTAATAAAAAATTGATATT-C
1 ATTTAATAAAAAATTAAT-TTAA
2533991 ATTTAATAAAAAATTAATTTAA
1 ATTTAATAAAAAATTAATTTAA
*
2534013 ATTTAATTATAAAAA-T-ATATAA
1 ATTTAA-TA-AAAAATTAATTTAA
* *
2534035 ATATTAATATACAATTAAT
1 AT-TTAATAAAAAATTAAT
2534054 ATTTTAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
21 5 0.10
22 33 0.63
23 9 0.17
24 5 0.10
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (22 bp):
ATTTAATAAAAAATTAATTTAA
Found at i:2534263 original size:37 final size:37
Alignment explanation
Indices: 2534222--2534303 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
2534212 GTGGATTGAT
* * *
2534222 CAATCCATTATGATTGTTAGTATTTGGGTAGCAGTGC
1 CAATCCACTATGATTGTTAGAATTTGGGTAGCAGCGC
*
2534259 CAATCCACTATGATTGTTAGAATTTGGGTGGCAGCGC
1 CAATCCACTATGATTGTTAGAATTTGGGTAGCAGCGC
2534296 CAATCCAC
1 CAATCCAC
2534304 AAAAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (37 bp):
CAATCCACTATGATTGTTAGAATTTGGGTAGCAGCGC
Found at i:2539576 original size:25 final size:21
Alignment explanation
Indices: 2539523--2539581 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
2539513 ATCTATGTGT
2539523 AATATTAATTAATTTTTAATC
1 AATATTAATTAATTTTTAATC
2539544 AATATTAATTAATTTTTAATC
1 AATATTAATTAATTTTTAATC
* *
2539565 AATGTTAGTTAATTTTT
1 AATATTAATTAATTTTT
2539582 TTCCATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
AATATTAATTAATTTTTAATC
Found at i:2539668 original size:3 final size:3
Alignment explanation
Indices: 2539660--2539701 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2539650 TGATAGTCAC
* *
2539660 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATG ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2539702 TCATCATGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2542947 original size:25 final size:25
Alignment explanation
Indices: 2542919--2542972 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2542909 AGCAATAGAA
2542919 TTAATAGATCATTGAAATTAGAGCT
1 TTAATAGATCATTGAAATTAGAGCT
2542944 TTAATAGATCATTGAAATTAGAGCT
1 TTAATAGATCATTGAAATTAGAGCT
2542969 TTAA
1 TTAA
2542973 CTTAGTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (25 bp):
TTAATAGATCATTGAAATTAGAGCT
Found at i:2544848 original size:33 final size:33
Alignment explanation
Indices: 2544811--2544894 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
2544801 GGATCTTCCC
*
2544811 TACTACTTGTGCTGCTTAAAGGAGCATCATCCA
1 TACTACTTGTCCTGCTTAAAGGAGCATCATCCA
* * *
2544844 TACTACTTGTCCGGATTAAAGGAGCATCATCCC
1 TACTACTTGTCCTGCTTAAAGGAGCATCATCCA
*
2544877 TACTAATTGTCCTGCTTA
1 TACTACTTGTCCTGCTTA
2544895 CAGTAATATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (33 bp):
TACTACTTGTCCTGCTTAAAGGAGCATCATCCA
Found at i:2550395 original size:14 final size:14
Alignment explanation
Indices: 2550365--2550405 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2550355 AAAGTTGATA
2550365 AATATAA-AAATAT
1 AATATAATAAATAT
2550378 --TATAATAAATAT
1 AATATAATAAATAT
2550390 AATATAATATAATAT
1 AATATAATA-AATAT
2550405 A
1 A
2550406 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
14 7 0.29
15 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATAATAAATAT
Found at i:2550462 original size:26 final size:28
Alignment explanation
Indices: 2550433--2550484 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
2550423 TTATAAATTC
2550433 AATATAT-TAATTAATAT-TTA-ATTTTT
1 AATATATATAA-TAATATATTATATTTTT
2550459 AATATATATAATAATATATTATATTT
1 AATATATATAATAATATATTATATTT
2550485 ATATTTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.57
27 6 0.26
28 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATATATAATAATATATTATATTTTT
Found at i:2551028 original size:15 final size:14
Alignment explanation
Indices: 2551003--2551033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2550993 ACAATTTAAG
2551003 ATATATTTATATAT
1 ATATATTTATATAT
2551017 ATATAGTTTATATAT
1 ATATA-TTTATATAT
2551032 AT
1 AT
2551034 TTTTAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATATTTATATAT
Found at i:2553813 original size:45 final size:43
Alignment explanation
Indices: 2553739--2553834 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 43
2553729 CTCGAACTTA
*
2553739 AAATAATATGTATTAATAAAAAATTATATTTAAAT-TTAATTAT
1 AAATAATATGTATTAATAAAAAATAATATTTAAATATT-ATTAT
* *
2553782 AAATAATATATTATTAATATAAAAATAATATTTTAATATTATTAT
1 AAATAATAT-GTATTAATA-AAAAATAATATTTAAATATTATTAT
2553827 AAATAATA
1 AAATAATA
2553835 AAATAAATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
43 9 0.19
44 8 0.17
45 28 0.60
46 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (43 bp):
AAATAATATGTATTAATAAAAAATAATATTTAAATATTATTAT
Found at i:2553817 original size:19 final size:19
Alignment explanation
Indices: 2553773--2553820 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
2553763 TATATTTAAA
2553773 TTTAATTATAAATAATATAT
1 TTTAA-TATAAATAATATAT
2553793 TATTAATATAAA-AATAATAT
1 T-TTAATATAAATAAT-ATAT
2553813 TTTAATAT
1 TTTAATAT
2553821 TATTATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATATAAATAATATAT
Found at i:2553819 original size:11 final size:12
Alignment explanation
Indices: 2553777--2553834 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 12
2553767 TTTAAATTTA
2553777 ATTATAAATAAT
1 ATTATAAATAAT
* *
2553789 A-TATTATTAAT
1 ATTATAAATAAT
*
2553800 A-TAAAAATAAT
1 ATTATAAATAAT
* *
2553811 ATT-TTAATATT
1 ATTATAAATAAT
2553822 ATTATAAATAAT
1 ATTATAAATAAT
2553834 A
1 A
2553835 AAATAAATTG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTATAAATAAT
Found at i:2555208 original size:2 final size:2
Alignment explanation
Indices: 2555201--2555234 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2555191 GTGTAAACAA
*
2555201 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2555235 TATTTCCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2555745 original size:23 final size:24
Alignment explanation
Indices: 2555699--2555746 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
2555689 AAAATAATAT
2555699 TATTAAAAAAATTATGTACTTTTTA
1 TATTAAAAAAATTATGTAC-TTTTA
*
2555724 TATTAAAAAAATTATTTA-TTTTA
1 TATTAAAAAAATTATGTACTTTTA
2555747 ATACTAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
25 17 0.77
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTAAAAAAATTATGTACTTTTA
Found at i:2555820 original size:18 final size:18
Alignment explanation
Indices: 2555765--2555819 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 18
2555755 CAAATTTAAA
*
2555765 AAAACTAATCATTCACTTTT
1 AAAA-TAATTATTCA-TTTT
2555785 AAAATAATTATTCATTTT
1 AAAATAATTATTCATTTT
*
2555803 AAAA-AATTATTTATTTT
1 AAAATAATTATTCATTTT
2555820 TTTATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 12 0.36
18 8 0.24
19 9 0.27
20 4 0.12
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATAATTATTCATTTT
Found at i:2565197 original size:45 final size:43
Alignment explanation
Indices: 2565142--2565290 Score: 137
Period size: 45 Copynumber: 3.4 Consensus size: 43
2565132 ATTTAATAAT
*
2565142 TTATATTATATTTATATATTTTATTATATCATAATCGTATTTAAA
1 TTATATTATATTTATATATTTT-TTATATCATAATC-TATTTATA
* * * *
2565187 TTATTTTATATTTATATAAATTTTTATATAATAAT-AATTTATA
1 TTATATTATATTTATAT-ATTTTTTATATCATAATCTATTTATA
*
2565230 TTATATTA-ATTTTAAAATATTTTTTATATC-TATATCATATTTATA
1 TTATATTATA-TTT-ATATATTTTTTATATCATA-ATC-TATTTATA
*
2565275 TTAT-TT-TTTTTATATA
1 TTATATTATATTTATATA
2565291 ATATTTAACA
Statistics
Matches: 85, Mismatches: 12, Indels: 17
0.75 0.11 0.15
Matches are distributed among these distances:
42 7 0.08
43 31 0.36
44 5 0.06
45 38 0.45
46 4 0.05
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (43 bp):
TTATATTATATTTATATATTTTTTATATCATAATCTATTTATA
Found at i:2565257 original size:88 final size:90
Alignment explanation
Indices: 2565127--2565296 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 90
2565117 TATATAAATT
* *
2565127 TAATAATTTAATAATTTATATTATATTTATATATTTTATTATATC-ATAATCGTATTTAAATTAT
1 TAATAATTTAATAATTTATATTATATTTAAATATTTTATTATATCTAT-ATCATATTTAAATTAT
2565191 TTTATATTTATATAA-ATTTTTATATAA
65 TTT-T-TTTATATAATATTTTTATATAA
*
2565218 TAATAATTT-AT-A-TTATATTA-ATTTTAAAATATTTT-TTATATCTATATCATATTTATATTA
1 TAATAATTTAATAATTTATATTATA-TTT-AAATATTTTATTATATCTATATCATATTTAAATTA
2565278 TTTTTTTTATATAATATTT
64 TTTTTTTTATATAATATTT
2565297 AACATTATCG
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
86 9 0.12
87 6 0.08
88 35 0.49
89 11 0.15
90 2 0.03
91 9 0.12
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (90 bp):
TAATAATTTAATAATTTATATTATATTTAAATATTTTATTATATCTATATCATATTTAAATTATT
TTTTTTATATAATATTTTTATATAA
Found at i:2565272 original size:29 final size:28
Alignment explanation
Indices: 2565224--2565294 Score: 70
Period size: 31 Copynumber: 2.4 Consensus size: 28
2565214 ATAATAATAA
*
2565224 TTTATATTATATTAATTTTAAAATATTT
1 TTTATATTATATCAATTTTAAAATATTT
** *
2565252 TTTATATCTATATCATATTTATATTATTTTT
1 TTTATAT-TATATCA-ATTT-TAAAATATTT
*
2565283 TTTATATAATAT
1 TTTATATTATAT
2565295 TTAACATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.20
29 6 0.17
30 8 0.23
31 14 0.40
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATATTATATCAATTTTAAAATATTT
Found at i:2565294 original size:45 final size:45
Alignment explanation
Indices: 2565157--2565296 Score: 125
Period size: 43 Copynumber: 3.1 Consensus size: 45
2565147 TTATATTTAT
* *
2565157 ATATTTTATTATATC-ATAATCGTATTTAAATTATTTTATATTTATATA
1 ATATTTT-TTATATCTAT-ATCATATTTATATTATTTT-T-TTTATATA
* *
2565205 A-A-TTTTTATA--TA-ATAATAATTTATATTATATTAATTTTA-A-A
1 ATATTTTTTATATCTATATCAT-ATTTATATTAT-TT-TTTTTATATA
2565246 ATATTTTTTATATCTATATCATATTTATATTATTTTTTTTATATA
1 ATATTTTTTATATCTATATCATATTTATATTATTTTTTTTATATA
2565291 ATATTT
1 ATATTT
2565297 AACATTATCG
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
41 2 0.03
42 5 0.07
43 27 0.36
44 7 0.09
45 25 0.33
46 7 0.09
47 1 0.01
48 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (45 bp):
ATATTTTTTATATCTATATCATATTTATATTATTTTTTTTATATA
Found at i:2566262 original size:12 final size:12
Alignment explanation
Indices: 2566245--2566295 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
2566235 GGGATGACAT
*
2566245 TAACAAAAATAA
1 TAACAATAATAA
2566257 TAACAATAATAA
1 TAACAATAATAA
*
2566269 TAATAATAATAA
1 TAACAATAATAA
*
2566281 TAATAATAATAA
1 TAACAATAATAA
2566293 TAA
1 TAA
2566296 AGCTCTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (12 bp):
TAACAATAATAA
Found at i:2566267 original size:3 final size:3
Alignment explanation
Indices: 2566252--2566295 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2566242 CATTAACAAA
*
2566252 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2566296 AGCTCTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2568097 original size:22 final size:22
Alignment explanation
Indices: 2568072--2568113 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2568062 TATTTTTATT
2568072 TAAAT-TTAATTATAAAAATATA
1 TAAATATT-ATTATAAAAATATA
2568094 TAAATATTATTATAAAAATA
1 TAAATATTATTATAAAAATA
2568114 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTATTATAAAAATATA
Found at i:2568353 original size:2 final size:2
Alignment explanation
Indices: 2568346--2568396 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2568336 GTTAAAGGTT
2568346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2568388 TA TA TA TA T
1 TA TA TA TA T
2568397 GGTAATTGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2568699 original size:2 final size:2
Alignment explanation
Indices: 2568692--2568720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2568682 TGTCAAAAAT
2568692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2568721 GGATTGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2570146 original size:2 final size:2
Alignment explanation
Indices: 2570139--2570164 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2570129 ATTACTTGGA
2570139 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
2570165 GAAATTATTT
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:2571521 original size:20 final size:20
Alignment explanation
Indices: 2571496--2571537 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2571486 ACTAATGGCC
2571496 ATAAAATATAAAATAATTCT
1 ATAAAATATAAAATAATTCT
*
2571516 ATAAAATATAAAGTAATTCT
1 ATAAAATATAAAATAATTCT
2571536 AT
1 AT
2571538 CTTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAAATATAAAATAATTCT
Found at i:2572900 original size:15 final size:15
Alignment explanation
Indices: 2572879--2572915 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2572869 AAATTAAGCT
2572879 TTAAATTTAA-TAAA
1 TTAAATTTAATTAAA
2572893 TATAAA-TTAATTAAA
1 T-TAAATTTAATTAAA
2572908 TTAAATTT
1 TTAAATTT
2572916 TAGACTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATTTAATTAAA
Found at i:2574013 original size:12 final size:13
Alignment explanation
Indices: 2573982--2574015 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2573972 TAAAATTTTA
2573982 ATTTTATTAAATT
1 ATTTTATTAAATT
2573995 ATTTTATTAAATT
1 ATTTTATTAAATT
2574008 -TTTTATTA
1 ATTTTATTA
2574016 TTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTATTAAATT
Found at i:2574243 original size:13 final size:14
Alignment explanation
Indices: 2574214--2574247 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2574204 ATTTAATTTA
2574214 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
2574228 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
2574241 TTAATAA
1 TTAATAA
2574248 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:2574472 original size:2 final size:2
Alignment explanation
Indices: 2574465--2574493 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2574455 AACTAAACCC
2574465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2574494 AGTTGGCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2574641 original size:2 final size:2
Alignment explanation
Indices: 2574634--2574665 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2574624 TTATAATAGG
2574634 AT AT 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 AT AT
2574666 GTCATGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2575833 original size:14 final size:15
Alignment explanation
Indices: 2575808--2575846 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2575798 AAAAAAATAA
2575808 AAAATATTAAAATTT
1 AAAATATTAAAATTT
2575823 AAAAT-TTAAAATTAT
1 AAAATATTAAAATT-T
*
2575838 TAAATATTA
1 AAAATATTA
2575847 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 8 0.38
15 10 0.48
16 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATATTAAAATTT
Found at i:2576026 original size:2 final size:2
Alignment explanation
Indices: 2576019--2576044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2576009 TATCAAACAT
2576019 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2576045 GATCGATAGA
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):
TA
Found at i:2580332 original size:14 final size:14
Alignment explanation
Indices: 2580313--2580345 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2580303 AATATTAAAA
*
2580313 TATTATTTTTATAT
1 TATTATTTATATAT
2580327 TATTATTTATATAT
1 TATTATTTATATAT
2580341 T-TTAT
1 TATTAT
2580346 AAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTATTTATATAT
Found at i:2581211 original size:3 final size:3
Alignment explanation
Indices: 2581203--2581228 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2581193 TTCAATTTAA
2581203 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2581229 ATCAAGATGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2581642 original size:2 final size:2
Alignment explanation
Indices: 2581635--2581666 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2581625 ATCCCAATTT
2581635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2581667 ATTTTGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2584121 original size:23 final size:22
Alignment explanation
Indices: 2584082--2584127 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
2584072 ATTTTTATTT
*
2584082 TAAATTTAATTATAAAATTATA
1 TAAATTTAATTATAAAATAATA
2584104 TAAATATTAA-TATAAAAATAATA
1 TAAAT-TTAATTAT-AAAATAATA
2584127 T
1 T
2584128 TTTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATTTAATTATAAAATAATA
Found at i:2586281 original size:22 final size:22
Alignment explanation
Indices: 2586256--2586316 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
2586246 TTCAAAATCA
* **
2586256 ATAATTAATTATTATATTTAAT
1 ATAATTAATTAATATAAATAAT
2586278 ATAAATT-ATTAATATAAATAAT
1 AT-AATTAATTAATATAAATAAT
*
2586300 AT-ATTAATTAATTTAAA
1 ATAATTAATTAATATAAA
2586317 AAATTCGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 10 0.30
22 16 0.48
23 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATTAATTAATATAAATAAT
Found at i:2587587 original size:26 final size:25
Alignment explanation
Indices: 2587557--2587623 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 25
2587547 TGAAATGTTC
*
2587557 ATATATCATATTTATATTATTTTTT
1 ATATATAATATTTATATTATTTTTT
2587582 ATTATATAATGATTTA-ATTATTTTTT
1 A-TATATAAT-ATTTATATTATTTTTT
*
2587608 ATATAGAATATTTATA
1 ATATATAATATTTATA
2587624 CCCAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 5 0.14
25 9 0.24
26 18 0.49
27 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (25 bp):
ATATATAATATTTATATTATTTTTT
Found at i:2589132 original size:2 final size:2
Alignment explanation
Indices: 2589125--2589150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2589115 TTATTAAGCC
2589125 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2589151 AGAAATTAAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2592035 original size:26 final size:27
Alignment explanation
Indices: 2591983--2592041 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
2591973 ATTTATATTT
*
2591983 AATAT-ATTTTTAAATATAAATATAAA
1 AATATAATTTTTAAATATAAATAAAAA
* *
2592009 AATATAATTTTTTAA-ATACATAAAAA
1 AATATAATTTTTAAATATAAATAAAAA
*
2592035 ATTATAA
1 AATATAA
2592042 AAGTAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATAATTTTTAAATATAAATAAAAA
Found at i:2592995 original size:14 final size:14
Alignment explanation
Indices: 2592978--2593019 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2592968 TTTGAAATAT
*
2592978 ATATTTATATTGTA
1 ATATTTATATTATA
*
2592992 ATATTT-TAATTATT
1 ATATTTAT-ATTATA
2593006 ATATTTATATTATA
1 ATATTTATATTATA
2593020 TTTATCTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATATTTATATTATA
Found at i:2593024 original size:20 final size:22
Alignment explanation
Indices: 2592982--2593024 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
2592972 AAATATATAT
*
2592982 TTATATTGTAATATTTTAATTA
1 TTATATTGTAATATTATAATTA
*
2593004 TTATATT-T-ATATTATATTTA
1 TTATATTGTAATATTATAATTA
2593024 T
1 T
2593025 CTAATCATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATATTGTAATATTATAATTA
Found at i:2596491 original size:71 final size:71
Alignment explanation
Indices: 2596347--2596495 Score: 165
Period size: 71 Copynumber: 2.0 Consensus size: 71
2596337 TTATTAGTAA
* * * *
2596347 AAAATTTATCACATTTATAAATAAAAATTCTAATTATATTGAAAATTTAGTTAAATTAATTTATC
1 AAAATTTATCACATTTATAAATAAAAATTCTAATTATATTAAAAATATAGGTAAATAAATTTATC
2596412 GAATAAT
66 -AATAAT
* * * *
2596419 AAAATTTATCACA-TTATGAATAAAAATTTTAATTTTATTAAAAAACTATGGGTAAATGAAATTT
1 AAAATTTATCACATTTATAAATAAAAATTCTAATTATATT-AAAAA-TATAGGTAAAT-AAATTT
*
2596483 ATTAAATAAT
63 A-TCAATAAT
2596493 AAA
1 AAA
2596496 TAAAAAATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
71 23 0.36
72 17 0.27
73 8 0.12
74 15 0.23
75 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (71 bp):
AAAATTTATCACATTTATAAATAAAAATTCTAATTATATTAAAAATATAGGTAAATAAATTTATC
AATAAT
Found at i:2596608 original size:24 final size:25
Alignment explanation
Indices: 2596573--2596619 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2596563 AAGTAAAAGG
* *
2596573 AAATATTTATATTAATTT-AATTTT
1 AAATATTAATATAAATTTGAATTTT
2596597 AAATATTAATATAAATTTGAATT
1 AAATATTAATATAAATTTGAATT
2596620 ATTTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATATTAATATAAATTTGAATTTT
Found at i:2596622 original size:19 final size:19
Alignment explanation
Indices: 2596581--2596627 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2596571 GGAAATATTT
* *
2596581 ATATTAAT-TTAATTTTAA
1 ATATTAATATAAATTTGAA
2596599 ATATTAATATAAATTTGAA
1 ATATTAATATAAATTTGAA
* *
2596618 TTATTTATAT
1 ATATTAATAT
2596628 TACATGTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATTAATATAAATTTGAA
Found at i:2596711 original size:21 final size:23
Alignment explanation
Indices: 2596682--2596736 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
2596672 TTTTTATAAG
2596682 ATAAATAGT-TTTCATA-ATATT
1 ATAAATAGTATTTCATATATATT
* *
2596703 ATAATTAGTATTTTATATTATATT
1 ATAAATAGTATTTCATA-TATATT
2596727 ATAAATAGTA
1 ATAAATAGTA
2596737 ATAAGATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.29
22 6 0.21
24 14 0.50
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (23 bp):
ATAAATAGTATTTCATATATATT
Found at i:2597909 original size:26 final size:26
Alignment explanation
Indices: 2597880--2597955 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
2597870 TTCGGTTCAT
*
2597880 TATTTTTTTAAATTTAAAAAAAAATC
1 TATTTTTTTAAATTTAAAAAAAAATA
2597906 TA-TTTTTTACTAATTTAAAAATAAAATA
1 TATTTTTTTA--AATTTAAAAA-AAAATA
*
2597934 T-TTATTTTTATATTATAAAAAA
1 TATT-TTTTTAAATT-TAAAAAA
2597956 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 7 0.17
26 2 0.05
27 14 0.33
28 13 0.31
29 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTTTTTTAAATTTAAAAAAAAATA
Found at i:2598689 original size:19 final size:18
Alignment explanation
Indices: 2598652--2598695 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2598642 TTAATATTTG
* *
2598652 TTTTAAATTTTTTTAAAA
1 TTTTATATTTTTTAAAAA
2598670 TTTTATATTTTTTAATAAA
1 TTTTATATTTTTTAA-AAA
*
2598689 TTATATA
1 TTTTATA
2598696 ATATAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATATTTTTTAAAAA
Found at i:2600708 original size:3 final size:3
Alignment explanation
Indices: 2600700--2600747 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2600690 TGATTATATG
2600700 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2600748 GTTTAATGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2601247 original size:17 final size:16
Alignment explanation
Indices: 2601222--2601274 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2601212 TAAACAGTTT
2601222 ATTTATTTATCATTTAA
1 ATTTATTTAT-ATTTAA
*
2601239 ATTTTTTTATATTTAA
1 ATTTATTTATATTTAA
*
2601255 TATATTATTTTTA-TTAA
1 -AT-TTATTTATATTTAA
2601272 ATT
1 ATT
2601275 AAAAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.03
16 8 0.26
17 15 0.48
18 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATATTTAA
Found at i:2603516 original size:27 final size:27
Alignment explanation
Indices: 2603467--2603519 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2603457 AAAAAATATA
*
2603467 ATTTTATTAATAATAATTTTTTAATTT
1 ATTTTATTAATAATAATTATTTAATTT
*
2603494 ATTTTAATTAA-AATTATTATTTAATT
1 ATTTT-ATTAATAATAATTATTTAATT
2603520 AATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTTATTAATAATAATTATTTAATTT
Found at i:2603545 original size:45 final size:45
Alignment explanation
Indices: 2603426--2603560 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
2603416 GACGTCACTG
* *
2603426 ATTATATATAAATATTTATAATTAATATATTAA--AAAATATAATTTT
1 ATTA-ATA-AAATATTTATAATTTATAT-TTAATTAAAATATAATTTA
* *
2603472 ATTAATAATAAT-TTTTTAATTTAT-TTTAATTAAAATTATTATTTA
1 ATTAATAA-AATATTTATAATTTATATTTAATTAAAA-TATAATTTA
*
2603517 ATTAATAAAATATTTAT-ATTTATATTTAATTATAAAAATAATTT
1 ATTAATAAAATATTTATAATTTATATTTAATTA-AAATATAATTT
2603561 TTTAATATTA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
42 4 0.05
43 1 0.01
44 24 0.32
45 39 0.52
46 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (45 bp):
ATTAATAAAATATTTATAATTTATATTTAATTAAAATATAATTTA
Found at i:2603596 original size:18 final size:17
Alignment explanation
Indices: 2603548--2603601 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2603538 ATATTTAATT
*
2603548 ATAAAAATAATTTTTTA
1 ATAAAAATAATATTTTA
*
2603565 ATATTATAAT-ATATTTTA
1 ATA--AAAATAATATTTTA
2603583 CATAAAAATAATATTTTA
1 -ATAAAAATAATATTTTA
2603601 A
1 A
2603602 ATTTAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
17 8 0.27
18 15 0.50
19 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAAATAATATTTTA
Found at i:2604008 original size:2 final size:2
Alignment explanation
Indices: 2604001--2604035 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2603991 TTTGTTCTTG
2604001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2604036 AAGTGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2604547 original size:34 final size:34
Alignment explanation
Indices: 2604484--2604700 Score: 260
Period size: 34 Copynumber: 6.4 Consensus size: 34
2604474 GGGGCAATAC
* *
2604484 TTGTTGATTAAAT-GGTGATTT-AGTAGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGA-TAGCTTACCA
* * * *
2604517 TTATTGATTAAATGGGTGATTTGATGGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGATAGCTTACCA
* *
2604551 TTGTTGACTAAAT-GGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGATAGCTTACCA
* *
2604584 TTGTTGATTAAATGGGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGATAGCTTACCA
* * *
2604618 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGATAGCTTACCA
* * *
2604652 TTGTTGACTAAATGGGAGATTTGATAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGATAGCTTACCA
2604686 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2604701 TGGTTTTTAC
Statistics
Matches: 161, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
33 40 0.25
34 120 0.75
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGATAGCTTACCA
Found at i:2604666 original size:68 final size:67
Alignment explanation
Indices: 2604484--2604702 Score: 303
Period size: 67 Copynumber: 3.3 Consensus size: 67
2604474 GGGGCAATAC
* * * * * *
2604484 TTGTTGATTAAATGGTGATTTAGTAGTTTACCATTATTGATTAAATGGGTGATTTGATGGTTTAC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGATAGCTTAC
2604549 CA
66 CA
* * * *
2604551 TTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGATAGCTTAC
2604616 CA
66 CA
* * * *
2604618 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGATAGGTTG
1 TTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGATAGCTTA
2604683 CCA
65 CCA
2604686 TTGTTGATTAAATGGTG
1 TTGTTGATTAAATGGTG
2604703 GTTTTTACCA
Statistics
Matches: 133, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 73 0.55
68 60 0.45
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (67 bp):
TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGATAGCTTAC
CA
Found at i:2609180 original size:34 final size:34
Alignment explanation
Indices: 2609111--2609328 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
2609101 AAGTGGGAGA
* * *
2609111 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2609144 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2609178 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2609211 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2609245 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2609279 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2609313 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2609329 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2609294 original size:68 final size:67
Alignment explanation
Indices: 2609111--2609330 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
2609101 AAGTGGGAGA
* * * * *
2609111 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
2609176 CC
66 CC
* * * *
2609178 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
2609243 CC
66 CC
* * *
2609245 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
2609310 GCC
65 GCC
2609313 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
2609331 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:2609674 original size:2 final size:2
Alignment explanation
Indices: 2609667--2609714 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
2609657 CCTAAATTTA
*
2609667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2609709 GT AT AT
1 AT AT AT
2609715 CGGTTGATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2610072 original size:3 final size:3
Alignment explanation
Indices: 2610064--2610097 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2610054 TGAAAGTTGA
2610064 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2610098 TAAATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2610132 original size:24 final size:23
Alignment explanation
Indices: 2610097--2610160 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
2610087 TTATTATTAT
*
2610097 TTAAA-TTT-TAAATTGATT-AA
1 TTAAATTTTATAAATTAATTAAA
2610117 TTATAATTTATATAAATTAATTAAA
1 TTA-AATTT-TATAAATTAATTAAA
*
2610142 TTAAATTTTTTAAATTAAT
1 TTAAATTTTATAAATTAAT
2610161 AATATCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 3 0.08
21 2 0.05
22 2 0.05
23 11 0.30
24 14 0.38
25 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAATTTTATAAATTAATTAAA
Found at i:2610461 original size:14 final size:14
Alignment explanation
Indices: 2610442--2610471 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2610432 TTGACTATAA
2610442 AAAATAAAAATTAT
1 AAAATAAAAATTAT
*
2610456 AAAATAATAATTAT
1 AAAATAAAAATTAT
2610470 AA
1 AA
2610472 TACAATATTT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATAAAAATTAT
Found at i:2612786 original size:29 final size:27
Alignment explanation
Indices: 2612731--2612784 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2612721 TAAAGTATTA
* **
2612731 AAAATATTTTTATAATTAAATTTAAAT
1 AAAATATATTTATAATTAAATAAAAAT
2612758 AAAATATATTTATTAATTAAATAAAAA
1 AAAATATATTTA-TAATTAAATAAAAA
2612785 ATTAAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATATATTTATAATTAAATAAAAAT
Found at i:2612894 original size:24 final size:24
Alignment explanation
Indices: 2612862--2612911 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2612852 AAGCCAGATA
*
2612862 AATAAGTTGATGTGAGAAAAAATT
1 AATAAGTTGATCTGAGAAAAAATT
*
2612886 AATAAGTTGATCTGAGAACAAATT
1 AATAAGTTGATCTGAGAAAAAATT
2612910 AA
1 AA
2612912 GACTATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (24 bp):
AATAAGTTGATCTGAGAAAAAATT
Found at i:2613446 original size:12 final size:12
Alignment explanation
Indices: 2613392--2613458 Score: 63
Period size: 12 Copynumber: 5.9 Consensus size: 12
2613382 ATATTAGATT
*
2613392 TATAATATCAAA
1 TATAATATAAAA
* *
2613404 TACAAT-TAATTA
1 TATAATATAA-AA
2613416 TATAA-A-AAAA
1 TATAATATAAAA
2613426 T-TAAT-TAAAA
1 TATAATATAAAA
2613436 TATAATATAAAA
1 TATAATATAAAA
2613448 TATAATATAAA
1 TATAATATAAA
2613459 TTTATGAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
9 3 0.07
10 7 0.16
11 8 0.18
12 26 0.59
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (12 bp):
TATAATATAAAA
Found at i:2613603 original size:16 final size:16
Alignment explanation
Indices: 2613554--2613603 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2613544 TTATAGAAAA
*
2613554 TATATAATA-TAAATA
1 TATATAATACTAAATT
* *
2613569 TATA-AATTACTCAACT
1 TATATAA-TACTAAATT
2613585 TATATAATACTAAATT
1 TATATAATACTAAATT
2613601 TAT
1 TAT
2613604 GATAGCAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 2 0.07
15 6 0.22
16 17 0.63
17 2 0.07
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATAATACTAAATT
Found at i:2614322 original size:34 final size:31
Alignment explanation
Indices: 2614269--2614330 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 31
2614259 AACTTTTTTC
*
2614269 TTTTTATTATAATTAAATTTAAATAAAAATA
1 TTTTTATTATAATAAAATTTAAATAAAAATA
2614300 TTTTTATTATTTAATAATAATTTAAATAAAA
1 TTTTTATTA--TAATAA-AATTTAAATAAAA
2614331 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTTTATTATAATAAAATTTAAATAAAAATA
Found at i:2614859 original size:20 final size:19
Alignment explanation
Indices: 2614819--2614893 Score: 54
Period size: 19 Copynumber: 4.1 Consensus size: 19
2614809 AAATTATGTC
2614819 ATAAAATTTATATATTTAT
1 ATAAAATTTATATATTTAT
*
2614838 ATAAATTTTA-ATATGTTA-
1 ATAAAATTTATATAT-TTAT
*
2614856 AT---ATTT-TATGATATAT
1 ATAAAATTTATAT-ATTTAT
*
2614872 ATAAAATCTAATATATTTAT
1 ATAAAAT-TTATATATTTAT
2614892 AT
1 AT
2614894 TTATATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 17
0.66 0.08 0.27
Matches are distributed among these distances:
15 7 0.17
16 4 0.10
18 6 0.14
19 14 0.33
20 8 0.19
21 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (19 bp):
ATAAAATTTATATATTTAT
Found at i:2614899 original size:14 final size:13
Alignment explanation
Indices: 2614882--2614963 Score: 53
Period size: 12 Copynumber: 6.3 Consensus size: 13
2614872 ATAAAATCTA
2614882 ATATATTTATATTT
1 ATATATTT-TATTT
2614896 ATATATTTGTATTAT
1 ATATATTT-TATT-T
*
2614911 ATTTATTTTATTT
1 ATATATTTTATTT
* *
2614924 -TTTATTTTATGT
1 ATATATTTTATTT
* **
2614936 A-ATAGTTTACAT
1 ATATATTTTATTT
*
2614948 A-ATATTTTAATT
1 ATATATTTTATTT
2614960 ATAT
1 ATAT
2614964 TATGTTAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
12 28 0.51
13 3 0.05
14 16 0.29
15 8 0.15
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (13 bp):
ATATATTTTATTT
Found at i:2615770 original size:8 final size:8
Alignment explanation
Indices: 2615759--2615787 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2615749 AATATAAATA
2615759 TAAATTTT
1 TAAATTTT
2615767 TAAATTTT
1 TAAATTTT
2615775 TAAATTTT
1 TAAATTTT
2615783 TAAAT
1 TAAAT
2615788 ACAAATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TAAATTTT
Found at i:2615831 original size:21 final size:20
Alignment explanation
Indices: 2615805--2615852 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2615795 TAATATATAA
2615805 TATATTATTCATTAAATTTAT
1 TATATTATT-ATTAAATTTAT
* *
2615826 TATATTATTTTTATATTTAT
1 TATATTATTATTAAATTTAT
2615846 TA-ATTAT
1 TATATTAT
2615853 ATAACATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTATTATTAAATTTAT
Found at i:2616046 original size:25 final size:23
Alignment explanation
Indices: 2616017--2616078 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
2616007 TTCAGTTAAT
2616017 TATTATTATGATTTAATAATAAAAA
1 TATTATTAT-ATTTAATAAT-AAAA
* *
2616042 TATTATTTAAATTTAATTATAAAA
1 TATTA-TTATATTTAATAATAAAA
*
2616066 TATTTTTATATTT
1 TATTATTATATTT
2616079 TATTATTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 14 0.44
26 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTATTATATTTAATAATAAAA
Found at i:2616080 original size:24 final size:25
Alignment explanation
Indices: 2616027--2616084 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
2616017 TATTATTATG
*
2616027 ATTTAATAATAAAAATATTATTTAA
1 ATTTAATTATAAAAATATTATTTAA
*
2616052 ATTTAATTAT-AAAATATT-TTTAT
1 ATTTAATTATAAAAATATTATTTAA
*
2616075 ATTTTATTAT
1 ATTTAATTAT
2616085 TTGATCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 13 0.43
24 8 0.27
25 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTAATTATAAAAATATTATTTAA
Found at i:2618269 original size:27 final size:27
Alignment explanation
Indices: 2618239--2618335 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 27
2618229 ATCATAATTA
* *
2618239 ATAATATTTAAAATATTATATATTTAT
1 ATAAAATTTAACATATTATATATTTAT
* *
2618266 ATAAAATTTTATACATCAATAATTTATATTAT
1 ATAAAA-TTTA-ACAT--ATTATATAT-TTAT
2618298 ATAAAATATTAACATATTTATATATTTAT
1 ATAAAAT-TTAACATA-TTATATATTTAT
*
2618327 ATAATATTT
1 ATAAAATTT
2618336 TTATATTATA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.09
28 6 0.11
29 14 0.25
30 6 0.11
31 12 0.21
32 13 0.23
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAAATTTAACATATTATATATTTAT
Found at i:2618333 original size:19 final size:18
Alignment explanation
Indices: 2618311--2618354 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2618301 AAATATTAAC
2618311 ATATTTATATATTTATATA
1 ATATTTATATA-TTATATA
* *
2618330 ATATTTTTATATTATATT
1 ATATTTATATATTATATA
2618348 ATATTTA
1 ATATTTA
2618355 AATTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTATATATTATATA
Found at i:2618964 original size:12 final size:12
Alignment explanation
Indices: 2618947--2618980 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2618937 AGATTAAGAG
2618947 TTTATTTTATA-T
1 TTTATTTT-TAGT
2618959 TTTATTTTTAGT
1 TTTATTTTTAGT
2618971 TTTATTTTTA
1 TTTATTTTTA
2618981 TAATATACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTATTTTTAGT
Done.