Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015260.1 Kokia drynarioides strain JFW-HI SEQ_130305, 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: 591355
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 484 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:125 original size:29 final size:29
Alignment explanation
Indices: 82--137 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
72 GATGTTACAC
* *
82 ATATATTAAAGATAATATAATATAAATTG
1 ATATATTAAAAATAAAATAATATAAATTG
111 ATATATTAAAAATAAAATAATATAAAT
1 ATATATTAAAAATAAAATAATATAAAT
138 ACACGGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
ATATATTAAAAATAAAATAATATAAATTG
Found at i:4337 original size:71 final size:71
Alignment explanation
Indices: 4252--4393 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
4242 AGCCACTATC
* *
4252 CTCACACTTATCATTTTTGTCACTCTCTGTTAATTTGCCATTACATACATTTACTTTGTTTACCC
1 CTCACACTTATCATTTTTGTCACCCTCTGTTAATTTGCCATTACAAACATTTACTTTGTTTACCC
4317 AATTTT
66 AATTTT
*
4323 CTCACACTTATCATTTTTGTTACCCTCTGTTAATTTGCCATTACAAACATTTACTTTGTTTACCC
1 CTCACACTTATCATTTTTGTCACCCTCTGTTAATTTGCCATTACAAACATTTACTTTGTTTACCC
4388 AATTTT
66 AATTTT
4394 AGTAAATTCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.23, C:0.24, G:0.06, T:0.47
Consensus pattern (71 bp):
CTCACACTTATCATTTTTGTCACCCTCTGTTAATTTGCCATTACAAACATTTACTTTGTTTACCC
AATTTT
Found at i:18655 original size:21 final size:22
Alignment explanation
Indices: 18624--18664 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18614 ATATTTCTCC
*
18624 TCTTGAATTATGTTATTTATGT
1 TCTTGAATTATATTATTTATGT
*
18646 TCTT-AATTATATTGTTTAT
1 TCTTGAATTATATTATTTAT
18665 AATTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (22 bp):
TCTTGAATTATATTATTTATGT
Found at i:19108 original size:19 final size:19
Alignment explanation
Indices: 19086--19130 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19076 TTTTATTAGG
19086 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
19105 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
19124 ATTTAAT
1 ATTTAAT
19131 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:21510 original size:21 final size:21
Alignment explanation
Indices: 21486--21534 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21476 GAATTTCAGT
*
21486 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
* *
21507 AGCAAACTTTGGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
21528 AGAAAAC
1 AGCAAAC
21535 CGAGACATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:26906 original size:31 final size:30
Alignment explanation
Indices: 26827--26909 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
26817 AAAAGACTTG
26827 TTTTATTT-TATTT-TATTTTAAAATATAAT
1 TTTTATTTGTATTTATA-TTTAAAATATAAT
* * * *
26856 TTTTATTAGGATTTAATATTTAAGATATTAT
1 TTTTATTTGTATTT-ATATTTAAAATATAAT
26887 TTATTATTTGTATTTATATTTAA
1 TT-TTATTTGTATTTATATTTAA
26910 TTTATGTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 7 0.16
30 4 0.09
31 21 0.48
32 12 0.27
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTATTTGTATTTATATTTAAAATATAAT
Found at i:26933 original size:14 final size:14
Alignment explanation
Indices: 26910--26939 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
26900 TTATATTTAA
*
26910 TTTATGTTTATCTT
1 TTTATATTTATCTT
26924 TTTATATTTATCTT
1 TTTATATTTATCTT
26938 TT
1 TT
26940 AGAGTTTAAA
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:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:28013 original size:17 final size:17
Alignment explanation
Indices: 27989--28062 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
27979 TTGGAAATTG
27989 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
28006 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
28023 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
28040 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
28057 AATTTA
1 AATTTA
28063 GAAAAGTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:28778 original size:3 final size:3
Alignment explanation
Indices: 28772--28804 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28762 TATAATATTC
28772 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28805 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28809 original size:3 final size:3
Alignment explanation
Indices: 28803--28840 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28793 ATAATAATAA
28803 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28841 ATAGCATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29904 original size:30 final size:28
Alignment explanation
Indices: 29838--30067 Score: 187
Period size: 30 Copynumber: 7.8 Consensus size: 28
29828 CCCTAAATTG
* * *
29838 TCCAAAAATTCCATTTTTATCCTCGAACT
1 TCCAAAAA-TCCATTTTTAACCCCAAACT
*
29867 TCTAAAAATCCAATTTTTAACCCCAAAACT
1 TCCAAAAATCC-ATTTTTAACCCC-AAACT
*
29897 TCCAAAAATCCCATTTTTACCCCCAAAACT
1 TCCAAAAAT-CCATTTTTAACCCC-AAACT
* *
29927 TCTAAAAATCCAATTTTTAACCCTGAAACT
1 TCCAAAAATCC-ATTTTTAACCC-CAAACT
* *
29957 TCCAAAAATTCCATTTTTACCCCCGAA-T
1 TCCAAAAA-TCCATTTTTAACCCCAAACT
*
29985 TACCAAAAATCCCA-TTTTAACCTCGAAACT
1 T-CCAAAAAT-CCATTTTTAACC-CCAAACT
* *
30015 TTCAAAAGGTCCATTTTT-ACCCTCAAACT
1 TCCAAAA-ATCCATTTTTAACCC-CAAACT
* *
30044 TCTAAAAATCCCATTTTTTACCCC
1 TCCAAAAAT-CCATTTTTAACCCC
30068 GAATTTTCCA
Statistics
Matches: 164, Mismatches: 22, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
28 15 0.09
29 64 0.39
30 80 0.49
31 5 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.32
Consensus pattern (28 bp):
TCCAAAAATCCATTTTTAACCCCAAACT
Found at i:29940 original size:60 final size:59
Alignment explanation
Indices: 29838--30089 Score: 294
Period size: 59 Copynumber: 4.3 Consensus size: 59
29828 CCCTAAATTG
* * * *
29838 TCCAAAAATTCCATTTTTATCCTCGAACTTCTAAAAATCCAATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCCGAAACT
* *
29897 TCCAAAAATCCCATTTTTACCCCCAAAACTTCTAAAAATCCAATTTTTAACCCTGAAACT
1 TCCAAAAATTCCATTTTTACCCCC-AAACTTCTAAAAATCCAATTTTTAACCCCGAAACT
* * * *
29957 TCCAAAAATTCCATTTTTACCCCCGAA-TTACCAAAAATCCCA-TTTTAACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACTT-CTAAAAATCCAATTTTTAACCCCGAAACT
* ** * * * **
30015 TTCAAAAGGTCCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTTACCCCGAATTT
1 TCCAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCCGAAACT
30074 TCC-AAAATTACCATTT
1 TCCAAAAATT-CCATTT
30090 CGTCCCCGAG
Statistics
Matches: 163, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
58 53 0.33
59 55 0.34
60 55 0.34
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATCCAATTTTTAACCCCGAAACT
Found at i:34511 original size:18 final size:18
Alignment explanation
Indices: 34488--34529 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
34478 TTTCAATTGT
34488 AATTAATTTAAAATT-TTC
1 AATTAA-TTAAAATTATTC
*
34506 AATTAATTAAATTTATTC
1 AATTAATTAAAATTATTC
34524 AATTAA
1 AATTAA
34530 AAATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAAAATTATTC
Found at i:34533 original size:16 final size:17
Alignment explanation
Indices: 34503--34538 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
34493 ATTTAAAATT
34503 TTCAATTAATTAAATTTA
1 TTCAATTAA-TAAATTTA
34521 TTCAATTAA-AAATTTA
1 TTCAATTAATAAATTTA
34537 TT
1 TT
34539 TTCATCTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCAATTAATAAATTTA
Found at i:34542 original size:18 final size:19
Alignment explanation
Indices: 34500--34542 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
34490 TTAATTTAAA
34500 ATTTTCAATTAATTAAATTT
1 ATTTTCAATTAA-TAAATTT
34520 A--TTCAATTAA-AAATTT
1 ATTTTCAATTAATAAATTT
34536 ATTTTCA
1 ATTTTCA
34543 TCTCAGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.33
18 13 0.62
20 1 0.05
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTCAATTAATAAATTT
Found at i:38043 original size:20 final size:20
Alignment explanation
Indices: 38018--38079 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
38008 CTCTATATAT
38018 ATATAATTAATTTTTAGGTA
1 ATATAATTAATTTTTAGGTA
38038 ATATAATTAATTTTTAGGTA
1 ATATAATTAATTTTTAGGTA
38058 ATATAATTAATTTTTAGGTA
1 ATATAATTAATTTTTAGGTA
38078 AT
1 AT
38080 GATGTGACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
ATATAATTAATTTTTAGGTA
Found at i:40595 original size:3 final size:3
Alignment explanation
Indices: 40587--40612 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40577 ACTTGAATGT
40587 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
40613 TAAAAAATTA
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:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:40851 original size:9 final size:9
Alignment explanation
Indices: 40837--41005 Score: 64
Period size: 9 Copynumber: 18.1 Consensus size: 9
40827 GTTGTGTCAT
40837 ATTATAAAA
1 ATTATAAAA
40846 ATTATAAAA
1 ATTATAAAA
* * *
40855 TTTGATATAT
1 ATT-ATAAAA
40865 A-T-TAAAA
1 ATTATAAAA
40872 ATTAT-AAA
1 ATTATAAAA
* *
40880 ATAATTAATA
1 ATTA-TAAAA
40890 ATTATAAAAA
1 ATTAT-AAAA
40900 ATTA-AAAA
1 ATTATAAAA
40908 AGTT-TAAAA
1 A-TTATAAAA
*
40917 ATCATAAAA
1 ATTATAAAA
40926 ATGT-TATAAA
1 AT-TATA-AAA
*
40936 AGTATAAAA
1 ATTATAAAA
* *
40945 CTTAT-AAT
1 ATTATAAAA
* *
40953 TTTAAAAAA
1 ATTATAAAA
40962 ATATATTAGAAA
1 AT-TA-TA-AAA
*
40974 CATTACAGAAA
1 -ATTATA-AAA
40985 ATTATGAAACA
1 ATTAT-AAA-A
40996 ATTATAAAA
1 ATTATAAAA
41005 A
1 A
41006 ATTAAAATAT
Statistics
Matches: 118, Mismatches: 23, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
7 4 0.03
8 18 0.15
9 43 0.36
10 33 0.28
11 13 0.11
12 5 0.04
13 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (9 bp):
ATTATAAAA
Found at i:40951 original size:28 final size:27
Alignment explanation
Indices: 40889--40951 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
40879 AATAATTAAT
*
40889 AATTATAAAAAATTAAAAAAGTTTAAA
1 AATTATAAAAAATTAAAAAAGTATAAA
* * *
40916 AATCATAAAAATGTTATAAAAGTATAAA
1 AATTATAAAAA-ATTAAAAAAGTATAAA
*
40944 ACTTATAA
1 AATTATAA
40952 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (27 bp):
AATTATAAAAAATTAAAAAAGTATAAA
Found at i:41006 original size:21 final size:19
Alignment explanation
Indices: 40966--41021 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 19
40956 AAAAAAATAT
*
40966 ATTAGAAACATTACAGAAA
1 ATTAGAAACATTACAAAAA
*
40985 ATTATGAAACAATTATAAAAA
1 ATTA-GAAAC-ATTACAAAAA
*
41006 ATTA-AAATA-TACAAAA
1 ATTAGAAACATTACAAAA
41022 TAAATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 6 0.19
18 1 0.03
19 7 0.23
20 5 0.16
21 12 0.39
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (19 bp):
ATTAGAAACATTACAAAAA
Found at i:48374 original size:2 final size:2
Alignment explanation
Indices: 48367--48392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48357 AAACATACAT
48367 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
48393 CAACCAACAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57734 original size:17 final size:18
Alignment explanation
Indices: 57712--57745 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
57702 TTTTATTAAA
57712 TATTGTAATATT-TTTAT
1 TATTGTAATATTATTTAT
*
57729 TATTGTATTATTATTTA
1 TATTGTAATATTATTTA
57746 AAACATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TATTGTAATATTATTTAT
Found at i:61502 original size:11 final size:11
Alignment explanation
Indices: 61486--61510 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61476 TATATTCCAC
61486 AAAGTAATACA
1 AAAGTAATACA
61497 AAAGTAATACA
1 AAAGTAATACA
61508 AAA
1 AAA
61511 CCTAGATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAGTAATACA
Found at i:62254 original size:14 final size:14
Alignment explanation
Indices: 62235--62263 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62225 TTAATTAATA
62235 TAAATATCCTAAAG
1 TAAATATCCTAAAG
62249 TAAATATCCTAAAG
1 TAAATATCCTAAAG
62263 T
1 T
62264 TGCTGATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
TAAATATCCTAAAG
Found at i:67216 original size:23 final size:23
Alignment explanation
Indices: 67190--67250 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
67180 TTATGTAACT
* *
67190 TTGTTGCACGTTTTTCCTTTACC
1 TTGTTGCACGCTTTTCCTCTACC
*
67213 TTG-TGACACGCTTTTCCTCTGCC
1 TTGTTG-CACGCTTTTCCTCTACC
* *
67236 TTGTGGCACACTTTT
1 TTGTTGCACGCTTTT
67251 GTCTTATGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 28 0.90
24 1 0.03
ACGTcount: A:0.10, C:0.28, G:0.16, T:0.46
Consensus pattern (23 bp):
TTGTTGCACGCTTTTCCTCTACC
Found at i:69182 original size:13 final size:13
Alignment explanation
Indices: 69161--69194 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
69151 ACAATATAAT
69161 AATAATAATCCTA
1 AATAATAATCCTA
*
69174 AATATTAATCCTA
1 AATAATAATCCTA
*
69187 AAAAATAA
1 AATAATAA
69195 AGTTTAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:70149 original size:21 final size:18
Alignment explanation
Indices: 70133--70179 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
70123 CTTTTTCTTC
70133 TTCTTTTTTCTGATTTTTTTT
1 TTCTTTTTTC-GA--TTTTTT
*
70154 TTCATTTTTCGATTTTTT
1 TTCTTTTTTCGATTTTTT
70172 TTCTTTTT
1 TTCTTTTT
70180 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 13 0.54
20 2 0.08
21 9 0.38
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.79
Consensus pattern (18 bp):
TTCTTTTTTCGATTTTTT
Found at i:71407 original size:15 final size:15
Alignment explanation
Indices: 71387--71418 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
71377 TTAAAACCTT
71387 AAATTTGAAACCCTA
1 AAATTTGAAACCCTA
*
71402 AAATTTGAAACTCTA
1 AAATTTGAAACCCTA
71417 AA
1 AA
71419 TCATTAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (15 bp):
AAATTTGAAACCCTA
Found at i:73869 original size:24 final size:24
Alignment explanation
Indices: 73842--73889 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
73832 AATTTTTTGT
73842 TGGAGTTAGATCTTCATTTTCTAC
1 TGGAGTTAGATCTTCATTTTCTAC
* *
73866 TGGATTTGGATCTTCATTTTCTAC
1 TGGAGTTAGATCTTCATTTTCTAC
73890 AAGTTCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TGGAGTTAGATCTTCATTTTCTAC
Found at i:74279 original size:19 final size:19
Alignment explanation
Indices: 74249--74294 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
74239 AATAAATCTG
74249 TTAAAAAT-AAATA-AAAT
1 TTAAAAATAAAATACAAAT
74266 TTAAATAATAAAATACAAAT
1 TTAAA-AATAAAATACAAAT
74286 TTAAAAATA
1 TTAAAAATA
74295 TATCAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 3 0.12
19 9 0.35
20 9 0.35
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAATAAAATACAAAT
Found at i:77254 original size:2 final size:2
Alignment explanation
Indices: 77247--77298 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
77237 CTCCCAAGGG
77247 AT AT AT AT AT 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 AT AT AT AT AT
77289 AT AT AT AT AT
1 AT AT AT AT AT
77299 GAGAGCAGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83539 original size:10 final size:10
Alignment explanation
Indices: 83524--83552 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
83514 TCTGGACAAT
83524 CAGAAAATGG
1 CAGAAAATGG
83534 CAGAAAATGG
1 CAGAAAATGG
83544 CAGAAAATG
1 CAGAAAATG
83553 AGGTTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.28, T:0.10
Consensus pattern (10 bp):
CAGAAAATGG
Found at i:86185 original size:31 final size:31
Alignment explanation
Indices: 86107--86187 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
86097 TTTGATTTGG
** **
86107 ATATCAAATTGAGCATTAAAATTAAACTCAA
1 ATATCAAATTGAATATTAAAACCAAACTCAA
*
86138 ATATCAAATTGAATATTAAAACCAAACTTAA
1 ATATCAAATTGAATATTAAAACCAAACTCAA
*
86169 GTATCAAA-TGACATATTAA
1 ATATCAAATTGA-ATATTAA
86188 TCCAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (31 bp):
ATATCAAATTGAATATTAAAACCAAACTCAA
Found at i:93124 original size:18 final size:18
Alignment explanation
Indices: 93086--93126 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
93076 ATTGCTTCTT
** *
93086 AAAAGTGCTTTTGGGGTC
1 AAAAGTGCTTTTGAAGCC
93104 AAAAGTGCTTTTGAAGCC
1 AAAAGTGCTTTTGAAGCC
93122 AAAAG
1 AAAAG
93127 CAATGCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (18 bp):
AAAAGTGCTTTTGAAGCC
Found at i:102563 original size:30 final size:31
Alignment explanation
Indices: 102495--102563 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
102485 TATTATAATC
* *
102495 TATATTATAATAATAGTTATATATGTATTAA
1 TATATTTTAATAATAGTTATATATGTATGAA
102526 TAT-TTTTAATAATAGTTATATAT-TA-GAA
1 TATATTTTAATAATAGTTATATATGTATGAA
102554 TATTATTTTA
1 TA-TATTTTA
102564 TGTATTAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.12
29 3 0.09
30 24 0.71
31 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (31 bp):
TATATTTTAATAATAGTTATATATGTATGAA
Found at i:102601 original size:3 final size:3
Alignment explanation
Indices: 102593--102664 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
102583 CATTATAATA
* *
102593 TAT TAT TA- TAT TAT GTAT TAT TAAT TTT TAT ATAT TA- TAT TAT TAA
1 TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT
*
102639 TAG TAT ATAT TA- TAT TAT TAT T-T TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT
102665 GCATTAGTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
2 8 0.14
3 36 0.64
4 12 0.21
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:102630 original size:42 final size:42
Alignment explanation
Indices: 102495--102681 Score: 111
Period size: 42 Copynumber: 4.4 Consensus size: 42
102485 TATTATAATC
*
102495 TATATTATAATA-A-TAGTTATA-TATGTATTAAT-ATTTTTAA
1 TATATTATAATATATTA-TTATATTATGTATTATTAATTTTT-A
* * * * ** *
102535 TAATAGTTATATATTAGAATATTATTTTATGTATTAGTAATACTAA
1 T-ATA-TTATA-A-TATATTATTATATTATGTATTATTAATTTTTA
*
102581 TACATTATAATATATTATTATATTATGTATTATTAATTTTTA
1 TATATTATAATATATTATTATATTATGTATTATTAATTTTTA
* *
102623 TATATTAT-AT-TATTAATAGTATATAT-TA-TATTATTATTTTA
1 TATATTATAATATATTATTA-TAT-TATGTATTATTAAT-TTTTA
**
102664 TGCATTAGTAATATATTA
1 TATATTA-TAATATATTA
102682 ATTTAGTATA
Statistics
Matches: 115, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
40 14 0.12
41 20 0.17
42 41 0.36
43 4 0.03
44 12 0.10
45 7 0.06
46 14 0.12
47 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (42 bp):
TATATTATAATATATTATTATATTATGTATTATTAATTTTTA
Found at i:102677 original size:29 final size:29
Alignment explanation
Indices: 102591--102677 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
102581 TACATTATAA
*
102591 TATATTATTATATTATGTATTATTAAT-T
1 TATATTATTATATTATGTATTAGTAATAT
* *
102619 TTTATATATTATATTAT-TAATAGTATATAT
1 TATAT-TATTATATTATGTATTAGTA-ATAT
* *
102649 TATATTATTATTTTATGCATTAGTAATAT
1 TATATTATTATATTATGTATTAGTAATAT
102678 ATTAATTTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 10 0.21
29 27 0.56
30 11 0.23
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (29 bp):
TATATTATTATATTATGTATTAGTAATAT
Found at i:103132 original size:15 final size:16
Alignment explanation
Indices: 103112--103145 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
103102 AGGCTTGAGC
*
103112 TTTTTT-GAGCTCATA
1 TTTTTTCGAGCTCAAA
103127 TTTTTTCGAGCTCAAA
1 TTTTTTCGAGCTCAAA
103143 TTT
1 TTT
103146 GTTATGGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.53
Consensus pattern (16 bp):
TTTTTTCGAGCTCAAA
Found at i:110286 original size:29 final size:27
Alignment explanation
Indices: 110247--110341 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 27
110237 AGGTCCAAAA
*
110247 AATTTAGATATCAAATTAAGAAAAAATC
1 AATTTAAATATCAAATTAA-AAAAAATC
*
110275 GAATTTAAATATCAAATCAAACAAAAA--
1 -AATTTAAATATCAAATTAAA-AAAAATC
*
110302 AA-TTAAATACCAAATTAAAAAAAATTC
1 AATTTAAATATCAAATTAAAAAAAA-TC
110329 AAGTTTAAATATC
1 AA-TTTAAATATC
110342 CTTATTTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
24 5 0.09
25 15 0.27
26 2 0.04
27 2 0.04
28 1 0.02
29 30 0.55
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.27
Consensus pattern (27 bp):
AATTTAAATATCAAATTAAAAAAAATC
Found at i:110307 original size:25 final size:24
Alignment explanation
Indices: 110279--110325 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
110269 AAAATCGAAT
*
110279 TTAAATATCAAATCAAACAAAAAAA
1 TTAAATACCAAATCAAA-AAAAAAA
*
110304 TTAAATACCAAATTAAAAAAAA
1 TTAAATACCAAATCAAAAAAAA
110326 TTCAAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (24 bp):
TTAAATACCAAATCAAAAAAAAAA
Found at i:110570 original size:46 final size:46
Alignment explanation
Indices: 110517--110614 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
110507 ATATAGAAGA
110517 ATCTAATCTTAATTAGTAGTTAAAATTGTCTCCAGCTCTGGATTCT
1 ATCTAATCTTAATTAGTAGTTAAAATTGTCTCCAGCTCTGGATTCT
110563 ATCTAATCTTAATTAGTAGTTAAAATTGTCTCCAGCTCTGGATTCT
1 ATCTAATCTTAATTAGTAGTTAAAATTGTCTCCAGCTCTGGATTCT
110609 ATCTAA
1 ATCTAA
110615 AGAAAGATTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (46 bp):
ATCTAATCTTAATTAGTAGTTAAAATTGTCTCCAGCTCTGGATTCT
Found at i:111012 original size:8 final size:8
Alignment explanation
Indices: 110981--111011 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
110971 CTCAGCCTTC
110981 ATTAAAAT
1 ATTAAAAT
110989 ATTAAAAT
1 ATTAAAAT
110997 ATTAAAAT
1 ATTAAAAT
111005 CATTAAA
1 -ATTAAA
111012 TGGTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (8 bp):
ATTAAAAT
Found at i:111394 original size:31 final size:31
Alignment explanation
Indices: 111334--111411 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
111324 CCCAAAAAAG
* ** *
111334 TTTAAGTACCAACTTTAAAAAAAATTGTCAAA
1 TTTAAGTACCAA-ATTATGAAAAAGTGTCAAA
*
111366 TTTAAGTACCTAATTATGAAAAAGTGTCAAA
1 TTTAAGTACCAAATTATGAAAAAGTGTCAAA
*
111397 TTTGAGTACCAAATT
1 TTTAAGTACCAAATT
111412 GGATTAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 28 0.72
32 11 0.28
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (31 bp):
TTTAAGTACCAAATTATGAAAAAGTGTCAAA
Found at i:111689 original size:15 final size:16
Alignment explanation
Indices: 111663--111692 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
111653 TAAAAGATAA
111663 AAAATAAATAAAAATC
1 AAAATAAATAAAAATC
111679 AAAAT-AATAAAAAT
1 AAAATAAATAAAAAT
111693 ATAAACCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATAAATAAAAATC
Found at i:120996 original size:7 final size:7
Alignment explanation
Indices: 120984--121016 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
120974 TAGAGATCTA
120984 AGAAGAG
1 AGAAGAG
120991 AGAAGAG
1 AGAAGAG
120998 AGAAGAG
1 AGAAGAG
121005 AGAAGAG
1 AGAAGAG
121012 AGAAG
1 AGAAG
121017 CAGTGACCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AGAAGAG
Found at i:125112 original size:22 final size:22
Alignment explanation
Indices: 125086--125139 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
125076 AACTTACGTT
125086 AATATAAATTCTCAATTCTTAA
1 AATATAAATTCTCAATTCTTAA
125108 AATATAAATTCTCAATTCTTAA
1 AATATAAATTCTCAATTCTTAA
125130 AATATAAATT
1 AATATAAATT
125140 ATATAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATAAATTCTCAATTCTTAA
Found at i:126228 original size:17 final size:17
Alignment explanation
Indices: 126203--126236 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
126193 ACGTCCTAAA
126203 GAAAATGAAAAGCAAAT
1 GAAAATGAAAAGCAAAT
* *
126220 GAAACTGAAATGCAAAT
1 GAAAATGAAAAGCAAAT
126237 TCAATCACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (17 bp):
GAAAATGAAAAGCAAAT
Found at i:127078 original size:22 final size:22
Alignment explanation
Indices: 127050--127091 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
127040 TAAAGTGGAT
127050 TCTATAAGAATATTAAGGTGAC
1 TCTATAAGAATATTAAGGTGAC
127072 TCTATAAGAATATTAAGGTG
1 TCTATAAGAATATTAAGGTG
127092 CCTATTAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (22 bp):
TCTATAAGAATATTAAGGTGAC
Found at i:130529 original size:40 final size:39
Alignment explanation
Indices: 130458--130595 Score: 97
Period size: 40 Copynumber: 3.5 Consensus size: 39
130448 CACTCCAGAA
* *
130458 TGAC-CCCTAGTGCCTCATCGGA-TAGTTCGAAGCAATAAAG
1 TGACACCC-AGTGTCTCATCGGACTAG-CCGAAG-AATAAAG
130498 TGACACCCAGTGTCTCATCGGACTAGCCGAAG--TAAAG
1 TGACACCCAGTGTCTCATCGGACTAGCCGAAGAATAAAG
** * * * *
130535 TGGTACCCAGTTTCTCATCGAATCTATCCGAAGTAA-AATAA
1 TGACACCCAGTGTCTCATCGGA-CTAGCCGAAG-AATAA-AG
* *
130576 TGACACTCAGTGTTTCATCG
1 TGACACCCAGTGTCTCATCG
130596 ACTCAAGGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
37 23 0.29
38 9 0.12
40 24 0.31
41 22 0.28
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (39 bp):
TGACACCCAGTGTCTCATCGGACTAGCCGAAGAATAAAG
Found at i:130543 original size:37 final size:38
Alignment explanation
Indices: 130493--130571 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
130483 TTCGAAGCAA
*
130493 TAAAGTGACACCCAGTGTCTCATCGGA-CTAGCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAATCTAGCCGAAG
** * *
130530 TAAAGTGGTACCCAGTTTCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAATCTAGCCGAAG
130568 TAAA
1 TAAA
130572 ATAATGACAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (38 bp):
TAAAGTGACACCCAGTGTCTCATCGAATCTAGCCGAAG
Found at i:130718 original size:23 final size:24
Alignment explanation
Indices: 130679--130728 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
130669 TAATAGGGAA
130679 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
130702 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
130726 TTT
1 TTT
130729 TACTTTCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:138066 original size:33 final size:33
Alignment explanation
Indices: 138029--138095 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
138019 ACAAAATACA
138029 AAAAATAAATTTATTTCTAAACGTAAGAACAGG
1 AAAAATAAATTTATTTCTAAACGTAAGAACAGG
*
138062 AAAAATAATTTTATTTCTAAACGTAAGAACAGG
1 AAAAATAAATTTATTTCTAAACGTAAGAACAGG
138095 A
1 A
138096 TGATTTCGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (33 bp):
AAAAATAAATTTATTTCTAAACGTAAGAACAGG
Found at i:164713 original size:18 final size:18
Alignment explanation
Indices: 164660--164719 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
164650 AAATTAAATC
164660 AAAATTAAATAAATTATTGA
1 AAAATT-AAT-AATTATTGA
* *
164680 AACAATTTATATTTATT-A
1 AA-AATTAATAATTATTGA
164698 TAAAATTAATAATTATTGA
1 -AAAATTAATAATTATTGA
164717 AAA
1 AAA
164720 TATTTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.48
19 9 0.27
20 4 0.12
21 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATTAATAATTATTGA
Found at i:164958 original size:41 final size:40
Alignment explanation
Indices: 164883--164968 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
164873 ACTTTCAATT
* *
164883 TAAAATTTTGATATTTTTTGTTAATAAAATTTATTTAATC
1 TAAAATTTTAATATTTTTTGTTAATAAAAGTTATTTAATC
* *
164923 TAAACTTTTAATAGTTTTATTGTT-ATAAACGTTATTTAATC
1 TAAAATTTTAATA-TTTT-TTGTTAATAAAAGTTATTTAATC
164964 TAAAA
1 TAAAA
164969 ATAATAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 11 0.28
41 23 0.59
42 5 0.13
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (40 bp):
TAAAATTTTAATATTTTTTGTTAATAAAAGTTATTTAATC
Found at i:164977 original size:42 final size:41
Alignment explanation
Indices: 164896--164977 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
164886 AATTTTGATA
* * **
164896 TTTTTTGTTAATAAAATTTATTTAATCTAAACTTTTAATAG
1 TTTTTTGTTAATAAAAGTTATTTAATCTAAAATAATAATAG
*
164937 TTTTATTGTT-ATAAACGTTATTTAATCTAAAAATAATAATA
1 TTTT-TTGTTAATAAAAGTTATTTAATCT-AAAATAATAATA
164978 ATAATAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 20 0.59
42 14 0.41
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (41 bp):
TTTTTTGTTAATAAAAGTTATTTAATCTAAAATAATAATAG
Found at i:166106 original size:3 final size:3
Alignment explanation
Indices: 166100--166125 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
166090 TATATTTATA
166100 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
166126 ATGAGACTTT
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:168479 original size:3 final size:3
Alignment explanation
Indices: 168471--168495 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
168461 AAGGGGAGTG
168471 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
168496 AAAAGTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:169190 original size:17 final size:17
Alignment explanation
Indices: 169168--169211 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
169158 ATTGTTTCTC
*
169168 AAAAATATTTTTTAGAT
1 AAAAATATTTTTTAAAT
169185 AAAAATA-TTTTTAAAT
1 AAAAATATTTTTTAAAT
169201 -AAAATATTTTT
1 AAAAATATTTTT
169212 GAGTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAAAATATTTTTTAAAT
Found at i:169204 original size:15 final size:16
Alignment explanation
Indices: 169168--169211 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
169158 ATTGTTTCTC
*
169168 AAAAATATTTTTTAGAT
1 AAAAATA-TTTTTAAAT
169185 AAAAATATTTTTAAAT
1 AAAAATATTTTTAAAT
169201 -AAAATATTTTT
1 AAAAATATTTTT
169212 GAGTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.42
16 8 0.31
17 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AAAAATATTTTTAAAT
Found at i:169234 original size:21 final size:23
Alignment explanation
Indices: 169192--169234 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
169182 GATAAAAATA
* *
169192 TTTTTAAATAAAATATTTTTGAG
1 TTTTTAAATAAAATACTATTGAG
169215 TTTTT-AA-AAAATACTATTGA
1 TTTTTAAATAAAATACTATTGA
169235 CACTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTTTAAATAAAATACTATTGAG
Found at i:199513 original size:28 final size:29
Alignment explanation
Indices: 199462--199522 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
199452 CCAAGAAATG
* *
199462 TATAAAAATACATAAATATTTTTAAAAAA
1 TATAAAAACAAATAAATATTTTTAAAAAA
*
199491 TATAAAAACAAATAAATATTTTAAAAAAA
1 TATAAAAACAAATAAATATTTTTAAAAAA
199520 TAT
1 TAT
199523 TTATGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
TATAAAAACAAATAAATATTTTTAAAAAA
Found at i:210402 original size:22 final size:20
Alignment explanation
Indices: 210365--210412 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
210355 GTTTTTTTTT
210365 TTAAAATTTAAAAATAAAAA
1 TTAAAATTTAAAAATAAAAA
210385 TTAAAACTTTAAAAAATAAAAA
1 TTAAAA-TTT-AAAAATAAAAA
*
210407 ATAAAA
1 TTAAAA
210413 AATATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 3 0.12
22 16 0.64
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAAATTTAAAAATAAAAA
Found at i:210404 original size:7 final size:7
Alignment explanation
Indices: 210374--210416 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
210364 TTTAAAATTT
210374 AAAAATA
1 AAAAATA
*
210381 AAAATTA
1 AAAAATA
**
210388 AAACTTTA
1 AAA-AATA
210396 AAAAATA
1 AAAAATA
210403 AAAAATA
1 AAAAATA
210410 AAAAATA
1 AAAAATA
210417 TTTAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAAATA
Found at i:217730 original size:103 final size:103
Alignment explanation
Indices: 217551--217756 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
217541 CCGATCCATG
* * *
217551 ATCAAATCAAGTTTAAAGTGAACAAGGCCATAGACAATGATTGATGATCTAAACAATACATTGAT
1 ATCAAATCAAGTTTAAAGTGAACAAGGCCATAGACAATGATGGATGATCTAAACAACACAGTGAT
217616 TAATGATCATAAACCAAAGATCATAGATGATCTAACAA
66 TAATGATCATAAACCAAAGATCATAGATGATCTAACAA
217654 ATCAAATCAAGTTTAAAGTGAACAAGGCCATAGACAATGATGGATGATCTAAACAACACAGTGAT
1 ATCAAATCAAGTTTAAAGTGAACAAGGCCATAGACAATGATGGATGATCTAAACAACACAGTGAT
*
217719 TAATGATCATAAACCAAAGATCATAGATGGTCTAACAA
66 TAATGATCATAAACCAAAGATCATAGATGATCTAACAA
217757 TAGAGGTCAA
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (103 bp):
ATCAAATCAAGTTTAAAGTGAACAAGGCCATAGACAATGATGGATGATCTAAACAACACAGTGAT
TAATGATCATAAACCAAAGATCATAGATGATCTAACAA
Found at i:221111 original size:27 final size:27
Alignment explanation
Indices: 221072--221132 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
221062 TTCTAAATAA
* * *
221072 TTTTGTTTAGTGACAAGACAATGTTTT
1 TTTTTTTTAGTGAAAAGACAATGTTAT
*
221099 TTTTTTTTTGTGAAAAGACAATGTTAT
1 TTTTTTTTAGTGAAAAGACAATGTTAT
*
221126 TTATTTT
1 TTTTTTT
221133 AGTTGTGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (27 bp):
TTTTTTTTAGTGAAAAGACAATGTTAT
Found at i:225964 original size:41 final size:41
Alignment explanation
Indices: 225919--226008 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
225909 TGTTCGTAGT
225919 GAATTCTTGTCAAGGTGGAGATTGTTAGAATTAGGTGACTA
1 GAATTCTTGTCAAGGTGGAGATTGTTAGAATTAGGTGACTA
* *
225960 GAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACTA
1 GAATTCTTGTCAAGGTGGAGATTGTTAGAATTAGGTGACTA
226001 GAATTCTT
1 GAATTCTT
226009 ATTAAAATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.28, C:0.07, G:0.29, T:0.37
Consensus pattern (41 bp):
GAATTCTTGTCAAGGTGGAGATTGTTAGAATTAGGTGACTA
Found at i:226649 original size:20 final size:20
Alignment explanation
Indices: 226612--226652 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
226602 ATAAAAGACA
* **
226612 TATAATTATTCATTTAATAT
1 TATAACTATTCAAGTAATAT
226632 TATAACTATTCAAGTAATAT
1 TATAACTATTCAAGTAATAT
226652 T
1 T
226653 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAACTATTCAAGTAATAT
Found at i:229742 original size:23 final size:22
Alignment explanation
Indices: 229700--229742 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
229690 TGATCATTGA
*
229700 AAATTTGAGCCAAAAGCAAATG
1 AAATTTGAACCAAAAGCAAATG
229722 AAATTTGCAACCACAAA-CAAA
1 AAATTTG-AACCA-AAAGCAAA
229743 AAGAAAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 8 0.44
24 3 0.17
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (22 bp):
AAATTTGAACCAAAAGCAAATG
Found at i:229935 original size:2 final size:2
Alignment explanation
Indices: 229928--229953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
229918 CCAGTTCCCC
229928 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
229954 AGATTTTAGG
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:230231 original size:21 final size:21
Alignment explanation
Indices: 230207--230267 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
230197 ATCTCAAATC
* * *
230207 TCAAATTTCGAACCTTAAACA
1 TCAAACTTCAAACCCTAAACA
230228 TCAAACTTCAAACCCTAAATC-
1 TCAAACTTCAAACCCTAAA-CA
*
230249 TTAAATCTT-AAACCCTAAA
1 TCAAA-CTTCAAACCCTAAA
230268 TCATGAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (21 bp):
TCAAACTTCAAACCCTAAACA
Found at i:230276 original size:21 final size:21
Alignment explanation
Indices: 230237--230276 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
230227 ATCAAACTTC
*
230237 AAACCCTAAATCTTAAATCTT
1 AAACCCTAAATCATAAATCTT
*
230258 AAACCCTAAATCATGAATC
1 AAACCCTAAATCATAAATC
230277 ATGAATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (21 bp):
AAACCCTAAATCATAAATCTT
Found at i:235345 original size:61 final size:60
Alignment explanation
Indices: 235124--235429 Score: 299
Period size: 59 Copynumber: 5.1 Consensus size: 60
235114 GGCATGGCCA
* * *
235124 ACACCCCTATTTATCTA-ATAAAAAAAATT--ACATTTTTTGGTGTTAGCCATGCAATGACTG
1 ACACCCCT-TTT-TC-AGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATGGCTG
235184 ACACTCCCTTTTTCA-A-AAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATGG-TCG
1 ACAC-CCCTTTTTCAGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATGGCT-G
* *
235243 ACACCCCTTTTCTCGGATTAAAAAAATTGC---ATTTTTTGGTGTTGGCCATGCAATGGCTG
1 ACACCCCTTTT-TCAGATAAAAAAAATT-CAAAATTTTTTGGTGTTGGCCATGCAATGGCTG
* * * * *
235302 ACACCCCTATTTTCAGAAAAAAAAAATTCAAAATTTTTTGGTGTAGGCTATGCAATGACCG
1 ACACCCCT-TTTTCAGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATGGCTG
* * * * * *
235363 ACACCCTCTGTTCTT-GGATTAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGCCG
1 ACACCC-CT-TT-TTCAGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATGGCTG
235425 ACACC
1 ACACC
235430 AACTTCCCCT
Statistics
Matches: 209, Mismatches: 22, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
57 10 0.05
58 11 0.05
59 82 0.39
60 12 0.06
61 44 0.21
62 48 0.23
63 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (60 bp):
ACACCCCTTTTTCAGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATGCAATGGCTG
Found at i:235367 original size:120 final size:118
Alignment explanation
Indices: 235144--235429 Score: 394
Period size: 120 Copynumber: 2.4 Consensus size: 118
235134 TTATCTAATA
* *
235144 AAAAAAATTACATTTTTTGGTGTTAGCCATGCAATGACTGACACTCCCTTTTTCAAAAAAAAAAT
1 AAAAAAATTACATTTTTTGGTGTTGGCCATGCAATGGCTGACAC-CCCTTTTTCAAAAAAAAAAT
* ** *
235209 TCAAAATTTTTTGGTGTTGGCCATGCAATGGTCGACACCC-CTTTTCTCGGATT
65 TCAAAATTTTTTGGTGTAGGCCATGCAATGACCGACACCCTCTGTTCTCGGATT
*
235262 AAAAAAATTGCATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTATTTTCAGAAAAAAAAA
1 AAAAAAATTACATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCT-TTTTC--AAAAAAAAA
* *
235327 ATTCAAAATTTTTTGGTGTAGGCTATGCAATGACCGACACCCTCTGTTCTTGGATT
63 ATTCAAAATTTTTTGGTGTAGGCCATGCAATGACCGACACCCTCTGTTCTCGGATT
* * * *
235383 AAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGCCGACACC
1 AAAAAAATT-ACA-TTTTTTGGTGTTGGCCATGCAATGGCTGACACC
235430 AACTTCCCCT
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
117 4 0.03
118 46 0.31
120 47 0.32
121 19 0.13
122 1 0.01
123 31 0.21
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (118 bp):
AAAAAAATTACATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCCTTTTTCAAAAAAAAAATT
CAAAATTTTTTGGTGTAGGCCATGCAATGACCGACACCCTCTGTTCTCGGATT
Found at i:239517 original size:85 final size:85
Alignment explanation
Indices: 239306--240074 Score: 1222
Period size: 85 Copynumber: 9.0 Consensus size: 85
239296 TTAACATTAT
** * * * * *
239306 TTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACA
1 TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATA
* *
239371 TTATTTATCAAATTTT-CATA
66 TTATTTAT-TAATTTTAAATA
* * *
239391 TTTAAAGT-ACAA--ATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGATAATG
1 -TTAAA-TAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATA
239453 TATTATTTATTAATTTTAAATA
64 TATTATTTATTAATTTTAAATA
*
239475 TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATGTA
1 TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATA
239540 TTATTTATTAATTTTAAATA
66 TTATTTATTAATTTTAAATA
* * *
239560 TTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATACA
1 TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATA
239625 TTATTTATTAATTTTAAATA
66 TTATTTATTAATTTTAAATA
* *
239645 TTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTATTGATTTGACAATGT
1 -TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAT
239710 ATTATTTATTAATTTTAAATA
65 ATTATTTATTAATTTTAAATA
* *
239731 TTAAATAAAAATTATTATTATTAAATTATAATTTTTATCAAATAATGTGTTGATTTGACAATGTA
1 TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATA
239796 TTATTTATTAATTTTAAATA
66 TTATTTATTAATTTTAAATA
* * *
239816 TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
1 TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATA
239881 TTATTTATTAATTTTAAATA
66 TTATTTATTAATTTTAAATA
*
239901 TGTAAATAAAAATTATTATTATTAAATTACAATTTTTATTAAATAATGTGTTGATTTGACAATAT
1 T-TAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAT
239966 ATTATTTATTAATTTTAAATA
65 ATTATTTATTAATTTTAAATA
*
239987 TTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 -TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATAT
*
240052 ATTATTTATTAATTTTAATTA
65 ATTATTTATTAATTTTAAATA
240073 TT
1 TT
240075 TATTATATTG
Statistics
Matches: 640, Mismatches: 35, Indels: 17
0.92 0.05 0.02
Matches are distributed among these distances:
82 1 0.00
83 14 0.02
84 56 0.09
85 318 0.50
86 249 0.39
87 2 0.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (85 bp):
TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATA
TTATTTATTAATTTTAAATA
Found at i:239717 original size:171 final size:171
Alignment explanation
Indices: 239290--240074 Score: 1242
Period size: 171 Copynumber: 4.6 Consensus size: 171
239280 TACATTTAAA
** * * *
239290 ATTAA-TTTAACATTATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGT
1 ATTAATTTTAA-A-TATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGT
* * * *
239354 GTTAATTTGACAATACATTATTTATCAAATTTT-CATATTTAAAGT-ACAA--ATTATTATTAAA
64 GTTGATTTGACAATACATTATTTAT-TAATTTTAAATA-TTAAA-TAAAAATTATTATTATTAAA
* *
239415 TTACAATTTTTATCAAATAATGTGTTGATTTGATAATGTATTATTT
126 TTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTT
239461 ATTAATTTTAAATA-TTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
** *
239525 TGATTTGACAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTATATTACA
66 TGATTTGACAATACATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAAATTACA
* *
239590 ATTTTTATCAAATAATGTGTTGATTTGATAATACATTATTT
131 ATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTT
*
239631 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTAT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
** *
239696 TGATTTGACAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAAATTATA
66 TGATTTGACAATACATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAAATTACA
*
239761 ATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTT
131 ATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTT
* *
239802 ATTAATTTTAAATA-TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
239866 TGATTTGACAATACATTATTTATTAATTTTAAATATGTAAATAAAAATTATTATTATTAAATTAC
66 TGATTTGACAATACATTATTTATTAATTTTAAATAT-TAAATAAAAATTATTATTATTAAATTAC
*
239931 AATTTTTATTAAATAATGTGTTGATTTGACAATATATTATTT
130 AATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTT
239973 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
*
240038 TGATTTGACAATACATTATTTATTAATTTTAATTATT
66 TGATTTGACAATACATTATTTATTAATTTTAAATATT
240075 TATTATATTG
Statistics
Matches: 575, Mismatches: 31, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
167 1 0.00
168 14 0.02
169 68 0.12
170 152 0.26
171 252 0.44
172 88 0.15
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (171 bp):
ATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATAATGTGT
TGATTTGACAATACATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAAATTACA
ATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTT
Found at i:239745 original size:256 final size:256
Alignment explanation
Indices: 239306--240074 Score: 1321
Period size: 256 Copynumber: 3.0 Consensus size: 256
239296 TTAACATTAT
* * * *
239306 TTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACA
1 TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
* * *
239371 TTATTTATCAAATTTT-CATATTTAAAGT-ACAA--ATTATTATTAAATTACAATTTTTATCAAA
66 TTATTTAT-TAATTTTAAATATTTAAA-TAAAAATTATTATTATTAAATTACAATTTTTATCAAA
*
239432 TAATGTGTTGATTTGATAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATT
129 TAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATT
239497 AAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA
194 AAATTACAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA
* *
239560 TTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATACA
1 TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
239625 TTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATA
66 TTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATA
*
239690 ATGTATTGATTTGACAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAA
131 ATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAA
*
239755 ATTATAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA
196 ATTACAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA
239816 TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
1 TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
* *
239881 TTATTTATTAATTTTAAATATGTAAATAAAAATTATTATTATTAAATTACAATTTTTATTAAATA
66 TTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATA
*
239946 ATGTGTTGATTTGACAATATATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTA
131 ATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA-TTAAATAAAAATTATTATTATTA
** *
240011 AATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAATTA
195 AATTACAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA
240073 TT
1 TT
240075 TATTATATTG
Statistics
Matches: 488, Mismatches: 22, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
253 7 0.01
254 79 0.16
256 319 0.65
257 83 0.17
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (256 bp):
TTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA
TTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATTAAATTACAATTTTTATCAAATA
ATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATATTAAATAAAAATTATTATTATTAA
ATTACAATTTTTATCAAATAATGTGTTGATTTGACAATGTATTATTTATTAATTTTAAATA
Found at i:239768 original size:20 final size:20
Alignment explanation
Indices: 239719--239768 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
239709 TATTATTTAT
* *
239719 TAATTTTAAATATTAAATAA
1 TAATTTTTATTATTAAATAA
* * *
239739 AAATTATTATTATTAAATTA
1 TAATTTTTATTATTAAATAA
239759 TAATTTTTAT
1 TAATTTTTAT
239769 CAAATAATGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTTTATTATTAAATAA
Found at i:240348 original size:111 final size:112
Alignment explanation
Indices: 240187--240392 Score: 274
Period size: 111 Copynumber: 1.8 Consensus size: 112
240177 CCAAAAATAT
* **
240187 AATTTTTTTATCCGAAAAAAAGGGTGTCGACCATTGCATGACCAACACAAAAAAATTTTGAAATT
1 AATTTTTTTATCAGAAAAAAAGGGTGTCGACCATTGCATGACCAACACAAAAAAAAATTG-AATT
240252 TTTT-TCT-G-AAAAAAGGGGTGTCGACCATTGCATGACCAAAATGCA
65 TTTTATCTGGCAAAAAAGGGGTGTCGACCATTGCATGACCAAAATGCA
* * * * * * *
240297 AATTTTTTTATCAGATAAATAAGGGTGTCGGCTATTGTATGATCAATACAAAAAAAAATTGTATT
1 AATTTTTTTATCAGA-AAAAAAGGGTGTCGACCATTGCATGACCAACACAAAAAAAAATTGAATT
*
240362 TTTTATCTGGCAAAAAAGGGGTGTCGGCCAT
65 TTTTATCTGGCAAAAAAGGGGTGTCGACCAT
240393 GCAAATTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
110 21 0.26
111 40 0.49
112 1 0.01
113 19 0.23
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (112 bp):
AATTTTTTTATCAGAAAAAAAGGGTGTCGACCATTGCATGACCAACACAAAAAAAAATTGAATTT
TTTATCTGGCAAAAAAGGGGTGTCGACCATTGCATGACCAAAATGCA
Found at i:243614 original size:166 final size:166
Alignment explanation
Indices: 243340--243668 Score: 606
Period size: 166 Copynumber: 2.0 Consensus size: 166
243330 GACTTTGATT
*
243340 TGCTCGCACATCTGAGGAACCTGTTTTTCAGATGCATAAGTCGTTACGGCAATAAAGAAACTTCG
1 TGCTCGCACATCTGAGGAACCTGTTTTTCAGATGCATAAGTCGTTACAGCAATAAAGAAACTTCG
*
243405 AGGTAGAAGGAAATGGCAAAGACAGGAAGACTAGGTTAATAACTGCAAAATTTCTGAAGAAAGTC
66 AGGTAGAAGGAAATGGCAAAGACAGGAAGACTAGGTTAATAACTGCAAAATTTCTGAAGAAAGAC
*
243470 GTGCAGGAA-TGTTTCAATAATGTTTATCTACTCAGA
131 GTGCAGGAATTG-TTCAATAATGTTCATCTACTCAGA
243506 TGCTCGCACATCTGAGGAACCTGTTTTTCAGATGCATAAGTCGTTACAGCAATAAAGAAACTTCG
1 TGCTCGCACATCTGAGGAACCTGTTTTTCAGATGCATAAGTCGTTACAGCAATAAAGAAACTTCG
*
243571 AGGTAGAAGGAAATGGCAAAGACAGGAAGACTGGGTTAATAACTGCAAAATTTCTGAAGAAAGAC
66 AGGTAGAAGGAAATGGCAAAGACAGGAAGACTAGGTTAATAACTGCAAAATTTCTGAAGAAAGAC
243636 GTGCAGGAATTGTTCAATAATGTTCATCTACTC
131 GTGCAGGAATTGTTCAATAATGTTCATCTACTC
243669 TGGATTGGGA
Statistics
Matches: 158, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
166 156 0.99
167 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (166 bp):
TGCTCGCACATCTGAGGAACCTGTTTTTCAGATGCATAAGTCGTTACAGCAATAAAGAAACTTCG
AGGTAGAAGGAAATGGCAAAGACAGGAAGACTAGGTTAATAACTGCAAAATTTCTGAAGAAAGAC
GTGCAGGAATTGTTCAATAATGTTCATCTACTCAGA
Found at i:248438 original size:13 final size:11
Alignment explanation
Indices: 248420--248454 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
248410 CCCAAGAAGT
248420 GAGAGAGAAAA
1 GAGAGAGAAAA
248431 GAGAGAGAAAA
1 GAGAGAGAAAA
248442 GAGAGAGACAAA
1 GAGAGAGA-AAA
248454 G
1 G
248455 CTTGCCTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.60, C:0.03, G:0.37, T:0.00
Consensus pattern (11 bp):
GAGAGAGAAAA
Found at i:251418 original size:29 final size:30
Alignment explanation
Indices: 251384--251449 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
251374 GATAGTTTAG
251384 GTACCACATTAGACATTT-TCAAAGTATAA
1 GTACCACATTAGACATTTATCAAAGTATAA
* * * *
251413 GTACCACATTGGACGTTTCATGAAAGTATAG
1 GTACCACATTAGACATTT-ATCAAAGTATAA
251444 GTACCA
1 GTACCA
251450 AATGTGACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
31 15 0.48
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (30 bp):
GTACCACATTAGACATTTATCAAAGTATAA
Found at i:251439 original size:92 final size:92
Alignment explanation
Indices: 251268--251449 Score: 229
Period size: 92 Copynumber: 2.0 Consensus size: 92
251258 ATGTAAGATA
* * * *
251268 ATAAAACACATATTGATAATTCAGGTACCACATTATATATTTTCAAAGTACACGTATCACATTGA
1 ATAAAACACATATTGATAATTCAGGTACCACATTAGACATTTTCAAAGTACAAGTACCACATTGA
*
251333 ACATTTTATAAAAGTACAAGTACCATG
66 ACATTTCATAAAAGTACAAGTACCATG
* * * * * *
251360 ATAAAACATATGTTGATAGTTTAGGTACCACATTAGACATTTTCAAAGTATAAGTACCACATTGG
1 ATAAAACACATATTGATAATTCAGGTACCACATTAGACATTTTCAAAGTACAAGTACCACATTGA
* * * *
251425 ACGTTTCATGAAAGTATAGGTACCA
66 ACATTTCATAAAAGTACAAGTACCA
251450 AATGTGACAT
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (92 bp):
ATAAAACACATATTGATAATTCAGGTACCACATTAGACATTTTCAAAGTACAAGTACCACATTGA
ACATTTCATAAAAGTACAAGTACCATG
Found at i:251877 original size:3 final size:3
Alignment explanation
Indices: 251869--251903 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
251859 AGAATAAATT
*
251869 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
251904 TTATTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:258215 original size:2 final size:2
Alignment explanation
Indices: 258208--258239 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
258198 TGCAATGAAC
258208 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
258240 TCTAGTGAAA
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:262145 original size:120 final size:120
Alignment explanation
Indices: 261940--262267 Score: 285
Period size: 120 Copynumber: 2.7 Consensus size: 120
261930 AACTGAGCAT
* *
261940 AACGAAGCAAAGCTCC-CCACAGAATCCCCTAACGTTAGGCATGACGATAACAAAAAGCTTGTCG
1 AACGAAGCAAAGC-CCTCCACAGAATCCCCTAACGTTAGACATGACGATAACAAAAAGCTTGTCA
* * * * *
262004 TTGACATAACTTACAATGAGGTCAACGGTGATGTATCAATAGC-GAGAACTGA-CCGG
65 TGGACATAACTTACAACGAGGTCAACGGCGACGTATCAATAGCGGA-AACTAATCC-G
*** * *
262060 AACGAAGCAAAGCCCTCCACAGAATCGTTTAATGTTAGACATGATGATAACAAAAAGCTTGTCAT
1 AACGAAGCAAAGCCCTCCACAGAATCCCCTAACGTTAGACATGACGATAACAAAAAGCTTGTCAT
* * * * *
262125 CGGA-A-AAGTTTATAACGAGGTCAATGGCGGCGTATCCATAGCGGAAACTAATCCG
66 -GGACATAA-CTTACAACGAGGTCAACGGCGACGTATCAATAGCGGAAACTAATCCG
* * * * * *
262180 AACGAAGTAAAGCTCTCCACA-ATGTCCCTTAATG-TAGGACATGACGATAA-AAATAAGCTTAT
1 AACGAAGCAAAGCCCTCCACAGA-ATCCCCTAACGTTA-GACATGACGATAACAAA-AAGCTTGT
* * * *
262242 CGTTGACACAACTTACAATGAGGTCA
63 CATGGACATAACTTACAACGAGGTCA
262268 TCAATGGCGA
Statistics
Matches: 169, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
119 12 0.07
120 149 0.88
121 8 0.05
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (120 bp):
AACGAAGCAAAGCCCTCCACAGAATCCCCTAACGTTAGACATGACGATAACAAAAAGCTTGTCAT
GGACATAACTTACAACGAGGTCAACGGCGACGTATCAATAGCGGAAACTAATCCG
Found at i:262402 original size:120 final size:122
Alignment explanation
Indices: 262253--262537 Score: 330
Period size: 120 Copynumber: 2.3 Consensus size: 122
262243 GTTGACACAA
* * * * * * * *
262253 CTTACAATGAGGTCATCAATGGCGACGTATTAGTAGCT-GAACCTGAGC-ATATCAAAGCAAAGC
1 CTTATAATGAAGTCATCAATGACGGCGTATCAGTAG-TGGAAACTAAGCAAAAT-AAAGCAAAGC
* *
262316 TCCCCAAAGAATCCTTTAATGTTG-G-GCATGATGATGGAAAGTTTGTCATTAACTC-G
64 TCCCCAAAGAATCCTTTAATGTTGCGAGCATGATGATGGAAAGTTTGACATTAACGCAG
*
262372 ACTTATAATGATA-TCATCAATGACGGCGTATCAGTAGTGGAAACTAAGCAAAATGAAGCAAAGC
1 -CTTATAATGA-AGTCATCAATGACGGCGTATCAGTAGTGGAAACTAAGCAAAATAAAGCAAAGC
* * *
262436 TCTCCAGAGAATCCTTTAATGTTGCGCAGGATGATGATGGAAAGTTTGACATTAACGCAG
64 TCCCCAAAGAATCCTTTAATGTTGCG-AGCATGATGATGGAAAGTTTGACATTAACGCAG
* * *
262496 CTTATAGTGAAGTCATGAATGACGGCGTATCAATAGTGGAAA
1 CTTATAATGAAGTCATCAATGACGGCGTATCAGTAGTGGAAA
262538 TGGAGCAAAA
Statistics
Matches: 140, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
119 1 0.01
120 69 0.49
121 4 0.03
122 1 0.01
123 64 0.46
124 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (122 bp):
CTTATAATGAAGTCATCAATGACGGCGTATCAGTAGTGGAAACTAAGCAAAATAAAGCAAAGCTC
CCCAAAGAATCCTTTAATGTTGCGAGCATGATGATGGAAAGTTTGACATTAACGCAG
Found at i:262522 original size:123 final size:120
Alignment explanation
Indices: 262307--262588 Score: 354
Period size: 123 Copynumber: 2.3 Consensus size: 120
262297 GAGCATATCA
* * *
262307 AAGCAAAGCTCCCCAAAGAATCCTTTAATGTTGGGCATGATGATGGAAAGTTTGTCATTAACTCG
1 AAGCAAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATGATGATGGAAAGTTTGACATTAACGCG
* *
262372 ACTTATAATGATATCATCAATGACGGCGTATCAGTAGTGGAAACT-AAGCAAAATG
66 ACTTATAATGATATCATCAATGACGGCGTATCAATAGTGGAAA-TGAAGCAAAACG
* *
262427 AAGCAAAGCTCTCCAGAGAATCCTTTAATGTTGCGCAGGATGATGATGGAAAGTTTGACATTAAC
1 AAGCAAAGCTCCCCAGAGAATCCTTTAATGTTG-G--GCATGATGATGGAAAGTTTGACATTAAC
* * *
262492 GC-AGCTTATAGTGA-AGTCATGAATGACGGCGTATCAATAGTGGAAATGGAGCAAAACG
63 GCGA-CTTATAATGATA-TCATCAATGACGGCGTATCAATAGTGGAAATGAAGCAAAACG
* * * * *
262550 TAGCGAAGCTCCCCAGAGAACCCCTGAATGTTGGGCATG
1 AAGCAAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATG
262589 GCGATAACAA
Statistics
Matches: 139, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
120 35 0.25
121 1 0.01
122 4 0.03
123 99 0.71
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (120 bp):
AAGCAAAGCTCCCCAGAGAATCCTTTAATGTTGGGCATGATGATGGAAAGTTTGACATTAACGCG
ACTTATAATGATATCATCAATGACGGCGTATCAATAGTGGAAATGAAGCAAAACG
Found at i:262603 original size:123 final size:123
Alignment explanation
Indices: 262353--262639 Score: 303
Period size: 123 Copynumber: 2.3 Consensus size: 123
262343 ATGATGATGG
* *
262353 AAAGTTTGTCATTAACTCGACTTATAATGATATCATCAATGACGGCGTATCAGTAGTGGAAACTA
1 AAAGTTTGTCATTAACGCGACTTATAATGATATCATCAATGACGGCGTATCAATAGTGGAAACTA
* * * * * * * ***
262418 AGCAAAATGAAGCAAAGCTCTCCAGAGAATCCTTTAATGTTGCGCAGGATGATGATGG
66 AGCAAAACGAAGCAAAGCTCCCCAGAGAACCCCTGAATGTTGCGCAGGACGATAACAA
* * *
262476 AAAGTTTGACATTAACGC-AGCTTATAGTGA-AGTCATGAATGACGGCGTATCAATAGTGGAAA-
1 AAAGTTTGTCATTAACGCGA-CTTATAATGATA-TCATCAATGACGGCGTATCAATAGTGGAAAC
* * * *
262538 TGGAGCAAAACGTAGCGAAGCTCCCCAGAGAACCCCTGAATGTTGGGCATGG-CGATAACAA
64 T-AAGCAAAACGAAGCAAAGCTCCCCAGAGAACCCCTGAATGTTGCGCA-GGACGATAACAA
* * * *
262599 AAAGTTTGTCATTGACACGACTTACAATGAGATCATCAATG
1 AAAGTTTGTCATTAACGCGACTTATAATGATATCATCAATG
262640 GCGACGTAAA
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
122 3 0.02
123 126 0.95
124 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.24
Consensus pattern (123 bp):
AAAGTTTGTCATTAACGCGACTTATAATGATATCATCAATGACGGCGTATCAATAGTGGAAACTA
AGCAAAACGAAGCAAAGCTCCCCAGAGAACCCCTGAATGTTGCGCAGGACGATAACAA
Found at i:262715 original size:93 final size:93
Alignment explanation
Indices: 262555--262734 Score: 229
Period size: 93 Copynumber: 1.9 Consensus size: 93
262545 AAACGTAGCG
* * * * *
262555 AAGCTCCCCAGAGAACCCCTGAATGTTGGGCATGGCGATAACAAAAAGTTTGTCATTGACACGAC
1 AAGCTCCCCACAGAACCCCTGAATGTTCGGCATGACGATAACAAAAAGCTTGTCATTGACACAAC
*
262620 TTACAATGA-GATCATCAATGGCGACGTA
66 TTACAATGATG-TCACCAATGGCGACGTA
* * * * *
262648 AAGCTCCCCACAGAATCCCTTAATGTTCGGCATGATGATAATGAAAAA-CTTGTCTTTGACACAA
1 AAGCTCCCCACAGAACCCCTGAATGTTCGGCATGACGATAA-CAAAAAGCTTGTCATTGACACAA
262712 CTTACAATGATGTCACCAATGGC
65 CTTACAATGATGTCACCAATGGC
262735 AGCCTATCAG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
93 68 0.92
94 6 0.08
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (93 bp):
AAGCTCCCCACAGAACCCCTGAATGTTCGGCATGACGATAACAAAAAGCTTGTCATTGACACAAC
TTACAATGATGTCACCAATGGCGACGTA
Found at i:263000 original size:123 final size:123
Alignment explanation
Indices: 262645--263144 Score: 429
Period size: 123 Copynumber: 4.1 Consensus size: 123
262635 CAATGGCGAC
* * *
262645 GTAAAGCTCCCCACAGAATCCC-TTAATGTTCG-GCATGATGATAATGAAAAACTTGTCTTTGAC
1 GTAAAGCTCCCCACAGAA-CCCTTTAATATT-GAGCATGATGATAATGAAAAGCTTGTCATTGAC
* * * * * *
262708 ACAACTTACAATGATGTCACCAATGGC-AGCCTATCAGTAGCGGAAATTGAGAAAAACAAA
64 ACAACTTACAATGAGGTCATCAATGGCGA-CGTATCAATAGCGGAAACTGAGCAAAACAAA
* * * ** * * * * *
262768 GCAAAGATCGCCAGTGAA-TCTCTTAATGTTGGGTATGATGATAACG-AAAGCTTCGTCATTGAC
1 GTAAAGCTCCCCACAGAACCCT-TTAATATTGAGCATGATGATAATGAAAAGCTT-GTCATTGAC
* * * * ** * * *
262831 ACAATTTATAATGAAGTCATCAACGATGGCATATCAGTAGCGGAAACTGAGCAAAACAAA
64 ACAACTTACAATGAGGTCATCAATGGCGACGTATCAATAGCGGAAACTGAGCAAAACAAA
* * *
262891 GTGAAGCTCCCCACAGAACCCTTTAATATTGAGCATGATGATAA-CAGAAAGCTTGTCGTTGACA
1 GTAAAGCTCCCCACAGAACCCTTTAATATTGAGCATGATGATAATGA-AAAGCTTGTCATTGACA
* ** * *
262955 CAACTTACAATGAGGTCATCAATGGCGACGTATTAATAGTTGAAACTGAGCATAACGAA
65 CAACTTACAATGAGGTCATCAATGGCGACGTATCAATAGCGGAAACTGAGCAAAACAAA
** ** * * **
263014 GTAAAGCTCCCCGTAGAATTCTTTAATATTGAGCATGTTGACAATGAAAAGCTTGTCAAAGACAC
1 GTAAAGCTCCCCACAGAACCCTTTAATATTGAGCATGATGATAATGAAAAGCTTGTCATTGACAC
* ** ** *
263079 AGCTTATGATGAGGTCA-CTAATGGCCTCGTATCAATAGCGGAAACTGAGCAAAACGAA
66 AACTTACAATGAGGTCATC-AATGGCGACGTATCAATAGCGGAAACTGAGCAAAACAAA
*
263137 GCAAAGCT
1 GTAAAGCT
263145 TCCTGCAAAG
Statistics
Matches: 299, Mismatches: 68, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
121 1 0.00
122 8 0.03
123 280 0.94
124 10 0.03
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (123 bp):
GTAAAGCTCCCCACAGAACCCTTTAATATTGAGCATGATGATAATGAAAAGCTTGTCATTGACAC
AACTTACAATGAGGTCATCAATGGCGACGTATCAATAGCGGAAACTGAGCAAAACAAA
Found at i:276844 original size:21 final size:21
Alignment explanation
Indices: 276798--276847 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
276788 TAAAAAATTT
*
276798 AAAATTTAATTAATTAAATCAT
1 AAAA-TTAATTAATTAAATCAC
*
276820 AAAATTAATTAAGTTTAAT-AC
1 AAAATTAATTAA-TTAAATCAC
276841 AAAATTA
1 AAAATTA
276848 TTTTATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTAATTAATTAAATCAC
Found at i:281096 original size:41 final size:42
Alignment explanation
Indices: 281034--281114 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 42
281024 TACTTGGTTT
*
281034 ATAAGACTTTTAACTTAGAATAATTATTGAAGGATATTATTC
1 ATAAGACTTTTAACTTAGAATAAATATTGAAGGATATTATTC
*
281076 ATAAGAC-TTTAACTTCGAATAAATATTGAAGGATATTAT
1 ATAAGACTTTTAACTTAGAATAAATATTGAAGGATATTAT
281115 GTAGGATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (42 bp):
ATAAGACTTTTAACTTAGAATAAATATTGAAGGATATTATTC
Found at i:287271 original size:30 final size:30
Alignment explanation
Indices: 287201--287273 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
287191 ATATAATCTA
*
287201 ATTAAAATTTTTAAATAATTAATATTAATT
1 ATTAAAATATTTAAATAATTAATATTAATT
*
287231 ACTTAGAAATATTT-AA-AATTAATATTTTATAT
1 A-TTA-AAATATTTAAATAATTAATA-TTAAT-T
287263 ATTAAAATATT
1 ATTAAAATATT
287274 AACAATAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 16 0.43
31 12 0.32
32 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
ATTAAAATATTTAAATAATTAATATTAATT
Found at i:294569 original size:18 final size:20
Alignment explanation
Indices: 294548--294585 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
294538 ATTCTTTTCA
294548 ATTGTTAT-ATTT-TAATTC
1 ATTGTTATAATTTATAATTC
*
294566 ATTGTTTTAATTTATAATTC
1 ATTGTTATAATTTATAATTC
294586 TTTTATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTGTTATAATTTATAATTC
Found at i:306226 original size:16 final size:16
Alignment explanation
Indices: 306194--306237 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
306184 TTTAAATTTT
306194 TAAAAATTCAAAAAAAA
1 TAAAAATT-AAAAAAAA
306211 TATAGAAATTAAAAAAAA
1 TA-A-AAATTAAAAAAAA
306229 TAAAAATTA
1 TAAAAATTA
306238 TTTAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.24
17 3 0.12
18 11 0.44
19 5 0.20
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
TAAAAATTAAAAAAAA
Found at i:307151 original size:97 final size:98
Alignment explanation
Indices: 306981--307174 Score: 266
Period size: 97 Copynumber: 2.0 Consensus size: 98
306971 TGGAAAATGA
* * *
306981 TATTCGATTATCTTGATTTGAAGACAAATCGCATCTAGTAAGTTAATGCACAAATTTTCAGAATC
1 TATTCGATTATCTTGATTTGAAGACAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATC
* *
307046 AGAGATAAAAAAACATTGCCTCGAT-TTAAGGG
66 AGAAATAAAAAAACATTACCTCGATATTAAGGG
* * * *
307078 TATTCGATTATTTTGATTTGAGGAGAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAACT
1 TATTCGATTATCTTGATTTGAAGACAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-T
* *
307143 C-GAAATAAAAGAATATTACCTCGATATTAAGG
65 CAGAAATAAAAAAACATTACCTCGATATTAAGG
307175 TTTTCGTGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
97 76 0.90
98 8 0.10
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (98 bp):
TATTCGATTATCTTGATTTGAAGACAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATC
AGAAATAAAAAAACATTACCTCGATATTAAGGG
Found at i:307195 original size:97 final size:97
Alignment explanation
Indices: 306996--307203 Score: 215
Period size: 97 Copynumber: 2.1 Consensus size: 97
306986 GATTATCTTG
* * * *
306996 ATTTGAAGACAAATCGCATCTAGTAAGTTAATGCACAAATTTTCAGAATCAGAGATAAAAAAACA
1 ATTTGAAGACAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAAAAACA
* * *** *
307061 TTGCCTCGATTTAAGGGTATTCGATTATTTTG
66 TTACCTCGATTTAAGGGTATTCGATGAAGATA
* * * * *
307093 ATTTGAGGAGAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAACTC-GAAATAAAAGAAT
1 ATTTGAAGACAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-TCAGAAATAAAAAAAC
*
307157 ATTACCTCGATATTAA-GGTTTTCG-TGAAGATA
65 ATTACCTCGAT-TTAAGGGTATTCGATGAAGATA
*
307189 ATTTTGAAAACAAAT
1 A-TTTGAAGACAAAT
307204 GTAAAATTTT
Statistics
Matches: 89, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
96 4 0.04
97 79 0.89
98 6 0.07
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (97 bp):
ATTTGAAGACAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAAAAACA
TTACCTCGATTTAAGGGTATTCGATGAAGATA
Found at i:307523 original size:29 final size:29
Alignment explanation
Indices: 307491--307678 Score: 154
Period size: 29 Copynumber: 6.5 Consensus size: 29
307481 CATTCGGGGG
307491 TAAAATGGTAATTTTAGAAAAATTAGGGT
1 TAAAATGGTAATTTTAGAAAAATTAGGGT
* * *
307520 TAAAAATGG-AATTTTTGGAAATTTGAGGG-
1 T-AAAATGGTAATTTTAGAAAAATT-AGGGT
* *
307549 TAAAATGATAATTTTGGAAAAATTAGGGT
1 TAAAATGGTAATTTTAGAAAAATTAGGGT
* * *
307578 CAAAAATGG-AATTTTAG--AAAGTAGGGG
1 -TAAAATGGTAATTTTAGAAAAATTAGGGT
* * *
307605 TAAAATGGTAATTTTTGGAAAAATCAAGGT
1 TAAAATGGTAA-TTTTAGAAAAATTAGGGT
* ** *
307635 CAAAAATGG-AATTTTAGAAAGTTTAGGGG
1 -TAAAATGGTAATTTTAGAAAAATTAGGGT
307664 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
307679 GGATAGTTTA
Statistics
Matches: 122, Mismatches: 26, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
26 7 0.06
27 10 0.08
28 22 0.18
29 51 0.42
30 25 0.20
31 7 0.06
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (29 bp):
TAAAATGGTAATTTTAGAAAAATTAGGGT
Found at i:307527 original size:58 final size:57
Alignment explanation
Indices: 307427--307681 Score: 300
Period size: 58 Copynumber: 4.4 Consensus size: 57
307417 TTGGACACTC
* * * * * *
307427 AGGGGCAAAATGGTAATTTTGGGAAAATTCGAGATCAAAAATGAAATTTTTA-AACATTC
1 AGGGGTAAAATGGTAATTTTGGAAAAATTAG-GGTCAAAAATGGAA-TTTTAGAA-ATTT
* * * *
307486 GGGGGTAAAATGGTAATTTTAGAAAAATTAGGGTTAAAAATGGAATTTTTGGAAATTT
1 AGGGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAA-TTTTAGAAATTT
* *
307544 -GAGGGTAAAATGATAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAA-GT
1 AG-GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAATTT
* *
307600 AGGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTAGAAAGTTT
1 AGGGGTAAAATGGTAA-TTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAA-TTT
307659 AGGGGTAAAATGGTAATTTTGGA
1 AGGGGTAAAATGGTAATTTTGGA
307682 TAGTTTAGGG
Statistics
Matches: 171, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
56 14 0.08
57 46 0.27
58 66 0.39
59 45 0.26
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (57 bp):
AGGGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAATTT
Found at i:307691 original size:29 final size:29
Alignment explanation
Indices: 307406--307681 Score: 162
Period size: 28 Copynumber: 9.6 Consensus size: 29
307396 CCCGGGAGCG
* * * *
307406 AAATGGTAATTTTGG-ACACTCAGGGGCA
1 AAATGGTAATTTTGGAAAAATTAGGGGTA
* * * *
307434 AAATGGTAATTTTGGGAAAATTCGAGATCAA
1 AAATGGTAATTTTGGAAAAATTAGGGGT--A
* * * *
307465 AAAT-GAAATTTT-TAAACATTCGGGGGTA
1 AAATGGTAATTTTGGAAAAATT-AGGGGTA
* *
307493 AAATGGTAATTTTAGAAAAATTAGGGTTAA
1 AAATGGTAATTTTGGAAAAATTAGGGGT-A
*
307523 AAATGG-AATTTTTGG--AAATTTGAGGGTA
1 AAATGGTAA-TTTTGGAAAAATTAG-GGGTA
*
307551 AAATGATAATTTTGGAAAAATTA-GGGTCAA
1 AAATGGTAATTTTGGAAAAATTAGGGGT--A
* *
307581 AAATGG-AATTTT--AGAAAGTAGGGGTA
1 AAATGGTAATTTTGGAAAAATTAGGGGTA
* *
307607 AAATGGTAATTTTTGGAAAAATCA-AGGTCAA
1 AAATGGTAA-TTTTGGAAAAATTAGGGGT--A
* **
307638 AAATGG-AATTTTAGAAAGTTTAGGGGTA
1 AAATGGTAATTTTGGAAAAATTAGGGGTA
307666 AAATGGTAATTTTGGA
1 AAATGGTAATTTTGGA
307682 TAGTTTAGGG
Statistics
Matches: 188, Mismatches: 37, Indels: 45
0.70 0.14 0.17
Matches are distributed among these distances:
26 7 0.04
27 8 0.04
28 57 0.30
29 55 0.29
30 49 0.26
31 12 0.06
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (29 bp):
AAATGGTAATTTTGGAAAAATTAGGGGTA
Found at i:309619 original size:6 final size:6
Alignment explanation
Indices: 309608--309738 Score: 89
Period size: 6 Copynumber: 22.8 Consensus size: 6
309598 GACTTCTATT
* ** *
309608 AATTTA AATTTA GAA--TA ATTTTA AATTTA AAAATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
** **
309655 AA-TTA AATTTA AATTTA AA-ACA AATTTA AATTTA AA-ACA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
309700 AATTTA AA-ATA AATCT- AATCTTA AA-ATA AATTTA AATTT
1 AATTTA AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTT
309739 TTTAAAAAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
4 1 0.01
5 24 0.25
6 66 0.69
7 4 0.04
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:309630 original size:17 final size:17
Alignment explanation
Indices: 309608--309738 Score: 174
Period size: 17 Copynumber: 7.6 Consensus size: 17
309598 GACTTCTATT
*
309608 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
309625 ATTTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
* *
309643 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
*
309660 AATTTAAATTTAAAACA
1 AATTTAAATTTAAAATA
*
309677 AATTTAAATTTAAAACA
1 AATTTAAATTTAAAATA
309694 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
309711 AATCT-AATCTTAAAATA
1 AATTTAAAT-TTAAAATA
309728 AATTTAAATTT
1 AATTTAAATTT
309739 TTTAAAAAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
16 3 0.03
17 80 0.80
18 17 0.17
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:309707 original size:23 final size:23
Alignment explanation
Indices: 309629--309690 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
309619 AGAATAATTT
**
309629 TAAATTTAAAAATAAATTTAAAC
1 TAAATTTAAATTTAAATTTAAAC
309652 TTAAA-TTAAATTTAAATTTAAAAC
1 -TAAATTTAAATTTAAATTT-AAAC
309676 -AAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
309691 ACAAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 3 0.09
23 23 0.68
24 8 0.24
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTTAAAC
Found at i:310699 original size:10 final size:10
Alignment explanation
Indices: 310686--310738 Score: 63
Period size: 11 Copynumber: 5.2 Consensus size: 10
310676 ATTTGAGAAC
*
310686 AAAAGGAGCA
1 AAAATGAGCA
310696 AAAATGAGCA
1 AAAATGAGCA
310706 AAAATTGAGCA
1 AAAA-TGAGCA
*
310717 AAAATTGAACA
1 AAAA-TGAGCA
310728 AAAA-GAGCA
1 AAAATGAGCA
310737 AA
1 AA
310739 TTTTAAGAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
9 6 0.15
10 13 0.33
11 20 0.51
ACGTcount: A:0.62, C:0.09, G:0.19, T:0.09
Consensus pattern (10 bp):
AAAATGAGCA
Found at i:310703 original size:21 final size:21
Alignment explanation
Indices: 310679--310738 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
310669 GGAGAGAATT
*
310679 TGAGAACAAAAGGAGCAAAAA
1 TGAGAACAAAAAGAGCAAAAA
310700 TGAG--CAAAAATTGAGCAAAAA
1 TGAGAACAAAAA--GAGCAAAAA
*
310721 T-TGAACAAAAAGAGCAAA
1 TGAGAACAAAAAGAGCAAA
310739 TTTTAAGAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 14 0.42
22 6 0.18
ACGTcount: A:0.60, C:0.10, G:0.20, T:0.10
Consensus pattern (21 bp):
TGAGAACAAAAAGAGCAAAAA
Found at i:310714 original size:11 final size:11
Alignment explanation
Indices: 310691--310731 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
310681 AGAACAAAAG
310691 GAGCAAAAA-T
1 GAGCAAAAATT
310701 GAGCAAAAATT
1 GAGCAAAAATT
310712 GAGCAAAAATT
1 GAGCAAAAATT
*
310723 GAACAAAAA
1 GAGCAAAAA
310732 GAGCAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.61, C:0.10, G:0.17, T:0.12
Consensus pattern (11 bp):
GAGCAAAAATT
Found at i:312149 original size:23 final size:23
Alignment explanation
Indices: 312119--312171 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
312109 TAAAGGGTTA
312119 TATTAATAGTA-TAGATAAA-TAAT
1 TATTAATA-TATTA-ATAAATTAAT
312142 TATTAATATATTAATAAATTAAT
1 TATTAATATATTAATAAATTAAT
312165 T-TTAATA
1 TATTAATA
312172 AACAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TATTAATATATTAATAAATTAAT
Found at i:312664 original size:20 final size:20
Alignment explanation
Indices: 312639--312691 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
312629 AAAAATACCC
* *
312639 TATGTATTGATATCTTATCT
1 TATGTATCGATACCTTATCT
*
312659 TATGTATCGATACCTTATCC
1 TATGTATCGATACCTTATCT
*
312679 AATGTATCGATAC
1 TATGTATCGATAC
312692 TTCCTTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (20 bp):
TATGTATCGATACCTTATCT
Found at i:321873 original size:18 final size:18
Alignment explanation
Indices: 321833--321884 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
321823 TTTTTAATTG
*
321833 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
321851 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
321869 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
321885 CTCGTACCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:333342 original size:49 final size:49
Alignment explanation
Indices: 333286--333384 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
333276 TAAAATTCTC
*
333286 TTTACAACTTTCTTTCTACAGTCACAACAACCACCATAACTCTCATCTT
1 TTTACAACTTTCTTTCTACAATCACAACAACCACCATAACTCTCATCTT
* * *
333335 TTTACAACTTTCTTTCTACAATCACAACCACCATCATAACTCTCTTCTT
1 TTTACAACTTTCTTTCTACAATCACAACAACCACCATAACTCTCATCTT
333384 T
1 T
333385 CTCAACCCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.29, C:0.32, G:0.01, T:0.37
Consensus pattern (49 bp):
TTTACAACTTTCTTTCTACAATCACAACAACCACCATAACTCTCATCTT
Found at i:340205 original size:24 final size:24
Alignment explanation
Indices: 340158--340216 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
340148 TAAAGTAAGT
*
340158 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATTA
340181 TATATTATAATTTTTACTAAT-TTA
1 TATATTATAATTTTT-CTAATATTA
*
340205 TATTTTAATAAT
1 TATATT-ATAAT
340217 AATTATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 17 0.55
25 10 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATTA
Found at i:340277 original size:58 final size:58
Alignment explanation
Indices: 340180--340346 Score: 205
Period size: 58 Copynumber: 2.8 Consensus size: 58
340170 TTCTAATATT
* * * *
340180 ATATATTATAATTTTTACTAATTTATATTTTAATAATAATTATATTAAAA-ACGTTATTAAA
1 ATATA-TATTATTTTTATTAAATTATA-TTTAATAATAATTATATTAAAATA--TAATTAAA
*
340241 ATATATATTA-TTTTATTTAATTATATTTAATAATAATTATATTAAAATATAATTAAA
1 ATATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAA
* *
340298 TTATTTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAAT
1 ATATATATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
340347 TTCATAATAA
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
57 15 0.16
58 57 0.60
59 14 0.15
60 4 0.04
61 5 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (58 bp):
ATATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAA
Found at i:340279 original size:16 final size:16
Alignment explanation
Indices: 340258--340335 Score: 53
Period size: 16 Copynumber: 5.2 Consensus size: 16
340248 TTATTTTATT
340258 TAATTATATTTAATAA
1 TAATTATATTTAATAA
340274 TAATTATA-TTAA-AA
1 TAATTATATTTAATAA
* *
340288 T-A-TA-ATTAAATTAT
1 TAATTATATTTAA-TAA
* * *
340302 TTATTAT-TTTTATTA
1 TAATTATATTTAATAA
340317 -AATTATATTTAATAA
1 TAATTATATTTAATAA
340332 TAAT
1 TAAT
340336 CTTATTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
11 1 0.02
12 5 0.11
13 1 0.02
14 10 0.22
15 12 0.27
16 16 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTATATTTAATAA
Found at i:340372 original size:28 final size:25
Alignment explanation
Indices: 340326--340376 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
340316 AAATTATATT
*
340326 TAATAATAATCTTATTAAAATTTCA
1 TAATAATAATCTTACTAAAATTTCA
340351 TAATAATAATCATTTACCTAAAATTT
1 TAATAATAATC--TTA-CTAAAATTT
340377 TTTTACTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
27 3 0.14
28 8 0.36
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATAATAATCTTACTAAAATTTCA
Found at i:340535 original size:16 final size:16
Alignment explanation
Indices: 340507--340576 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
340497 TGAATTACTG
* *
340507 ATTACAATCATATTTC
1 ATTACAATTATATTCC
*
340523 ATTACAGTTATATTCC
1 ATTACAATTATATTCC
* *
340539 ATTACAACTCTATTCC
1 ATTACAATTATATTCC
*
340555 ATTACAATTCTATTCC
1 ATTACAATTATATTCC
340571 ATTACA
1 ATTACA
340577 GCAAACCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTACAATTATATTCC
Found at i:340558 original size:32 final size:32
Alignment explanation
Indices: 340507--340576 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
340497 TGAATTACTG
* *
340507 ATTACAATCATATTTCATTACAGTTATATTCC
1 ATTACAATCATATTCCATTACAATTATATTCC
*
340539 ATTACAACTC-TATTCCATTACAATTCTATTCC
1 ATTACAA-TCATATTCCATTACAATTATATTCC
340571 ATTACA
1 ATTACA
340577 GCAAACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.41
Consensus pattern (32 bp):
ATTACAATCATATTCCATTACAATTATATTCC
Found at i:343669 original size:18 final size:18
Alignment explanation
Indices: 343642--343719 Score: 51
Period size: 18 Copynumber: 4.5 Consensus size: 18
343632 TATTTAATAT
*
343642 TAAATTTTATTAAATTAA
1 TAAATATTATTAAATTAA
343660 TAAATATTATCTACAA--AA
1 TAAATATTAT-TA-AATTAA
*
343678 TAAATA-T-TTAATTTAA
1 TAAATATTATTAAATTAA
* *
343694 T--TTAATATTAAATTAA
1 TAAATATTATTAAATTAA
343710 TAAAATATTA
1 T-AAATATTA
343720 ATAAGATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 17
0.66 0.09 0.25
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 13 0.29
17 1 0.02
18 17 0.38
19 6 0.13
20 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATTATTAAATTAA
Found at i:345086 original size:18 final size:18
Alignment explanation
Indices: 345046--345088 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
345036 TTTTCAATTG
345046 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
345064 CAATTAA-TTAAATTTGTT
1 TAATTAATTTAAAATT-TT
345082 TAATTAA
1 TAATTAA
345089 AATTTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:346613 original size:3 final size:3
Alignment explanation
Indices: 346605--346639 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
346595 CCTAAACCAA
346605 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
346640 AATGATGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.