Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011066.1 Kokia drynarioides strain JFW-HI SEQ_126038, 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: 248974
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:577 original size:3 final size:3
Alignment explanation
Indices: 569--613 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
559 AATAGTATAA
569 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
614 GTAGCTAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3280 original size:20 final size:21
Alignment explanation
Indices: 3255--3300 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3245 TTTTAATTTT
3255 TTTGTAACTC-ACTAATTATG
1 TTTGTAACTCTACTAATTATG
* *
3275 TTTGTAACTCTTCTCATTATG
1 TTTGTAACTCTACTAATTATG
3296 TTTGT
1 TTTGT
3301 TTTCAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (21 bp):
TTTGTAACTCTACTAATTATG
Found at i:3703 original size:19 final size:18
Alignment explanation
Indices: 3655--3703 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3645 AGTATACTTG
3655 TTATTTTTTTAAAATTTA
1 TTATTTTTTTAAAATTTA
** *
3673 TTATTAAATTTAAATTTTA
1 TTATT-TTTTTAAAATTTA
3692 TTTATTTTTTTA
1 -TTATTTTTTTA
3704 TATAATGTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTTTTAAAATTTA
Found at i:9912 original size:23 final size:23
Alignment explanation
Indices: 9881--9927 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9871 CTAGTCTGAC
9881 AGAAAGAAACAGAAAAATTACAG
1 AGAAAGAAACAGAAAAATTACAG
* *
9904 AGAAGGAAACAGGAAAATTACAG
1 AGAAAGAAACAGAAAAATTACAG
9927 A
1 A
9928 TAGACAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.09, G:0.21, T:0.09
Consensus pattern (23 bp):
AGAAAGAAACAGAAAAATTACAG
Found at i:19046 original size:23 final size:23
Alignment explanation
Indices: 18961--19040 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
18951 AGCACGTCTC
* *
18961 GTGCTCTCTGTTATTAGCACTATAT
1 GTGCTCTCTG--ATTAGCACTTTGT
*
18986 GTGCTCTCTGATTAGCATTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
19009 GTGTTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
19032 GTGCTCTCT
1 GTGCTCTCT
19041 ATTTAGAACT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 38 0.79
25 10 0.21
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:19654 original size:69 final size:66
Alignment explanation
Indices: 19532--19671 Score: 174
Period size: 69 Copynumber: 2.0 Consensus size: 66
19522 TATACGGAAC
* * *
19532 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACATAAGTGTTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCT--G-AACAGAGAACACACACAG
19597 TGCT
63 TGCT
*
19601 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAACACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAAAGAGCACA-AAAGTGCTGAA-CAGAGAACACACACA
19665 GTGCT
62 GTGCT
19670 AA
1 AA
19672 TAATAAAGAG
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
68 2 0.03
69 34 0.54
70 11 0.17
71 10 0.16
72 6 0.10
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.13
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCTGAACAGAGAACACACACAGTGC
T
Found at i:19672 original size:23 final size:23
Alignment explanation
Indices: 19581--19672 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
19571 TGTTGGGCAA
* *
19581 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
* *
19604 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
19627 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
19650 CAGAGAACACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
19673 AATAAAGAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:24930 original size:16 final size:17
Alignment explanation
Indices: 24899--24932 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24889 AAATGTTTTT
*
24899 TTATTGTAGTATAGAAA
1 TTATTGTAGGATAGAAA
24916 TTATT-TAGGATAGAAA
1 TTATTGTAGGATAGAAA
24932 T
1 T
24933 GTAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TTATTGTAGGATAGAAA
Found at i:25745 original size:22 final size:23
Alignment explanation
Indices: 25720--25780 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
25710 TCTCCGATTA
25720 TTAGCACATTAGTGCTCCTC-GT
1 TTAGCACATTAGTGCTCCTCTGT
*
25742 TTAGCACA-TACATGCT-CTCTGT
1 TTAGCACATTA-GTGCTCCTCTGT
* *
25764 ATAGCACCTTAGTGCTC
1 TTAGCACATTAGTGCTC
25781 TTTGTTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 5 0.16
22 24 0.77
23 2 0.06
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (23 bp):
TTAGCACATTAGTGCTCCTCTGT
Found at i:26088 original size:42 final size:42
Alignment explanation
Indices: 26041--26124 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
26031 TATTTACCAC
*
26041 CTTGTAGTGCTTACTAAGCTTTCATCGACTTAACGCGCTTAT
1 CTTGTAGTGCTTACTAAGCCTTCATCGACTTAACGCGCTTAT
*
26083 CTTGTAGTGCTTACTAAGCCTTCATCGACTTAACGCGTTTAT
1 CTTGTAGTGCTTACTAAGCCTTCATCGACTTAACGCGCTTAT
26125 TTTAACGCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (42 bp):
CTTGTAGTGCTTACTAAGCCTTCATCGACTTAACGCGCTTAT
Found at i:26952 original size:19 final size:19
Alignment explanation
Indices: 26928--26970 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
26918 TTTATATTGG
26928 GTACATACAGTCAAACCGA
1 GTACATACAGTCAAACCGA
26947 GTACATACAGTCAAACCGA
1 GTACATACAGTCAAACCGA
26966 GTACA
1 GTACA
26971 GGGGTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (19 bp):
GTACATACAGTCAAACCGA
Found at i:33257 original size:41 final size:41
Alignment explanation
Indices: 33200--33352 Score: 108
Period size: 41 Copynumber: 3.5 Consensus size: 41
33190 GTGTTTAAAA
* *
33200 TAAATATTTTATTTTTAAAAAAGATTTTTTAACAGTAATAT
1 TAAATATTTAAATTTTAAAAAAGATTTTTTAACAGTAATAT
* * * * *
33241 TAAATATTTAAATTTTAAATCATGCTTTTTAAAAATATATAATCACATCAAT
1 TAAATATTTAAATTTTAAA-AAAGATTTTT-----TA-ACAGT-A-AT--AT
* * * *
33293 AAAATATTTTATTTTTGAAAAAGATTTTTTAACAGTAATAT
1 TAAATATTTAAATTTTAAAAAAGATTTTTTAACAGTAATAT
33334 TAAATATTTAAATTTTAAA
1 TAAATATTTAAATTTTAAA
33353 TTATACTTTT
Statistics
Matches: 81, Mismatches: 20, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
41 34 0.42
42 7 0.09
43 2 0.02
44 1 0.01
45 3 0.04
46 2 0.02
47 2 0.02
48 3 0.04
49 1 0.01
50 2 0.02
51 7 0.09
52 17 0.21
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (41 bp):
TAAATATTTAAATTTTAAAAAAGATTTTTTAACAGTAATAT
Found at i:33298 original size:93 final size:93
Alignment explanation
Indices: 33201--33386 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
33191 TGTTTAAAAT
*
33201 AAATATTTTATTTTTAAAAAAGATTTTTTAACAGTAATATTAAATATTTAAATTTTAAATCATGC
1 AAATATTTTATTTTTAAAAAAGATTTTTTAACAGTAATATTAAATATTTAAATTTTAAATCATAC
33266 TTTTTAAAAATATATAATCACATCAATA
66 TTTTTAAAAATATATAATCACATCAATA
* *
33294 AAATATTTTATTTTTGAAAAAGATTTTTTAACAGTAATATTAAATATTTAAATTTTAAATTATAC
1 AAATATTTTATTTTTAAAAAAGATTTTTTAACAGTAATATTAAATATTTAAATTTTAAATCATAC
33359 TTTTTAAAAATATATAATCACATCAATA
66 TTTTTAAAAATATATAATCACATCAATA
33387 CCTTAAAAGA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (93 bp):
AAATATTTTATTTTTAAAAAAGATTTTTTAACAGTAATATTAAATATTTAAATTTTAAATCATAC
TTTTTAAAAATATATAATCACATCAATA
Found at i:35964 original size:20 final size:21
Alignment explanation
Indices: 35939--35977 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35929 CAAAACGATG
35939 TAGTTTGTATT-TTAATTTAA
1 TAGTTTGTATTATTAATTTAA
*
35959 TAGTTTTTATTATTAATTT
1 TAGTTTGTATTATTAATTT
35978 TAGAAAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
TAGTTTGTATTATTAATTTAA
Found at i:36332 original size:23 final size:23
Alignment explanation
Indices: 36289--36332 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
36279 GAAGCTAACT
**
36289 TATAATTTTTATTATAATAAAAA
1 TATAATTTTTAAAATAATAAAAA
*
36312 TATAATTTTTAAAATATTAAA
1 TATAATTTTTAAAATAATAAA
36333 TTAAAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAATTTTTAAAATAATAAAAA
Found at i:37724 original size:22 final size:22
Alignment explanation
Indices: 37699--37741 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
37689 TTTTATTGTT
37699 TTGCTATTATTTCGTTATTATA
1 TTGCTATTATTTCGTTATTATA
* *
37721 TTGCTATTATTTTGTTGTTAT
1 TTGCTATTATTTCGTTATTAT
37742 TGTTTGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.12, T:0.63
Consensus pattern (22 bp):
TTGCTATTATTTCGTTATTATA
Found at i:45261 original size:15 final size:18
Alignment explanation
Indices: 45227--45262 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
45217 AAACCGTTAG
45227 TTTTATTAATAAATTATA
1 TTTTATTAATAAATTATA
45245 TTTT-TTAA-AAA-TATA
1 TTTTATTAATAAATTATA
45260 TTT
1 TTT
45263 AAATCCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 4 0.22
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATTAATAAATTATA
Found at i:67821 original size:44 final size:44
Alignment explanation
Indices: 67758--67847 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
67748 CGGGCCATAT
67758 TCACACTTATGTTGCAGATGAAATTTTTGAATCCATTCAGCCTA
1 TCACACTTATGTTGCAGATGAAATTTTTGAATCCATTCAGCCTA
67802 TCACACTTATGTTGCAGATGAAATTTTTGAATCCATTCAGCCTA
1 TCACACTTATGTTGCAGATGAAATTTTTGAATCCATTCAGCCTA
67846 TC
1 TC
67848 TTAGTTGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (44 bp):
TCACACTTATGTTGCAGATGAAATTTTTGAATCCATTCAGCCTA
Found at i:71723 original size:24 final size:24
Alignment explanation
Indices: 71665--71722 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
71655 AAAAAGTCAA
*
71665 AACAACCAAAATAACAACTAAAAC
1 AACAACAAAAATAACAACTAAAAC
* * *
71689 AATAGCAAAAATAACAGC-AAAAC
1 AACAACAAAAATAACAACTAAAAC
71712 AACAACAAAAA
1 AACAACAAAAA
71723 ACAAAAATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACAACTAAAAC
Found at i:71803 original size:17 final size:17
Alignment explanation
Indices: 71781--71815 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
71771 CCAAAACAAC
71781 AATCAAAACAATAAAAA
1 AATCAAAACAATAAAAA
*
71798 AATCAAAACAGTAAAAA
1 AATCAAAACAATAAAAA
71815 A
1 A
71816 CAACAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.11
Consensus pattern (17 bp):
AATCAAAACAATAAAAA
Found at i:72192 original size:41 final size:42
Alignment explanation
Indices: 72111--72192 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
72101 AAACATTTCT
* *
72111 TATATTTTTATACTTTTTAAATAATTTTAATTTTTCAAAAAA
1 TATATTTTCATACTTTTTAAATAATTTTAAATTTTCAAAAAA
**
72153 TATATTTTCATACTTTTT-TTTAATTTTAAAATTTT-AAAAA
1 TATATTTTCATACTTTTTAAATAATTTT-AAATTTTCAAAAA
72193 GTTAATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (42 bp):
TATATTTTCATACTTTTTAAATAATTTTAAATTTTCAAAAAA
Found at i:72991 original size:19 final size:19
Alignment explanation
Indices: 72969--73023 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
72959 TTTTAGAAAA
*
72969 TTTT-TAATATTTTAATACT
1 TTTTATAATTTTTTAA-ACT
* *
72988 TTTTAGAATTTTTTAAATT
1 TTTTATAATTTTTTAAACT
73007 TTTTATAATTTTTTAAA
1 TTTTATAATTTTTTAAA
73024 AATATAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTAAACT
Found at i:73008 original size:8 final size:9
Alignment explanation
Indices: 72969--73023 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
72959 TTTTAGAAAA
72969 TTTTT-AAT
1 TTTTTAAAT
* *
72977 ATTTTAATAC
1 TTTTTAA-AT
72987 TTTTTAGAAT
1 TTTTTA-AAT
72997 TTTTTAAAT
1 TTTTTAAAT
73006 TTTTTATAAT
1 TTTTTA-AAT
73016 TTTTTAAA
1 TTTTTAAA
73024 AATATAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 4 0.10
9 12 0.31
10 22 0.56
11 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:73010 original size:29 final size:28
Alignment explanation
Indices: 72959--73019 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
72949 AAAATTATCA
*
72959 TTTTAGAAAATTTTTAATATTTTAATACT
1 TTTTAGAAAATTTTTAATATTTT-ATAAT
* *
72988 TTTTAG-AATTTTTTAAATTTTTTATAAT
1 TTTTAGAAAATTTTT-AATATTTTATAAT
73016 TTTT
1 TTTT
73020 TAAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTAGAAAATTTTTAATATTTTATAAT
Found at i:73049 original size:18 final size:18
Alignment explanation
Indices: 73008--73050 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
72998 TTTTAAATTT
* *
73008 TTTATAATTTTTTAAAAA
1 TTTATAAATTTTGAAAAA
73026 --TATAAATTTTGAAAAA
1 TTTATAAATTTTGAAAAA
73042 TTTATAAAT
1 TTTATAAAT
73051 ATTTTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 14 0.67
18 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTATAAATTTTGAAAAA
Found at i:73395 original size:16 final size:17
Alignment explanation
Indices: 73363--73396 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
73353 TTTAACCGTC
*
73363 TAAAATTTAATTAATTT
1 TAAAATTAAATTAATTT
73380 TAAAATTAAATT-ATTT
1 TAAAATTAAATTAATTT
73396 T
1 T
73397 CTCAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATTAAATTAATTT
Found at i:80341 original size:13 final size:13
Alignment explanation
Indices: 80323--80347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80313 CACACCCTCA
80323 ATTAAATAACAAC
1 ATTAAATAACAAC
80336 ATTAAATAACAA
1 ATTAAATAACAA
80348 ATCAATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
ATTAAATAACAAC
Found at i:80362 original size:23 final size:23
Alignment explanation
Indices: 80336--80413 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
80326 AAATAACAAC
80336 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAATTAAAA
* *
80359 ATTAAATTAAAGAAAACAA--AAAA
1 ATTAAA-T-AACAAATCAATTAAAA
* *
80382 CTTAAAATAATCAAATTAATTAACAA
1 ATT-AAATAA-CAAATCAATTAA-AA
80408 ATTAAA
1 ATTAAA
80414 ATATTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
22 2 0.05
23 18 0.44
24 4 0.10
25 13 0.32
26 4 0.10
ACGTcount: A:0.65, C:0.08, G:0.01, T:0.26
Consensus pattern (23 bp):
ATTAAATAACAAATCAATTAAAA
Found at i:80368 original size:12 final size:12
Alignment explanation
Indices: 80322--80413 Score: 57
Period size: 12 Copynumber: 7.6 Consensus size: 12
80312 ACACACCCTC
80322 AATTAAATAACA
1 AATTAAATAACA
80334 ACATTAAATAACA
1 A-ATTAAATAACA
* *
80347 AATCAATTAA-A
1 AATTAAATAACA
80358 AATTAAATTAA-A
1 AATTAAA-TAACA
* * *
80370 GA--AAACAAAA
1 AATTAAATAACA
80380 AACTTAAAATAATCA
1 AA-TT-AAATAA-CA
*
80395 AATTAATTAACA
1 AATTAAATAACA
80407 AATTAAA
1 AATTAAA
80414 ATATTTATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
9 2 0.03
10 5 0.08
11 6 0.10
12 21 0.34
13 17 0.28
14 7 0.11
15 3 0.05
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.25
Consensus pattern (12 bp):
AATTAAATAACA
Found at i:80626 original size:13 final size:13
Alignment explanation
Indices: 80608--80640 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
80598 ACGTGTCAGG
80608 TATTTTTTTCTCA
1 TATTTTTTTCTCA
80621 TA--TTTTTCTCA
1 TATTTTTTTCTCA
80632 TATTTTTTT
1 TATTTTTTT
80641 TGAAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.61
13 7 0.39
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTTTTTCTCA
Found at i:80637 original size:10 final size:11
Alignment explanation
Indices: 80612--80638 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
80602 GTCAGGTATT
80612 TTTTTCTCATA
1 TTTTTCTCATA
80623 TTTTTCTCATA
1 TTTTTCTCATA
80634 TTTTT
1 TTTTT
80639 TTTGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTCTCATA
Found at i:80966 original size:8 final size:8
Alignment explanation
Indices: 80953--80994 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
80943 CTATTTCAAC
80953 AAAAATAA
1 AAAAATAA
*
80961 AAAAAT-T
1 AAAAATAA
*
80968 AAAAATTA
1 AAAAATAA
80976 AAAAATAA
1 AAAAATAA
80984 AAAAATAA
1 AAAAATAA
80992 AAA
1 AAA
80995 TTATATACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:80973 original size:15 final size:15
Alignment explanation
Indices: 80953--80997 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
80943 CTATTTCAAC
80953 AAAAATAAAAAAATT
1 AAAAATAAAAAAATT
*
80968 AAAAATTAAAAAA-T
1 AAAAATAAAAAAATT
80982 AAAAA-AATAAAAATT
1 AAAAATAA-AAAAATT
80997 A
1 A
80998 TATACAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
15 14 0.54
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAATAAAAAAATT
Found at i:89835 original size:13 final size:13
Alignment explanation
Indices: 89814--89847 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
89804 ATATAATAAT
89814 AATAATAATCCTA
1 AATAATAATCCTA
*
89827 AATATTAATCCTA
1 AATAATAATCCTA
*
89840 AAAAATAA
1 AATAATAA
89848 AGTTTAAATT
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:92337 original size:177 final size:177
Alignment explanation
Indices: 92041--92395 Score: 647
Period size: 177 Copynumber: 2.0 Consensus size: 177
92031 TCCAGAAACA
92041 TCTAAATCTGGGCACACATTTGTCTAGACTCAATTCTTATGTAGTTTTATTTAGTAGTTAATTTT
1 TCTAAATCTGGGCACACATTTGTCTAGACTCAATTCTTATGTAGTTTTATTTAGTAGTTAATTTT
* * *
92106 CAAAAAATAAAAGAGTAGAGGTAAAATTGAATAAATGTGTAAATATTAGGGGTTATATTTGTAAT
66 CAAAAAATAAAAGAATAAAGGTAAAATTGAATAAATGTGTAAATATTAGGGGTTATATTTATAAT
*
92171 TATTCCTTATACGTAAAATGCCAACTTAAGCATTTTTGATGGAATTT
131 TATTCCTTATACGTAAAATGCCAACTTAAGCATTTTTGATAGAATTT
*
92218 TCTAAATCTGGGCACACATTTGTCTAGACTCATTTCTTATGTAGTTTTATTTAGTAGTTAATTTT
1 TCTAAATCTGGGCACACATTTGTCTAGACTCAATTCTTATGTAGTTTTATTTAGTAGTTAATTTT
*
92283 CAAAAAATAAAAGAATAAAGGTAAAATTGAATAAATGTGTAAATATTGGGGGTTATATTTATAAT
66 CAAAAAATAAAAGAATAAAGGTAAAATTGAATAAATGTGTAAATATTAGGGGTTATATTTATAAT
*
92348 TATTCCTTATACGTAAAATGTCAACTTAAGCATTTTTGATAGAATTT
131 TATTCCTTATACGTAAAATGCCAACTTAAGCATTTTTGATAGAATTT
92395 T
1 T
92396 AACGGAGTGG
Statistics
Matches: 171, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
177 171 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (177 bp):
TCTAAATCTGGGCACACATTTGTCTAGACTCAATTCTTATGTAGTTTTATTTAGTAGTTAATTTT
CAAAAAATAAAAGAATAAAGGTAAAATTGAATAAATGTGTAAATATTAGGGGTTATATTTATAAT
TATTCCTTATACGTAAAATGCCAACTTAAGCATTTTTGATAGAATTT
Found at i:96089 original size:16 final size:15
Alignment explanation
Indices: 96062--96119 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 15
96052 ATCTTCTTTG
96062 AATCCCTAAAATATTGA
1 AATCCCT-AAATATT-A
96079 AATCCCTAAATATTA
1 AATCCCTAAATATTA
*
96094 AAGTCCCCAAATCATTA
1 AA-TCCCTAAAT-ATTA
96111 AATCCCTAA
1 AATCCCTAA
96120 CCTCATGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 3 0.08
16 21 0.57
17 13 0.35
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.28
Consensus pattern (15 bp):
AATCCCTAAATATTA
Found at i:98084 original size:24 final size:24
Alignment explanation
Indices: 98052--98109 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
98042 TATCACTAAA
98052 AAAAC-ATAAGTAGTATTTGAGAG
1 AAAACAATAAGTAGTATTTGAGAG
** *
98075 AAAACAATAACAAGTTTTTGAGAG
1 AAAACAATAAGTAGTATTTGAGAG
*
98099 AGAACAA-AAGT
1 AAAACAATAAGT
98110 TATTTCTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (24 bp):
AAAACAATAAGTAGTATTTGAGAG
Found at i:103785 original size:41 final size:39
Alignment explanation
Indices: 103740--103852 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 39
103730 CTTTGTAGCG
* *
103740 ACATAGAATGTCTATGTTGCGACAAACACCCTTATGTCGCA
1 ACATA-AATGTCTATGTTACGACAAAC-CCCTTATGTCACA
* *
103781 ACATAAAATGTCTATGTCATGACAAACCCCCTTATGTCACA
1 ACAT-AAATGTCTATGTTACGACAAA-CCCCTTATGTCACA
* *
103822 ACACAACATGTTTATGTTACGACAAACCCCT
1 ACATAA-ATGTCTATGTTACGACAAACCCCT
103853 AAAGATGTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 7 0.11
41 52 0.85
42 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (39 bp):
ACATAAATGTCTATGTTACGACAAACCCCTTATGTCACA
Found at i:106802 original size:11 final size:11
Alignment explanation
Indices: 106786--106826 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
106776 AAATGTTTTT
106786 ATAATAAATAC
1 ATAATAAATAC
106797 ATAATAAATAC
1 ATAATAAATAC
* * *
106808 ATATTAAGTAA
1 ATAATAAATAC
106819 ATAATAAA
1 ATAATAAA
106827 GAAAGGAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (11 bp):
ATAATAAATAC
Found at i:107908 original size:30 final size:30
Alignment explanation
Indices: 107885--108039 Score: 145
Period size: 30 Copynumber: 5.2 Consensus size: 30
107875 TTGACACCCG
107885 AACTTTTTAAAAATTATATTTTGACCCCTT
1 AACTTTTTAAAAATTATATTTTGACCCCTT
* * *
107915 AAGTTTTAAAAAATTATATTTCGA-CCCTT
1 AACTTTTTAAAAATTATATTTTGACCCCTT
* * * *
107944 AAATTTTTTTAAAATCATATTTTAACCCCTT
1 -AACTTTTTAAAAATTATATTTTGACCCCTT
* * *
107975 AACTTTTTTAAAATTACATTTTGA-CCCTA
1 AACTTTTTAAAAATTATATTTTGACCCCTT
* ** *
108004 AACTCTTCCAAAATTACATTTTGA-CCCTT
1 AACTTTTTAAAAATTATATTTTGACCCCTT
108033 AAACTTT
1 -AACTTT
108040 CCTAAATTTA
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
29 34 0.33
30 64 0.62
31 5 0.05
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (30 bp):
AACTTTTTAAAAATTATATTTTGACCCCTT
Found at i:107952 original size:60 final size:59
Alignment explanation
Indices: 107885--108098 Score: 171
Period size: 60 Copynumber: 3.6 Consensus size: 59
107875 TTGACACCCG
* *
107885 AACTTTTTAAAAATTATATTTTGACCCCTTAAGTTTTAAAAAATTATATTTCGACCCTTA
1 AACTTTTTAAAAATTATATTTTGACCCCTTAACTTTTAAAAAATTACATTTCGACCC-TA
* * * * ** *
107945 AATTTTTTTAAAATCATATTTTAACCCCTTAACTTTTTTAAAATTACATTTTGACCCTA
1 AACTTTTTAAAAATTATATTTTGACCCCTTAACTTTTAAAAAATTACATTTCGACCCTA
* ** * *** * ** *
108004 AACTCTTCCAAAATTACATTTTGA-CCCTTAAACTTTCCTAAATTTACATTTTAACTGCTA
1 AACTTTTTAAAAATTATATTTTGACCCCTT-AACTTTTAAAAAATTACATTTCGAC-CCTA
* * *
108064 AACTTCTCT-AAAATTACATTTTGACCCCTAAACTT
1 AACTT-TTTAAAAATTATATTTTGACCCCTTAACTT
108099 CCCAAAATCA
Statistics
Matches: 125, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
58 5 0.04
59 40 0.32
60 75 0.60
61 5 0.04
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.43
Consensus pattern (59 bp):
AACTTTTTAAAAATTATATTTTGACCCCTTAACTTTTAAAAAATTACATTTCGACCCTA
Found at i:108051 original size:30 final size:29
Alignment explanation
Indices: 107924--108122 Score: 163
Period size: 30 Copynumber: 6.8 Consensus size: 29
107914 TAAGTTTTAA
* * * **
107924 AAAATTATATTTCGACCCTTAAATTTTTTT
1 AAAATTACATTTTGACCC-TAAACTTTCCT
* * * * **
107954 AAAATCATATTTTAACCCCTTAACTTTTTT
1 AAAATTACATTTTGA-CCCTAAACTTTCCT
107984 AAAATTACATTTTGACCCTAAACTCTTCC-
1 AAAATTACATTTTGACCCTAAACT-TTCCT
108013 AAAATTACATTTTGACCCTTAAACTTTCCT
1 AAAATTACATTTTGACCC-TAAACTTTCCT
* * *
108043 AAATTTACATTTTAACTGCTAAAC-TTCTCT
1 AAAATTACATTTTGAC-CCTAAACTTTC-CT
*
108073 AAAATTACATTTTGACCCCTAAAC-TTCCC
1 AAAATTACATTTTGA-CCCTAAACTTTCCT
*
108102 AAAATCACATTTTGA-CCTAAA
1 AAAATTACATTTTGACCCTAAA
108123 AATTCTCAAA
Statistics
Matches: 143, Mismatches: 19, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.04
29 48 0.34
30 84 0.59
31 5 0.03
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCTAAACTTTCCT
Found at i:108058 original size:89 final size:89
Alignment explanation
Indices: 107885--108118 Score: 254
Period size: 89 Copynumber: 2.6 Consensus size: 89
107875 TTGACACCCG
* * ** ** * * *
107885 AACTTTTTAAAAATTATATTTTGACCCCTTAAGTTTTAAAAAATTATATTTCGACCCTTAAATTT
1 AACTTTTTTAAAATTACATTTTGACCCC-TAAACTTTCCAAAATTACATTTTGACCCTTAAACTT
** * *
107950 TTTTAAAATCATATTTTAACCCCTT
65 TCCTAAAATCACATTTTAACCCCTA
107975 AACTTTTTTAAAATTACATTTTGA-CCCTAAACTCTTCCAAAATTACATTTTGACCCTTAAACTT
1 AACTTTTTTAAAATTACATTTTGACCCCTAAACT-TTCCAAAATTACATTTTGACCCTTAAACTT
* * **
108039 TCCTAAATTTACATTTTAACTGCTA
65 TCCTAAAATCACATTTTAACCCCTA
* * * *
108064 AACTTCTCTAAAATTACATTTTGACCCCTAAACTTCCCAAAATCACATTTTGACC
1 AACTTTTTTAAAATTACATTTTGACCCCTAAACTTTCCAAAATTACATTTTGACC
108119 TAAAAATTCT
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
88 4 0.03
89 86 0.71
90 31 0.26
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (89 bp):
AACTTTTTTAAAATTACATTTTGACCCCTAAACTTTCCAAAATTACATTTTGACCCTTAAACTTT
CCTAAAATCACATTTTAACCCCTA
Found at i:123951 original size:4 final size:4
Alignment explanation
Indices: 123942--123970 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
123932 CAAGCAACTA
123942 AAAC AAAC AAAC AAAC AAAC AAA- AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
123971 TATCACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:132312 original size:25 final size:23
Alignment explanation
Indices: 132284--132329 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
132274 GTTGGATCCA
132284 AATTAAATTCTAAAAAAATAATTTG
1 AATTAAA-TCT-AAAAAATAATTTG
*
132309 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
132330 CCTTGATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:133326 original size:66 final size:66
Alignment explanation
Indices: 133248--133380 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
133238 AACACCAATT
133248 AAACCTTTAATTTAACACATAATCAGGCAAATTTAACAAATTATCCATAATATCACTCACCTTCG
1 AAACCTTTAATTTAACACATAATCAGGCAAATTTAACAAATTATCCATAATATCACTCACCTTCG
133313 C
66 C
*
133314 AAACCTTTAATTTAACACATAATCAGGCAAATTTAACAAATTGTCCATAATATCACTCACCTTCG
1 AAACCTTTAATTTAACACATAATCAGGCAAATTTAACAAATTATCCATAATATCACTCACCTTCG
133379 C
66 C
133380 A
1 A
133381 TTTAGCTCTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (66 bp):
AAACCTTTAATTTAACACATAATCAGGCAAATTTAACAAATTATCCATAATATCACTCACCTTCG
C
Found at i:138722 original size:40 final size:41
Alignment explanation
Indices: 138631--138735 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 41
138621 CGTGACATAA
*
138631 AATGTCTATGTCGCGACAAACCCCACTAAGTCGCAACATAG
1 AATGTCTATGTCGCGACAAACCCCACTAAGTCGCAACACAG
* * * *
138672 AATGTCTATGTCGTGACAAACTCC-TTATGTCGCAACACA-
1 AATGTCTATGTCGCGACAAACCCCACTAAGTCGCAACACAG
* * *
138711 ACATGTTTATGTCACAACAAACCCC
1 A-ATGTCTATGTCGCGACAAACCCC
138736 TAAAGATGTC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 30 0.57
41 22 0.42
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (41 bp):
AATGTCTATGTCGCGACAAACCCCACTAAGTCGCAACACAG
Found at i:141681 original size:41 final size:41
Alignment explanation
Indices: 141635--141730 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
141625 TGATTTTTTT
*
141635 TTAACAAGAATTCTAGTCACCCAATTTTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
141676 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* *
141717 TTGACAATAATTCT
1 TTAACAAGAATTCT
141731 CTATGAACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:155116 original size:21 final size:21
Alignment explanation
Indices: 155068--155119 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
155058 GGAGTTTTTA
*
155068 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGAATGACAT
* *
155089 GTTTCGGTAGAAGTAAT-ACTT
1 GTATCGGTAGAAG-AATGACAT
155110 GTATCGGTAG
1 GTATCGGTAG
155120 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGAATGACAT
Found at i:161495 original size:11 final size:11
Alignment explanation
Indices: 161481--161513 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
161471 TAAAATATAC
161481 AAATTAATAAA
1 AAATTAATAAA
161492 AAATT-ATAAA
1 AAATTAATAAA
161502 AAATTACATAAA
1 AAATTA-ATAAA
161514 GAACCTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 5 0.25
12 5 0.25
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATTAATAAA
Found at i:166740 original size:31 final size:30
Alignment explanation
Indices: 166682--166741 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
166672 AGATTTAGGG
*
166682 TTTTTTTAATTAAGATTTAATATTTAAAAT
1 TTTTTTTAATTAAGATTTAATAATTAAAAT
*
166712 TTTTTATTAATTAA-ATTTATTTAATTAAAA
1 TTTTT-TTAATTAAGATTTA-ATAATTAAAA
166742 ATTTATTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTTTTAATTAAGATTTAATAATTAAAAT
Found at i:166743 original size:16 final size:15
Alignment explanation
Indices: 166702--166748 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
166692 TAAGATTTAA
*
166702 TATTTAAAATTT-TT
1 TATTAAAAATTTATT
166716 TATTAATTAAATTTATT
1 TATTAA--AAATTTATT
166733 TAATTAAAAATTTATT
1 T-ATTAAAAATTTATT
166749 CTCATTCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.18
16 15 0.54
17 3 0.11
18 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTAAAAATTTATT
Found at i:171351 original size:29 final size:30
Alignment explanation
Indices: 171309--171400 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 30
171299 TAAAATGAGG
171309 TTTTAGGT-TCCTTAAAAGTTAGAAAAA-AA
1 TTTTAGGTCT-CTTAAAAGTTAGAAAAAGAA
171338 TTTTAGGTCTCTT-AAAGATT-GATAAAAGAA
1 TTTTAGGTCTCTTAAAAG-TTAGA-AAAAGAA
* * *
171368 TTTTTGGCCT-TTAAAAGTTAAAAAAAGAA
1 TTTTAGGTCTCTTAAAAGTTAGAAAAAGAA
171397 TTTT
1 TTTT
171401 TTTTGGACCC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
28 6 0.11
29 32 0.59
30 16 0.30
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (30 bp):
TTTTAGGTCTCTTAAAAGTTAGAAAAAGAA
Found at i:173010 original size:58 final size:58
Alignment explanation
Indices: 172920--173040 Score: 233
Period size: 58 Copynumber: 2.1 Consensus size: 58
172910 CAAATTCCAC
*
172920 ACATTACTTGACCTAGAAACTCCACAGAGCATCTTTCAATGCATTCCCTTTGCCATTT
1 ACATTACTTGACCTAGAAACTCCACAAAGCATCTTTCAATGCATTCCCTTTGCCATTT
172978 ACATTACTTGACCTAGAAACTCCACAAAGCATCTTTCAATGCATTCCCTTTGCCATTT
1 ACATTACTTGACCTAGAAACTCCACAAAGCATCTTTCAATGCATTCCCTTTGCCATTT
173036 ACATT
1 ACATT
173041 GCTCTTGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (58 bp):
ACATTACTTGACCTAGAAACTCCACAAAGCATCTTTCAATGCATTCCCTTTGCCATTT
Found at i:184139 original size:2 final size:2
Alignment explanation
Indices: 184132--184159 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
184122 TAAATTTAGA
184132 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
184160 CATGATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190580 original size:29 final size:29
Alignment explanation
Indices: 190534--190603 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
190524 TTGGTTTTGG
* * *
190534 TTTTTTTATAATTTATAAAATTGT-ATTTT
1 TTTTTTTA-AAATAATAAAATTGTGATTTA
* *
190563 TATTTTTTAAAATAATAAATTTTTGATTTA
1 T-TTTTTTAAAATAATAAAATTGTGATTTA
190593 TTTTTTTAAAA
1 TTTTTTTAAAA
190604 AAATTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTTTTTAAAATAATAAAATTGTGATTTA
Found at i:190792 original size:2 final size:2
Alignment explanation
Indices: 190743--190776 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
190733 AAAAAATTAA
190743 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
190777 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193875 original size:8 final size:9
Alignment explanation
Indices: 193857--193890 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
193847 AAAATTAATT
193857 AATTTTAAA
1 AATTTTAAA
193866 AATTTTAAA
1 AATTTTAAA
**
193875 AATTCAAAA
1 AATTTTAAA
193884 AATTTTA
1 AATTTTA
193891 TGAAAATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
AATTTTAAA
Found at i:198862 original size:16 final size:15
Alignment explanation
Indices: 198841--198894 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
198831 TAAGTTATTG
198841 ATTACAGTCATATTCC
1 ATTACAGTC-TATTCC
*
198857 ATTACAGCTCTATTAC
1 ATTACAG-TCTATTCC
*
198873 ATTACAATTCTATTCC
1 ATTAC-AGTCTATTCC
198889 ATTACA
1 ATTACA
198895 ACGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 1 0.03
16 29 0.88
17 3 0.09
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (15 bp):
ATTACAGTCTATTCC
Found at i:198895 original size:16 final size:16
Alignment explanation
Indices: 198851--198896 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
198841 ATTACAGTCA
*
198851 TATTCCATTACAGCTC
1 TATTCCATTACAACTC
* *
198867 TATTACATTACAATTC
1 TATTCCATTACAACTC
198883 TATTCCATTACAAC
1 TATTCCATTACAAC
198897 GAACCAAACG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (16 bp):
TATTCCATTACAACTC
Found at i:199535 original size:20 final size:20
Alignment explanation
Indices: 199507--199572 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
199497 CCACGTTAGC
*
199507 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
199527 AAATTATTTTTTAAA-TA-TA
1 AAATTA-TTTTAAAATTATTA
199546 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
199566 AAATTAT
1 AAATTAT
199573 AATCATCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
16 5 0.14
17 2 0.05
19 8 0.22
20 15 0.41
21 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:199573 original size:28 final size:28
Alignment explanation
Indices: 199516--199574 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
199506 CAAATGATTT
*
199516 TAAAATTATTAAAATTATTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTAAAATA
199544 TAAAATTATTAAAATTA-TTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTAAAA-TA
199572 TAA
1 TAA
199575 TCATCATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:206418 original size:2 final size:2
Alignment explanation
Indices: 206411--206443 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
206401 TAAACAATGC
*
206411 CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
206444 AAGTCGCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
CT
Found at i:213637 original size:22 final size:21
Alignment explanation
Indices: 213594--213647 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
213584 TGAAGTTTAC
*
213594 ATTTTT-TTTTTATTAAATTA
1 ATTTTTATTTTAATTAAATTA
213614 ATTTTTATTTTAATTAAATATA
1 ATTTTTATTTTAATTAAAT-TA
*
213636 ATTATTAATTTT
1 ATT-TTTATTTT
213648 TCAGTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 5 0.17
23 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTATTTTAATTAAATTA
Found at i:221288 original size:9 final size:9
Alignment explanation
Indices: 221274--221326 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
221264 GTAAATGATT
221274 TTAAAATTA
1 TTAAAATTA
221283 TTAAAATTA
1 TTAAAATTA
*
221292 TT----TTT
1 TTAAAATTA
221297 TTAAAA-TA
1 TTAAAATTA
221305 -TAAAATTA
1 TTAAAATTA
221313 TTAAAATTA
1 TTAAAATTA
221322 TTAAA
1 TTAAA
221327 TAAATCATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
5 4 0.11
7 5 0.14
8 3 0.08
9 24 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:222328 original size:20 final size:22
Alignment explanation
Indices: 222305--222346 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
222295 AAGTAATTTT
222305 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
222325 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
222347 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:227272 original size:46 final size:49
Alignment explanation
Indices: 227219--227313 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 49
227209 TTTTTTATTT
227219 TATATTG-TTTCAAG-TTTT-TTTTTAATTAATGTTTATAATTAATAAA
1 TATATTGTTTTCAAGTTTTTATTTTTAATTAATGTTTATAATTAATAAA
* *
227265 TATATTGTTTTCAAGTTTTTCATTTTTAATTCATGTTTTTAATTAATAA
1 TATATTGTTTTCAAGTTTTT-ATTTTTAATTAATGTTTATAATTAATAA
227314 TTCTTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 7 0.16
47 7 0.16
48 4 0.09
50 25 0.58
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (49 bp):
TATATTGTTTTCAAGTTTTTATTTTTAATTAATGTTTATAATTAATAAA
Done.