Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002799.1 Hibiscus syriacus cultivar Beakdansim tig00005762_pilon, 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: 63412
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:114 original size:20 final size:21
Alignment explanation
Indices: 81--119 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
71 AAAACCTTTC
81 ATCAAAAGGATAAGTCTTTTA
1 ATCAAAAGGATAAGTCTTTTA
*
102 ATCAAAA-GTTAAGTCTTT
1 ATCAAAAGGATAAGTCTTT
120 CATCGTAAGG
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:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAAAGGATAAGTCTTTTA
Found at i:2999 original size:21 final size:21
Alignment explanation
Indices: 2975--3024 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2965 AAGCCATTTC
2975 ATCAAAAGGAGAAGTCTTTTA
1 ATCAAAAGGAGAAGTCTTTTA
** *
2996 ATCAAAAGGTTAAGTCTTTTC
1 ATCAAAAGGAGAAGTCTTTTA
*
3017 ATCGAAAG
1 ATCAAAAG
3025 ATCTTAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
ATCAAAAGGAGAAGTCTTTTA
Found at i:9672 original size:35 final size:35
Alignment explanation
Indices: 9632--9704 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
9622 AGAAATCTAA
* *
9632 GAGAAGCTGCTAAGGGTGTTAATTGTTATCGATCC
1 GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
9667 GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
1 GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
9702 GAG
1 GAG
9705 CTCAAGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (35 bp):
GAGAAGCTGCTAAGGGCGTTAATTGTTATCAATCC
Found at i:14483 original size:29 final size:29
Alignment explanation
Indices: 14431--14518 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
14421 TTTACTTTGG
* *
14431 TCATT-AAC-TTTAAAACTTGT-ATTACAA
1 TCATTAAACTTTTAAATCTT-TCATTACGA
14458 TCATTAAACTTTTAAATCTTTCATTACGA
1 TCATTAAACTTTTAAATCTTTCATTACGA
14487 TCATTAAACTTTTAAATCTTTCATTACGA
1 TCATTAAACTTTTAAATCTTTCATTACGA
14516 TCA
1 TCA
14519 CCGTCGTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
27 5 0.09
28 4 0.07
29 47 0.84
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.43
Consensus pattern (29 bp):
TCATTAAACTTTTAAATCTTTCATTACGA
Found at i:15242 original size:26 final size:26
Alignment explanation
Indices: 15175--15236 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
15165 CAGTAGTTAG
*
15175 TTTAAGCAA-CTGA-TTGATTAGCTGA
1 TTTAAG-AATCTGATTTGATTAACTGA
15200 TTTAAGAATCTGATTTGATTAACTGA
1 TTTAAGAATCTGATTTGATTAACTGA
15226 TTATATAGAAT
1 TT-TA-AGAAT
15237 TGTTTGGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 2 0.06
25 10 0.31
26 13 0.41
27 2 0.06
28 5 0.16
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (26 bp):
TTTAAGAATCTGATTTGATTAACTGA
Found at i:15418 original size:20 final size:20
Alignment explanation
Indices: 15393--15438 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
15383 ATTCCTTAAG
15393 AAAATTAGAGAATAT-TTTTT
1 AAAATT-GAGAATATATTTTT
*
15413 AAAATTGTGAATATATTTTT
1 AAAATTGAGAATATATTTTT
*
15433 TAAATT
1 AAAATT
15439 TAATAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (20 bp):
AAAATTGAGAATATATTTTT
Found at i:16182 original size:16 final size:16
Alignment explanation
Indices: 16163--16193 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16153 TTAGAACATA
*
16163 CAAAATTATAAAATTT
1 CAAAAGTATAAAATTT
16179 CAAAAGTATAAAATT
1 CAAAAGTATAAAATT
16194 ATATCATCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
CAAAAGTATAAAATTT
Found at i:18821 original size:74 final size:70
Alignment explanation
Indices: 18741--19043 Score: 311
Period size: 73 Copynumber: 4.1 Consensus size: 70
18731 AGTATATAAA
* * * **
18741 ATATATTTCGAAAAACGTTTTCGAAGCCTATACATATGGTATATTTTCAAAAGCGTTTTAAAATT
1 ATATATTTC--AAAATGTTTTCGAA-ACTATATATATTATATATTTTCAAAAG-GTTTTAAAATT
18806 ATATATTAT
62 ATATATTAT
*
18815 ATATATTTTCAAAATGTTTTCAAAACTATATATATTATATATATTTCAAAAGGTTTTTAAAATTA
1 ATATA-TTTCAAAATGTTTTCGAAACTATATATATTATATAT-TTTCAAAAGG-TTTTAAAATTA
18880 TATATTAT
63 TATATTAT
* *
18888 ATATATTTTTAAAATGTTTTCAGAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAA
1 ATATA-TTTCAAAATGTTTTC-GAAACTATATA-TAT-TATATATTTTCAAAAGGTTTT--AAAA
*
18953 CTATATATTAT
60 TTATATATTAT
* * **
18964 ATATATTTTCAAAATGTTTTCAAAAACTATATAT-TATATATATATTCAAAATATTTTCAAAAAT
1 ATATA-TTTCAAAATGTTTTC-GAAACTATATATAT-TATATATTTTCAAAAGGTTTT--AAAAT
19028 TATATATTAT
61 TATATATTAT
*
19038 AGATAT
1 ATATAT
19044 ATTTTCGAAA
Statistics
Matches: 205, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
72 15 0.07
73 61 0.30
74 60 0.29
75 17 0.08
76 52 0.25
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (70 bp):
ATATATTTCAAAATGTTTTCGAAACTATATATATTATATATTTTCAAAAGGTTTTAAAATTATAT
ATTAT
Found at i:18871 original size:37 final size:37
Alignment explanation
Indices: 18780--19054 Score: 341
Period size: 37 Copynumber: 7.4 Consensus size: 37
18770 ATACATATGG
*
18780 TATATTTTCAAAAGCGTTTT-AAAAT-TATATATTATA
1 TATATTTTCAAAA-TGTTTTCAAAATATATATATTATA
18816 TATATTTTCAAAATGTTTTCAAAACTATATATATTATA
1 TATATTTTCAAAATGTTTTCAAAA-TATATATATTATA
* *
18854 TATA-TTTCAAAAGGTTTTTAAAAT-TATATATTATA
1 TATATTTTCAAAATGTTTTCAAAATATATATATTATA
*
18889 TATATTTTTAAAATGTTTTCAGAAACTATATAT-TATATA
1 TATATTTTCAAAATGTTTTCA-AAA-TATATATAT-TATA
18928 TATATTTTCAAAATGTTTTCAAAA-ACTATATATTATA
1 TATATTTTCAAAATGTTTTCAAAATA-TATATATTATA
18965 TATATTTTCAAAATGTTTTCAAAA-ACTATATATTATA
1 TATATTTTCAAAATGTTTTCAAAATA-TATATATTATA
* *
19002 TATATATTCAAAATATTTTCAAAA-ATTATATATTATAGA
1 TATATTTTCAAAATGTTTTCAAAATA-TATATATTAT--A
19041 TATATTTTCGAAAA
1 TATATTTTC-AAAA
19055 ATTATATATA
Statistics
Matches: 215, Mismatches: 11, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
35 20 0.09
36 32 0.15
37 100 0.47
38 21 0.10
39 38 0.18
40 4 0.02
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATTTTCAAAATGTTTTCAAAATATATATATTATA
Found at i:19049 original size:76 final size:75
Alignment explanation
Indices: 18780--19054 Score: 384
Period size: 76 Copynumber: 3.7 Consensus size: 75
18770 ATACATATGG
*
18780 TATAT-TTTCAAAAGCGTTTT--AAAATTATATATTATATATATTTTCAAAATGTTTTC-AAAAC
1 TATATATTTCAAAA-TGTTTTCAAAAATTATATATTATATATATTTTCAAAATGTTTTCAAAAAC
18841 TATATA-TATTA
65 TATATATTA-TA
* * * *
18852 TATATATTTCAAAAGGTTTT-TAAAATTATATATTATATATATTTTTAAAATGTTTTCAGAAACT
1 TATATATTTCAAAATGTTTTCAAAAATTATATATTATATATATTTTCAAAATGTTTTCAAAAACT
18916 ATATATTATA
66 ATATATTATA
*
18926 TATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAAC
1 TATATA-TTTCAAAATGTTTTCAAAAATTATATATTATATATATTTTCAAAATGTTTTCAAAAAC
18991 TATATATTATA
65 TATATATTATA
*
19002 TATATA-TTCAAAATATTTTCAAAAATTATATATTATAGATATATTTTCGAAAA
1 TATATATTTCAAAATGTTTTCAAAAATTATATATTAT--ATATATTTTC-AAAA
19055 ATTATATATA
Statistics
Matches: 184, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
72 10 0.05
73 43 0.23
74 46 0.25
75 15 0.08
76 66 0.36
77 4 0.02
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (75 bp):
TATATATTTCAAAATGTTTTCAAAAATTATATATTATATATATTTTCAAAATGTTTTCAAAAACT
ATATATTATA
Found at i:19062 original size:29 final size:30
Alignment explanation
Indices: 18996--19077 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 30
18986 AAAACTATAT
*
18996 ATTATATATATATTCA-AAATATTTTCAAAA
1 ATTATATATATATT-AGATATATTTTCAAAA
19026 ATTATATAT-TA-TAGATATATTTTCGAAAA
1 ATTATATATATATTAGATATATTTTC-AAAA
*
19055 ATTATATATATATTATATATATT
1 ATTATATATATATTAGATATATT
19078 AAATAGAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 10 0.22
29 15 0.33
30 11 0.24
31 9 0.20
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTATATATATATTAGATATATTTTCAAAA
Found at i:24491 original size:58 final size:58
Alignment explanation
Indices: 24421--26949 Score: 3735
Period size: 58 Copynumber: 43.7 Consensus size: 58
24411 TCCAGTTAAT
* * * *
24421 AAATAAATTCAACAATCTATTTTCTTTACAAAGTTATAATCATTAAAGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
24479 AAATAAAGTCAACAATCTAATTTCCTTACAAAGTTAGAATTATTTAAGATTCTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
24537 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
24595 AAATAAATTCAACAATCTATTTTCCTTACAAAGATAGAATCATTTAGGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
24653 AAATAAATTTAACAATCTATTTTACTTACAAAGTTATAATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
24711 AAATAAATTCAACAATCTATTTTCCTTGCAAAGTTAGAATCATTTAAGATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
24769 TAATAAATTCAACAATCTATTTTACTTACAAAGTTAGAATCATTTAAGATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * **
24827 TAATAAATTCAACAATCTATTTTCCTTATAAAGTTAGAATTGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
24885 AATTAAATTAAACAATCTATTTT-CTTACAAAGTTAGAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
24942 AAATAAATTCAACAATCTATTTTTCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
25000 AATTAAATTAAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
25058 AAATAAATTCATCAATCTATTTTCCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * *
25116 AATTAAATTAAACAATATATTTTTCTTACAAAGTTAGAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
25174 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTATAATCATTAAAGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * *
25232 AAATAAAGTCAACAATCTATTTTCTTTACAAAATTAGAATCATTTAAGATTCACAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
25290 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
25348 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTT-AGAATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAG-ATTCTCAAGG
* * ** *
25406 AAATAAATTCAACAATATATTTTCCGTACAAAGTTAGAATTGTTTAAGATTCTGAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
25464 AAATAAATTAAACAATATATTTTCCTTACAAAGTTAGAATCATTTAGGGTTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
25522 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
** *
25580 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATTGTTTAAGATTCTGAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
25638 AAATAAATTAAACAATATATTTTCCTTACAAAGTTAGAATCATTTAGGGTTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * **
25696 AAATAAATTCAACAATCTATTTTCCTTACAAATTTATAATCATTAAAGATTCTCAATA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
25754 AAATAAAGTCAACAATCTATTTTCCTCACAAAGTTAGAATCATTTAAGATTCTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
25812 AAATAAATTCAACAATCTATTTTCTTTACAAAGTT--AATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
25868 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAATATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
25926 TAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAATATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
25984 TAATAAATTCAACAATCTATTTTCCTTACAAAATTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * **
26042 AATTAAATTAAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAGGGTTCTCAATT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
26100 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * *
26158 -AATTAATTAAACAATCTATTTTCCTTATAAAGTTAAAATCATTTAGGATTCTCAATG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
26215 CAATAAATTCAACAATCTATTTTTCTTACAAAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * * * **
26273 AAATAAATTCAATAATGTA-TTTCCTGACAAAGTTAGAACCATTTAGGATTCTCAATC
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
26330 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCGTTTAAGGTTTTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
26388 AAATAAATTCAACAATCTATTTTCCTTAGAAAGTTAGAATCATTTAGGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * * *
26446 AAATAAATTAAACAATCTATTTTCATTACAAAGTTATAATCATTAAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
26504 AAATAAATCCAGCAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
26562 AAATAAATTCAACAATCTATTCTCCTTACAAAGTTAGAATAATTTAAGATTCTCAAGT
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
26620 TAATAAATTCAACAATCTATTTT-CTTAC-AAGTTAGAATCGTTTAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
26676 AATTAAATTAAACAATCTATTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* *
26734 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTTTCAAGA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
* * *
26792 AAACAAATTCATCAATTTATTTTCCTTACAAAGTTAGAATCA-TTAAGTATTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAG-ATTCTCAAGG
* *
26850 AAATAAATTCAACAATCTATTTTACTTACAAAGTTAGAATCATTTAAGTTTCTCAAGG
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
*
26908 AAATAAATTCAACCATCTATTTTCCTTACAAAGTTAGAATCA
1 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCA
26950 ACACATGATT
Statistics
Matches: 2213, Mismatches: 247, Indels: 22
0.89 0.10 0.01
Matches are distributed among these distances:
56 99 0.04
57 164 0.07
58 1943 0.88
59 7 0.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (58 bp):
AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
Found at i:27128 original size:39 final size:40
Alignment explanation
Indices: 27082--27191 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 40
27072 AACATAAATA
*
27082 AAAAGGAATTAATCCTTTAATTTTAC-CAA-CCAAATAATC
1 AAAAGGAATTAATCCTTTGATTTTACGCAATCC-AATAATC
*
27121 AAAAGGAACTAATCCTTTGATTTTAATTTTCGCAATCCAATAATC
1 AAAAGGAATTAATCCTTTGATTTT-A----CGCAATCCAATAATC
*
27166 GAAAGGAATTAATCCTTTGATTTTAC
1 AAAAGGAATTAATCCTTTGATTTTAC
27192 TTTTGGCAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
39 22 0.37
40 2 0.03
44 2 0.03
45 32 0.53
46 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (40 bp):
AAAAGGAATTAATCCTTTGATTTTACGCAATCCAATAATC
Found at i:27163 original size:45 final size:44
Alignment explanation
Indices: 27097--27215 Score: 150
Period size: 45 Copynumber: 2.6 Consensus size: 44
27087 GAATTAATCC
27097 TTTAATTTTAC-CAACCAAATAATCAAAAGGAACTAATCCTTTGAT
1 TTTAATTTT-CGCAACC-AATAATCAAAAGGAACTAATCCTTTGAT
* *
27142 TTTAATTTTCGCAATCCAATAATCGAAAGGAATTAATCCTTTGAT
1 TTTAATTTTCGCAA-CCAATAATCAAAAGGAACTAATCCTTTGAT
* * *
27187 TTTACTTTTGGCAACATAATAATCAAAAG
1 TTTAATTTTCGCAAC-CAATAATCAAAAG
27216 CCTTGGATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
44 2 0.03
45 61 0.94
46 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.35
Consensus pattern (44 bp):
TTTAATTTTCGCAACCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:29768 original size:19 final size:19
Alignment explanation
Indices: 29744--29782 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29734 AATTATGTGA
29744 ATCTTCTCTAAGTGAAGTT
1 ATCTTCTCTAAGTGAAGTT
*
29763 ATCTTCTTTAAGTGAAGTT
1 ATCTTCTCTAAGTGAAGTT
29782 A
1 A
29783 ACTCAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (19 bp):
ATCTTCTCTAAGTGAAGTT
Found at i:41147 original size:211 final size:208
Alignment explanation
Indices: 40768--41184 Score: 750
Period size: 211 Copynumber: 2.0 Consensus size: 208
40758 GAACTCAACT
40768 TGGATAATGATGCATACTGCCTTAAGGCAAAGGGAAACATTGCAAATTTCACGATTTTTTCGAGA
1 TGGATAATGATGCATACTGCCTTAAGGCAAAGGGAAACATTGCAAATTTCACGATTTTTTCGAGA
*
40833 GGGGTCATGTCCCAAACATTTATCGGATTCGAGTTGGGAAACTATAAGCCAAAAATACCCGATTT
66 GGGGTCATGTCCCAAACATTTATCGGATTCGAGTTGGGAAACTATAAGCCAAAAATAACCGATTT
40898 GCTTGAGGTTTTTAAAAATGCAACAACTTTTTTATCCGGTGTTTATTACCCTACTAGCCCGTTGG
131 GCTTGAGGTTTTTAAAAATGCAACAACTTTTTTATCCGGTGTTTATTACCCTACTAGCCCGTTGG
40963 TTC-TAATCAATA
196 TTCTTAATCAATA
40975 TGGATAATGATGCATACTGCCTTAAGGCAAAGGGAAACATTGCAAACATTTCACGATCGGTTTTT
1 TGGATAATGATGCATACTGCCTTAAGGCAAAGGGAAACATTGC-AA-ATTTCACGAT---TTTTT
41040 CGAGAGGGGTCATGTCCCAAACATTTATCCGGATTCGAGTTGGGAAACTAT-AGCC-AAAATAAC
61 CGAGAGGGGTCATGTCCCAAACATTTAT-CGGATTCGAGTTGGGAAACTATAAGCCAAAAATAAC
41103 CGATTTGCTTGAGGTTTTTAAAAATGCAACAACTTTTTTATCCGGTGTTTATTACCCTACTAGCC
125 CGATTTGCTTGAGGTTTTTAAAAATGCAACAACTTTTTTATCCGGTGTTTATTACCCTACTAGCC
41168 CGTTGGTTCTTAATCAA
190 CGTTGGTTCTTAATCAA
41185 ATATTTTGTT
Statistics
Matches: 202, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
207 43 0.21
208 2 0.01
209 10 0.05
211 81 0.40
212 44 0.22
213 22 0.11
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (208 bp):
TGGATAATGATGCATACTGCCTTAAGGCAAAGGGAAACATTGCAAATTTCACGATTTTTTCGAGA
GGGGTCATGTCCCAAACATTTATCGGATTCGAGTTGGGAAACTATAAGCCAAAAATAACCGATTT
GCTTGAGGTTTTTAAAAATGCAACAACTTTTTTATCCGGTGTTTATTACCCTACTAGCCCGTTGG
TTCTTAATCAATA
Found at i:42024 original size:21 final size:21
Alignment explanation
Indices: 42000--42041 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41990 AGTTTATTTT
*
42000 TAAACTTTATTTTAATTATCG
1 TAAACTTTATTTCAATTATCG
*
42021 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
42042 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:42078 original size:32 final size:33
Alignment explanation
Indices: 42030--42137 Score: 152
Period size: 32 Copynumber: 3.4 Consensus size: 33
42020 GTAAACTTTG
42030 TTTCAA-TTATCGAACTT-GAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* *
42061 TTTGAATTTATCAAACTTGGAAG-TTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* *
42093 TTTTAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
42126 TTTCAA-TTATCG
1 TTTCAATTTATCG
42138 TAAACTTTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.07
32 46 0.68
33 17 0.25
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
Found at i:42218 original size:17 final size:18
Alignment explanation
Indices: 42198--42231 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42188 GTTTTTTTAT
42198 AACCGG-ATTTTTAAAAA
1 AACCGGTATTTTTAAAAA
*
42215 AACCGGTTTTTTTAAAA
1 AACCGGTATTTTTAAAA
42232 CCGAAGCCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
AACCGGTATTTTTAAAAA
Found at i:42231 original size:15 final size:15
Alignment explanation
Indices: 42179--42234 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
42169 TTTAATAATA
*
42179 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
42194 TTATAACCGGATTTTT
1 TTAAAACCGG-TTTTT
**
42210 AAAAAAACCGGTTTTT
1 -TTAAAACCGGTTTTT
42226 TTAAAACCG
1 TTAAAACCG
42235 AAGCCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 15 0.47
16 10 0.31
17 7 0.22
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:43998 original size:14 final size:14
Alignment explanation
Indices: 43979--44005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43969 TTATTCCGTC
43979 AAAATTTGAATTTT
1 AAAATTTGAATTTT
43993 AAAATTTGAATTT
1 AAAATTTGAATTT
44006 ATTTATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AAAATTTGAATTTT
Found at i:44501 original size:35 final size:35
Alignment explanation
Indices: 44462--44571 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
44452 AAAACAATCC
*
44462 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* *
44497 TCAATTTCACTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
** *
44532 TCAATTAAATTCT-AA-CCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
44565 TCAATTT
1 TCAATTT
44572 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
33 22 0.33
34 2 0.03
35 42 0.64
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:46665 original size:35 final size:35
Alignment explanation
Indices: 46614--46719 Score: 140
Period size: 35 Copynumber: 3.0 Consensus size: 35
46604 ATTCTAAACC
* * *
46614 TTAAGTTGAAGTATTTTAGAAATTGGGGTTTAGAAT
1 TTAA-TTGAATTATTTTGGAATTTGGGGTTTAGAAT
*
46650 TTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 TTAATTGAATTATTTTGGAATTTGGGGTTTAGAAT
** *
46685 GAAATTGAATTACTTTGGAATTTGGGGTTTAGAAT
1 TTAATTGAATTATTTTGGAATTTGGGGTTTAGAAT
46720 GAAATTAAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
35 58 0.94
36 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (35 bp):
TTAATTGAATTATTTTGGAATTTGGGGTTTAGAAT
Found at i:46720 original size:35 final size:35
Alignment explanation
Indices: 46636--46725 Score: 144
Period size: 35 Copynumber: 2.6 Consensus size: 35
46626 ATTTTAGAAA
** *
46636 TTGGGGTTTAGAATTTAATTGAATTATTTTGGAAT
1 TTGGGGTTTAGAATGAAATTGAATTACTTTGGAAT
*
46671 TTAGGGTTTAGAATGAAATTGAATTACTTTGGAAT
1 TTGGGGTTTAGAATGAAATTGAATTACTTTGGAAT
46706 TTGGGGTTTAGAATGAAATT
1 TTGGGGTTTAGAATGAAATT
46726 AAGGACTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.43
Consensus pattern (35 bp):
TTGGGGTTTAGAATGAAATTGAATTACTTTGGAAT
Found at i:51219 original size:16 final size:16
Alignment explanation
Indices: 51194--51236 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
51184 TAGTTAGTAA
*
51194 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
*
51210 TTAGCTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
51226 TTAGCGGTTAG
1 TTAGCGGTTAG
51237 CGGTTAGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:51372 original size:119 final size:121
Alignment explanation
Indices: 51232--51464 Score: 314
Period size: 119 Copynumber: 1.9 Consensus size: 121
51222 AAAGTTAGCG
*
51232 GTTAGCGGTTAGCATAGTCCGAACCATAATAAAGTGGATCATACCACAG-ATCTAG-TCACCACA
1 GTTAGCGGTTAGCATAGTCCGAACCATAATAAAGTGGATCATACC-CAGTATC-AGATAACCACA
51295 AGGTCAAATAGAATAATTCAAACAAAT-TA-ACAAAATAAAAT-AAATAAAACAAAAAA
64 AGGTCAAATAGAATAATTCAAACAAATATATA-AAAATAAAATAAAATAAAACAAAAAA
* * * * *
51351 GTTAGTGGTTAGCATGGTCCGAACCATAATAATGTGGATCATACCCCGTATCGGATAACCACAAG
1 GTTAGCGGTTAGCATAGTCCGAACCATAATAAAGTGGATCATACCCAGTATCAGATAACCACAAG
** * *
51416 GTTGAATATAATTATTCAAACAAATATATAAAAATAAAATAAAATAAAA
66 GTCAAATAGAATAATTCAAACAAATATATAAAAATAAAATAAAATAAAA
51465 TAAATAAAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
118 3 0.03
119 75 0.76
120 12 0.12
121 9 0.09
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (121 bp):
GTTAGCGGTTAGCATAGTCCGAACCATAATAAAGTGGATCATACCCAGTATCAGATAACCACAAG
GTCAAATAGAATAATTCAAACAAATATATAAAAATAAAATAAAATAAAACAAAAAA
Found at i:51456 original size:5 final size:5
Alignment explanation
Indices: 51446--51478 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
51436 CAAATATATA
51446 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
51479 AAGGTTAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:51471 original size:9 final size:9
Alignment explanation
Indices: 51447--51477 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
51437 AAATATATAA
51447 AAATAAAAT
1 AAATAAAAT
51456 AAAATAAAAT
1 -AAATAAAAT
51466 AAATAAAAT
1 AAATAAAAT
51475 AAA
1 AAA
51478 AAAGGTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:51471 original size:14 final size:15
Alignment explanation
Indices: 51446--51478 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
51436 CAAATATATA
51446 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
51461 AAAAT-AAATAAAAT
1 AAAATAAAATAAAAT
51475 AAAA
1 AAAA
51479 AAGGTTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:51612 original size:131 final size:128
Alignment explanation
Indices: 51326--51584 Score: 326
Period size: 131 Copynumber: 2.0 Consensus size: 128
51316 ACAAATTAAC
* *
51326 AAAATAAAATAAATAAAACAAAAAAGTTAGTGGTTAGCATGGTCCGAACCATAATAATGTGGATC
1 AAAATAAAATAAAT-AAA-ATAAAAGTTAGTGGTTAGCATGGTCCGAACCATAATAATGCGGATC
* * *
51391 ATACCCCGTATCGGATAACCACAAGGTTGAATATAATTATTCAAACAAATATATAAAAATAAAAT
64 ATACCCCGTATCGGATAACCACAAGGTCGAATAGAATTATTCAAACAAATAAATAAAAATAAAAT
*
51456 AAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCA-GAGTCTGAACCATAATAATGCGGA
1 AAAATAAAATAAATAAAAT--AAAA-GTTAGTGGTTAGCATG-GTCCGAACCATAATAATGCGGA
* * * *
51520 TCATACCCCGTATCGGGTCACCACAAGGTCGAATCGAA-TATTAGAAAC-AATAAATACATAAAT
62 TCATACCCCGTATCGGATAACCACAAGGTCGAATAGAATTATT-CAAACAAATAAATA-A-AAAT
51583 AA
124 AA
51585 CAATGGTTAG
Statistics
Matches: 112, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
128 1 0.01
129 3 0.03
130 30 0.27
131 72 0.64
132 6 0.05
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (128 bp):
AAAATAAAATAAATAAAATAAAAGTTAGTGGTTAGCATGGTCCGAACCATAATAATGCGGATCAT
ACCCCGTATCGGATAACCACAAGGTCGAATAGAATTATTCAAACAAATAAATAAAAATAAAAT
Found at i:51622 original size:29 final size:29
Alignment explanation
Indices: 51597--51652 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
51587 ATGGTTAGAG
51597 TGCAATAAAATAAAAGTTAGTAGTTAATA
1 TGCAATAAAATAAAAGTTAGTAGTTAATA
51626 TGCAATAAAATAAAAGTTAGTAGTTAA
1 TGCAATAAAATAAAAGTTAGTAGTTAA
51653 CTTAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (29 bp):
TGCAATAAAATAAAAGTTAGTAGTTAATA
Found at i:51661 original size:29 final size:29
Alignment explanation
Indices: 51600--51663 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
51590 GTTAGAGTGC
**
51600 AATAAAATAAAAGTTAGTAGTTAATATGC
1 AATAAAATAAAAGTTAGTAGTTAATATAA
51629 AATAAAATAAAAGTTAGTAGTTAACT-TAA
1 AATAAAATAAAAGTTAGTAGTTAA-TATAA
51658 AATAAA
1 AATAAA
51664 TAACATAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (29 bp):
AATAAAATAAAAGTTAGTAGTTAATATAA
Found at i:53276 original size:277 final size:278
Alignment explanation
Indices: 52756--53356 Score: 774
Period size: 277 Copynumber: 2.2 Consensus size: 278
52746 ATATTTGAAT
* * *
52756 ATAATTTGAAGACAACACGATTCCTTCGTGATGAGGAAGTCTGATTGCCTGAAGATGATGTTGCT
1 ATAATTTGAAGACAACACGATTCCTACGTGATGAGAAAGTCTGATTACCTGAAGATGATGTTGCT
* * * * ** *
52821 CATTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAATCA
66 CATACATATTGAGGAGATCTAGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAACCA
* * *
52886 TCTTTATGGATAATTTGGAGACAACAAGATTCCTACGTGATGAGGAAGTCTGGTTATTTGAGGAT
131 TCTTTAGGGATAATTTGGAGACAACAAGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGAT
*
52951 GACGCTGCTCCTACGCATTAAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGAC
196 GACGCTGCTCCTACGCATTAAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGAC
* **
53016 TTCTAGCTGTCTTT-AGAG
261 GTCTAGCCATCTTTAAG-G
* * * * * *
53034 ATACTTTGAAGACAACA-GGTTCCTACGTGATGAGAAAGTCTGGTTATCTGAGGATGGTGTTGCT
1 ATAATTTGAAGACAACACGATTCCTACGTGATGAGAAAGTCTGATTACCTGAAGATGATGTTGCT
* * * * * *
53098 CCTACATATTGTGGAGATCTAGTTGGTGGACAACATTGTTCCTACGTGATGAGGATGTCTAGCCG
66 CATACATATTGAGGAGATCTAGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAACCA
* * * *
53163 TCTTTAGGGATAATTTGGAGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCTAAGGAT
131 TCTTTAGGGATAATTTGGAGACAACAAGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGAT
* * * * * * * ** *
53228 GGCGTTGTTCCTACGCGTTTAGGAGATTTGATTGGTGGATGACATTGTTTCTACGTGATGAGGAC
196 GACGCTGCTCCTACGCATTAAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGAC
53293 GTCTAGCCATCTTTAAGG
261 GTCTAGCCATCTTTAAGG
* *
53311 ATAATTTGGAGACAACACGTTTCCTACGTGATGAGAAAGTCTGATT
1 ATAATTTGAAGACAACACGATTCCTACGTGATGAGAAAGTCTGATT
53357 GTCTAAGGGT
Statistics
Matches: 274, Mismatches: 47, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
277 230 0.84
278 44 0.16
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (278 bp):
ATAATTTGAAGACAACACGATTCCTACGTGATGAGAAAGTCTGATTACCTGAAGATGATGTTGCT
CATACATATTGAGGAGATCTAGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAACCA
TCTTTAGGGATAATTTGGAGACAACAAGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGAT
GACGCTGCTCCTACGCATTAAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGAC
GTCTAGCCATCTTTAAGG
Found at i:53362 original size:139 final size:139
Alignment explanation
Indices: 52756--53402 Score: 674
Period size: 139 Copynumber: 4.7 Consensus size: 139
52746 ATATTTGAAT
* * * ** *
52756 ATAATTTGAAGACAACACGATTCCTTCGTGATGAGGAAGTCTGATTGCCTGAA-GATGATGTTGC
1 ATAATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGGTTATCT-AAGGATGACGTTGC
* * ** * * ** **
52820 TCATTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAATC
65 TCCTACGCATTTAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
*
52885 ATCTTTATGG
130 ATCTTTAAGG
* * * *
52895 ATAATTTGGAGACAACAAGATTCCTACGTGATGAGGAAGTCTGGTTATTTGAGGATGACGCTGCT
1 ATAATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGTTGCT
* * * **
52960 CCTACGCATTAAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACTTCTAGCTG
66 CCTACGCATTTAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCA
53025 TCTTT-AGAG
131 TCTTTAAG-G
* * * * * **
53034 ATACTTTGAAGACAACA-GGTTCCTACGTGATGAGAAAGTCTGGTTATCTGAGGATGGTGTTGCT
1 ATAATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGTTGCT
** * *
53098 CCTACATATTGT-GGAGATCT-AGTTGGTGGACAACATTGTTCCTACGTGATGAGGATGTCTAGC
66 CCTACGCATT-TAGGAGATCTGA-TCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGC
* *
53161 CGTCTTTAGGG
129 CATCTTTAAGG
* * * * *
53172 ATAATTTGGAGATAACACGGTTCCTACGTGATGAGGACGTCTGGTTATCTAAGGATGGCGTTGTT
1 ATAATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGTTGCT
* * * ** *
53237 CCTACGCGTTTAGGAGATTTGATTGGTGGATGACATTGTTTCTACGTGATGAGGACGTCTAGCCA
66 CCTACGCATTTAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCA
53302 TCTTTAAGG
131 TCTTTAAGG
* * * * * ** *
53311 ATAATTTGGAGACAACACGTTTCCTACGTGATGAGAAAGTCTGATTGTCTAAGGGTGACACTACT
1 ATAATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGTTGCT
* * *
53376 CCTTCGCGTTTAGGATATCTGATCGGT
66 CCTACGCATTTAGGAGATCTGATCGGT
53403 TTCCAATGAT
Statistics
Matches: 426, Mismatches: 74, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
138 119 0.28
139 306 0.72
140 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (139 bp):
ATAATTTGGAGACAACACGATTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGTTGCT
CCTACGCATTTAGGAGATCTGATCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCA
TCTTTAAGG
Found at i:54087 original size:154 final size:153
Alignment explanation
Indices: 53747--54107 Score: 383
Period size: 154 Copynumber: 2.3 Consensus size: 153
53737 TTGTGTCTTA
* * * * * * *
53747 AGGAAGACTGTCTCAATTGAGACAAAATTTGTTTGGTGAAAAAAAATCTCAAAATGTTTATGTTT
1 AGGAAAACAGTCTCAAGTGAGACGAAATTTGTTTCGAGAAAAAAAATATCAAAA-GTTTATGTTT
** *
53812 CAAGAGAAAATGTCTCAAGCAATACGAAATTTTATTTGGGAAAATAATCTCAAATGAGATCAATT
65 CAAGAGAAAATGTCTCAAGCAATAC-AAATTTTATTTGAAAAAACAATCTCAAATGAGATCAATT
*
53877 TTGTTTCAAAAATTTCAAAATTTGT
129 TTGTTTAAAAAATTTCAAAATTTGT
* * * ** *
53902 A-GAAAGCTA-TCTCAAGAGAAACGAAGCTTGTTTCGAGAGAAAAAATATCAATAA-TTTATGTT
1 AGGAAAAC-AGTCTCAAGTGAGACGAAATTTGTTTCGAGAAAAAAAATATCAA-AAGTTTATGTT
* * *
53964 TCAAGAGAAATTGTCTCAAGCGAGATA-AACTTTGT-TTTGAAAGAAACAATCTCAAGTGAGATC
64 TCAAGAGAAAATGTCTCAAGC-A-ATACAAATTT-TATTTGAAA-AAACAATCTCAAATGAGATC
54027 AATTTTGTTTAAAAAATTTCAAAATTTG-
125 AATTTTGTTTAAAAAATTTCAAAATTTGT
* ** * *
54055 AGGAAAACAGTCTCAAGTGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAA
1 AGGAAAACAGTCTCAAGTGAGACGAAATTTGTTTCGAGAAAAAAAATATCAAA
54108 GGCTTATAGA
Statistics
Matches: 167, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
153 41 0.25
154 120 0.72
155 6 0.04
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (153 bp):
AGGAAAACAGTCTCAAGTGAGACGAAATTTGTTTCGAGAAAAAAAATATCAAAAGTTTATGTTTC
AAGAGAAAATGTCTCAAGCAATACAAATTTTATTTGAAAAAACAATCTCAAATGAGATCAATTTT
GTTTAAAAAATTTCAAAATTTGT
Found at i:55807 original size:25 final size:26
Alignment explanation
Indices: 55779--55839 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
55769 ATTTTCAAAA
**
55779 TTTTGAAAAAT-ATCAATTAAATTTT
1 TTTTGAAAAATGATCAATTAAAAATT
* *
55804 TTTTGAAAAATGTTTAATTAAAAATT
1 TTTTGAAAAATGATCAATTAAAAATT
55830 TTTTGAAAAA
1 TTTTGAAAAA
55840 ATATTACCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (26 bp):
TTTTGAAAAATGATCAATTAAAAATT
Found at i:56745 original size:11 final size:11
Alignment explanation
Indices: 56731--56777 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
56721 CTCTTTCTTC
56731 TTTTGTCTTTG
1 TTTTGTCTTTG
*
56742 TTTTGTCTTTT
1 TTTTGTCTTTG
*
56753 TTTTTTGCTTT-
1 TTTTGT-CTTTG
56764 TTTTG-CTTTG
1 TTTTGTCTTTG
56774 TTTT
1 TTTT
56778 TTTTCATTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 4 0.13
10 4 0.13
11 19 0.61
12 4 0.13
ACGTcount: A:0.00, C:0.09, G:0.13, T:0.79
Consensus pattern (11 bp):
TTTTGTCTTTG
Found at i:56790 original size:22 final size:21
Alignment explanation
Indices: 56743--56797 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
56733 TTGTCTTTGT
* *
56743 TTTGTCTTTTTTTTTTGCTTTT
1 TTTG-CTTTTTTTTTTGCATTC
*
56765 TTTGCTTTGTTTTTTTTCATTC
1 TTTGCTTT-TTTTTTTGCATTC
56787 TTTG-TTTTTTT
1 TTTGCTTTTTTT
56798 CTCTTTGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.14
21 7 0.24
22 18 0.62
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (21 bp):
TTTGCTTTTTTTTTTGCATTC
Found at i:56802 original size:14 final size:14
Alignment explanation
Indices: 56749--56808 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
56739 TTGTTTTGTC
56749 TTTTTTT-TTTGCT
1 TTTTTTTCTTTGCT
* *
56762 TTTTTTGCTTTGTTT
1 TTTTTTTCTTTG-CT
56777 TTTTTCATTCTTTG-T
1 TTTTT--TTCTTTGCT
56792 TTTTTTCTCTTTGCT
1 TTTTTT-TCTTTGCT
56807 TT
1 TT
56809 GATTTGATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 7 0.18
14 10 0.26
15 15 0.39
17 6 0.16
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTTGCT
Found at i:60625 original size:15 final size:17
Alignment explanation
Indices: 60590--60626 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
60580 TTAAAGAAAA
60590 TAAATGTGCATAAATTT
1 TAAATGTGCATAAATTT
60607 TAAA-GTGCATAAA-TT
1 TAAATGTGCATAAATTT
60622 TAAAT
1 TAAAT
60627 AACAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 9 0.47
17 4 0.21
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (17 bp):
TAAATGTGCATAAATTT
Found at i:60713 original size:16 final size:16
Alignment explanation
Indices: 60672--60734 Score: 76
Period size: 16 Copynumber: 4.1 Consensus size: 16
60662 TAGTTTGTAA
*
60672 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
**
60688 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
60704 TTAGCGGTT--AAAAG
1 TTAGCGGTTAGAAAAG
*
60718 TTAGCGGTTAGCAAAG
1 TTAGCGGTTAGAAAAG
60734 T
1 T
60735 CTGAACCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 14 0.36
16 25 0.64
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:60718 original size:14 final size:14
Alignment explanation
Indices: 60699--60727 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60689 TAGTTGTTAG
60699 AAAAGTTAGCGGTT
1 AAAAGTTAGCGGTT
60713 AAAAGTTAGCGGTT
1 AAAAGTTAGCGGTT
60727 A
1 A
60728 GCAAAGTCTG
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:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (14 bp):
AAAAGTTAGCGGTT
Found at i:60728 original size:30 final size:32
Alignment explanation
Indices: 60672--60734 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
60662 TAGTTTGTAA
**
60672 TTAGCGGTTAGAAAGGTTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAGGTTAGCGGTTAGAAAAG
*
60704 TTAGCGGTTA-AAA-GTTAGCGGTTAGCAAAG
1 TTAGCGGTTAGAAAGGTTAGCGGTTAGAAAAG
60734 T
1 T
60735 CTGAACCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 3 0.11
32 10 0.36
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (32 bp):
TTAGCGGTTAGAAAGGTTAGCGGTTAGAAAAG
Found at i:60936 original size:120 final size:121
Alignment explanation
Indices: 60713--60948 Score: 298
Period size: 120 Copynumber: 2.0 Consensus size: 121
60703 GTTAGCGGTT
* * * * *
60713 AAAAGTTAGCGGTTAGCAAAGTCTGAACCATAATAATATGGATCATACCCCGAATCTGGTCACCA
1 AAAAATTAGCGGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCACGAATCGGGTCAACA
60778 CAAGGTCGAATCGAATAATTCAAACAAATTAACAAAATAAAAT-AAATAAAACAAA
66 CAAGGTCGAATCGAATAATTCAAACAAATTAACAAAATAAAATAAAATAAAACAAA
* ** * * * * * *
60833 AAAAATTAGTGGTTAGCATGGTCCGAACCTTAATAATGTGGATTATACCATGGATCGGGTTAACA
1 AAAAATTAGCGGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCACGAATCGGGTCAACA
*
60898 CAAGGTCGAATCGAATAATTCAAA-TAATATATA-AAAATAAAATAAAATAAA
66 CAAGGTCGAATCGAATAATTCAAACAAAT-TA-ACAAAATAAAATAAAATAAA
60949 TAAAATAAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
119 3 0.03
120 87 0.89
121 8 0.08
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (121 bp):
AAAAATTAGCGGTTAGCAAAGTCCGAACCATAATAATATGGATCATACCACGAATCGGGTCAACA
CAAGGTCGAATCGAATAATTCAAACAAATTAACAAAATAAAATAAAATAAAACAAA
Found at i:60941 original size:5 final size:5
Alignment explanation
Indices: 60931--60971 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
60921 ATAATATATA
60931 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT --AAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
60972 AAGGTTAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 4 0.12
5 26 0.79
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:60949 original size:27 final size:27
Alignment explanation
Indices: 60919--60971 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
60909 CGAATAATTC
*
60919 AAATAATATATAAA-AATAAAATAAAAT
1 AAATAAAATA-AAATAATAAAATAAAAT
60946 AAATAAAATAAAATAATAAAATAAAA
1 AAATAAAATAAAATAATAAAATAAAA
60972 AAGGTTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (27 bp):
AAATAAAATAAAATAATAAAATAAAAT
Found at i:60955 original size:19 final size:18
Alignment explanation
Indices: 60931--60971 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
60921 ATAATATATA
60931 AAAATAAAATAAAATAAAT
1 AAAATAAAATAAAA-AAAT
*
60950 AAAATAAAATAATAAAAT
1 AAAATAAAATAAAAAAAT
60968 AAAA
1 AAAA
60972 AAGGTTAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAATAAAAAAAT
Found at i:60965 original size:13 final size:13
Alignment explanation
Indices: 60920--60971 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
60910 GAATAATTCA
*
60920 AATAATATATAAA-
1 AATAAAATA-AAAT
60933 AATAAAATAAAAT
1 AATAAAATAAAAT
60946 AAATAAAATAAAAT
1 -AATAAAATAAAAT
60960 AATAAAATAAAA
1 AATAAAATAAAA
60972 AAGGTTAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 3 0.08
13 20 0.56
14 13 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:61119 original size:29 final size:29
Alignment explanation
Indices: 61094--61149 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
61084 ATGGTTAGAG
61094 TGCAATAAAATAAAAGTTAGTAGTTAATA
1 TGCAATAAAATAAAAGTTAGTAGTTAATA
61123 TGCAATAAAATAAAAGTTAGTAGTTAA
1 TGCAATAAAATAAAAGTTAGTAGTTAA
61150 CTTGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (29 bp):
TGCAATAAAATAAAAGTTAGTAGTTAATA
Found at i:61158 original size:29 final size:29
Alignment explanation
Indices: 61097--61160 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
61087 GTTAGAGTGC
*
61097 AATAAAATAAAAGTTAGTAGTTAATATGC
1 AATAAAATAAAAGTTAGTAGTTAATATGA
61126 AATAAAATAAAAGTTAGTAGTTAACT-TGA
1 AATAAAATAAAAGTTAGTAGTTAA-TATGA
61155 AATAAA
1 AATAAA
61161 TAACATAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (29 bp):
AATAAAATAAAAGTTAGTAGTTAATATGA
Done.