Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007090.1 Hibiscus syriacus cultivar Beakdansim tig00018511_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: 76970
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1041 original size:12 final size:12
Alignment explanation
Indices: 1024--1053 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1014 TCCCTTGAAA
1024 CACTCTTAGTAG
1 CACTCTTAGTAG
1036 CACTCTTAGTAG
1 CACTCTTAGTAG
1048 CACTCT
1 CACTCT
1054 GTTCAAACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33
Consensus pattern (12 bp):
CACTCTTAGTAG
Found at i:6393 original size:53 final size:50
Alignment explanation
Indices: 6311--6410 Score: 119
Period size: 53 Copynumber: 1.9 Consensus size: 50
6301 ATTGTCCTTA
* * * * *
6311 TTATATATTTTTTTTTAACAAGTTGAATTCTATTATAATATTATATAATTAAT
1 TTATATATTTTCTTTAAAAAAGTTAAATTC-A-TAAAAT-TTATATAATTAAT
*
6364 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATAATT
1 TTATATATTTTCTTTAAAAAAGTTAAATTCATAAAATTTATATAATT
6411 TTTTACAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 10 0.24
51 5 0.12
52 1 0.02
53 25 0.61
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (50 bp):
TTATATATTTTCTTTAAAAAAGTTAAATTCATAAAATTTATATAATTAAT
Found at i:16050 original size:31 final size:31
Alignment explanation
Indices: 15956--16050 Score: 163
Period size: 31 Copynumber: 3.1 Consensus size: 31
15946 GGGTCGAGGG
*
15956 TTACCTATGTTCTTCGGGACATATGGACTAT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
15987 TTACCTATGTTCTTCGGGACATATGAACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
16018 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
16049 TT
1 TT
16051 CTTCGGGACA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:16096 original size:53 final size:52
Alignment explanation
Indices: 15994--16114 Score: 145
Period size: 53 Copynumber: 2.3 Consensus size: 52
15984 TATTTACCTA
** * * *
15994 TGTTCTTCGGGACATATGAACTGTTTACCTATGTTCTTCGGGACATATGGAT
1 TGTTCTTCGGGACATATGAACCATTTACCTAGGTTCTTCGGAACATATGGAC
*
16046 TGTTTCTTCGGGACATATGGACCATTTACCTAGGTTCTTCGGAATC-TATGGAC
1 TG-TTCTTCGGGACATATGAACCATTTACCTAGGTTCTTCGGAA-CATATGGAC
*
16099 TGATCATTCGGGACAT
1 TGTTC-TTCGGGACAT
16115 TTATACGAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
52 4 0.07
53 54 0.92
54 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (52 bp):
TGTTCTTCGGGACATATGAACCATTTACCTAGGTTCTTCGGAACATATGGAC
Found at i:16849 original size:22 final size:22
Alignment explanation
Indices: 16824--16868 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16814 GGTACACTGT
*
16824 AGCACTGTTCATGGTATTGTTC
1 AGCACTGATCATGGTATTGTTC
16846 AGCACTGATCATGGTATTGTTC
1 AGCACTGATCATGGTATTGTTC
16868 A
1 A
16869 TACCGTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (22 bp):
AGCACTGATCATGGTATTGTTC
Found at i:19501 original size:2 final size:2
Alignment explanation
Indices: 19494--19518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19484 TTTAACCTTT
19494 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19519 TGGGAGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20400 original size:21 final size:21
Alignment explanation
Indices: 20374--20413 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
20364 ATATAAATAC
20374 CATCGATTATAACAAAATAAT
1 CATCGATTATAACAAAATAAT
20395 CATCGATTATAACAAAATA
1 CATCGATTATAACAAAATA
20414 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (21 bp):
CATCGATTATAACAAAATAAT
Found at i:25620 original size:59 final size:59
Alignment explanation
Indices: 25536--25648 Score: 190
Period size: 59 Copynumber: 1.9 Consensus size: 59
25526 GATAAGTATA
* * *
25536 CTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTCTAAGTGTC
1 CTATCGAACCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGACTCTAAGTGTC
*
25595 CTATCGAATCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGACTCTAA
1 CTATCGAACCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGACTCTAA
25649 CCAACCCTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (59 bp):
CTATCGAACCCTCCTAGTCACAATGAAAAGACAAACTCGATAATATGACTCTAAGTGTC
Found at i:29973 original size:150 final size:154
Alignment explanation
Indices: 29624--29979 Score: 418
Period size: 150 Copynumber: 2.3 Consensus size: 154
29614 CTATTGTGTA
*
29624 TATGAGCATGTGGTTCAAATTT-AGTAAAAGAAAGACTTAAAATAAAGGATGAATTGAAGAAATA
1 TATGAGCATGTGGTTCAAATTTGA-TAAAAGAAAGACTTAAAATAAAGGACGAATTGAAGAAATA
* * * * * *
29688 AGGAAAATATAAAAGATCAAGGGACTAGATTGAAAAATAAAAAATTTGTTATCAAAAGGAGGAAT
65 AAGAAAATAGAAAAAATCAAGGGACTAAATT---AAATAAAAAA-TTGTTATAAAAAAGAGGAAT
* * ** * *
29753 TGAAAGTACATGTGCATTTTATGATGGTT
126 TGAAAGTAAATATGCATTCCAAGATGATT
** *
29782 TATGAGCATGTGGTTCAAATTTGATAAAAGATGGACCTAAAATAAAGGACGAATTGAAGAAATAA
1 TATGAGCATGTGGTTCAAATTTGATAAAAGAAAGACTTAAAATAAAGGACGAATTGAAGAAATAA
* *
29847 AGAAAATAGGAAAAAAT-AA-GGACTAAATT-AA-AAAAAA-TGTTATAAAAAAGATGAGTTGAA
66 AGAAAATA-GAAAAAATCAAGGGACTAAATTAAATAAAAAATTGTTATAAAAAAGAGGAATTGAA
*
29907 AGTAAATATGTATTCCAAGATGATT
130 AGTAAATATGCATTCCAAGATGATT
* *
29932 TATGAGCATGTAGTTCAAATTTGATAAAAAAAAGACTTAAAATGAAAG
1 TATGAGCATGTGGTTCAAATTTGATAAAAGAAAGACTTAAAAT-AAAG
29980 AAAAATTGAA
Statistics
Matches: 171, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
150 75 0.44
151 4 0.02
152 6 0.04
153 2 0.01
157 9 0.05
158 68 0.40
159 7 0.04
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (154 bp):
TATGAGCATGTGGTTCAAATTTGATAAAAGAAAGACTTAAAATAAAGGACGAATTGAAGAAATAA
AGAAAATAGAAAAAATCAAGGGACTAAATTAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAA
GTAAATATGCATTCCAAGATGATT
Found at i:31091 original size:36 final size:37
Alignment explanation
Indices: 31042--31163 Score: 103
Period size: 36 Copynumber: 3.4 Consensus size: 37
31032 AATCTAGAGA
*
31042 CAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAAT
1 CAAAAGAAATTAAATGTCTAAAGTTCAATGAGTAAAT
* * ** *
31079 CAAAA-AAATTAAAAGTACGATGAA-TGAAAT-AG-AGA-
1 CAAAAGAAATTAAATGT-C--TAAAGTTCAATGAGTAAAT
*
31114 CAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAAT
1 CAAAAGAAATTAAATGTCTAAAGTTCAATGAGTAAAT
*
31151 CGAAA-AAATTAAA
1 CAAAAGAAATTAAA
31164 AGTACGATGA
Statistics
Matches: 63, Mismatches: 14, Indels: 17
0.67 0.15 0.18
Matches are distributed among these distances:
33 3 0.05
34 4 0.06
35 8 0.13
36 29 0.46
37 12 0.19
38 4 0.06
39 3 0.05
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (37 bp):
CAAAAGAAATTAAATGTCTAAAGTTCAATGAGTAAAT
Found at i:31157 original size:72 final size:72
Alignment explanation
Indices: 31036--31182 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
31026 GTAAATAATC
31036 TAGAGACAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAATCAAAAAAATTAAAAGTACGATG
1 TAGAGACAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAATCAAAAAAATTAAAAGTACGATG
31101 AATGAAA
66 AATGAAA
*
31108 TAGAGACAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAATCGAAAAAATTAAAAGTACGATG
1 TAGAGACAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAATCAAAAAAATTAAAAGTACGATG
31173 AATGAAA
66 AATGAAA
31180 TAG
1 TAG
31183 GAGAGTAAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (72 bp):
TAGAGACAAAAGAAGTTAAATGTCTAAAGTTCAATGAGTAAATCAAAAAAATTAAAAGTACGATG
AATGAAA
Found at i:36673 original size:19 final size:19
Alignment explanation
Indices: 36651--36688 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
36641 TCTAAAATTA
36651 CAAATGTTGTCCATTTAGG
1 CAAATGTTGTCCATTTAGG
36670 CAAATGTTGTCCATTTAGG
1 CAAATGTTGTCCATTTAGG
36689 TGTCTGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (19 bp):
CAAATGTTGTCCATTTAGG
Found at i:40450 original size:19 final size:18
Alignment explanation
Indices: 40415--40450 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40405 AAAGTTGATT
*
40415 CTTCAAATTTTGGGGACG
1 CTTCAAATTTGGGGGACG
40433 CTTCAAATTCTGGGGGAC
1 CTTCAAATT-TGGGGGAC
40451 ATCGCGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (18 bp):
CTTCAAATTTGGGGGACG
Found at i:41521 original size:21 final size:21
Alignment explanation
Indices: 41497--41559 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
41487 TTATTAATGC
41497 ATGCATGTATGTATAATATGT
1 ATGCATGTATGTATAATATGT
*
41518 ATGCATATATGTATAAT-T-T
1 ATGCATGTATGTATAATATGT
** * *
41537 ATTAATGCATGTATGATATGT
1 ATGCATGTATGTATAATATGT
41558 AT
1 AT
41560 ATTAATGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.38
20 2 0.06
21 19 0.56
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (21 bp):
ATGCATGTATGTATAATATGT
Found at i:41562 original size:23 final size:23
Alignment explanation
Indices: 41488--41566 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
41478 ATATATAATT
*
41488 TATTAATGCATGCATG-TATGTA
1 TATTAATGCATGTATGATATGTA
* *
41510 TAATATGTATGCATATATGTATAAT-T-
1 T-AT-T-AATGCATGTATG-AT-ATGTA
41536 TATTAATGCATGTATGATATGTA
1 TATTAATGCATGTATGATATGTA
41559 TATTAATG
1 TATTAATG
41567 TAATATGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 2 0.05
22 4 0.09
23 20 0.45
24 2 0.05
25 11 0.25
26 1 0.02
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (23 bp):
TATTAATGCATGTATGATATGTA
Found at i:41634 original size:40 final size:40
Alignment explanation
Indices: 41585--41662 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
41575 ATAGTATTTC
*
41585 TATAAACTATAT-AAGTAATTTACTTTATATAGTTTATATA
1 TATAAACTATATAAAGTAAATTAC-TTATATAGTTTATATA
*
41625 TATATACTATATAAAGTAAATTACTTATATAGTTTATA
1 TATAAACTATATAAAGTAAATTACTTATATAGTTTATA
41663 GAATACTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 25 0.71
41 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (40 bp):
TATAAACTATATAAAGTAAATTACTTATATAGTTTATATA
Found at i:41735 original size:21 final size:21
Alignment explanation
Indices: 41709--41779 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
41699 TAGTTTATAG
41709 AAACCCTAAATCATAAACCAT
1 AAACCCTAAATCATAAACCAT
* * *
41730 ACACCCTAACT-TTAAACCAT
1 AAACCCTAAATCATAAACCAT
*
41750 AAACACTAAA-CACTAAACCAT
1 AAACCCTAAATCA-TAAACCAT
41771 AAACCCTAA
1 AAACCCTAA
41780 TATAAATGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 15 0.38
21 25 0.62
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAATCATAAACCAT
Found at i:41926 original size:13 final size:13
Alignment explanation
Indices: 41894--41920 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41884 TAATTTACAT
41894 TTAAATAATTTTA
1 TTAAATAATTTTA
41907 TTAAATAATTTTA
1 TTAAATAATTTTA
41920 T
1 T
41921 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:41965 original size:29 final size:27
Alignment explanation
Indices: 41933--41996 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
41923 AATATGTATG
*
41933 TATAAACCATGTATAGTATATATAAACTA
1 TATAAA-CATATATA-TATATATAAACTA
*
41962 TATATATATATATATATATATATAAACTA
1 TATA-A-ACATATATATATATATAAACTA
41991 TATAAA
1 TATAAA
41997 GTACTTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 21 0.68
30 7 0.23
31 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (27 bp):
TATAAACATATATATATATATAAACTA
Found at i:41994 original size:2 final size:2
Alignment explanation
Indices: 41944--41985 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
41934 ATAAACCATG
*
41944 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
41986 AACTATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 33 0.92
3 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:42018 original size:24 final size:24
Alignment explanation
Indices: 41991--42066 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
41981 ATATAAACTA
41991 TATAAAGTACTTACTTATATAGTT
1 TATAAAGTACTTACTTATATAGTT
** * * *
42015 TATAGAAACACTATAC--ATAAACTA
1 TATA-AAGTACT-TACTTATATAGTT
42039 TATAAAGTACTTACTTATATAGTT
1 TATAAAGTACTTACTTATATAGTT
42063 TATA
1 TATA
42067 GAAACACTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 3 0.08
23 5 0.13
24 22 0.58
25 5 0.13
26 3 0.08
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (24 bp):
TATAAAGTACTTACTTATATAGTT
Found at i:42018 original size:26 final size:26
Alignment explanation
Indices: 41989--42066 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
41979 ATATATAAAC
41989 TATATAAAGTACTTACTTATATAGTT
1 TATATAAAGTACTTACTTATATAGTT
* * **
42015 TATAGAAA-CACTATAC--ATA-A-AC
1 TATATAAAGTACT-TACTTATATAGTT
42037 TATATAAAGTACTTACTTATATAGTT
1 TATATAAAGTACTTACTTATATAGTT
42063 TATA
1 TATA
42067 GAAACACTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
22 10 0.26
23 4 0.11
24 6 0.16
25 4 0.11
26 14 0.37
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (26 bp):
TATATAAAGTACTTACTTATATAGTT
Found at i:42037 original size:48 final size:48
Alignment explanation
Indices: 41978--42119 Score: 239
Period size: 48 Copynumber: 3.0 Consensus size: 48
41968 TATATATATA
*
41978 TATATATAAACTATATAAAGTACTTACTTATATAGTTTATAGAAACAC
1 TATACATAAACTATATAAAGTACTTACTTATATAGTTTATAGAAACAC
42026 TATACATAAACTATATAAAGTACTTACTTATATAGTTTATAGAAACAC
1 TATACATAAACTATATAAAGTACTTACTTATATAGTTTATAGAAACAC
* * **
42074 TATACATAAACTATATAAAGTAGTAAAATATATAGTTTATAGAAAC
1 TATACATAAACTATATAAAGTACTTACTTATATAGTTTATAGAAAC
42120 CTTAAATCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 89 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (48 bp):
TATACATAAACTATATAAAGTACTTACTTATATAGTTTATAGAAACAC
Found at i:42040 original size:22 final size:22
Alignment explanation
Indices: 42015--42088 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
42005 TTATATAGTT
42015 TATAGAAACACTATACATAAAC
1 TATAGAAACACTATACATAAAC
* * **
42037 TATATAAAGTACT-TACTTATATAGTT
1 TATAGAAA-CACTATAC--ATA-A-AC
42063 TATAGAAACACTATACATAAAC
1 TATAGAAACACTATACATAAAC
42085 TATA
1 TATA
42089 TAAAGTAGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
22 14 0.37
23 4 0.11
24 6 0.16
25 4 0.11
26 10 0.26
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (22 bp):
TATAGAAACACTATACATAAAC
Found at i:42140 original size:21 final size:20
Alignment explanation
Indices: 42116--42180 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
42106 TAGTTTATAG
42116 AAACCTTAAATCATAAACCCT
1 AAACC-TAAATCATAAACCCT
*
42137 AAACCCTAAA-CTTTAAACCAC-
1 AAA-CCTAAATC-ATAAACC-CT
*
42158 AAACACTAAATCATAAATCCT
1 AAAC-CTAAATCATAAACCCT
42179 AA
1 AA
42181 TATAAATGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
20 3 0.09
21 28 0.80
22 4 0.11
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.22
Consensus pattern (20 bp):
AAACCTAAATCATAAACCCT
Found at i:42540 original size:23 final size:22
Alignment explanation
Indices: 42488--42534 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
42478 TAATTTACAT
*
42488 TTAAATAATTTTATTAATTTTA
1 TTAAATAATTTTATTAATTGTA
42510 TTAAATAATTTTATATAATATGTA
1 TTAAATAATTTTAT-TAAT-TGTA
42534 T
1 T
42535 ATATAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 4 0.18
24 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAAATAATTTTATTAATTGTA
Found at i:42570 original size:20 final size:20
Alignment explanation
Indices: 42521--42574 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
42511 TAAATAATTT
42521 TATATAATATGTATATATAAAC
1 TATAT-ATA-GTATATATAAAC
* *
42543 CATGTATAGTATATATAAAC
1 TATATATAGTATATATAAAC
42563 TATATATA-TATA
1 TATATATAGTATA
42575 AACTATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 3 0.11
22 3 0.11
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (20 bp):
TATATATAGTATATATAAAC
Found at i:42572 original size:15 final size:16
Alignment explanation
Indices: 42547--42581 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
42537 ATAAACCATG
42547 TATAGTATATATAAAC
1 TATAGTATATATAAAC
42563 TATA-TATATATAAAC
1 TATAGTATATATAAAC
42578 TATA
1 TATA
42582 ATAAAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (16 bp):
TATAGTATATATAAAC
Found at i:42687 original size:14 final size:14
Alignment explanation
Indices: 42665--42729 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
42655 ATAGAAACCT
*
42665 TAAATCCTAAATCA
1 TAAACCCTAAATCA
*
42679 TAAACCCTAATTC-
1 TAAACCCTAAATCA
**
42692 TAAACTTTAAA-CTA
1 TAAACCCTAAATC-A
*
42706 TAAACACTAAATCA
1 TAAACCCTAAATCA
42720 TAAACCCTAA
1 TAAACCCTAA
42730 TTTAAATGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 1 0.03
13 8 0.20
14 30 0.75
15 1 0.03
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:42922 original size:23 final size:23
Alignment explanation
Indices: 42892--42935 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42882 TTATTTTTTC
42892 TTTATATAAATTAAACTATATCA
1 TTTATATAAATTAAACTATATCA
*
42915 TTTATATAAATTAAATTATAT
1 TTTATATAAATTAAACTATAT
42936 TAATTTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATCA
Found at i:43232 original size:16 final size:16
Alignment explanation
Indices: 43213--43247 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
43203 TCATTTACAA
43213 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAG
43229 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAG
43245 GTC
1 GTC
43248 GGGTAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.20
Consensus pattern (16 bp):
GTCAGGTTGAAAACAG
Found at i:43828 original size:19 final size:18
Alignment explanation
Indices: 43793--43828 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43783 AAAGTTGATT
*
43793 CTTCAAATTTTGGGGACG
1 CTTCAAATTTAGGGGACG
43811 CTTCAAATTCTAGGGGAC
1 CTTCAAATT-TAGGGGAC
43829 ATCGCGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (18 bp):
CTTCAAATTTAGGGGACG
Found at i:44592 original size:21 final size:21
Alignment explanation
Indices: 44568--44630 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
44558 TTATTAATGC
44568 ATGCATGTATGTATAATATGT
1 ATGCATGTATGTATAATATGT
*
44589 ATGCATATATGTATAAT-T-T
1 ATGCATGTATGTATAATATGT
** * *
44608 ATTAATGCATGTATGATATGT
1 ATGCATGTATGTATAATATGT
44629 AT
1 AT
44631 ATTAATGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.38
20 2 0.06
21 19 0.56
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (21 bp):
ATGCATGTATGTATAATATGT
Found at i:44633 original size:23 final size:23
Alignment explanation
Indices: 44559--44637 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
44549 ATATATAATT
*
44559 TATTAATGCATGCATG-TATGTA
1 TATTAATGCATGTATGATATGTA
* *
44581 TAATATGTATGCATATATGTATAAT-T-
1 T-AT-T-AATGCATGTATG-AT-ATGTA
44607 TATTAATGCATGTATGATATGTA
1 TATTAATGCATGTATGATATGTA
44630 TATTAATG
1 TATTAATG
44638 TAATATGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 2 0.05
22 4 0.09
23 20 0.45
24 2 0.05
25 11 0.25
26 1 0.02
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (23 bp):
TATTAATGCATGTATGATATGTA
Found at i:44705 original size:40 final size:40
Alignment explanation
Indices: 44656--44733 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
44646 ATAGTGTTTC
*
44656 TATAAACTATAT-AAGTAATTTACTTTATATAGTTTATATA
1 TATAAACTATATAAAGTAAATTAC-TTATATAGTTTATATA
*
44696 TATATACTATATAAAGTAAATTACTTATATAGTTTATA
1 TATAAACTATATAAAGTAAATTACTTATATAGTTTATA
44734 GAAATACTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 25 0.71
41 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (40 bp):
TATAAACTATATAAAGTAAATTACTTATATAGTTTATATA
Found at i:44750 original size:40 final size:41
Alignment explanation
Indices: 44656--44743 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 41
44646 ATAGTGTTTC
* * *
44656 TATAAACTATAT-AAGTAATTTACTTTATATAGTTTATATA
1 TATATACTATATAAAGTAAATTACTTTATATAGTTTATAGA
44696 TATATACTATATAAAGTAAATTAC-TTATATAGTTTATAGA
1 TATATACTATATAAAGTAAATTACTTTATATAGTTTATAGA
44736 -A-ATACTAT
1 TATATACTAT
44744 GCATAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 7 0.16
39 1 0.02
40 26 0.59
41 10 0.23
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (41 bp):
TATATACTATATAAAGTAAATTACTTTATATAGTTTATAGA
Found at i:45056 original size:15 final size:15
Alignment explanation
Indices: 45031--45067 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
45021 ATAAACCATG
45031 TATAGTATATATAAAC
1 TATA-TATATATAAAC
45047 TATATATATATAAAC
1 TATATATATATAAAC
45062 TATATA
1 TATATA
45068 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:45144 original size:48 final size:49
Alignment explanation
Indices: 45051--45144 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
45041 ATAAACTATA
* * **
45051 TATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
1 TATACATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACAC
*
45100 TATACATAAACTATATAAAGT-AGTAAAATATATAGTTTATAGAAA
1 TATACATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAA
45145 TCTTAAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 20 0.50
49 20 0.50
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.35
Consensus pattern (49 bp):
TATACATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACAC
Found at i:45172 original size:21 final size:21
Alignment explanation
Indices: 45148--45206 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
45138 ATAGAAATCT
*
45148 TAAATCATAAACCCTAAACCC
1 TAAATCATAAACCCTAAACAC
*
45169 TAAA-CTTTAAACCAC-AAACAC
1 TAAATC-ATAAACC-CTAAACAC
45190 TAAATCATAAACCCTAA
1 TAAATCATAAACCCTAA
45207 TGTAAATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAATCATAAACCCTAAACAC
Found at i:45596 original size:20 final size:21
Alignment explanation
Indices: 45547--45597 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
45537 TAAATATTTT
*
45547 TATATAATATGTATGTATAAAC
1 TATAT-ATATGTATATATAAAC
* *
45569 CATGTATA-GTATATATAAAC
1 TATATATATGTATATATAAAC
45589 TATATATAT
1 TATATATAT
45598 AAAAACTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 3 0.13
22 3 0.13
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (21 bp):
TATATATATGTATATATAAAC
Found at i:45598 original size:15 final size:16
Alignment explanation
Indices: 45573--45607 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
45563 ATAAACCATG
*
45573 TATAGTATATATAAAC
1 TATAGTATATAAAAAC
45589 TATA-TATATAAAAAC
1 TATAGTATATAAAAAC
45604 TATA
1 TATA
45608 ATAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (16 bp):
TATAGTATATAAAAAC
Found at i:45944 original size:23 final size:23
Alignment explanation
Indices: 45917--45960 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
45907 TTATTTTTTC
45917 TTTATATAAATTAAACTATATCA
1 TTTATATAAATTAAACTATATCA
*
45940 TTTATATAAATTAAATTATAT
1 TTTATATAAATTAAACTATAT
45961 TAATTTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATCA
Found at i:46255 original size:16 final size:16
Alignment explanation
Indices: 46234--46272 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
46224 TGGATCATTT
46234 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
46250 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
46266 ACAGGTC
1 ACAGGTC
46273 GGGTAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:47145 original size:2 final size:2
Alignment explanation
Indices: 47105--47130 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47095 CTTAACATTA
47105 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
47131 CTTAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47177 original size:15 final size:16
Alignment explanation
Indices: 47157--47198 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
47147 TAAAATATAT
47157 TTTTATTTATA-TAAA
1 TTTTATTTATATTAAA
47172 TTTTATTTCTATATTAAA
1 TTTTA-TT-TATATTAAA
47190 TTTTATTTA
1 TTTTATTTA
47199 CATTTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.21
16 4 0.17
17 6 0.25
18 9 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTATTTATATTAAA
Found at i:47184 original size:17 final size:18
Alignment explanation
Indices: 47164--47197 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47154 TATTTTTATT
47164 TATA-TAAATTTTATTTC
1 TATATTAAATTTTATTTC
47181 TATATTAAATTTTATTT
1 TATATTAAATTTTATTT
47198 ACATTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTAAATTTTATTTC
Found at i:47306 original size:40 final size:40
Alignment explanation
Indices: 47260--47357 Score: 151
Period size: 40 Copynumber: 2.4 Consensus size: 40
47250 TGTATTTTTA
47260 TTTTTATTTTTATATATTTAAAATATATTGAAAAATATAT
1 TTTTTATTTTTATATATTTAAAATATATTGAAAAATATAT
* *
47300 TTTTTATTTTTATACATTTTAAATATATTGAAAAATATAT
1 TTTTTATTTTTATATATTTAAAATATATTGAAAAATATAT
* *
47340 TTTTATATATTTAAATAT
1 TTTT-TATTTTTATATAT
47358 ATTTTATCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
40 42 0.81
41 10 0.19
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (40 bp):
TTTTTATTTTTATATATTTAAAATATATTGAAAAATATAT
Found at i:49025 original size:31 final size:31
Alignment explanation
Indices: 48953--49013 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
48943 AACTCGGGTG
*
48953 ACCACATCTTAATTAAATAAAAACGAAAGTA
1 ACCATATCTTAATTAAATAAAAACGAAAGTA
*
48984 ACCGTATCTTAATTAAATAAAAACGAAAGT
1 ACCATATCTTAATTAAATAAAAACGAAAGT
49014 GGTCATATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAAACGAAAGTA
Found at i:50266 original size:14 final size:14
Alignment explanation
Indices: 50243--50280 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
50233 TCTGTCTATA
*
50243 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
50256 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
50271 TGCAGGGATT
1 TGCAGGGATT
50281 ACTTCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:53147 original size:26 final size:27
Alignment explanation
Indices: 53111--53167 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
53101 ATAAATACTT
* *
53111 ATAATTAAATTTAAATAAAAACT-TAA
1 ATAATTAAATTCAAATAAAAAATATAA
* *
53137 ATAATTTAATTCAATTAAAAAATATAA
1 ATAATTAAATTCAAATAAAAAATATAA
53164 ATAA
1 ATAA
53168 GATTAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAATTAAATTCAAATAAAAAATATAA
Found at i:54547 original size:12 final size:12
Alignment explanation
Indices: 54530--54560 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
54520 AATAAATAGT
54530 ATATAAATTAAA
1 ATATAAATTAAA
54542 ATATAAATTAAA
1 ATATAAATTAAA
54554 ATATAAA
1 ATATAAA
54561 CTAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAAATTAAA
Found at i:59687 original size:36 final size:37
Alignment explanation
Indices: 59573--59693 Score: 100
Period size: 36 Copynumber: 3.3 Consensus size: 37
59563 AACTTGGACT
* * * * * *
59573 AATTTTTTTTCATGAGAAAATATCTCAAGTAAGATGCA
1 AATTTTATTTCAAGGGAAACTATCTAAAGTAAGAT-AA
* * * * *
59611 ACTTTTGTTTCAAGGGAAACTGTTTAAAGTAAGATGA
1 AATTTTATTTCAAGGGAAACTATCTAAAGTAAGATAA
* * *
59648 AA-TTTATTTCAAGGGAAATTATCTCAAGTGAGATAA
1 AATTTTATTTCAAGGGAAACTATCTAAAGTAAGATAA
59684 AATTTTATTT
1 AATTTTATTT
59694 TGAGAAAAAT
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
36 29 0.45
37 9 0.14
38 27 0.42
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (37 bp):
AATTTTATTTCAAGGGAAACTATCTAAAGTAAGATAA
Found at i:59821 original size:35 final size:37
Alignment explanation
Indices: 59773--59847 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 37
59763 AATTGTTTCG
*
59773 AGTGAGACGAATTTGTT-TTAAG-GA-AAACTATCCCA
1 AGTGAGACAAATTT-TTATTAAGAGAGAAACTATCCCA
* * *
59808 AGTGAGGCAAATTTTTATTTAGAGAGAAACTATCTCA
1 AGTGAGACAAATTTTTATTAAGAGAGAAACTATCCCA
59845 AGT
1 AGT
59848 ACTGAGATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.06
35 16 0.48
36 2 0.06
37 13 0.39
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (37 bp):
AGTGAGACAAATTTTTATTAAGAGAGAAACTATCCCA
Found at i:70960 original size:49 final size:49
Alignment explanation
Indices: 70823--70967 Score: 227
Period size: 49 Copynumber: 3.0 Consensus size: 49
70813 GAAAACACGG
* *
70823 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGAAAAGCGCGT
1 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
*
70872 ATTGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
1 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
* * * *
70921 ATCGTCATCATCGTCTTCGTTAAACCTCTGACATATATGGAAGGCGC
1 ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGC
70968 AAATCATGGT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (49 bp):
ATCGTCATCTTCGTCTTCGATGAACCTTTGACATATATGGAAGGCGCGT
Found at i:75522 original size:29 final size:29
Alignment explanation
Indices: 75489--75641 Score: 127
Period size: 29 Copynumber: 5.4 Consensus size: 29
75479 ATTTTGTGTT
*
75489 TTAGTACTTTAAATTTCTGTTTTGCTTTG
1 TTAGTCCTTTAAATTTCTGTTTTGCTTTG
* * * * * *
75518 TTAGTCCCTTAACTTTCGGTTTTACTATC
1 TTAGTCCTTTAAATTTCTGTTTTGCTTTG
* * *
75547 ATAGCCCTTTAAGTTTCTGTTTTGTCTTT-
1 TTAGTCCTTTAAATTTCTGTTTTG-CTTTG
* *
75576 TTATTCCTTTAATTTTCTGTTTTGCTTTG
1 TTAGTCCTTTAAATTTCTGTTTTGCTTTG
* * *
75605 TTAG-CCTTTAACTTTAT-TTTTGC--TA
1 TTAGTCCTTTAAATTTCTGTTTTGCTTTG
75630 TTAGTCCTTTAA
1 TTAGTCCTTTAA
75642 CTGTCTATTT
Statistics
Matches: 99, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
25 5 0.05
26 7 0.07
27 6 0.06
28 15 0.15
29 63 0.64
30 3 0.03
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.56
Consensus pattern (29 bp):
TTAGTCCTTTAAATTTCTGTTTTGCTTTG
Found at i:75638 original size:26 final size:29
Alignment explanation
Indices: 75605--75682 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
75595 TTTTGCTTTG
*
75605 TTAG-CCTTTAACT-T-TATTTTTGCTA-
1 TTAGTCCTTTAACTGTCTATTTTTACTAT
75630 TTAGTCCTTTAACTGTCTATTTTTACTAT
1 TTAGTCCTTTAACTGTCTATTTTTACTAT
* * *
75659 TTAATCCTTTAAGTTTCTATTTTT
1 TTAGTCCTTTAACTGTCTATTTTT
75683 GTTTGCTGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.09
26 9 0.20
27 1 0.02
28 10 0.22
29 21 0.47
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (29 bp):
TTAGTCCTTTAACTGTCTATTTTTACTAT
Found at i:75676 original size:83 final size:84
Alignment explanation
Indices: 75478--75736 Score: 220
Period size: 83 Copynumber: 3.0 Consensus size: 84
75468 TGGTTTATTT
* * * **
75478 TATTTTGTGT-TTTAGTACTTTAAATTTCTGTTTTGCTTTGTTAGTCCC-TTAACTTTCGGTTTT
1 TATTTTGTCTATTTAATCCTTTAAATTTCTGTTTTGCTTTGTTAG-CCCTTTAACTTT-ATTTTT
* * *
75541 ACTATCATAGCCCTTTAAGTTTC
64 GCTAT--TAGCCCTTTAACTGTC
* * * *
75564 TGTTTTGTCTTTTTATTCCTTTAATTTTCTGTTTTGCTTTGTTAG-CCTTTAACTTTATTTTTGC
1 TATTTTGTCTATTTAATCCTTTAAATTTCTGTTTTGCTTTGTTAGCCCTTTAACTTTATTTTTGC
*
75628 TATTAGTCCTTTAACTGTC
66 TATTAGCCCTTTAACTGTC
* * *
75647 TATTTT-TACTATTTAATCCTTTAAGTTTCTATTTTTGTTTGCTGTGTTAGCCCTTTAACTTTAT
1 TATTTTGT-CTATTTAATCCTTTAAATTTC----TGT-TTTGCTTTGTTAGCCCTTTAACTTTA-
75711 GTTTTTGCTATGTTAGCCCTTTAACT
59 -TTTTTGCTA--TTAGCCCTTTAACT
75737 ATTTTTTATT
Statistics
Matches: 142, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
82 1 0.01
83 36 0.25
85 10 0.07
86 16 0.11
87 33 0.23
88 12 0.08
89 12 0.08
91 9 0.06
93 13 0.09
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (84 bp):
TATTTTGTCTATTTAATCCTTTAAATTTCTGTTTTGCTTTGTTAGCCCTTTAACTTTATTTTTGC
TATTAGCCCTTTAACTGTC
Found at i:75716 original size:34 final size:30
Alignment explanation
Indices: 75595--75736 Score: 107
Period size: 30 Copynumber: 4.8 Consensus size: 30
75585 TAATTTTCTG
*
75595 TTTTGCTTTGTTAG-CCTTTAAC-TT-TAT
1 TTTTGCTATGTTAGCCCTTTAACTTTATAT
* * *
75622 TTTTGCTA--TTAGTCCTTTAACTGTCTAT
1 TTTTGCTATGTTAGCCCTTTAACTTTATAT
* ** * *
75650 TTTTACTAT-TTAATCCTTTAAGTTTCTATTTT
1 TTTTGCTATGTTAGCCCTTTAA-CTT-TA-TAT
* *
75682 TGTTTGCTGTGTTAGCCCTTTAACTTTATGT
1 T-TTTGCTATGTTAGCCCTTTAACTTTATAT
75713 TTTTGCTATGTTAGCCCTTTAACT
1 TTTTGCTATGTTAGCCCTTTAACT
75737 ATTTTTTATT
Statistics
Matches: 91, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
25 4 0.04
26 8 0.09
27 8 0.09
28 10 0.11
29 11 0.12
30 23 0.25
31 4 0.04
32 5 0.05
33 8 0.09
34 10 0.11
ACGTcount: A:0.17, C:0.16, G:0.11, T:0.56
Consensus pattern (30 bp):
TTTTGCTATGTTAGCCCTTTAACTTTATAT
Done.