Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007610.1 Hibiscus syriacus cultivar Beakdansim tig00022531_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: 83313
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:431 original size:19 final size:18
Alignment explanation
Indices: 391--457 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
381 CAAGGATTGA
*
391 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTT-GAGTTT-GG
411 TTTAGGGTTTGAGTTTGGG
1 TTTAGGGTTTGAGTTT-GG
*
430 TTTA-GGTTTGAGTTCTAG
1 TTTAGGGTTTGAGTT-TGG
448 TTTAGGGTTT
1 TTTAGGGTTT
458 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.36
19 17 0.40
20 10 0.24
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTGAGTTTGG
Found at i:450 original size:18 final size:18
Alignment explanation
Indices: 410--453 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
400 TAAAGTTTAG
*
410 GTTTAGGGTTTGAGTTTGG
1 GTTTA-GGTTTGAGTTTGA
429 GTTTAGGTTTGAGTTCT-A
1 GTTTAGGTTTGAGTT-TGA
447 GTTTAGG
1 GTTTAGG
454 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (18 bp):
GTTTAGGTTTGAGTTTGA
Found at i:902 original size:25 final size:25
Alignment explanation
Indices: 861--1015 Score: 97
Period size: 25 Copynumber: 6.1 Consensus size: 25
851 TGTTTCTTTT
861 TATATATA-TATA-T-ATATATATA
1 TATATATATTATATTAATATATATA
*
883 TATATATATTATATTAATATACATA
1 TATATATATTATATTAATATATATA
* * * *
908 CATATATACTATATTAGTATAAAT-
1 TATATATATTATATTAATATATATA
* *
932 TATAATATAACTATATTTTATATATTTATA
1 TAT-ATAT-A-T-TATATTA-ATATATATA
* *
962 CATATATAGTT-TATATACATATATTTA
1 TATATATA-TTATAT-TA-ATATATATA
* *
989 TATATATACTATA-TAATATAAATA
1 TATATATATTATATTAATATATATA
1013 TAT
1 TAT
1016 TTTATAAACT
Statistics
Matches: 101, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
22 8 0.08
23 4 0.04
24 13 0.13
25 34 0.34
26 4 0.04
27 19 0.19
28 8 0.08
29 9 0.09
30 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (25 bp):
TATATATATTATATTAATATATATA
Found at i:976 original size:81 final size:84
Alignment explanation
Indices: 861--1067 Score: 239
Period size: 81 Copynumber: 2.5 Consensus size: 84
851 TGTTTCTTTT
* * *
861 TATATATATATATATATATATATATATA-TATTATATTA-ATATACATACATATATACTATATTA
1 TATATATTTATATATTTATACATATATAGT-TTATATTACATATACATACATATATACTATA-TA
*
924 GTATAAAT-TATAATAT-AAC
64 ATATAAATATATAATATAAAC
** *
943 TATAT-TTTATATATTTATACATATATAGTTTATA-TACATATATTTATATATATACTATATAAT
1 TATATATTTATATATTTATACATATATAGTTTATATTACATATACATACATATATACTATATAAT
**
1006 ATAAATATATTTTATAAAC
66 ATAAATATATAATATAAAC
*
1025 TATATACTTTTTATAGTTTATACATATATAGTTTATA-TACATA
1 TATATA-TTTATATA-TTTATACATATATAGTTTATATTACATA
1068 GTTTATATAT
Statistics
Matches: 108, Mismatches: 10, Indels: 11
0.84 0.08 0.09
Matches are distributed among these distances:
80 11 0.10
81 49 0.45
82 14 0.13
84 7 0.06
85 27 0.25
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (84 bp):
TATATATTTATATATTTATACATATATAGTTTATATTACATATACATACATATATACTATATAAT
ATAAATATATAATATAAAC
Found at i:1017 original size:68 final size:71
Alignment explanation
Indices: 932--1063 Score: 180
Period size: 68 Copynumber: 1.9 Consensus size: 71
922 TAGTATAAAT
* * * *
932 TATAATATAACTATATTTTATATA-TTTATAC-ATATATAGTTTATATACATATA-TTTATATAT
1 TATAATATAAATATATTTTATAAACTATATACTATATATAGTTTATACACATATAGTTTATATAT
994 ATACTA
66 ATACTA
* * *
1000 TATAATATAAATATATTTTATAAACTATATACTTTTTATAGTTTATACATATATAGTTTATATA
1 TATAATATAAATATATTTTATAAACTATATACTATATATAGTTTATACACATATAGTTTATATA
1064 CATAGTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
68 22 0.41
69 6 0.11
70 18 0.33
71 8 0.15
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.50
Consensus pattern (71 bp):
TATAATATAAATATATTTTATAAACTATATACTATATATAGTTTATACACATATAGTTTATATAT
ATACTA
Found at i:1030 original size:2 final size:2
Alignment explanation
Indices: 861--1015 Score: 112
Period size: 2 Copynumber: 79.5 Consensus size: 2
851 TGTTTCTTTT
861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
900 TA TA CA TA CA TA TA TA CTA TA T- TA GTA TA AA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
941 -A CTA TA T- TT TA TA TA TT TA TA CA TA TA TA GTT TA TA TA CA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
983 TA TT TA TA TA TA TA CTA TA TA -A TA TA AA TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T
1016 TTTATAAACT
Statistics
Matches: 120, Mismatches: 19, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
1 9 0.08
2 103 0.86
3 8 0.07
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1056 original size:15 final size:14
Alignment explanation
Indices: 1036--1137 Score: 56
Period size: 15 Copynumber: 7.1 Consensus size: 14
1026 ATATACTTTT
1036 TATAGTTTATACATA
1 TATAGTTTATA-ATA
1051 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
1064 CATAG-TT-T-ATA
1 TATAGTTTATAATA
*
1075 TATAGTTCACATAATCA
1 TATAGTT--TATAAT-A
1092 TA-A--TTATATATA
1 TATAGTTTATA-ATA
1104 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
1122 TATAGTTTATAATA
1 TATAGTTTATAATA
1136 TA
1 TA
1138 AATATAGTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 29
0.68 0.04 0.28
Matches are distributed among these distances:
11 8 0.12
12 9 0.13
13 10 0.14
14 5 0.07
15 15 0.22
16 5 0.07
17 7 0.10
18 10 0.14
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:1063 original size:85 final size:80
Alignment explanation
Indices: 909--1078 Score: 234
Period size: 85 Copynumber: 2.1 Consensus size: 80
899 ATATACATAC
*
909 ATATATACTATATTAGTATAAATTATAATATAACTATATTTTATATATTTATACATATATAGTTT
1 ATATATACTATATTAATATAAATTATAATATAACTATATTTTATATATTTATACATATATAGTTT
974 ATATACATATATTTAT
66 ATATACATA-ATTTAT
** *
990 ATATATACTATA-TAATATAAATATATTTTATAAACTATATACTTTTTATAGTTTATACATATAT
1 ATATATACTATATTAATATAAAT-TATAATAT-AACTATAT--TTTATATA-TTTATACATATAT
*
1054 AGTTTATATACATAGTTTAT
61 AGTTTATATACATAATTTAT
1074 ATATA
1 ATATA
1079 GTTCACATAA
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
80 9 0.11
81 18 0.23
82 8 0.10
84 17 0.22
85 27 0.34
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (80 bp):
ATATATACTATATTAATATAAATTATAATATAACTATATTTTATATATTTATACATATATAGTTT
ATATACATAATTTAT
Found at i:1068 original size:13 final size:13
Alignment explanation
Indices: 1037--1076 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
1027 TATACTTTTT
*
1037 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
1052 ATAGTTTATATAC
1 ATAGTTTATATAC
1065 ATAGTTTATATA
1 ATAGTTTATATA
1077 TAGTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:1137 original size:85 final size:85
Alignment explanation
Indices: 909--1137 Score: 226
Period size: 85 Copynumber: 2.7 Consensus size: 85
899 ATATACATAC
* * * *
909 ATATATACTATATTAGTATAAAT-TATAATAT-AACTATAT--TTTATATA-TTTATACATATAT
1 ATATATACTACA-TAATATAAATATATTATATAAACTATATACATTATATAGTTTATACATATAT
969 AGTTTATATACATATATTTAT
65 AGTTTATATACATATATTTAT
* * * *
990 ATATATACTATATAATATAAATATATTTTATAAACTATATACTTTTTATAGTTTATACATATATA
1 ATATATACTACATAATATAAATATATTATATAAACTATATACATTATATAGTTTATACATATATA
*
1055 GTTTATATACATA-GTTTAT
66 GTTTATATACATATATTTAT
* * *
1074 ATATAGTTC-ACATAATCATAATTATA-TATATATAGCTTATAATA-ATTATATAGTTTATA-AT
1 ATATA-TACTACATAAT-ATAAATATATTATATA-AAC-TAT-ATACATTATATAGTTTATACAT
1135 ATA
61 ATA
1138 AATATAGTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
80 9 0.07
81 18 0.14
82 8 0.06
84 28 0.22
85 44 0.35
86 16 0.13
87 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (85 bp):
ATATATACTACATAATATAAATATATTATATAAACTATATACATTATATAGTTTATACATATATA
GTTTATATACATATATTTAT
Found at i:1142 original size:18 final size:18
Alignment explanation
Indices: 1097--1150 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
1087 AATCATAATT
*
1097 ATATATATATAGCTTATA
1 ATATATATATAGTTTATA
1115 ATA-ATTATATAGTTTATA
1 ATATA-TATATAGTTTATA
*
1133 ATATAAATATAGTTTATA
1 ATATATATATAGTTTATA
1151 TGTAAACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATATATATAGTTTATA
Found at i:12168 original size:16 final size:16
Alignment explanation
Indices: 12144--12214 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
12134 GGTATTACCC
*
12144 GACCAGTTTTCAACCT
1 GACCTGTTTTCAACCT
12160 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
12176 GGCCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
12192 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
12208 GACCTGT
1 GACCTGT
12215 AAATGATCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:12521 original size:23 final size:24
Alignment explanation
Indices: 12484--12533 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
12474 ATGAAAATAA
12484 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
12508 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
12531 AAA
1 AAA
12534 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:12738 original size:49 final size:50
Alignment explanation
Indices: 12685--12787 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
12675 AGTGCTTATG
** * ** *
12685 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
* * *
12734 GTTT-ATGCATAGTATTTCTATAAATTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
12783 GTTTA
1 GTTTA
12788 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (50 bp):
GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:12797 original size:15 final size:15
Alignment explanation
Indices: 12777--12813 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
12767 TAATTTACTT
12777 TATATAGTTTATATA
1 TATATAGTTTATATA
12792 TATATAGTTTATATA
1 TATATAGTTTATATA
12807 TACTATA
1 TA-TATA
12814 TATGGTTTAT
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:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:12815 original size:20 final size:20
Alignment explanation
Indices: 12786--12839 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
12776 TTATATAGTT
12786 TATA-TATATATAGTTTATA
1 TATACTATATATAGTTTATA
*
12805 TATACTATATATGGTTTATA
1 TATACTATATATAGTTTATA
*
12825 CATACATATTATATA
1 TATAC-TA-TATATA
12840 AATTATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 2 0.07
22 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TATACTATATATAGTTTATA
Found at i:14274 original size:15 final size:17
Alignment explanation
Indices: 14240--14282 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
14230 TTTAATGATA
14240 TATATATACATATATAT
1 TATATATACATATATAT
*
14257 TATATATACATA-GT-T
1 TATATATACATATATAT
14272 TATATATACAT
1 TATATATACAT
14283 GTACTATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 12 0.48
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATATACATATATAT
Found at i:14406 original size:19 final size:18
Alignment explanation
Indices: 14366--14432 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
14356 CAAGGATTGA
*
14366 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTT-GAGTTT-GG
14386 TTTAGGGTTTGAGTTTGGG
1 TTTAGGGTTTGAGTTT-GG
*
14405 TTTA-GGTTTGAGTTCTAG
1 TTTAGGGTTTGAGTT-TGG
14423 TTTAGGGTTT
1 TTTAGGGTTT
14433 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.36
19 17 0.40
20 10 0.24
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTGAGTTTGG
Found at i:14425 original size:18 final size:18
Alignment explanation
Indices: 14385--14428 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14375 TAAAGTTTAG
*
14385 GTTTAGGGTTTGAGTTTGG
1 GTTTA-GGTTTGAGTTTGA
14404 GTTTAGGTTTGAGTTCT-A
1 GTTTAGGTTTGAGTT-TGA
14422 GTTTAGG
1 GTTTAGG
14429 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (18 bp):
GTTTAGGTTTGAGTTTGA
Found at i:14532 original size:2 final size:2
Alignment explanation
Indices: 14525--14554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14515 ATATGGTTTT
14525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14555 CATAGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14647 original size:34 final size:34
Alignment explanation
Indices: 14575--14653 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
14565 ACATACATGT
* *
14575 ACTATAAGTTACATATAGTTTACATTGTATACAT
1 ACTATAAGTTACATATAGTTAACATTGTATACAG
* *
14609 ACTATAAGTTACATATA-TTAACTATTGTTTATAG
1 ACTATAAGTTACATATAGTTAAC-ATTGTATACAG
*
14643 ACTATATGTTA
1 ACTATAAGTTA
14654 ATTTGACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (34 bp):
ACTATAAGTTACATATAGTTAACATTGTATACAG
Found at i:14846 original size:2 final size:2
Alignment explanation
Indices: 14839--14980 Score: 100
Period size: 2 Copynumber: 72.0 Consensus size: 2
14829 TGTTTCTTTA
* *
14839 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
14879 AT AT AT ACT AT AT -T AGT AT AA AT -T AT A- AT AT AT AA ACT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * *
14919 AT AT -T TT AT AT A- AT TT AT AC AT AT AT AGT TT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
*
14960 AT TT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT A-T AT AT
14981 TAATATAAAT
Statistics
Matches: 109, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
1 7 0.06
2 94 0.86
3 8 0.07
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14979 original size:89 final size:88
Alignment explanation
Indices: 14877--15058 Score: 285
Period size: 89 Copynumber: 2.1 Consensus size: 88
14867 TTATACATAC
* *
14877 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATA-TTTTATATAATTTATACAT
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTT-TATAATTTATACAT
14941 ATATAGTTTATATACATATATTTAT
65 ATATAGTTTATATACATA-ATTTAT
* * *
14966 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACATA
*
15031 TATAGTTTATATACATAGTTTAT
66 TATAGTTTATATACATAATTTAT
15054 ATATA
1 ATATA
15059 GTTCACATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
88 10 0.12
89 72 0.84
90 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (88 bp):
ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACATA
TATAGTTTATATACATAATTTAT
Found at i:15036 original size:15 final size:14
Alignment explanation
Indices: 15016--15120 Score: 58
Period size: 15 Copynumber: 7.1 Consensus size: 14
15006 ATATACTTTT
15016 TATAGTTTATACATA
1 TATAGTTTATA-ATA
15031 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
15044 CATAG-TT-T-ATA
1 TATAGTTTATAATA
*
15055 TATAGTTCACATAATCA
1 TATAGTT--TATAAT-A
*
15072 TA-ATTTATATATATA
1 TATAGTT-TATA-ATA
15087 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
15105 TATAGTTTATAATA
1 TATAGTTTATAATA
15119 TA
1 TA
15121 AATATAGTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 23
0.72 0.06 0.23
Matches are distributed among these distances:
11 8 0.11
12 3 0.04
13 7 0.10
14 4 0.05
15 22 0.30
16 9 0.12
17 10 0.14
18 10 0.14
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:15048 original size:13 final size:13
Alignment explanation
Indices: 15017--15056 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
15007 TATACTTTTT
*
15017 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
15032 ATAGTTTATATAC
1 ATAGTTTATATAC
15045 ATAGTTTATATA
1 ATAGTTTATATA
15057 TAGTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:15055 original size:24 final size:26
Alignment explanation
Indices: 15028--15084 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
15018 TAGTTTATAC
* * *
15028 ATATATAGTTTATAT-A-CATAGTTT
1 ATATATAGTTCACATAATCATAATTT
15052 ATATATAGTTCACATAATCATAATTT
1 ATATATAGTTCACATAATCATAATTT
15078 ATATATA
1 ATATATA
15085 TATATAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 13 0.46
25 1 0.04
26 14 0.50
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAGTTCACATAATCATAATTT
Found at i:15109 original size:89 final size:89
Alignment explanation
Indices: 14877--15120 Score: 250
Period size: 89 Copynumber: 2.8 Consensus size: 89
14867 TTATACATAC
* * * * ** *
14877 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATATTTTATATAATTTATACATA
1 ATATATATACTACATTAATATAAATAATATTATATAAACTATATACATTATATAGTTTATACATA
14942 TATAGTTTATATACATATATTTAT
66 TATAGTTTATATACATATATTTAT
* * * *
14966 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTACATTAATATAAATAATATTATATAAACTATATACATTATATAGTTTATACATA
*
15031 TATAGTTTATATACATA-GTTTAT
66 TATAGTTTATATACATATATTTAT
* * *
15054 ATATAGT-T-C-ACA-TAATCATAATTTATATATATATATAGCTTATAATA-ATTATATAGTTTA
1 ATATA-TATACTACATTAAT-ATAAATAATAT-TATATA-AAC-TAT-ATACATTATATAGTTTA
15114 TA-ATATA
60 TACATATA
15121 AATATAGTTT
Statistics
Matches: 134, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
85 4 0.03
86 11 0.08
87 6 0.04
88 18 0.13
89 92 0.69
90 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (89 bp):
ATATATATACTACATTAATATAAATAATATTATATAAACTATATACATTATATAGTTTATACATA
TATAGTTTATATACATATATTTAT
Found at i:15125 original size:18 final size:18
Alignment explanation
Indices: 15075--15133 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
15065 ATAATCATAA
15075 TTTAT-ATATATATATAG
1 TTTATAATATATATATAG
*
15092 CTTATAATA-ATTATATAG
1 TTTATAATATA-TATATAG
*
15110 TTTATAATATAAATATAG
1 TTTATAATATATATATAG
15128 TTTATA
1 TTTATA
15134 TGTAAACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.14
18 30 0.83
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTATAATATATATATAG
Found at i:26162 original size:16 final size:16
Alignment explanation
Indices: 26138--26208 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
26128 GGTATTACCC
*
26138 GACCAGTTTTCAACCT
1 GACCTGTTTTCAACCT
26154 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
26170 GGCCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
26186 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
26202 GACCTGT
1 GACCTGT
26209 AAATGATCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:26513 original size:23 final size:24
Alignment explanation
Indices: 26476--26525 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
26466 ATGAAAATAA
26476 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
26500 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
26523 AAA
1 AAA
26526 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:26730 original size:49 final size:50
Alignment explanation
Indices: 26677--26779 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
26667 AGTGCTTATG
** * ** *
26677 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
* * *
26726 GTTT-ATGCATAGTATTTCTATAAATTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
26775 GTTTA
1 GTTTA
26780 TATATATAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (50 bp):
GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:26787 original size:13 final size:13
Alignment explanation
Indices: 26769--26798 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
26759 TAATTTACTT
26769 TATATAGTTTATA
1 TATATAGTTTATA
26782 TATATAGTTTATA
1 TATATAGTTTATA
26795 TATA
1 TATA
26799 CTATATGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:26809 original size:18 final size:18
Alignment explanation
Indices: 26778--26821 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
26768 TTATATAGTT
26778 TATA-TATATAGTTTATA
1 TATACTATATAGTTTATA
*
26795 TATACTATATGGTTTATA
1 TATACTATATAGTTTATA
*
26813 CATAC-ATAT
1 TATACTATAT
26822 TATATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (18 bp):
TATACTATATAGTTTATA
Found at i:28268 original size:19 final size:18
Alignment explanation
Indices: 28226--28270 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
28216 ATGTTTAATG
28226 ATATATATATACATATAT
1 ATATATATATACATATAT
*
28244 ATTATATATATACATAGTTT
1 A-TATATATATACATA-TAT
28264 ATATATA
1 ATATATA
28271 CATGTACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 20 0.83
20 3 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATATATATACATATAT
Found at i:28397 original size:19 final size:18
Alignment explanation
Indices: 28357--28423 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
28347 CAAGGATTGA
*
28357 TTTAGGGTTTAAAGTTTAGG
1 TTTAGGGTTT-GAGTTT-GG
28377 TTTAGGGTTTGAGTTTGGG
1 TTTAGGGTTTGAGTTT-GG
*
28396 TTTA-GGTTTGAGTTCTAG
1 TTTAGGGTTTGAGTT-TGG
28414 TTTAGGGTTT
1 TTTAGGGTTT
28424 AGAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.36
19 17 0.40
20 10 0.24
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTGAGTTTGG
Found at i:28416 original size:18 final size:18
Alignment explanation
Indices: 28376--28419 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28366 TAAAGTTTAG
*
28376 GTTTAGGGTTTGAGTTTGG
1 GTTTA-GGTTTGAGTTTGA
28395 GTTTAGGTTTGAGTTCT-A
1 GTTTAGGTTTGAGTT-TGA
28413 GTTTAGG
1 GTTTAGG
28420 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (18 bp):
GTTTAGGTTTGAGTTTGA
Found at i:28527 original size:2 final size:2
Alignment explanation
Indices: 28516--28549 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
28506 ATATGGTTTT
28516 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28550 CATAGTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28644 original size:34 final size:35
Alignment explanation
Indices: 28570--28650 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
28560 ACATACATGT
* *
28570 ACTATAAGTTACATATATAGTTTACATTGTATACAT
1 ACTATAAGTTACA-ATATAGTTAACATTGTATACAG
* *
28606 ACTATAAGTTAC-ATATA-TTAACTATTGTTTATAG
1 ACTATAAGTTACAATATAGTTAAC-ATTGTATACAG
*
28640 ACTATATGTTA
1 ACTATAAGTTA
28651 ATTTGACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 4 0.10
34 23 0.59
36 12 0.31
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (35 bp):
ACTATAAGTTACAATATAGTTAACATTGTATACAG
Found at i:28843 original size:2 final size:2
Alignment explanation
Indices: 28836--28977 Score: 86
Period size: 2 Copynumber: 73.0 Consensus size: 2
28826 TGTTTCTTTA
* *
28836 AT AT AT AT AT AT AT AT AT -T AT AT -T A- AT -T AT AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
28874 AT AT AT ACT AT AT -T AGT AT AA AT -T AT A- AT AT AT AA ACT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * *
28914 AT AT -T TT AT AT A- AT TT AT AC AT AT AT AGT TT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
*
28955 AT TT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT
28978 TAATATAAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
1 9 0.08
2 90 0.84
3 8 0.07
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28912 original size:29 final size:30
Alignment explanation
Indices: 28840--28985 Score: 97
Period size: 29 Copynumber: 4.8 Consensus size: 30
28830 TCTTTAATAT
*
28840 ATATATATA-TATATTATAT-TAATTATAC
1 ATATATAAACTATATTATATATAATTATAC
28868 ATACATATATATACTATATTAGTATA-AATTATA-
1 AT--ATATA-A-ACTATATTA-TATATAATTATAC
*
28901 ATATATAAACTATATATTTTATATAATTTATAC
1 ATATATAAAC--TATATTATATATAA-TTATAC
*** * * *
28934 ATATATAGTTTATA-TACATATATTTATAT
1 ATATATAAACTATATTATATATAATTATAC
*
28963 ATATATATACTATATTA-ATATAA
1 ATATATAAACTATATTATATATAA
28986 ATAATATTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
28 2 0.02
29 23 0.25
30 18 0.20
31 17 0.18
32 6 0.07
33 16 0.17
34 10 0.11
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (30 bp):
ATATATAAACTATATTATATATAATTATAC
Found at i:28968 original size:91 final size:90
Alignment explanation
Indices: 28872--29057 Score: 293
Period size: 91 Copynumber: 2.1 Consensus size: 90
28862 TTATACATAC
* *
28872 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATA-TTTTATATAATTTATACAT
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTT-TATAATTTATACAT
28936 ATATAGTTTATATACATATATTTATAT
65 ATATAGTTTATATACATA-ATTTATAT
* * *
28963 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACATA
*
29028 TATAGTTTATATACATAGTTTATAT
66 TATAGTTTATATACATAATTTATAT
29053 ATATA
1 ATATA
29058 GTTCACATAA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
90 12 0.14
91 72 0.82
92 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (90 bp):
ATATATATACTATATTAATATAAATAATAATATATAAACTATATACTTTTTATAATTTATACATA
TATAGTTTATATACATAATTTATAT
Found at i:29045 original size:13 final size:13
Alignment explanation
Indices: 29013--29085 Score: 74
Period size: 13 Copynumber: 5.3 Consensus size: 13
29003 ATATACTTTT
29013 TATAGTTTATACATA
1 TATAGTTTAT--ATA
29028 TATAGTTTATATA
1 TATAGTTTATATA
*
29041 CATAGTTTATATA
1 TATAGTTTATATA
* *
29054 TATAGTTCACATAA
1 TATAGTTTATAT-A
*
29068 TCATAATTTATATA
1 T-ATAGTTTATATA
29082 TATA
1 TATA
29086 TATAGCTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
13 27 0.55
14 4 0.08
15 18 0.37
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:29047 original size:28 final size:29
Alignment explanation
Indices: 29014--29087 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
29004 TATACTTTTT
* *
29014 ATAGTTTATACATATATAGTTTATAT-A-C
1 ATAGTTTATA-ATATATAGTTCACATAATC
29042 ATAGTTTAT-ATATATAGTTCACATAATC
1 ATAGTTTATAATATATAGTTCACATAATC
*
29070 ATAATTTATATATATATA
1 ATAGTTTATA-ATATATA
29088 TAGCTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 13 0.33
27 1 0.03
28 18 0.46
30 7 0.18
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (29 bp):
ATAGTTTATAATATATAGTTCACATAATC
Found at i:29108 original size:91 final size:91
Alignment explanation
Indices: 28872--29119 Score: 258
Period size: 91 Copynumber: 2.7 Consensus size: 91
28862 TTATACATAC
* * * * ** *
28872 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATATTTTATATAATTTATACATA
1 ATATATATACTACATTAATATAAATAATATTATATAAACTATATACATTATATAGTTTATACATA
28937 TATAGTTTATATACATATATTTATAT
66 TATAGTTTATATACATATATTTATAT
* * * *
28963 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTACATTAATATAAATAATATTATATAAACTATATACATTATATAGTTTATACATA
*
29028 TATAGTTTATATACATA-GTTTATAT
66 TATAGTTTATATACATATATTTATAT
* * *
29053 ATATAGT-T-C-ACA-TAATCATAATTTATATATATATATAGCTTATAATA-ATTATATAGTTTA
1 ATATA-TATACTACATTAAT-ATAAATAATAT-TATATA-AAC-TAT-ATACATTATATAGTTTA
29113 TA-ATATA
60 TACATATA
29120 AATATAGTTT
Statistics
Matches: 136, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
87 4 0.03
88 11 0.08
89 6 0.04
90 20 0.15
91 92 0.68
92 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (91 bp):
ATATATATACTACATTAATATAAATAATATTATATAAACTATATACATTATATAGTTTATACATA
TATAGTTTATATACATATATTTATAT
Found at i:29115 original size:15 final size:15
Alignment explanation
Indices: 29013--29132 Score: 65
Period size: 13 Copynumber: 7.7 Consensus size: 15
29003 ATATACTTTT
29013 TATAGTTTATACA-TA
1 TATAGTTTATA-ATTA
29028 TATAGTTTAT-A-TA
1 TATAGTTTATAATTA
*
29041 CATAGTTTAT-A-TA
1 TATAGTTTATAATTA
* *
29054 TATAGTTCACATAATCA
1 TATAGTT--TATAATTA
29071 TA-A-TTTATATATATA
1 TATAGTTTATA-AT-TA
29086 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAATTA
29104 TATAGTTTATAATATAAA
1 TATAGTTTATAAT-T--A
29122 TATAGTTTATA
1 TATAGTTTATA
29133 TGTAAACTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 25
0.73 0.05 0.22
Matches are distributed among these distances:
13 24 0.28
14 2 0.02
15 22 0.26
16 5 0.06
17 5 0.06
18 21 0.25
19 3 0.04
20 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAGTTTATAATTA
Found at i:29124 original size:18 final size:18
Alignment explanation
Indices: 29074--29132 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
29064 ATAATCATAA
29074 TTTAT-ATATATATATAG
1 TTTATAATATATATATAG
*
29091 CTTATAATA-ATTATATAG
1 TTTATAATATA-TATATAG
*
29109 TTTATAATATAAATATAG
1 TTTATAATATATATATAG
29127 TTTATA
1 TTTATA
29133 TGTAAACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.14
18 30 0.83
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTATAATATATATATAG
Found at i:29133 original size:15 final size:15
Alignment explanation
Indices: 29013--29133 Score: 63
Period size: 15 Copynumber: 7.8 Consensus size: 15
29003 ATATACTTTT
* *
29013 TATAGTTTATACATA
1 TATAGTTTATATAAA
29028 TATAGTTTATAT--A
1 TATAGTTTATATAAA
*
29041 CATAGTTTATAT--A
1 TATAGTTTATATAAA
* *
29054 TATAGTTCACAT-AA
1 TATAGTTTATATAAA
*
29068 TCATAATTTATATATATA
1 T-ATAGTTTATATA-A-A
*
29086 TATAGCTTATAATAATTA
1 TATAGTTTAT-ATAA--A
29104 TATAGTTTATAATATAAA
1 TATAG-TT-T-ATATAAA
29122 TATAGTTTATAT
1 TATAGTTTATAT
29134 GTAAACTTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 20
0.73 0.09 0.17
Matches are distributed among these distances:
13 22 0.26
14 2 0.02
15 23 0.27
16 1 0.01
17 11 0.13
18 18 0.21
19 1 0.01
20 5 0.06
21 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAGTTTATATAAA
Found at i:32811 original size:15 final size:15
Alignment explanation
Indices: 32793--32823 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
32783 TTAATCAGAG
32793 TTTTAAATCACGGTC
1 TTTTAAATCACGGTC
32808 TTTTAAATCACGGTC
1 TTTTAAATCACGGTC
32823 T
1 T
32824 GAAAACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
TTTTAAATCACGGTC
Found at i:38473 original size:18 final size:17
Alignment explanation
Indices: 38450--38492 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38440 ATATATACAT
38450 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
38468 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
38485 ATAA-AATA
1 ATAATAATA
38493 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:39832 original size:105 final size:105
Alignment explanation
Indices: 39645--40206 Score: 945
Period size: 105 Copynumber: 5.4 Consensus size: 105
39635 GCATTGTTCA
* * **
39645 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
39705 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
39745 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
39810 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
39850 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGGCAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
39915 CAGCGGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
39955 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
40020 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
40060 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
40125 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
40165 AAGTCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
40207 GCTGTAAAAA
Statistics
Matches: 436, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
100 36 0.08
101 1 0.00
102 2 0.00
103 2 0.00
104 2 0.00
105 393 0.90
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:40799 original size:22 final size:22
Alignment explanation
Indices: 40774--40821 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
40764 TGTTTGGTCT
40774 AAGGTTTGGCATTTGATGCTCA
1 AAGGTTTGGCATTTGATGCTCA
*
40796 AAGGTTTGGTATTTGATGCTCA
1 AAGGTTTGGCATTTGATGCTCA
40818 AAGG
1 AAGG
40822 ATTGATGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.35
Consensus pattern (22 bp):
AAGGTTTGGCATTTGATGCTCA
Found at i:41446 original size:19 final size:20
Alignment explanation
Indices: 41424--41467 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
41414 TTTGTCCCTT
*
41424 TTTTTATTTTTGTTCTTT-C
1 TTTTTATTCTTGTTCTTTCC
* *
41443 TTTTTGTTCTTGTTTTTTCC
1 TTTTTATTCTTGTTCTTTCC
41463 TTTTT
1 TTTTT
41468 TGCTTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTATTCTTGTTCTTTCC
Found at i:41468 original size:22 final size:23
Alignment explanation
Indices: 41443--41490 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
41433 TTGTTCTTTC
41443 TTTTTG-TTCTTGT-TTTTTCCT
1 TTTTTGCTTCTTGTCTTTTTCCT
* *
41464 TTTTTGCTTCTTTTCTTTTTTCT
1 TTTTTGCTTCTTGTCTTTTTCCT
41487 TTTT
1 TTTT
41491 GCCCTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 6 0.26
23 11 0.48
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTTGCTTCTTGTCTTTTTCCT
Found at i:41491 original size:22 final size:21
Alignment explanation
Indices: 41439--41492 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
41429 ATTTTTGTTC
41439 TTTCTTTTTG-TTCTTGTTTT
1 TTTCTTTTTGCTTCTTGTTTT
* *
41459 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTC-TTTTTGCTTCTTGT-TTT
41482 TTTCTTTTTGC
1 TTTCTTTTTGC
41493 CCTTTTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.11
21 6 0.21
22 13 0.46
23 6 0.21
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTCTTTTTGCTTCTTGTTTT
Found at i:45137 original size:18 final size:17
Alignment explanation
Indices: 45114--45156 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
45104 ATATATACAT
45114 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
45132 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
45149 ATAA-AATA
1 ATAATAATA
45157 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:48338 original size:16 final size:16
Alignment explanation
Indices: 48314--48384 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
48304 GGTATTACCC
*
48314 GACCAGTTTTCAACCT
1 GACCTGTTTTCAACCT
48330 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
48346 GGCCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
48362 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
48378 GACCTGT
1 GACCTGT
48385 AAATGATCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:48691 original size:23 final size:24
Alignment explanation
Indices: 48654--48703 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
48644 ATGAAAATAA
48654 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
48678 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
48701 AAA
1 AAA
48704 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:48908 original size:49 final size:50
Alignment explanation
Indices: 48855--48957 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
48845 AGTGCTTATG
** * ** *
48855 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-TTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
* * *
48904 GTTT-ATGCATAGTATTTCTATAAATTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
48953 GTTTA
1 GTTTA
48958 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 23 0.53
49 20 0.47
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (50 bp):
GTTTAAAGCATAGGATTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:48967 original size:15 final size:15
Alignment explanation
Indices: 48947--48983 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
48937 TAATTTACTT
48947 TATATAGTTTATATA
1 TATATAGTTTATATA
48962 TATATAGTTTATATA
1 TATATAGTTTATATA
48977 TACTATA
1 TA-TATA
48984 TATGGTTTAT
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:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:48985 original size:20 final size:20
Alignment explanation
Indices: 48956--49009 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
48946 TTATATAGTT
48956 TATA-TATATATAGTTTATA
1 TATACTATATATAGTTTATA
*
48975 TATACTATATATGGTTTATA
1 TATACTATATATAGTTTATA
*
48995 CATACATATTATATA
1 TATAC-TA-TATATA
49010 AAATTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 2 0.07
22 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TATACTATATATAGTTTATA
Found at i:50442 original size:15 final size:17
Alignment explanation
Indices: 50408--50450 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
50398 TGTTTAATGA
50408 TATATATACATATATAT
1 TATATATACATATATAT
*
50425 TATATATACATA-GT-T
1 TATATATACATATATAT
50440 TATATATACAT
1 TATATATACAT
50451 GTACTATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 12 0.48
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATATACATATATAT
Found at i:50573 original size:18 final size:18
Alignment explanation
Indices: 50546--50595 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
50536 TAGGGTTTAA
50546 AGTTTAGGTTTAGGTTTG
1 AGTTTAGGTTTAGGTTTG
*
50564 AGTTTGGGTTTAGGTTTG
1 AGTTTAGGTTTAGGTTTG
50582 AGTTCTA-GTTTAGG
1 AGTT-TAGGTTTAGG
50596 GTTTAGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (18 bp):
AGTTTAGGTTTAGGTTTG
Found at i:50703 original size:2 final size:2
Alignment explanation
Indices: 50692--50734 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
50682 ATATGGTTTT
50692 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50733 TA
1 TA
50735 CATAGTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:50829 original size:34 final size:35
Alignment explanation
Indices: 50755--50835 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
50745 ACATACATGT
* *
50755 ACTATAAGTTACATATATAGTTTACATTGTATACAT
1 ACTATAAGTTACA-ATATAGTTAACATTGTATACAG
* *
50791 ACTATAAGTTAC-ATATA-TTAACTATTGTTTATAG
1 ACTATAAGTTACAATATAGTTAAC-ATTGTATACAG
*
50825 ACTATATGTTA
1 ACTATAAGTTA
50836 ATTTGACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 4 0.10
34 23 0.59
36 12 0.31
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (35 bp):
ACTATAAGTTACAATATAGTTAACATTGTATACAG
Found at i:51028 original size:2 final size:2
Alignment explanation
Indices: 51021--51177 Score: 79
Period size: 2 Copynumber: 82.5 Consensus size: 2
51011 TGTTTCTTTA
* *
51021 AT AT AT AT AT AT AT AT AT -T AT AT -T A- AT -T AT AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
51059 AT AT AT ACT AT AT -T AGT AT AA AT -T AT A- AT AT AT AA ACT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
51099 AT AT -T TT AT AT A- AT -T AT AC AT AT AT AGT TT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
51139 AT TT AT AT AT AT ACT AT AT -T A- AT AT AA AT A- AT AT TT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
51178 AACTATATAC
Statistics
Matches: 116, Mismatches: 21, Indels: 36
0.67 0.12 0.21
Matches are distributed among these distances:
1 13 0.11
2 95 0.82
3 8 0.07
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51122 original size:23 final size:25
Alignment explanation
Indices: 51082--51140 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
51072 TAGTATAAAT
*
51082 TATAATATATAAACTATATATTTTA
1 TATAATATATAAACTATATAGTTTA
*
51107 TATAAT-TATACA-TATATAGTTTA
1 TATAATATATAAACTATATAGTTTA
51130 TATACATATAT
1 TATA-ATATAT
51141 TTATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 14 0.47
24 7 0.23
25 9 0.30
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (25 bp):
TATAATATATAAACTATATAGTTTA
Found at i:51165 original size:86 final size:83
Alignment explanation
Indices: 51057--51234 Score: 252
Period size: 86 Copynumber: 2.1 Consensus size: 83
51047 TTATACATAC
* *
51057 ATATATATACTATATTAGTATAAATTATAATATATAAACTATATA-TTTTATATA-ATTATACAT
1 ATATATATACTATATTAATATAAATAAT-ATATATAAACTATATACTTTT-TATAGATTATACAT
51120 ATATAGTTTATATACATATATTT
64 ATATAG-TT-TATACATA-ATTT
* *
51143 ATATATATACTATATTAATATAAATAATATTTATAAACTATATACTTTTTATAGTTTATACATAT
1 ATATATATACTATATTAATATAAATAATATATATAAACTATATACTTTTTATAGATTATACATAT
*
51208 ATAGTTTATACATAGTTT
66 ATAGTTTATACATAATTT
51226 ATATATATA
1 ATATATATA
51235 GTTCACATAA
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
83 12 0.14
84 8 0.09
85 21 0.25
86 44 0.52
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (83 bp):
ATATATATACTATATTAATATAAATAATATATATAAACTATATACTTTTTATAGATTATACATAT
ATAGTTTATACATAATTT
Found at i:51185 original size:13 final size:14
Alignment explanation
Indices: 51058--51185 Score: 54
Period size: 15 Copynumber: 9.0 Consensus size: 14
51048 TATACATACA
*
51058 TATATATACTATAT
1 TATATAAACTATAT
* *
51072 TAGTATAAATTATAA
1 TA-TATAAACTATAT
51087 TATATAAACTATA-
1 TATATAAACTATAT
**
51100 TAT-TTTA-TATAAT
1 TATATAAACTAT-AT
* *
51113 TATACATA-TATAGT
1 TATATAAACTATA-T
*
51127 T-TATATACATATATT
1 TATATAAAC-TATA-T
51142 TATATATATACTATAT
1 TATATA-A-ACTATAT
51158 TAATATAAA-TAATAT
1 T-ATATAAACT-ATAT
51173 T-TATAAACTATAT
1 TATATAAACTATAT
51186 ACTTTTTATA
Statistics
Matches: 90, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
11 3 0.03
12 3 0.03
13 22 0.24
14 21 0.23
15 23 0.26
16 7 0.08
17 9 0.10
18 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (14 bp):
TATATAAACTATAT
Found at i:51212 original size:15 final size:15
Alignment explanation
Indices: 51192--51221 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51182 ATATACTTTT
51192 TATAGTTTATACATA
1 TATAGTTTATACATA
51207 TATAGTTTATACATA
1 TATAGTTTATACATA
51222 GTTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:51272 original size:28 final size:28
Alignment explanation
Indices: 51197--51273 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
51187 CTTTTTATAG
* * *
51197 TTTATACATATATAGTTTAT-A-CATAG
1 TTTATATATATATAGCTTATAATCATAA
* **
51223 TTTATATATATAGT-TCACATAATCATAA
1 TTTATATATATA-TAGCTTATAATCATAA
51251 TTTATATATATATAGCTTATAAT
1 TTTATATATATATAGCTTATAAT
51274 AATTATATAG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
26 13 0.34
27 3 0.08
28 22 0.58
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (28 bp):
TTTATATATATATAGCTTATAATCATAA
Found at i:51299 original size:18 final size:18
Alignment explanation
Indices: 51254--51307 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
51244 ATCATAATTT
*
51254 ATATATATATAGCTTATA
1 ATATATATATAGTTTATA
51272 ATA-ATTATATAGTTTATA
1 ATATA-TATATAGTTTATA
*
51290 ATATAAATATAGTTTATA
1 ATATATATATAGTTTATA
51308 TGTAAACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATATATATAGTTTATA
Found at i:60622 original size:18 final size:17
Alignment explanation
Indices: 60599--60641 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
60589 ATATATACAT
60599 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
60617 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
60634 ATAA-AATA
1 ATAATAATA
60642 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:61981 original size:105 final size:105
Alignment explanation
Indices: 61794--62355 Score: 945
Period size: 105 Copynumber: 5.4 Consensus size: 105
61784 GCATTGTTCA
* * **
61794 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
61854 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
61894 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
61959 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
61999 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGGCAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
62064 CAGCGGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
62104 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
62169 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
62209 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
62274 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
62314 AAGTCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
62356 GCTGTAAAAA
Statistics
Matches: 436, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
100 36 0.08
101 1 0.00
102 2 0.00
103 2 0.00
104 2 0.00
105 393 0.90
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:62948 original size:22 final size:22
Alignment explanation
Indices: 62923--62970 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
62913 TGTTTGGTCT
62923 AAGGTTTGGCATTTGATGCTCA
1 AAGGTTTGGCATTTGATGCTCA
*
62945 AAGGTTTGGTATTTGATGCTCA
1 AAGGTTTGGCATTTGATGCTCA
62967 AAGG
1 AAGG
62971 ATTGATGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.35
Consensus pattern (22 bp):
AAGGTTTGGCATTTGATGCTCA
Found at i:63598 original size:20 final size:21
Alignment explanation
Indices: 63575--63634 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
63565 TTTGTCCCTT
*
63575 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
63595 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
63616 TTTTTTGCTTCTT-TTCTTT
1 TTTTTT-ATTCTTGTTCTTT
63635 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 12 0.36
22 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:63645 original size:22 final size:22
Alignment explanation
Indices: 63591--63643 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
63581 ATTTTTGTTC
63591 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
63612 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
63635 TTTCTTTTT
1 TTTCTTTTT
63644 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:67012 original size:17 final size:17
Alignment explanation
Indices: 66969--67012 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
66959 AAATAATAAT
66969 ATAATAATAATAAAAAAA
1 ATAAT-ATAATAAAAAAA
** *
66987 CGAAAATAATAAAAAAA
1 ATAATATAATAAAAAAA
67004 ATAATATAA
1 ATAATATAA
67013 ATATATAAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
ATAATATAATAAAAAAA
Found at i:67289 original size:18 final size:17
Alignment explanation
Indices: 67266--67308 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
67256 ATATATACAT
67266 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
67284 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
67301 ATAA-AATA
1 ATAATAATA
67309 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:70484 original size:16 final size:16
Alignment explanation
Indices: 70460--70530 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
70450 GGTATTACCC
*
70460 GACCAGTTTTCAACCT
1 GACCTGTTTTCAACCT
70476 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
70492 GGCCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
70508 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
70524 GACCTGT
1 GACCTGT
70531 AAATGATCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:70836 original size:23 final size:24
Alignment explanation
Indices: 70799--70848 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
70789 ATGAAAATAA
70799 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
*
70823 AAATT-ATATGGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
70846 AAA
1 AAA
70849 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:71127 original size:20 final size:19
Alignment explanation
Indices: 71098--71149 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
71088 TTTATATAGT
71098 TATATATATATAGTTTATA
1 TATATATATATAGTTTATA
* *
71117 TATACTATATATGGTTTACA
1 TATA-TATATATAGTTTATA
*
71137 TACATATTATATA
1 TATATA-TATATA
71150 AAATTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (19 bp):
TATATATATATAGTTTATA
Found at i:72554 original size:15 final size:15
Alignment explanation
Indices: 72534--72573 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
72524 ATGTTTAATG
72534 ATATATAT-CATA-T
1 ATATATATACATAGT
72547 ATATATATACATAGT
1 ATATATATACATAGT
*
72562 TTATATATACAT
1 ATATATATACAT
72574 GTACTATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 8 0.33
14 4 0.17
15 12 0.50
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (15 bp):
ATATATATACATAGT
Found at i:72581 original size:15 final size:14
Alignment explanation
Indices: 72534--72581 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
72524 ATGTTTAATG
*
72534 ATATATAT-CATAT
1 ATATATATACATGT
72547 ATATATATACATAGT
1 ATATATATACAT-GT
*
72562 TTATATATACATGT
1 ATATATATACATGT
72576 ACTATA
1 A-TATA
72582 AGCTACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 8 0.28
14 5 0.17
15 16 0.55
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (14 bp):
ATATATATACATGT
Found at i:72702 original size:18 final size:18
Alignment explanation
Indices: 72668--72720 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
72658 TTAGGGTTAA
72668 AGTTTGGTTTAAGGTTTG
1 AGTTTGGTTTAAGGTTTG
72686 AGTTTGGGTTT-AGGTTTG
1 AGTTT-GGTTTAAGGTTTG
* *
72704 AGTTTAGTTTAGGGTTT
1 AGTTTGGTTTAAGGTTT
72721 AGAATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (18 bp):
AGTTTGGTTTAAGGTTTG
Found at i:72721 original size:12 final size:11
Alignment explanation
Indices: 72680--72722 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
72670 TTTGGTTTAA
72680 GGTTTGAGTTTG
1 GGTTT-AGTTTG
72692 GGTTTAGGTTTG
1 GGTTTA-GTTTG
*
72704 AGTTTAGTTTAG
1 GGTTTAGTTT-G
72716 GGTTTAG
1 GGTTTAG
72723 AATTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (11 bp):
GGTTTAGTTTG
Found at i:72818 original size:2 final size:2
Alignment explanation
Indices: 72807--72853 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
72797 ATATGGTTTT
* *
72807 TA TA TA -A TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72848 TA TA TA
1 TA TA TA
72854 CATGTACTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:73127 original size:2 final size:2
Alignment explanation
Indices: 73120--73248 Score: 69
Period size: 2 Copynumber: 67.0 Consensus size: 2
73110 GTGTTTCTTA
* *
73120 AT AT AT AT AT AT AT AT -T AT AT -T A- AT -T AT AC AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
73158 AT AT AT -T AGT AT AA AT -T AT A- AT AT AA ACT AT AT -T TT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * *
73198 A- AT TT AT AC AT AT AT AGT TT AT AT AC AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
73240 AT ACT AT AT
1 AT A-T AT AT
73249 TAATATAAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 26
0.68 0.14 0.19
Matches are distributed among these distances:
1 9 0.09
2 80 0.84
3 6 0.06
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73222 original size:17 final size:16
Alignment explanation
Indices: 73193--73321 Score: 66
Period size: 17 Copynumber: 7.4 Consensus size: 16
73183 AACTATATTT
*
73193 TATATAATT-TATACA
1 TATATATTTATATACA
73208 TATATAGTTTATATACA
1 TATATA-TTTATATACA
*
73225 TATAT-TTATATATATA
1 TATATATT-TATATACA
* *
73241 TACTATATTAATATAAA
1 TA-TATATTTATATACA
*
73258 TA-ATATTTTATAAACTA
1 TATATA-TTTATATAC-A
*
73275 TATACTTTTTATAGTTTATACA
1 TATA--TATT-TA---TATACA
73297 TATATAGTTTATATACA
1 TATATA-TTTATATACA
73314 TAGTATAT
1 TA-TATAT
73322 ATAGTTCACA
Statistics
Matches: 88, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
15 11 0.12
16 17 0.19
17 34 0.39
18 7 0.08
19 2 0.02
20 6 0.07
21 2 0.02
22 5 0.06
23 4 0.05
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATATTTATATACA
Found at i:73321 original size:73 final size:73
Alignment explanation
Indices: 73176--73321 Score: 172
Period size: 73 Copynumber: 2.0 Consensus size: 73
73166 GTATAAATTA
* * * *
73176 TAATATAAACTATATTTTATATAATTTATACATATATAGTTTATATACATATATTTATATATATA
1 TAATATAAACTATATTTTATATAATATATACATATATAGTTTATACACATATAGTTATATATACA
73241 TACTATAT
66 TACTATAT
* * *
73249 TAATATAAA-TAATATTTTATA-AACTATATACTTTTTATAGTTTATACATATATAGTT-TATAT
1 TAATATAAACT-ATATTTTATATAA-TATATAC-ATATATAGTTTATACACATATAGTTATATAT
*
73311 ACATAGTATAT
63 ACATACTATAT
73322 ATAGTTCACA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
72 3 0.05
73 39 0.63
74 20 0.32
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (73 bp):
TAATATAAACTATATTTTATATAATATATACATATATAGTTTATACACATATAGTTATATATACA
TACTATAT
Found at i:73339 original size:24 final size:22
Alignment explanation
Indices: 73296--73348 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
73286 TAGTTTATAC
* * *
73296 ATATATAGTTTATATACATAGT
1 ATATATAGTTCACATACATAAT
73318 ATATATAGTTCACATAATCATAAT
1 ATATATAGTTCACAT-A-CATAAT
*
73342 TTATATA
1 ATATATA
73349 TATAGCTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 13 0.52
23 1 0.04
24 11 0.44
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (22 bp):
ATATATAGTTCACATACATAAT
Found at i:73374 original size:16 final size:17
Alignment explanation
Indices: 73343--73399 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 17
73333 AATCATAATT
* *
73343 TATATATATAGCTTATA
1 TATAAATATAGTTTATA
*
73360 -ATAATTATAGTTTATAA
1 TATAAATATAGTTTAT-A
73377 TATAAATATAGTTTATA
1 TATAAATATAGTTTATA
*
73394 TGTAAA
1 TATAAA
73400 CTTATTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 12 0.36
17 7 0.21
18 14 0.42
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (17 bp):
TATAAATATAGTTTATA
Done.