Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012006.1 Kokia drynarioides strain JFW-HI SEQ_127004, 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: 139472
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:1136 original size:29 final size:28
Alignment explanation
Indices: 1091--1594 Score: 416
Period size: 29 Copynumber: 17.2 Consensus size: 28
1081 CCCCAAAGTT
* *
1091 CCCT-AAACTATCTAAAAATTACCGTTTTA
1 CCCTCAAACT-TCCAAAAA-TACCATTTTA
* *
1120 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATACCA-TTTT-A
1150 CCC-CGAAACTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAA-TACCATTTTA
* *
1179 CCCTCAAACTTCTAAAAATCCCAATTTTAA
1 CCCTCAAACTTCCAAAAATACC-ATTTT-A
*
1209 ACCTCAAAACTTCCAAAAATTACCA-TTTA
1 CCCTC-AAACTTCCAAAAA-TACCATTTTA
*
1238 CCC-CTAAACTTCCAAAAATCCCATTTTTA
1 CCCTC-AAACTTCCAAAAATACCA-TTTTA
*
1267 ACCTCTAAACTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAA-TACCATTTTA
* *
1297 CCC-CTAAACTTCTAAAAATCCCATTTTTAA
1 CCCTC-AAACTTCCAAAAATACCA-TTTT-A
* *
1327 CCCTAAAACTTCCAAAAATTATCATTTTA
1 CCCTCAAACTTCCAAAAA-TACCATTTTA
*
1356 CCCTCAAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATACCA-TTTT-A
1386 CCC-CAAAACTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAA-TACCATTTTA
* * *
1415 CCCAT-GAACTT-CTAAAATCCCATTTTA
1 CCC-TCAAACTTCCAAAAATACCATTTTA
*
1442 ACCTCGAAACTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAA-TACCATTTTA
* *
1472 CCCTCGAACTTCCAAAAATCCCATTTTGA
1 CCCTCAAACTTCCAAAAATACCATTTT-A
1501 -CCTCGAAACTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAA-TACCATTTTA
* * * *
1530 CCCCCGAACTCCCAAAAATATCATTTTTGA
1 CCCTCAAACTTCCAAAAATACCA-TTTT-A
*
1560 CCC-CAAAACTTCCAAAAAATACCTTTTTTA
1 CCCTC-AAACTTCC-AAAAATACC-ATTTTA
1590 CCCTC
1 CCCTC
1595 GAATGTCCGA
Statistics
Matches: 390, Mismatches: 47, Indels: 74
0.76 0.09 0.14
Matches are distributed among these distances:
26 1 0.00
27 15 0.04
28 53 0.14
29 143 0.37
30 134 0.34
31 41 0.11
32 3 0.01
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.30
Consensus pattern (28 bp):
CCCTCAAACTTCCAAAAATACCATTTTA
Found at i:1196 original size:59 final size:59
Alignment explanation
Indices: 1095--1594 Score: 627
Period size: 59 Copynumber: 8.5 Consensus size: 59
1085 AAAGTTCCCT
* * * * *
1095 AAACTATCTAAAAATTACCGTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * *
1155 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCTAAAAATCCCAATTTTAAACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCC-ATTTTTAACCCCA
* *
1215 AAACTTCCAAAAATTACCA-TTTACCC-CTAAACTTCCAAAAATCCCATTTTTAACCTCT
1 AAACTTCCAAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCA
* *
1273 AAACTTCCAAAAATTACCATTTTACCC-CTAAACTTCTAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCA
* *
1332 AAACTTCCAAAAATTATCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1391 AAACTTCCAAAAATTACCATTTTACCCAT-GAACTT-CTAAAATCCCA-TTTTAACCTCG
1 AAACTTCCAAAAATTACCATTTTACCC-TCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1448 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * ** *
1506 AAACTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATATCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* *
1565 AAACTTCCAAAAAATACCTTTTTTACCCTC
1 AAACTTCCAAAAATTACC-ATTTTACCCTC
1595 GAATGTCCGA
Statistics
Matches: 395, Mismatches: 36, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
56 1 0.00
57 41 0.10
58 104 0.26
59 205 0.52
60 44 0.11
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.30
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:7167 original size:24 final size:25
Alignment explanation
Indices: 7126--7181 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
7116 TAACGAAAAG
*
7126 AATTATA--AAAATTGAAGTAT-CA
1 AATTATATCAAAATTAAAGTATACA
*
7148 AATTATATCAAAATTAAAGTATATA
1 AATTATATCAAAATTAAAGTATACA
7173 AATTATATC
1 AATTATATC
7182 TTAAATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.24
24 12 0.41
25 10 0.34
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (25 bp):
AATTATATCAAAATTAAAGTATACA
Found at i:9148 original size:20 final size:20
Alignment explanation
Indices: 9097--9149 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9087 AAAATATAAA
*
9097 ATTTGAAATTTTTAAAAATC
1 ATTTCAAATTTTTAAAAATC
* * * *
9117 ATTTTAACTTTTTGAAAATT
1 ATTTCAAATTTTTAAAAATC
9137 ATTTCAAATTTTT
1 ATTTCAAATTTTT
9150 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (20 bp):
ATTTCAAATTTTTAAAAATC
Found at i:12675 original size:37 final size:37
Alignment explanation
Indices: 12625--12699 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
12615 ATAGACACAT
12625 AGCTTCTTTCTTTCACATTTTCCATGTTTTAACAACC
1 AGCTTCTTTCTTTCACATTTTCCATGTTTTAACAACC
12662 AGCTTCTTTCTTTCACATTTTCCATGTTTTAACAACC
1 AGCTTCTTTCTTTCACATTTTCCATGTTTTAACAACC
12699 A
1 A
12700 ACGACAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.27, G:0.05, T:0.45
Consensus pattern (37 bp):
AGCTTCTTTCTTTCACATTTTCCATGTTTTAACAACC
Found at i:16863 original size:22 final size:20
Alignment explanation
Indices: 16838--16907 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
16828 TATATTGTTG
16838 TTTTGGTGCTGTTTGTTTACTA
1 TTTTGGTG-TGTTT-TTTACTA
* *
16860 TTTTAGTTGTTGTTTTTTACTG
1 TTTT-GGTG-TGTTTTTTACTA
* *
16882 TTTTAGTGTTTTTTTTTACTA
1 TTTTGGTG-TGTTTTTTACTA
16903 TTTTG
1 TTTTG
16908 ATTGTTGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 17 0.44
22 14 0.36
23 8 0.21
ACGTcount: A:0.10, C:0.06, G:0.17, T:0.67
Consensus pattern (20 bp):
TTTTGGTGTGTTTTTTACTA
Found at i:16896 original size:21 final size:22
Alignment explanation
Indices: 16847--16918 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
16837 GTTTTGGTGC
16847 TGTTTGTTTACTATTTTAGTTGT
1 TGTTT-TTTACTATTTTAGTTGT
*
16870 TGTTTTTTACTGTTTTAG-TGT
1 TGTTTTTTACTATTTTAGTTGT
*
16891 TTTTTTTTACTATTTT-GATTGT
1 TGTTTTTTACTATTTTAG-TTGT
16913 TGTTTT
1 TGTTTT
16919 GATGCTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 1 0.02
21 17 0.40
22 20 0.47
23 5 0.12
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.69
Consensus pattern (22 bp):
TGTTTTTTACTATTTTAGTTGT
Found at i:16927 original size:21 final size:21
Alignment explanation
Indices: 16903--16945 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16893 TTTTTTACTA
*
16903 TTTTGATTGTTGTTTTGATGC
1 TTTTGATTATTGTTTTGATGC
**
16924 TTTTTTTTATTGTTTTGATGC
1 TTTTGATTATTGTTTTGATGC
16945 T
1 T
16946 GTTATTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.05, G:0.19, T:0.67
Consensus pattern (21 bp):
TTTTGATTATTGTTTTGATGC
Found at i:16965 original size:12 final size:12
Alignment explanation
Indices: 16945--17010 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
16935 GTTTTGATGC
16945 TGTTATTTTTGT
1 TGTTATTTTTGT
*
16957 TG-T-TGTTT-T
1 TGTTATTTTTGT
*
16966 TGTTATTCTTGT
1 TGTTATTTTTGT
* *
16978 TGTT-GTTTTGC
1 TGTTATTTTTGT
* *
16989 TGCTATTTTGGT
1 TGTTATTTTTGT
17001 TGTTATTTTT
1 TGTTATTTTT
17011 ATGCATTTTT
Statistics
Matches: 38, Mismatches: 12, Indels: 8
0.66 0.21 0.14
Matches are distributed among these distances:
9 3 0.08
10 5 0.13
11 11 0.29
12 19 0.50
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:16971 original size:21 final size:21
Alignment explanation
Indices: 16945--17010 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
16935 GTTTTGATGC
16945 TGTTATTTTTGTTGTTGTTTT
1 TGTTATTTTTGTTGTTGTTTT
*
16966 TGTTATTCTTGTTGTTGTTTT
1 TGTTATTTTTGTTGTTGTTTT
* * *
16987 GCTGCTATTTTGGTTGTTATTTT
1 --TGTTATTTTTGTTGTTGTTTT
17010 T
1 T
17011 ATGCATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 21 0.55
23 17 0.45
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.70
Consensus pattern (21 bp):
TGTTATTTTTGTTGTTGTTTT
Found at i:28360 original size:12 final size:12
Alignment explanation
Indices: 28338--28372 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
28328 ATTTTATTAT
28338 AATTGTATAATAA
1 AATT-TATAATAA
28351 AATTTATAATAA
1 AATTTATAATAA
28363 AATTTTATAA
1 AA-TTTATAA
28373 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (12 bp):
AATTTATAATAA
Found at i:28369 original size:13 final size:13
Alignment explanation
Indices: 28338--28372 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
28328 ATTTTATTAT
*
28338 AATTGTATAATAA
1 AATTTTATAATAA
28351 AA-TTTATAATAA
1 AATTTTATAATAA
28363 AATTTTATAA
1 AATTTTATAA
28373 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
AATTTTATAATAA
Found at i:40427 original size:3 final size:3
Alignment explanation
Indices: 40419--40444 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40409 ATTGTGCAGT
40419 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
40445 TTTGTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40504 original size:29 final size:32
Alignment explanation
Indices: 40444--40506 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
40434 GAAGAAGAAG
40444 ATTTGTAATGGCTGTATAATATTATATATTTAA
1 ATTTGTAATGGCTGTAT-ATATTATATATTTAA
*
40477 ATTTGTAATGGTTGTAT-T-TTA-ATATTTAA
1 ATTTGTAATGGCTGTATATATTATATATTTAA
40506 A
1 A
40507 ATATAGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 9 0.31
30 3 0.10
31 1 0.03
33 16 0.55
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.51
Consensus pattern (32 bp):
ATTTGTAATGGCTGTATATATTATATATTTAA
Found at i:41875 original size:28 final size:29
Alignment explanation
Indices: 41813--41930 Score: 84
Period size: 28 Copynumber: 4.2 Consensus size: 29
41803 CAACTCTGGA
* * *
41813 TTTTAGCTCGGATAGAGCA-TAATTTTGA-
1 TTTTGGCTCGGGTAGAGCATTAATTCT-AT
*
41841 TTCTGGCTCGGGTAGAGC-TTAATTCTAT
1 TTTTGGCTCGGGTAGAGCATTAATTCTAT
* **
41869 TTTTGGCTTGGGTAGAGCATT-ATTCTGC
1 TTTTGGCTCGGGTAGAGCATTAATTCTAT
* ** * *
41897 TTTTAGCTCGATTAGAGCGTTAA-TCTGT
1 TTTTGGCTCGGGTAGAGCATTAATTCTAT
41925 TTTTGG
1 TTTTGG
41931 TTCAAAAATA
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
27 1 0.01
28 67 0.94
29 3 0.04
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (29 bp):
TTTTGGCTCGGGTAGAGCATTAATTCTAT
Found at i:43224 original size:23 final size:23
Alignment explanation
Indices: 43194--43238 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
43184 TTATAGTTAA
43194 TGTAAAAATATCAATGATGGTAG
1 TGTAAAAATATCAATGATGGTAG
*
43217 TGTAAAAATATCAGTGATGGTA
1 TGTAAAAATATCAATGATGGTA
43239 AGATTAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.31
Consensus pattern (23 bp):
TGTAAAAATATCAATGATGGTAG
Found at i:44041 original size:30 final size:30
Alignment explanation
Indices: 44005--44065 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
43995 TTTTTAAACC
* *
44005 CTAAACCCTTTTCCACATACCTCTCTTCTT
1 CTAAACCCATTTCCACACACCTCTCTTCTT
*
44035 CTAAACCCATTTCCACACACTTCTCTTCTT
1 CTAAACCCATTTCCACACACCTCTCTTCTT
44065 C
1 C
44066 ATCATTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (30 bp):
CTAAACCCATTTCCACACACCTCTCTTCTT
Found at i:44811 original size:22 final size:20
Alignment explanation
Indices: 44754--44802 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
44744 TTGGTTGTTA
*
44754 TTTTTGTGTTTTTTTTACTG
1 TTTTGGTGTTTTTTTTACTG
*
44774 TTTTGGAGCTTTTTTTTTACTG
1 TTTTGGTG--TTTTTTTTACTG
44796 TTTTGGT
1 TTTTGGT
44803 TGTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
22 18 0.75
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.69
Consensus pattern (20 bp):
TTTTGGTGTTTTTTTTACTG
Found at i:44842 original size:15 final size:13
Alignment explanation
Indices: 44830--44864 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
44820 TTTTGCTGTT
44830 ATTTTTGTTGCTG
1 ATTTTTGTTGCTG
*
44843 CTTTTTGTTGCT-
1 ATTTTTGTTGCTG
44855 ATTTTTGTTG
1 ATTTTTGTTG
44865 TTTTTAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.06, C:0.09, G:0.20, T:0.66
Consensus pattern (13 bp):
ATTTTTGTTGCTG
Found at i:44847 original size:13 final size:12
Alignment explanation
Indices: 44819--44864 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
44809 TTTCATGTTG
* *
44819 TTTTTGCTGTTA
1 TTTTTGTTGCTA
*
44831 TTTTTGTTGCTGC
1 TTTTTGTTGCT-A
44844 TTTTTGTTGCTA
1 TTTTTGTTGCTA
44856 TTTTTGTTG
1 TTTTTGTTG
44865 TTTTTAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.04, C:0.09, G:0.20, T:0.67
Consensus pattern (12 bp):
TTTTTGTTGCTA
Found at i:44885 original size:22 final size:22
Alignment explanation
Indices: 44860--44901 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
44850 TTGCTATTTT
* *
44860 TGTTGTTTTTAATGTTGTTTAC
1 TGTTATTTTTAATGCTGTTTAC
*
44882 TGTTATTTTTACTGCTGTTT
1 TGTTATTTTTAATGCTGTTT
44902 TGGTTGTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (22 bp):
TGTTATTTTTAATGCTGTTTAC
Found at i:44891 original size:43 final size:43
Alignment explanation
Indices: 44851--44935 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
44841 TGCTTTTTGT
*
44851 TGCTATTTTTGTTGTT-TTTAATGTTGTTT-ACTGTTATTTTTAC
1 TGCTATTTTGGTTGTTATTT-ATGTTGTTTGA-TGTTATTTTTAC
* *
44894 TGCTGTTTTGGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 TGCTATTTTGGTTGTTATTTATGTTGTTT-GATGTTATTTTT
44936 TATGCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 22 0.61
44 13 0.36
45 1 0.03
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.66
Consensus pattern (43 bp):
TGCTATTTTGGTTGTTATTTATGTTGTTTGATGTTATTTTTAC
Found at i:45133 original size:38 final size:38
Alignment explanation
Indices: 45047--45131 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
45037 CTTAATATAA
* * *
45047 ATTTTTTTAATGTATTTTAAATTTATTTATTTTTTAAT
1 ATTTTTTTAATGTATTTTAAATGTATTTATATATTAAT
*
45085 ATTTGTTTTAATGT-TTTTAAGTGTATTTGATATATTATAT
1 ATTT-TTTTAATGTATTTTAAATGTATTT-ATATATTA-AT
45125 ATTTTTT
1 ATTTTTT
45132 AAATTTGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 16 0.40
39 18 0.45
40 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (38 bp):
ATTTTTTTAATGTATTTTAAATGTATTTATATATTAAT
Found at i:50376 original size:16 final size:16
Alignment explanation
Indices: 50357--50403 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
50347 AATTTTTAAT
50357 AAATAAAAAATATATA
1 AAATAAAAAATATATA
* *
50373 AAATTAATACATAT-TA
1 AAA-TAAAAAATATATA
50389 AAATAAAACAATATA
1 AAATAAAA-AATATA
50404 AATATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 4 0.17
16 12 0.50
17 8 0.33
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:55440 original size:4 final size:4
Alignment explanation
Indices: 55431--55471 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
55421 AATAGATGGT
* *
55431 TGTA TGTA TGTA TGTA TGTA TGTA TGTT TGTA CGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
55472 TCTTTGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:57693 original size:21 final size:22
Alignment explanation
Indices: 57667--57709 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
57657 GTAAATATTA
* *
57667 AATATAAATATTTA-TGAAGAT
1 AATATAAAAATATATTGAAGAT
57688 AATATAAAAATATATTGAAGAT
1 AATATAAAAATATATTGAAGAT
57710 TGATAGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (22 bp):
AATATAAAAATATATTGAAGAT
Found at i:82388 original size:59 final size:59
Alignment explanation
Indices: 82320--82645 Score: 329
Period size: 59 Copynumber: 5.5 Consensus size: 59
82310 TTCGGACATC
* * * * *
82320 CGGGAGTAAAATAGTAATTTTTTGATGTTTCGAGGTCAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* * * * *
82379 CGGGGGTAAAATGTTAATTTTTAGAAGTTT-TAGGGTTAAAAATAGGATTTTTGGGAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGAAGTT
** * * **
82438 TAGGGGTAAAATGATAATTTTTAGAAGGTTC-AGGGTCAAAAATGAAATTTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGAAG-TT
* *
82498 AGGGGGT-AAATGGTAA-TTTTAGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTA-GAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
** * * **
82556 CGATGGTAAAATGGTAA-TTTTAGGAAGTTTCGGGGTTAAAAATGATATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTA-GAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
* *
82615 CGAGGGTAAAATGGTAATTTTTGGACAGTTT
1 CGGGGGTAAAATGGTAATTTTTAGA-AGTTT
82646 AAGGACCTTC
Statistics
Matches: 225, Mismatches: 34, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
58 12 0.05
59 197 0.88
60 16 0.07
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:82389 original size:29 final size:29
Alignment explanation
Indices: 82357--82644 Score: 173
Period size: 29 Copynumber: 9.8 Consensus size: 29
82347 TTTCGAGGTC
* *
82357 AAAAATGGGATTTTTGAAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* * ** *
82386 -AAAATGTTAATTTTTAGAAGTTTTAGGGTT
1 AAAAATG-GAATTTTTGGAAG-TTCGGGGGT
* **
82416 AAAAATAGG-ATTTTTGGGAGTTTAGGGGT
1 AAAAAT-GGAATTTTTGGAAGTTCGGGGGT
* * *
82445 -AAAATGATAATTTTTAGAAGGTTC-AGGGT
1 AAAAATG-GAATTTTTGGAA-GTTCGGGGGT
* *
82474 CAAAAATGAAATTTTTGGAAGTTTAGGGGGT
1 -AAAAATGGAATTTTTGGAAG-TTCGGGGGT
*
82505 --AAATGGTAATTTTAGGAAGTTTC-GGGGT
1 AAAAATGG-AATTTTTGGAAG-TTCGGGGGT
* **
82533 CAAAAATGGGATTTTTGGAAGTTCGATGGT
1 -AAAAATGGAATTTTTGGAAGTTCGGGGGT
* *
82563 -AAAATGGTAATTTTAGGAAGTTTCGGGGTT
1 AAAAATGG-AATTTTTGGAAG-TTCGGGGGT
*
82593 AAAAAT-GATATTTTTGGAAGTTCGAGGGT
1 AAAAATGGA-ATTTTTGGAAGTTCGGGGGT
82622 -AAAATGGTAATTTTTGGACAGTT
1 AAAAATGG-AATTTTTGGA-AGTT
82645 TAAGGACCTT
Statistics
Matches: 201, Mismatches: 35, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.00
28 33 0.16
29 75 0.37
30 65 0.32
31 26 0.13
32 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:82429 original size:30 final size:28
Alignment explanation
Indices: 82395--82501 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 28
82385 TAAAATGTTA
82395 ATTTTTAGAAGTTTTAGGGTTAAAAATAGG
1 ATTTTTAGAAG-TTTAGGGTTAAAAATA-G
* * *
82425 ATTTTTGGGAGTTTAGGGGTAAAATGATA-
1 ATTTTTAGAAGTTTAGGGTTAAAA--ATAG
* * *
82454 ATTTTTAGAAGGTTCAGGGTCAAAAATGAA
1 ATTTTTAGAA-GTTTAGGGTTAAAAAT-AG
*
82484 ATTTTTGGAAGTTTAGGG
1 ATTTTTAGAAGTTTAGGG
82502 GGTAAATGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
28 2 0.03
29 28 0.45
30 29 0.47
31 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (28 bp):
ATTTTTAGAAGTTTAGGGTTAAAAATAG
Found at i:84457 original size:6 final size:6
Alignment explanation
Indices: 84441--84511 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
84431 ATTATTTAAA
* * *
84441 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT CAAA-A TAAACT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* *
84488 TAATTT TAAA-A TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
84512 GTTGGGCCCG
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.04
5 9 0.18
6 33 0.66
7 6 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:84468 original size:17 final size:17
Alignment explanation
Indices: 84448--84511 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
84438 AAATAAATTT
*
84448 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
84465 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
* *
84482 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
84499 TAAATTTAAATTT
1 TAAATTTAAATTT
84512 GTTGGGCCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:92652 original size:2 final size:2
Alignment explanation
Indices: 92645--92669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
92635 AAATATCTTC
92645 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
92670 TATTACAAGG
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:95282 original size:24 final size:24
Alignment explanation
Indices: 95261--95312 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
95251 TACTTGTACT
* *
95261 TGAAATTGAGATTGCATCTGTATC
1 TGAAACTGAGAATGCATCTGTATC
*
95285 TGAAACTGAGAATGTATCTGTATC
1 TGAAACTGAGAATGCATCTGTATC
95309 TGAA
1 TGAA
95313 TTGCATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (24 bp):
TGAAACTGAGAATGCATCTGTATC
Found at i:97305 original size:16 final size:17
Alignment explanation
Indices: 97277--97308 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
97267 CAAATATTTT
97277 TATAAATATATTTTCAA
1 TATAAATATATTTTCAA
97294 TATAAA-ATATTTTCA
1 TATAAATATATTTTCA
97309 TTCATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAAATATATTTTCAA
Found at i:100709 original size:24 final size:24
Alignment explanation
Indices: 100680--100736 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
100670 CTATCGTCTG
100680 CCACCGCTGAAGGAAGCCTTACCA
1 CCACCGCTGAAGGAAGCCTTACCA
*
100704 CCACCGCTGAAGGAAGCTTTACCA
1 CCACCGCTGAAGGAAGCCTTACCA
*
100728 CCACTGCTG
1 CCACCGCTG
100737 TGTAACCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.37, G:0.21, T:0.16
Consensus pattern (24 bp):
CCACCGCTGAAGGAAGCCTTACCA
Found at i:101875 original size:30 final size:30
Alignment explanation
Indices: 101710--101994 Score: 187
Period size: 29 Copynumber: 9.9 Consensus size: 30
101700 TTTAGGAAAA
* *
101710 TTTGAGGTTTAAAAATGGAATTTTTAGACA--
1 TTTGAGG-GTAAAAATGGAATTTTTGGA-AGT
* **
101740 TTCGAGGGTAAAAGGGGTAA-TTTT-GAGAGT
1 TTTGAGGGTAAAAATGG-AATTTTTGGA-AGT
101770 TTT-AGGGGTAAAAATGGAA--TTTGGAAGT
1 TTTGA-GGGTAAAAATGGAATTTTTGGAAGT
* **
101798 TTCG-GGGGCAAAATGGAATTTTTGGAAGT
1 TTTGAGGGTAAAAATGGAATTTTTGGAAGT
101827 TTTG-GGGT-----T-GAGATTTTTGGAAGT
1 TTTGAGGGTAAAAATGGA-ATTTTTGGAAGT
*
101851 TTTGAGGTTAAAAATGGAATTTTTGGAAG-
1 TTTGAGGGTAAAAATGGAATTTTTGGAAGT
* *
101880 TTTGGGGGTAAAAATGGGATTTTTGGAAGT
1 TTTGAGGGTAAAAATGGAATTTTTGGAAGT
** *
101910 TCAG-GGGTAAAAATGGGATTTTTGGAAGT
1 TTTGAGGGTAAAAATGGAATTTTTGGAAGT
* *
101939 TTCG-GAGTCAAAAAT-GAGATTTTTGGAAG-
1 TTTGAGGGT-AAAAATGGA-ATTTTTGGAAGT
* * *
101968 TTCGGGGGTAAAAATGGGATTTTTGGA
1 TTTGAGGGTAAAAATGGAATTTTTGGA
101995 CAATTTAAGG
Statistics
Matches: 209, Mismatches: 25, Indels: 43
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.01
24 17 0.08
25 3 0.01
27 12 0.06
28 11 0.05
29 107 0.51
30 55 0.26
31 2 0.01
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (30 bp):
TTTGAGGGTAAAAATGGAATTTTTGGAAGT
Found at i:101952 original size:59 final size:58
Alignment explanation
Indices: 101835--101994 Score: 230
Period size: 59 Copynumber: 2.7 Consensus size: 58
101825 GTTTTGGGGT
** * * * *
101835 TGAGATTTTTGGAAGTTTTGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAA
1 TGAGATTTTTGGAAGTTCAG-GGGTAAAAATGGGATTTTTGGAAGTTTCGGAGTAAAAA
*
101894 TGGGATTTTTGGAAGTTCAGGGGTAAAAATGGGATTTTTGGAAGTTTCGGAGTCAAAAA
1 TGAGATTTTTGGAAGTTCAGGGGTAAAAATGGGATTTTTGGAAGTTTCGGAGT-AAAAA
*
101953 TGAGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGA
1 TGAGATTTTTGGAAGTTCAGGGGTAAAAATGGGATTTTTGGA
101995 CAATTTAAGG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 29 0.32
59 62 0.68
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.35
Consensus pattern (58 bp):
TGAGATTTTTGGAAGTTCAGGGGTAAAAATGGGATTTTTGGAAGTTTCGGAGTAAAAA
Found at i:102547 original size:14 final size:14
Alignment explanation
Indices: 102528--102566 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
102518 AAAAAAAACC
102528 AAATCCTCTCCAAA
1 AAATCCTCTCCAAA
102542 AAATCCTCTCCAAA
1 AAATCCTCTCCAAA
102556 AAATCCTCTCC
1 AAATCCTCTCC
102567 TCCTTCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCTCTCCAAA
Found at i:103191 original size:3 final size:3
Alignment explanation
Indices: 103086--103173 Score: 79
Period size: 3 Copynumber: 28.0 Consensus size: 3
103076 TTTTCCTTTT
* * * **
103086 TTA TTA TTAA TGA TTA ATA TTA TTA TTA TTA TTA TTA TTGA TGA GGCA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA
103134 GTTA TTA CTTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
103174 ATAGCACATT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
2 2 0.03
3 59 0.83
4 10 0.14
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:103985 original size:17 final size:17
Alignment explanation
Indices: 103947--104017 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
103937 TAATGGACTT
*
103947 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAAATT-AA
*
103965 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATTAA
* *
103982 TTTATATTTAAAATAAA
1 TTTAAATTTAAAATTAA
* *
103999 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATTAA
104016 TT
1 TT
104018 AAAAAGGGGC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 32 0.71
18 13 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:104523 original size:35 final size:33
Alignment explanation
Indices: 104445--104524 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 33
104435 AAATGAGTAA
* *
104445 ATTTCCATTTTGATTCTTTTGTATTTTTTATTT
1 ATTTCAATTTTGATCCTTTTGTATTTTTTATTT
*
104478 GTTTCAATTTT-ATCCTTTTGTACTATTTTTAATTT
1 ATTTCAATTTTGATCCTTTTGTA-T-TTTTT-ATTT
*
104513 ATTTCGATTTTG
1 ATTTCAATTTTG
104525 CCCAATAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
32 10 0.26
33 10 0.26
34 5 0.13
35 13 0.34
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (33 bp):
ATTTCAATTTTGATCCTTTTGTATTTTTTATTT
Found at i:104697 original size:30 final size:30
Alignment explanation
Indices: 104635--104699 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
104625 TTTTATTTAG
* *
104635 AAATTGTGTTTTGACCCTCAAACTATCCAA
1 AAATTATGTTTTGACCCTCAAACTATCAAA
* *
104665 AAATTATGTTTTGA-CCTCCAAATTGTCAAA
1 AAATTATGTTTTGACCCT-CAAACTATCAAA
104695 AAATT
1 AAATT
104700 CGAATTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.35
Consensus pattern (30 bp):
AAATTATGTTTTGACCCTCAAACTATCAAA
Found at i:104728 original size:30 final size:29
Alignment explanation
Indices: 104693--104892 Score: 79
Period size: 30 Copynumber: 6.7 Consensus size: 29
104683 CAAATTGTCA
104693 AAAAATTCGAATTTGACCCCTAAACTTTTC
1 AAAAATT-GAATTTGACCCCTAAACTTTTC
* * *
104723 AAAAATT-ATCTTTTAACCCTTAAAC-TTTC
1 AAAAATTGA--ATTTGACCCCTAAACTTTTC
* * *
104752 TAAACATT-AAGTTTTAACCCCTTTAA-TTTTCC
1 -AAAAATTGAA--TTTGACCCC-TAAACTTTT-C
* * **
104784 AAAAATTTGGATTTAACCCCTAAACTTCCC
1 AAAAA-TTGAATTTGACCCCTAAACTTTTC
* *
104814 AAAAATTTAGATTTGACCCC-AAACTTTTG
1 AAAAATTGA-ATTTGACCCCTAAACTTTTC
* * * *
104843 AAAGATTCAAATTTGGCCCCAAAAC-TTTC
1 AAAAATT-GAATTTGACCCCTAAACTTTTC
* **
104872 TAAAATTTGTTTTTGACCCCT
1 -AAAAATTGAATTTGACCCCT
104893 TTTCCTAATT
Statistics
Matches: 126, Mismatches: 29, Indels: 31
0.68 0.16 0.17
Matches are distributed among these distances:
28 1 0.01
29 38 0.30
30 62 0.49
31 21 0.17
32 3 0.02
33 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAAATTGAATTTGACCCCTAAACTTTTC
Found at i:104837 original size:29 final size:30
Alignment explanation
Indices: 104703--104839 Score: 98
Period size: 30 Copynumber: 4.6 Consensus size: 30
104693 AAAAATTCGA
* ** *
104703 ATTTGACCCCTAAACTTTTCAAAAA-TTATC
1 ATTTAACCCCTAAACTTCCCAAAAATTTA-G
* * * * * *
104733 TTTTAACCCTTAAACTTTCTAAACATTAAG
1 ATTTAACCCCTAAACTTCCCAAAAATTTAG
* * * * *
104763 TTTTAACCCCTTTAATTTTCCAAAAATTTGG
1 ATTTAACCCC-TAAACTTCCCAAAAATTTAG
104794 ATTTAACCCCTAAACTTCCCAAAAATTTAG
1 ATTTAACCCCTAAACTTCCCAAAAATTTAG
*
104824 ATTTGACCCC-AAACTT
1 ATTTAACCCCTAAACTT
104840 TTGAAAGATT
Statistics
Matches: 84, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
29 6 0.07
30 53 0.63
31 25 0.30
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
ATTTAACCCCTAAACTTCCCAAAAATTTAG
Found at i:109834 original size:2 final size:2
Alignment explanation
Indices: 109829--109874 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
109819 TATGGTGTAC
109829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109871 AT AT
1 AT AT
109875 CTATTTTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111818 original size:29 final size:29
Alignment explanation
Indices: 111686--112021 Score: 165
Period size: 29 Copynumber: 11.4 Consensus size: 29
111676 TTCTTGGGGC
* *
111686 AAAATGGTAATTTTGGGAAAGTTCG-GGGTTAA
1 AAAATGG-AATTTTTGG-AGGTTCGAGGG-T-A
* * ** *
111718 AAAATGAAATTTTTAGACATTTGAGGGT-
1 AAAATGGAATTTTTGGAGGTTCGAGGGTA
* *
111746 AAAAGGGTAA-TTTTGAGAGTTTCGA-GGTCA
1 AAAATGG-AATTTTTG-GAGGTTCGAGGGT-A
*
111776 AAAATAG-ATATTTTGGAGGTTCGAGGGTA
1 AAAATGGAAT-TTTTGGAGGTTCGAGGGTA
* * *
111805 AATATGGAATTTTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGG-AGGTTCGAGGGT-A
* * * * *
111835 AAAAAGGTA-TTTTGGAAGTTTGA-GGAA
1 AAAATGGAATTTTTGGAGGTTCGAGGGTA
* * * *
111862 AAAATGGAATTTTTGAAAGTT-TAGAGATA
1 AAAATGGAATTTTTGGAGGTTCGAG-GGTA
* * *
111891 AAAATGAAATTTTTGGAAGTTTCG-GGATCA
1 AAAATGGAATTTTTGG-AGGTTCGAGGGT-A
* * *
111921 AAAATGGAATTTTTGAAAGTTTC-AAGGTA
1 AAAATGGAATTTTTG-GAGGTTCGAGGGTA
*
111950 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGG-AGGTTCGAGGGT-A
* *
111980 AAAATGGAATTTTTGAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAGGTTCGAGGGTA
112009 AAAATGGAATTTT
1 AAAATGGAATTTT
112022 CGGACAGTTT
Statistics
Matches: 236, Mismatches: 44, Indels: 51
0.71 0.13 0.15
Matches are distributed among these distances:
27 9 0.04
28 30 0.13
29 102 0.43
30 79 0.33
31 10 0.04
32 6 0.03
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAGGTTCGAGGGTA
Found at i:111826 original size:59 final size:58
Alignment explanation
Indices: 111756--112021 Score: 251
Period size: 59 Copynumber: 4.6 Consensus size: 58
111746 AAAAGGGTAA
* *
111756 TTTTGAGAGTTTCGAGGTCAAAAATAGATATTTTGG-AGGTTCGAGGGT-AAATATGGAAT
1 TTTTGAAAGTTTCGAGGT-AAAAATAGA-ATTTTGGAAGGTTCGA-GGTCAAAAATGGAAT
* * * * * *
111815 TTTTGGAAGTTTTGGGGTCAAAAA-AGGTATTTTGGAA-GTTTGAGG-AAAAAATGGAAT
1 TTTTGAAAGTTTCGAGGT-AAAAATA-GAATTTTGGAAGGTTCGAGGTCAAAAATGGAAT
* * *
111872 TTTTGAAAGTTTAGAGATAAAAAT-GAAATTTTTGGAAGTTTCG-GGATCAAAAATGGAAT
1 TTTTGAAAGTTTCGAGGTAAAAATAG-AA-TTTTGGAAGGTTCGAGG-TCAAAAATGGAAT
* * *
111931 TTTTGAAAGTTTCAAGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTGAAAGTTTCGAGGTAAAAATAGAA-TTTTGGAAGGTTCGAGGTCAAAAATGGAAT
*
111990 TTTTGAAAG-TTCGAGGGTAAAAATGGAATTTT
1 TTTTGAAAGTTTCGA-GGTAAAAATAGAATTTT
112022 CGGACAGTTT
Statistics
Matches: 176, Mismatches: 19, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
55 1 0.01
56 6 0.03
57 36 0.20
58 24 0.14
59 106 0.60
60 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
TTTTGAAAGTTTCGAGGTAAAAATAGAATTTTGGAAGGTTCGAGGTCAAAAATGGAAT
Found at i:111926 original size:30 final size:29
Alignment explanation
Indices: 111786--112036 Score: 219
Period size: 29 Copynumber: 8.6 Consensus size: 29
111776 AAAATAGATA
* * *
111786 TTTTGG-AGGTTCGAGGGTAAATATGGAAT
1 TTTTGGAAGTTTCG-GGATAAAAATGGAAT
* * * *
111815 TTTTGGAAGTTTTGGGGTCAAAAAAGGTA-
1 TTTTGGAAGTTTCGGGAT-AAAAATGGAAT
111844 TTTTGGAAGTTT-GAGGA-AAAAATGGAAT
1 TTTTGGAAGTTTCG-GGATAAAAATGGAAT
* * * *
111872 TTTTGAAAGTTTAGAGATAAAAATGAAAT
1 TTTTGGAAGTTTCGGGATAAAAATGGAAT
111901 TTTTGGAAGTTTCGGGATCAAAAATGGAAT
1 TTTTGGAAGTTTCGGGAT-AAAAATGGAAT
* *
111931 TTTTGAAAGTTTCAAGG-TAAAAATGGAAT
1 TTTTGGAAGTTTC-GGGATAAAAATGGAAT
111960 TTTTGGAAGTTTCGAGG-TCAAAAATGGAAT
1 TTTTGGAAGTTTCG-GGAT-AAAAATGGAAT
* *
111990 TTTTGAAAG-TTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCG-GGATAAAAATGGAAT
* *
112019 TTTCGGACAGTTTAGGGA
1 TTTTGGA-AGTTTCGGGA
112037 CCTTCAGGGC
Statistics
Matches: 185, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
27 8 0.04
28 14 0.08
29 99 0.54
30 59 0.32
31 5 0.03
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
TTTTGGAAGTTTCGGGATAAAAATGGAAT
Found at i:112035 original size:29 final size:27
Alignment explanation
Indices: 111741--112035 Score: 182
Period size: 29 Copynumber: 10.1 Consensus size: 27
111731 TAGACATTTG
*
111741 AGGGT-AAAAGGGTAATTTT-GAGAGTTT
1 AGGGTAAAAATGG-AATTTTGGA-AGTTT
* * * *
111768 CGAGGTCAAAAATAGATATTTTGGAGGTTCG
1 AG-GGT-AAAAATGGA-ATTTTGGAAGTT-T
*
111799 AGGGTAAATATGGAATTTTTGGAAGTTTT
1 AGGGTAAAAATGGAA-TTTTGGAAG-TTT
* * *
111828 GGGGTCAAAAAAGGTATTTTGGAAGTTT
1 AGGGT-AAAAATGGAATTTTGGAAGTTT
* *
111856 -GAGGAAAAAATGGAATTTTTGAAAGTTT
1 AG-GGTAAAAATGGAA-TTTTGGAAGTTT
* *
111884 AGAGATAAAAATGAAATTTTTGGAAGTTT
1 AG-GGTAAAAATGGAA-TTTTGGAAGTTT
* *
111913 CGGGATCAAAAATGGAATTTTTGAAAGTTT
1 AGGG-T-AAAAATGGAA-TTTTGGAAGTTT
*
111943 CAAGGTAAAAATGGAATTTTTGGAAGTTT
1 -AGGGTAAAAATGGAA-TTTTGGAAGTTT
* * *
111972 CGAGGTCAAAAATGGAATTTTTGAAAGTTCG
1 AG-GGT-AAAAATGGAA-TTTTGGAAGTT-T
112003 AGGGTAAAAATGGAATTTTCGGACAGTTT
1 AGGGTAAAAATGGAATTTT-GGA-AGTTT
112032 AGGG
1 AGGG
112036 ACCTTCAGGG
Statistics
Matches: 212, Mismatches: 36, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
27 10 0.05
28 25 0.12
29 96 0.45
30 75 0.35
31 6 0.03
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (27 bp):
AGGGTAAAAATGGAATTTTGGAAGTTT
Found at i:115668 original size:27 final size:27
Alignment explanation
Indices: 115636--115696 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
115626 CACCTTGAGG
115636 CGATTATCATACTCTTTTTATCCTTCA
1 CGATTATCATACTCTTTTTATCCTTCA
115663 CGATTATCATACTCTTTTTATCCTTCA
1 CGATTATCATACTCTTTTTATCCTTCA
*
115690 TGATTAT
1 CGATTAT
115697 TCATTCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (27 bp):
CGATTATCATACTCTTTTTATCCTTCA
Found at i:120431 original size:96 final size:96
Alignment explanation
Indices: 120257--120438 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
120247 AAGGATGTTT
* * * *
120257 GATTATCTCGATTTGAGGAAAGATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAGTCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAACTCGAAGA
120322 TAAGAAAACATTGCCTCGATTAAGGGTATTC
66 TAAGAAAACATTGCCTCGATTAAGGGTATTC
* * * *
120353 GATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAATGTGCAAATTTTCGAAACTCGAA-
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-AAACTCGAAG
* *
120417 ATAA-AAGAATATTGCCTTGATT
65 ATAAGAA-AACATTGCCTCGATT
120439 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
95 2 0.03
96 65 0.88
97 7 0.09
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAACTCGAAGA
TAAGAAAACATTGCCTCGATTAAGGGTATTC
Found at i:121831 original size:18 final size:19
Alignment explanation
Indices: 121798--121837 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
121788 AAGATTGTAA
121798 TTTGGACTTTGTATTT-AT
1 TTTGGACTTTGTATTTAAT
121816 TTTGGACTTT-TAATTTAAT
1 TTTGGACTTTGT-ATTTAAT
121835 TTT
1 TTT
121838 ATTTGGGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 14 0.70
19 5 0.25
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.62
Consensus pattern (19 bp):
TTTGGACTTTGTATTTAAT
Found at i:136112 original size:7 final size:7
Alignment explanation
Indices: 136100--136124 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
136090 TGAAGGGAGA
136100 CAATTTG
1 CAATTTG
136107 CAATTTG
1 CAATTTG
136114 CAATTTG
1 CAATTTG
136121 CAAT
1 CAAT
136125 CAGTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (7 bp):
CAATTTG
Found at i:139023 original size:18 final size:18
Alignment explanation
Indices: 138989--139023 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
138979 AACAAGACAA
* *
138989 AATAAAATTTATTTTAAC
1 AATAAAATTAATATTAAC
139007 AATAAAATTAATATTAA
1 AATAAAATTAATATTAA
139024 TACATTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAAAATTAATATTAAC
Done.