Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014847.1 Kokia drynarioides strain JFW-HI SEQ_129890, 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: 36462
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:858 original size:15 final size:15
Alignment explanation
Indices: 835--864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
825 ACCTGATAGA
835 TTTTGTAAATTATTT
1 TTTTGTAAATTATTT
*
850 TTTTTTAAATTATTT
1 TTTTGTAAATTATTT
865 ATGTCTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTGTAAATTATTT
Found at i:11819 original size:14 final size:14
Alignment explanation
Indices: 11790--11829 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
11780 CATTACATAT
*
11790 TTTGTTCTTTTGTTC
1 TTTGTT-TTTTCTTC
11805 TTTGTTTTTTCTTC
1 TTTGTTTTTTCTTC
11819 TTTGTCTTTTT
1 TTTGT-TTTTT
11830 GTCTGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (14 bp):
TTTGTTTTTTCTTC
Found at i:12997 original size:233 final size:227
Alignment explanation
Indices: 12529--13083 Score: 663
Period size: 233 Copynumber: 2.4 Consensus size: 227
12519 ATTTGTTTTA
* * *
12529 ACCCACTTCTCCGTACCTCACTAGGAAGATGAGATTTGAAGTCTCACTCCACT--CCACTGTAAC
1 ACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCACCACTGTATC
* * * *
12592 CTCAAGGACATTGAGCTCTACTTCGTTGTTTTAATCTAACCTACTATTTTGACCCACTTCTCTAT
66 CTCAAGGACGTTGAGCTCTACTTCATTGTTTTGATCTAACCTACTATTTTAACCCACTTCTCTAT
* * * * *
12657 ACGTCAGGAAGATGGGATTTGAAGTCTCACCCCACTCCACTGAATTCTCAAGGACGTTGAGCTTG
131 ACCTCAGGAAGATGGGATTTAAAGTCTCACCCCACTCCACTGAATCCTCAAGGACGTTAAGCTCG
** *
12722 GCTTTGTTGTTTTGATTCAACACACTATTTTG
196 GCTTCATTGTTTTGATTCAACACACTATATTG
*
12754 ACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGCACTGT
1 ACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACT-CAC--CACTGT
* * *
12819 ATCCTTAAGGACGTTGAGCTCGACTTCATTGTTTTGATTTAACAC-ACTATTTTAACCCACTTCT
63 ATCCTCAAGGACGTTGAGCTCTACTTCATTGTTTTGATCTAAC-CTACTATTTTAACCCACTTCT
* * * * * * *
12883 CTGTTCCTCACCAGGAAGATGGGATTTAAAGTCTCTCTCTACTCCACT-ATATCCTTAGGGACGT
127 CTATACCT---CAGGAAGATGGGATTTAAAGTCTCACCCCACTCCACTGA-ATCCTCAAGGACGT
* * *
12947 TAAGCTCGGCTTCATTGTTTTGATTCAACATATTGTATTG
188 TAAGCTCGGCTTCATTGTTTTGATTCAACACACTATATTG
* * * * *
12987 ACCTACTTCTCTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCA--CACCATTGTATC
1 ACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCACCACTGTATC
* * *
13050 CTCAGGGACGTTGAGCTCTACCTCATTATTTTGA
66 CTCAAGGACGTTGAGCTCTACTTCATTGTTTTGA
13084 CCCACTTCTT
Statistics
Matches: 281, Mismatches: 39, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
225 50 0.18
228 38 0.14
230 68 0.24
231 1 0.00
232 1 0.00
233 123 0.44
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (227 bp):
ACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTCCACTCACCACTGTATC
CTCAAGGACGTTGAGCTCTACTTCATTGTTTTGATCTAACCTACTATTTTAACCCACTTCTCTAT
ACCTCAGGAAGATGGGATTTAAAGTCTCACCCCACTCCACTGAATCCTCAAGGACGTTAAGCTCG
GCTTCATTGTTTTGATTCAACACACTATATTG
Found at i:13006 original size:114 final size:114
Alignment explanation
Indices: 12524--13083 Score: 610
Period size: 114 Copynumber: 4.9 Consensus size: 114
12514 TCACTATTTG
* * * * *
12524 TTTTAACCCACTTCTCCGTACCTCACTAGGAAGATGAGATTTGAAGTCTCACTCCACTCCACTGT
1 TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTAT
* * * * *
12589 AACCTCAAGGACATTGAGCTCTACTTCGTTGTTTT-AATCTAAC-CTACTA
66 ATCCTCAAGGACGTTGAGCTCGACTTCATTGTTTTGATTC-AACAC-ACTA
* * *
12638 TTTTGACCCACTTCTCTATACGT---CAGGAAGATGGGATTTGAAGTCTCACCCCACTCCACTGA
1 TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT-A
* * * **
12700 -ATTCTCAAGGACGTTGAGCTTGGCTTTGTTGTTTTGATTCAACACACTA
65 TATCCTCAAGGACGTTGAGCTCGACTTCATTGTTTTGATTCAACACACTA
12749 TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGC
1 TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT--
* *
12814 ACTGTATCCTTAAGGACGTTGAGCTCGACTTCATTGTTTTGATTTAACACACTA
64 A---TATCCTCAAGGACGTTGAGCTCGACTTCATTGTTTTGATTCAACACACTA
* * * * *
12868 TTTTAACCCACTTCTCTGTTCCTCACCAGGAAGATGGGATTTAAAGTCTCTCTCTACTCCACTAT
1 TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTAT
* * * * * * *
12933 ATCCTTAGGGACGTTAAGCTCGGCTTCATTGTTTTGATTCAACATATTG
66 ATCCTCAAGGACGTTGAGCTCGACTTCATTGTTTTGATTCAACACACTA
* * * * * * * *
12982 TATTGACCTACTTCTCTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCACACCATTGT
1 TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTAT
* * * *
13047 ATCCTCAGGGACGTTGAGCTCTACCTCATTATTTTGA
66 ATCCTCAAGGACGTTGAGCTCGACTTCATTGTTTTGA
13084 CCCACTTCTT
Statistics
Matches: 377, Mismatches: 58, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
111 90 0.24
112 4 0.01
114 181 0.48
115 1 0.00
117 1 0.00
119 100 0.27
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (114 bp):
TTTTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTAT
ATCCTCAAGGACGTTGAGCTCGACTTCATTGTTTTGATTCAACACACTA
Found at i:13153 original size:96 final size:96
Alignment explanation
Indices: 12984--13260 Score: 410
Period size: 96 Copynumber: 2.9 Consensus size: 96
12974 ACATATTGTA
* * * *
12984 TTGACCTACTTCTCTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCACACCATTGTAT
1 TTGACCCACTTCTTTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCACTCCACTGTAT
*
13049 CCTCAGGGACGTTGAGCTCTACCTCATTATT
66 CCTTAGGGACGTTGAGCTCTACCTCATTATT
* * *
13080 TTGACCCACTTCTTTGTACCTCACCAGGAAGATGTGATTTGAAGTTTCACTCTACTCTACTGTAT
1 TTGACCCACTTCTTTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCACTCCACTGTAT
* *
13145 CCTTAGGGACGTTGGGCTCTACTTCATTATT
66 CCTTAGGGACGTTGAGCTCTACCTCATTATT
* * * * *
13176 TTGACTCACTTCTTTATACCTCACCAAGAAGATGTGATTTGAAGTCTCACTCCACTCCACTATAA
1 TTGACCCACTTCTTTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCACTCCACTGTAT
*
13241 CTTTAGGGACGTTGAGCTCT
66 CCTTAGGGACGTTGAGCTCT
13261 GCTTTGTTGT
Statistics
Matches: 161, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 161 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (96 bp):
TTGACCCACTTCTTTGTACCTCACCAAGAAGATGTGATTTGAAGTTTCACTCCACTCCACTGTAT
CCTTAGGGACGTTGAGCTCTACCTCATTATT
Found at i:13524 original size:49 final size:49
Alignment explanation
Indices: 13471--13829 Score: 309
Period size: 49 Copynumber: 7.4 Consensus size: 49
13461 CTAGCCCTTC
*
13471 ACATCTCTAAGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCCTCT
1 ACATCTCTAGGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCCTCT
** * * *
13520 ACATCTCTAACGTATAAGGTTCA-CTGTTGCGGTTTCAACCTTTTCCTCC
1 ACATCTCTAGGGTATAAGGTTCATC-GTTGCGGCTTCAACCTTTCCCTCT
** **
13569 ACATCTCTAGGGTATAAGGTTCGCCGTTATGGCTTCAACCTTTTCCCT-T
1 ACATCTCTAGGGTATAAGGTTCATCGTTGCGGCTTCAACC-TTTCCCTCT
* * * * * *
13618 CATATCTCTAGGGTACAAGATTCATTGTTACGGCTTCAAGCTTTCCCATC-
1 -ACATCTCTAGGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCC-TCT
* * * *
13668 ACATTTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCTCT
1 ACATCTCTAGGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCCTCT
* * * * ** *
13717 --ATCTCTAGGGTATAAGATT-TTCCTTTGCGGCTTCAATCTTTTTCTCA
1 ACATCTCTAGGGTATAAGGTTCAT-CGTTGCGGCTTCAACCTTTCCCTCT
* * ** * * *
13764 AC-GCTCTAGGGTATAAGGCTCGCCATTGCGGCTTCAACCTGTCCTTCT
1 ACATCTCTAGGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCCTCT
*
13812 ACATCTTTAGGGTATAAG
1 ACATCTCTAGGGTATAAG
13830 ATTCGCCATT
Statistics
Matches: 246, Mismatches: 52, Indels: 24
0.76 0.16 0.07
Matches are distributed among these distances:
46 1 0.00
47 37 0.15
48 38 0.15
49 130 0.53
50 40 0.16
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (49 bp):
ACATCTCTAGGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCCTCT
Found at i:13677 original size:148 final size:146
Alignment explanation
Indices: 13465--13732 Score: 378
Period size: 148 Copynumber: 1.8 Consensus size: 146
13455 TTCAATCTAG
* * *
13465 CCCTTCACATCTCTAAGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCCCTCTACATCTCTAA
1 CCCTTCACATCTCTAAGGTACAAGATTCATCGTTACGGCTTCAACCTTTCCCTCTACATCTCTAA
*
13530 CGTATAAGGTTCACT-GTTGCGGTTTCAACCTTTTCCTCCACATCTCTAGGGTATAAGGTTCGCC
66 CGTATAAGGTTC-CTCGTTGCGGCTTCAACCTTTTCCT-C-CATCTCTAGGGTATAAGGTTCGCC
13594 GTTATGGCTTCAACCTTTT
128 GTTATGGCTTCAACCTTTT
* * * * *
13613 CCCTTCATATCTCTAGGGTACAAGATTCATTGTTACGGCTTCAAGCTTTCCCATC-ACATTTCTA
1 CCCTTCACATCTCTAAGGTACAAGATTCATCGTTACGGCTTCAACCTTTCCC-TCTACATCTCTA
* * *
13677 AGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCTCTATCTCTAGGGTATAAG
65 ACGTATAAGGTTCCTCGTTGCGGCTTCAACCTTTTCCTCCATCTCTAGGGTATAAG
13733 ATTTTCCTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
146 16 0.15
147 2 0.02
148 86 0.81
149 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.36
Consensus pattern (146 bp):
CCCTTCACATCTCTAAGGTACAAGATTCATCGTTACGGCTTCAACCTTTCCCTCTACATCTCTAA
CGTATAAGGTTCCTCGTTGCGGCTTCAACCTTTTCCTCCATCTCTAGGGTATAAGGTTCGCCGTT
ATGGCTTCAACCTTTT
Found at i:13683 original size:99 final size:97
Alignment explanation
Indices: 13469--13869 Score: 357
Period size: 99 Copynumber: 4.1 Consensus size: 97
13459 ATCTAGCCCT
* * **
13469 TCACATCTCTAAGGTATAAGGTTCATCGTTGCGGCTTCAACC-TTTCCCTCTACATCTCTAACGT
1 TCACATCTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCCTC-ATATCTCTAGGGT
* * * *
13533 ATAAGGTTCACTGTTGCGGTTTCAACCTTTTCC
65 ATAAGATTCACTGTTACGGCTTCAACCTTTCCC
* * **
13566 TCCACATCTCTAGGGTATAAGGTTCGCCGTTATGGCTTCAACCTTTTCCCTTCATATCTCTAGGG
1 T-CACATCTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCC-TCATATCTCTAGGG
* * *
13631 TACAAGATTCATTGTTACGGCTTCAAGCTTTCCC
64 TATAAGATTCACTGTTACGGCTTCAACCTTTCCC
*
13665 ATCACATTTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTT-CCTC-TATCTCTAGGGT
1 -TCACATCTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCCTCATATCTCTAGGGT
* * **
13728 ATAAGATTTTC-CT-TTGCGGCTTCAATCTTTTTC
65 ATAAGA--TTCACTGTTACGGCTTCAACCTTTCCC
* * * * * * * * *
13761 TCA-ACGCTCTAGGGTATAAGGCTCGCCATTGCGGCTTCAACC-TGTCCTTCTACATCTTTAGGG
1 TCACA-TCTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCCTC-ATATCTCTAGGG
* ** * **
13824 TATAAGATTCGCCATTACGACTTCAATTTTTCCC
64 TATAAGATTCACTGTTACGGCTTCAACCTTTCCC
13858 TTCACATCTCTA
1 -TCACATCTCTA
13870 GAGTATAGGA
Statistics
Matches: 247, Mismatches: 43, Indels: 27
0.78 0.14 0.09
Matches are distributed among these distances:
94 3 0.01
95 40 0.16
96 34 0.14
97 35 0.14
98 49 0.20
99 83 0.34
100 3 0.01
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (97 bp):
TCACATCTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCCTCATATCTCTAGGGTA
TAAGATTCACTGTTACGGCTTCAACCTTTCCC
Found at i:13836 original size:49 final size:49
Alignment explanation
Indices: 13466--13876 Score: 304
Period size: 49 Copynumber: 8.4 Consensus size: 49
13456 TCAATCTAGC
* **
13466 CCTTC-ACATCTCTAAGGTATAAGGTTCATCGTTGCGGCTTCAACCTTT
1 CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTT
* ** * * *
13514 CCCTCTACATCTCTAACGTATAAGGTTCACTGTTGCGGTTTCAACCTTTT
1 CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACC-TTT
* **
13564 CC-TCCACATCTCTAGGGTATAAGGTTCGCCGTTATGGCTTCAACCTTTT
1 CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACC-TTT
* * * *** * *
13613 CCCTTC-ATATCTCTAGGGTACAAGATTCATTGTTACGGCTTCAAGCTTT
1 -CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTT
* * * *
13662 CCCATC-ACATTTCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTT
1 -CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACC-TTT
* ** * *
13712 CC-TCT--ATCTCTAGGGTATAAGATTTTCCTTTGCGGCTTCAATCTTT
1 CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTT
* * * *
13758 --TTCT-CAACGCTCTAGGGTATAAGGCTCGCCATTGCGGCTTCAACCTGT
1 CCTTCTAC-A-TCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTT
* * * * * **
13806 CCTTCTACATCTTTAGGGTATAAGATTCGCCATTACGACTTCAATTTTT
1 CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTT
*
13855 CCCTTC-ACATCTCTAGAGTATA
1 -CCTTCTACATCTCTAGGGTATA
13877 GGATTCAATG
Statistics
Matches: 291, Mismatches: 58, Indels: 27
0.77 0.15 0.07
Matches are distributed among these distances:
45 3 0.01
46 3 0.01
47 31 0.11
48 38 0.13
49 161 0.55
50 52 0.18
51 3 0.01
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (49 bp):
CCTTCTACATCTCTAGGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTT
Found at i:13854 original size:95 final size:94
Alignment explanation
Indices: 13673--13855 Score: 217
Period size: 95 Copynumber: 1.9 Consensus size: 94
13663 CCATCACATT
* * * * **
13673 TCTAAGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTTCCTCTATCTCTAGGGTATAAGATTTT
1 TCTAAGGTATAAGGCTCGCCATTGCGGCTTCAACCTTGTCCTCTATCTCTAGGGTATAAGATTCG
* * *
13738 CCTTTGCGGCTTCAATCTTTTTCTCAACGC
66 CCATTACGACTTCAA-CTTTTTCTCAACGC
* *
13768 TCTAGGGTATAAGGCTCGCCATTGCGGCTTCAACC-TGTCCTTCTACATCTTTAGGGTATAAGAT
1 TCTAAGGTATAAGGCTCGCCATTGCGGCTTCAACCTTGTCC-TCT--ATCTCTAGGGTATAAGAT
13832 TCGCCATTACGACTTCAA-TTTTTC
63 TCGCCATTACGACTTCAACTTTTTC
13856 CCTTCACATC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
94 4 0.05
95 40 0.54
97 30 0.41
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (94 bp):
TCTAAGGTATAAGGCTCGCCATTGCGGCTTCAACCTTGTCCTCTATCTCTAGGGTATAAGATTCG
CCATTACGACTTCAACTTTTTCTCAACGC
Found at i:14838 original size:6 final size:6
Alignment explanation
Indices: 14829--14889 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
14819 CGACCTCTCC
* * * *
14829 TTTTCT TTTTCC TTCTCT TTTTCT TTTCCT TGTTCTT TTTTCTT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTC-T TTTTCT
14879 TTTTCT CTTTT
1 TTTTCT -TTTT
14890 TATTATTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
6 29 0.64
7 16 0.36
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:14864 original size:20 final size:21
Alignment explanation
Indices: 14824--14890 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
14814 CACCTCGACC
*
14824 TCTCCTTTTCTTTTTCC---T
1 TCTCTTTTTCTTTTTCCTTGT
14842 TCTCTTTTTC-TTTTCCTTGT
1 TCTCTTTTTCTTTTTCCTTGT
* *
14862 TCT-TTTTTCTTTTTTCTTTT
1 TCTCTTTTTCTTTTTCCTTGT
14882 TCTCTTTTT
1 TCTCTTTTT
14891 ATTATTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.15
18 9 0.22
19 6 0.15
20 15 0.37
21 5 0.12
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (21 bp):
TCTCTTTTTCTTTTTCCTTGT
Found at i:14873 original size:7 final size:7
Alignment explanation
Indices: 14829--14890 Score: 54
Period size: 7 Copynumber: 8.4 Consensus size: 7
14819 CGACCTCTCC
14829 TTTTCTT
1 TTTTCTT
*
14836 TTTCCTT
1 TTTTCTT
14843 CTCTTT-TT
1 -T-TTTCTT
*
14851 CTTTTCCT
1 -TTTTCTT
*
14859 TGTTCTT
1 TTTTCTT
14866 TTTTCTT
1 TTTTCTT
14873 TTTTCTT
1 TTTTCTT
14880 TTTCTCTT
1 TTT-TCTT
14888 TTT
1 TTT
14891 ATTATTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
7 30 0.67
8 13 0.29
9 2 0.04
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:21216 original size:15 final size:14
Alignment explanation
Indices: 21177--21218 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
21167 ACATTACATA
21177 TTTGTTCTTTTCTTC
1 TTTGTT-TTTTCTTC
21192 TTTGTTTTTTCTTC
1 TTTGTTTTTTCTTC
21206 TTTGTCTTTTTCT
1 TTTGT-TTTTTCT
21219 CTGTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTGTTTTTTCTTC
Found at i:21500 original size:24 final size:24
Alignment explanation
Indices: 21472--21521 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
21462 TGGGGTGTAA
21472 TTGGG-TTTTGATGTAAATGGACAT
1 TTGGGATTTTG-TGTAAATGGACAT
*
21496 TTGGGTATTTTGTGTAAATTGACAT
1 TTGGG-ATTTTGTGTAAATGGACAT
21521 T
1 T
21522 AACATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 13 0.57
26 5 0.22
ACGTcount: A:0.24, C:0.04, G:0.26, T:0.46
Consensus pattern (24 bp):
TTGGGATTTTGTGTAAATGGACAT
Found at i:27304 original size:293 final size:293
Alignment explanation
Indices: 26770--27356 Score: 1111
Period size: 293 Copynumber: 2.0 Consensus size: 293
26760 AAATTAATAG
26770 TATAGTTACGATGAGCACAAATATCATTCCCACAAGGACTAAAAATAACTGTCTTCCTATTATCT
1 TATAGTTACGATGAGCACAAATATCATTCCCACAAGGACTAAAAATAACTGTCTTCCTATTATCT
26835 AACTATTGAATAAAGTGATTGTTTTAAACTAAAATTAACTAAATTAATAAACTAAAAGTGCAACA
66 AACTATTGAATAAAGTGATTGTTTTAAACTAAAATTAACTAAATTAATAAACTAAAAGTGCAACA
* *
26900 AAGATTAAAGCAAGAAATAACAATTGTTTTAATGCCAAGAAGCAAACAATACCAAGGAAAGACTC
131 AAGATTAAAGCAAGAAATAACAAGTGTTTTAATGCCAAGAAGCAAACAATACCAAGGAAACACTC
* *
26965 TGCCTAGATTTCATCTGTCATTATCATTTTGAATTAATTTATTTATTCACTTAGTATTTTGATCC
196 TGCCTAGATTTCATCTGCCATTATCATTTTGAATTAATTAATTTATTCACTTAGTATTTTGATCC
*
27030 GTAGAAATCCCTAAATTATGTTAATACCTCTAT
261 GTAAAAATCCCTAAATTATGTTAATACCTCTAT
*
27063 TATAGTTACGGTGAGCACAAATATCATTCCCACAAGGACTAAAAATAACTGTCTTCCTATTATCT
1 TATAGTTACGATGAGCACAAATATCATTCCCACAAGGACTAAAAATAACTGTCTTCCTATTATCT
27128 AACTATTGAATAAAGTGATTGTTTTAAACTAAAATTAACTAAATTAATAAACTAAAAGTGCAACA
66 AACTATTGAATAAAGTGATTGTTTTAAACTAAAATTAACTAAATTAATAAACTAAAAGTGCAACA
27193 AAGATTAAAGCAAGAAATAACAAGTGTTTTAATGCCAAGAAGCAAACAATACCAAGGAAACACTC
131 AAGATTAAAGCAAGAAATAACAAGTGTTTTAATGCCAAGAAGCAAACAATACCAAGGAAACACTC
*
27258 TGTCTAGATTTCATCTGCCATTATCATTTTGAATTAATTAATTTATTCACTTAGTATTTTGATCC
196 TGCCTAGATTTCATCTGCCATTATCATTTTGAATTAATTAATTTATTCACTTAGTATTTTGATCC
27323 GTAAAAATCCCTAAATTATGTTAATACCTCTAT
261 GTAAAAATCCCTAAATTATGTTAATACCTCTAT
27356 T
1 T
27357 CAAGCATAAA
Statistics
Matches: 287, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
293 287 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (293 bp):
TATAGTTACGATGAGCACAAATATCATTCCCACAAGGACTAAAAATAACTGTCTTCCTATTATCT
AACTATTGAATAAAGTGATTGTTTTAAACTAAAATTAACTAAATTAATAAACTAAAAGTGCAACA
AAGATTAAAGCAAGAAATAACAAGTGTTTTAATGCCAAGAAGCAAACAATACCAAGGAAACACTC
TGCCTAGATTTCATCTGCCATTATCATTTTGAATTAATTAATTTATTCACTTAGTATTTTGATCC
GTAAAAATCCCTAAATTATGTTAATACCTCTAT
Found at i:28022 original size:25 final size:23
Alignment explanation
Indices: 27994--28039 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
27984 GTTGGATCCA
27994 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
28019 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
28040 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:31088 original size:13 final size:14
Alignment explanation
Indices: 31059--31088 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31049 TTCAGTACAT
31059 TGACATTTAACCTC
1 TGACATTTAACCTC
31073 TGACATTTAA-CTC
1 TGACATTTAACCTC
31086 TGA
1 TGA
31089 TTGCGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Done.