Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009735.1 Kokia drynarioides strain JFW-HI SEQ_124454, 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: 68718
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:4221 original size:3 final size:3
Alignment explanation
Indices: 4213--4248 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4203 AAGTATTAAT
4213 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4249 ATATCTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5660 original size:26 final size:26
Alignment explanation
Indices: 5598--5679 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
5588 TATTCTATCT
* *
5598 GGCTCATAAGAGCGATATTCT-TTTT
1 GGCTCATAAGAGCGATACTCTGTTTA
* * *
5623 TGCTCAAAAGAGCGATACTCTGTTTG
1 GGCTCATAAGAGCGATACTCTGTTTA
* ** *
5649 GGCTCGTAAGAGATAAACTCTGTTTA
1 GGCTCATAAGAGCGATACTCTGTTTA
5675 GGCTC
1 GGCTC
5680 GTTTGAGCTA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 18 0.40
26 27 0.60
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (26 bp):
GGCTCATAAGAGCGATACTCTGTTTA
Found at i:13813 original size:25 final size:25
Alignment explanation
Indices: 13774--13874 Score: 130
Period size: 25 Copynumber: 4.0 Consensus size: 25
13764 AGACGATGAA
* *
13774 GATATTCTATCTGGCTCGTAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
*
13799 GATATTATGTTTGGCTCGTAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
*
13824 GATATTCTGTTTGGCTCGAAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* * *
13849 GAAACTCTGTCTGGCCTCGTAAGAGC
1 GATATTCTGTTTGG-CTCGTAAGAGC
13875 TAAACTCTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 56 0.85
26 10 0.15
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (25 bp):
GATATTCTGTTTGGCTCGTAAGAGC
Found at i:15623 original size:25 final size:25
Alignment explanation
Indices: 15588--15642 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
15578 CATCATTATT
*
15588 ATAATATCAATAATAATAAAATATA
1 ATAATACCAATAATAATAAAATATA
15613 ATAATACCAATAATAATAAAATATA
1 ATAATACCAATAATAATAAAATATA
15638 A-AATA
1 ATAATA
15643 AAATATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (25 bp):
ATAATACCAATAATAATAAAATATA
Found at i:15642 original size:12 final size:13
Alignment explanation
Indices: 15597--15653 Score: 73
Period size: 12 Copynumber: 4.5 Consensus size: 13
15587 TATAATATCA
15597 ATAATAATAAAAT
1 ATAATAATAAAAT
**
15610 ATAATAATACCA-
1 ATAATAATAAAAT
15622 ATAATAATAAAAT
1 ATAATAATAAAAT
15635 ATAA-AATAAAAT
1 ATAATAATAAAAT
*
15647 ATTATAA
1 ATAATAA
15654 CTTATTCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 21 0.57
13 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAATAAAAT
Found at i:21105 original size:47 final size:47
Alignment explanation
Indices: 21049--21148 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
21039 TTTTATTTTA
*
21049 AACCCTAAACCCAATAAATAATAAACTTGTGTCAAAATACCATAACT
1 AACCCTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
*
21096 AACCCTAAACCCAATAAATAATAAACTTGTATGAAAATACCATAACT
1 AACCCTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
21143 AACCCT
1 AACCCT
21149 TTACAAAAGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.23
Consensus pattern (47 bp):
AACCCTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
Found at i:21201 original size:6 final size:6
Alignment explanation
Indices: 21192--21217 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21182 TTAAACATAA
21192 TACCCT TACCCT TACCCT TACCCT TA
1 TACCCT TACCCT TACCCT TACCCT TA
21218 TATTTGCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.00, T:0.35
Consensus pattern (6 bp):
TACCCT
Found at i:22962 original size:143 final size:139
Alignment explanation
Indices: 22697--22979 Score: 426
Period size: 143 Copynumber: 2.0 Consensus size: 139
22687 TTGTTCATTC
* *
22697 ATGATTATATATTTTATAGACAAATAAATTCAAAAGGATCTAATTTTGTCATGTTTGAATGTGCA
1 ATGATTATATATTTTATAGACAAATAAATTCAAAAAGAGCTAATTTTGTCATGTTTGAATGTGCA
*
22762 TCTGTACTGTCATTGCTATTTGTTAGTCTAAGTCCTCAGTCAGGAAGCATTCTAAGGTGCCCAAG
66 TCTGTACTGTCA-TGCTATTTGTTAGTCTAAGTCCTCAGTCAGGAAGCATCCTAAGGTGCCCAAG
22827 AATTCTGCAA
130 AATTCTGCAA
*
22837 ATGATTATATATTTTATAGACAAATAAATTCAGAAGAATAGAGGCTATTTTTGTCATGTTTGAAT
1 ATGATTATATATTTTATAGACAAATAAATTC--AA-AA-AGA-GCTAATTTTGTCATGTTTGAAT
* * *
22902 GTGCATCTGT-CTTGTCA-GCTTTTTGTTAGTCTAAGTCGTCAGTCAGGTAGCATCCTAAGGTGC
61 GTGCATCTGTAC-TGTCATGCTATTTGTTAGTCTAAGTCCTCAGTCAGGAAGCATCCTAAGGTGC
22965 CCAAGAATTCTGCAA
125 CCAAGAATTCTGCAA
22980 GTTTGAGGAA
Statistics
Matches: 130, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
140 31 0.24
142 2 0.02
143 59 0.45
144 3 0.02
145 35 0.27
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (139 bp):
ATGATTATATATTTTATAGACAAATAAATTCAAAAAGAGCTAATTTTGTCATGTTTGAATGTGCA
TCTGTACTGTCATGCTATTTGTTAGTCTAAGTCCTCAGTCAGGAAGCATCCTAAGGTGCCCAAGA
ATTCTGCAA
Found at i:26040 original size:16 final size:17
Alignment explanation
Indices: 26021--26056 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
26011 AAATGTTTAG
26021 TATTTTAA-ATATGAAA
1 TATTTTAACATATGAAA
26037 TATTTTAACATATGAAA
1 TATTTTAACATATGAAA
26054 TAT
1 TAT
26057 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
TATTTTAACATATGAAA
Found at i:26727 original size:24 final size:22
Alignment explanation
Indices: 26700--26744 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
26690 AATCGAACAT
26700 GTTCACGAACATATAATTGAATAC
1 GTTCACGAACA-ATAA-TGAATAC
* *
26724 GTTCAGGAATAATAATGAATA
1 GTTCACGAACAATAATGAATA
26745 ATAAACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 4 0.21
24 9 0.47
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (22 bp):
GTTCACGAACAATAATGAATAC
Found at i:31737 original size:34 final size:34
Alignment explanation
Indices: 31655--31739 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
31645 ACATATACGA
* * *
31655 ATATCATATTAGAATGTCACATTACTAGAAATAT
1 ATATCATATTAGAATGTCACATTACAAAAAACAT
* * * * * *
31689 ATAGCAAATCAGAATTTCATATTTCAAAAAACAT
1 ATATCATATTAGAATGTCACATTACAAAAAACAT
31723 ATATCATATTAGAATGT
1 ATATCATATTAGAATGT
31740 TATATCAGAT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (34 bp):
ATATCATATTAGAATGTCACATTACAAAAAACAT
Found at i:32150 original size:12 final size:12
Alignment explanation
Indices: 32124--32210 Score: 77
Period size: 12 Copynumber: 7.0 Consensus size: 12
32114 AGTAAAAGAT
*
32124 AATGA-AAAGTA
1 AATGATAAAATA
32135 AATGATAAAATA
1 AATGATAAAATA
*
32147 AATGATAAACTA
1 AATGATAAAATA
* *
32159 AGTACGAAAAAATA
1 A--ATGATAAAATA
*
32173 AATGATAAACTA
1 AATGATAAAATA
*
32185 AATGCAAAAAAATA
1 AATG--ATAAAATA
32199 AATGATAAAATA
1 AATGATAAAATA
32211 TAAATGGTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
11 5 0.08
12 36 0.60
14 19 0.32
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (12 bp):
AATGATAAAATA
Found at i:32175 original size:26 final size:26
Alignment explanation
Indices: 32141--32207 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
32131 AGTAAATGAT
* *
32141 AAAATAAATGATAAACTAAGTACGAA
1 AAAATAAATGATAAACTAAATACAAA
*
32167 AAAATAAATGATAAACTAAATGCAAA
1 AAAATAAATGATAAACTAAATACAAA
32193 AAAATAAATGATAAA
1 AAAATAAATGATAAA
32208 ATATAAATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (26 bp):
AAAATAAATGATAAACTAAATACAAA
Found at i:32202 original size:14 final size:13
Alignment explanation
Indices: 32165--32216 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
32155 ACTAAGTACG
32165 AAAAAATAAATG-
1 AAAAAATAAATGA
* *
32177 ATAAACTAAATGCA
1 AAAAAATAAATG-A
32191 AAAAAATAAATGA
1 AAAAAATAAATGA
*
32204 TAAAATATAAATG
1 -AAAAAATAAATG
32217 GTATGTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 10 0.31
13 1 0.03
14 21 0.66
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (13 bp):
AAAAAATAAATGA
Found at i:36409 original size:74 final size:74
Alignment explanation
Indices: 36329--36476 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
36319 TTAGAATAAG
*
36329 AAAAAAATAAAACCACCTGAAATAAAATCATATGCAACAAAAGAAAATTAAAAAGAAAAGAAAAC
1 AAAAAAATAAAACCACCTGAAATAAAATCACATGCAACAAAAGAAAATTAAAAAGAAAAGAAAAC
36394 TTTAAATAT
66 TTTAAATAT
36403 AAAAAAATAAAACCACCTGAAATAAAATCACATGCAACAAAAGAAAATTAAAAAGAAAAGAAAAC
1 AAAAAAATAAAACCACCTGAAATAAAATCACATGCAACAAAAGAAAATTAAAAAGAAAAGAAAAC
36468 TTTAAATAT
66 TTTAAATAT
36477 TCCGAAAGGG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.65, C:0.11, G:0.07, T:0.17
Consensus pattern (74 bp):
AAAAAAATAAAACCACCTGAAATAAAATCACATGCAACAAAAGAAAATTAAAAAGAAAAGAAAAC
TTTAAATAT
Found at i:36843 original size:19 final size:21
Alignment explanation
Indices: 36805--36844 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36795 TGTTTATGAG
*
36805 CTTAATATCATGACATTCTTC
1 CTTAACATCATGACATTCTTC
36826 CTTAACATCA-GA-ATTCTTC
1 CTTAACATCATGACATTCTTC
36845 ACAGCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (21 bp):
CTTAACATCATGACATTCTTC
Found at i:39666 original size:38 final size:38
Alignment explanation
Indices: 39624--39696 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
39614 ATAACCACCT
* *
39624 GCACAAAGCCTACTAGGCACTAAGCCCAATAAACATCG
1 GCACAAAGCCTACTAAGCACAAAGCCCAATAAACATCG
* * * *
39662 GCACATAGCCTGCTAAGCACAAAGCTCGATAAACA
1 GCACAAAGCCTACTAAGCACAAAGCCCAATAAACA
39697 CTAGCACATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.40, C:0.30, G:0.16, T:0.14
Consensus pattern (38 bp):
GCACAAAGCCTACTAAGCACAAAGCCCAATAAACATCG
Found at i:42863 original size:71 final size:71
Alignment explanation
Indices: 42766--43080 Score: 382
Period size: 71 Copynumber: 4.4 Consensus size: 71
42756 ATCATCAGAA
* * **
42766 TGCCATAGCTCAGCTATGGTCTTACATATATACACTGCCATGTTCCAACCATGGTCTTATGTCTG
1 TGCCATAGCTCAACTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACATCTG
42831 AATAAT
66 AATAAT
* * * * * ** *
42837 TGTCATAGCTCAACCATGGCCTTACATATATACATTGCCATGGTCCAACTATGGTCTTATGTTTG
1 TGCCATAGCTCAACTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACATCTG
42902 AATAAT
66 AATAAT
* * * * *
42908 TGCCATAGCCCAACTATGGTCTTACGTATATACACTGTCATGGTCTAACCATGGTCTTACATCTA
1 TGCCATAGCTCAACTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACATCTG
*
42973 AATAAC
66 AATAAT
*
42979 TGCCATAG-TCCAACTATGGTCTTACGTTATATACACTGCCATGGTCCAACCATGGTCTTACATC
1 TGCCATAGCT-CAACTATGGTCTTAC-ATATATACACTGCCATGGTCCAACCATGGTCTTACATC
*
43043 TCAATAAT
64 TGAATAAT
* * *
43051 TGCCATAG-TGTAGCTATGGTCTTACGTATA
1 TGCCATAGCT-CAACTATGGTCTTACATATA
43081 AATGCAACTT
Statistics
Matches: 210, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
71 147 0.70
72 63 0.30
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (71 bp):
TGCCATAGCTCAACTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACATCTG
AATAAT
Found at i:42928 original size:107 final size:106
Alignment explanation
Indices: 42810--43039 Score: 245
Period size: 107 Copynumber: 2.2 Consensus size: 106
42800 CTGCCATGTT
* * * * *
42810 CCAACCATGGTCTTATGTCTGAATA-ATTGTCATAGCTC-AACCATGGCCTTACA-TATATACAT
1 CCAACCATGGTCTTACGTAT--ATACACTGTCAT-GCTCTAACCATGGCCTTACACTAAATA-AC
*
42872 TGCCATGGTCCAACTATGGTCTTATGTTTGAATAATTGCCATAGC
62 TGCCATAGTCCAACTATGGTCTTATGTTTGAATAATTGCCATAGC
* * *
42917 CCAACTATGGTCTTACGTATATACACTGTCATGGTCTAACCATGGTCTTACATCTAAATAACTGC
1 CCAACCATGGTCTTACGTATATACACTGTCATGCTCTAACCATGGCCTTACA-CTAAATAACTGC
* * * *
42982 CATAGTCCAACTATGGTCTTACG-TT-ATATACACTGCCATGGT
65 CATAGTCCAACTATGGTCTTATGTTTGA-ATA-ATTGCCATAGC
43024 CCAACCATGGTCTTAC
1 CCAACCATGGTCTTAC
43040 ATCTCAATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
105 7 0.07
106 26 0.25
107 65 0.63
108 5 0.05
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (106 bp):
CCAACCATGGTCTTACGTATATACACTGTCATGCTCTAACCATGGCCTTACACTAAATAACTGCC
ATAGTCCAACTATGGTCTTATGTTTGAATAATTGCCATAGC
Found at i:43017 original size:36 final size:36
Alignment explanation
Indices: 42781--43039 Score: 205
Period size: 36 Copynumber: 7.3 Consensus size: 36
42771 TAGCTCAGCT
*
42781 ATGGTCTTAC-ATATATACACTGCCAT-GTTCCAACC
1 ATGGTCTTACGTTATATACACTGCCATAG-TCCAACC
* * *
42816 ATGGTCTTATGTCTGA-ATA-ATTGTCATAG-CTCAACC
1 ATGGTCTTACGT-T-ATATACACTGCCATAGTC-CAACC
* * * * *
42852 ATGGCCTTAC-ATATATACATTGCCATGGTCCAACT
1 ATGGTCTTACGTTATATACACTGCCATAGTCCAACC
* * * *
42887 ATGGTCTTATGTT-TGAATA-ATTGCCATAGCCCAACT
1 ATGGTCTTACGTTAT--ATACACTGCCATAGTCCAACC
* * *
42923 ATGGTCTTACG-TATATACACTGTCATGGTCTAACC
1 ATGGTCTTACGTTATATACACTGCCATAGTCCAACC
* * *
42958 ATGGTCTTACATCTAAATA-ACTGCCATAGTCCAACT
1 ATGGTCTTACGT-TATATACACTGCCATAGTCCAACC
*
42994 ATGGTCTTACGTTATATACACTGCCATGGTCCAACC
1 ATGGTCTTACGTTATATACACTGCCATAGTCCAACC
43030 ATGGTCTTAC
1 ATGGTCTTAC
43040 ATCTCAATAA
Statistics
Matches: 176, Mismatches: 32, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
33 1 0.01
34 7 0.04
35 58 0.33
36 96 0.55
37 13 0.07
38 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (36 bp):
ATGGTCTTACGTTATATACACTGCCATAGTCCAACC
Found at i:43070 original size:36 final size:35
Alignment explanation
Indices: 42766--43075 Score: 193
Period size: 36 Copynumber: 8.7 Consensus size: 35
42756 ATCATCAGAA
* *
42766 TGCCATAG-CTCAGCTATGGTCTTACATAT-ATACAC
1 TGCCATAGTC-CAACTATGGTCTTACATCTAATA-AC
* ** *
42801 TGCCAT-GTTCCAACCATGGTCTTATGTCTGAATAAT
1 TGCCATAG-TCCAACTATGGTCTTACATCT-AATAAC
* * * * *
42837 TGTCATAG-CTCAACCATGGCCTTACATAT-ATACAT
1 TGCCATAGTC-CAACTATGGTCTTACATCTAATA-AC
* ** * *
42872 TGCCATGGTCCAACTATGGTCTTATGTTTGAATAAT
1 TGCCATAGTCCAACTATGGTCTTACATCT-AATAAC
* * *
42908 TGCCATAGCCCAACTATGGTCTTACGTAT-ATACAC
1 TGCCATAGTCCAACTATGGTCTTACATCTAATA-AC
* * * *
42943 TGTCATGGTCTAACCATGGTCTTACATCTAAATAAC
1 TGCCATAGTCCAACTATGGTCTTACATCT-AATAAC
*
42979 TGCCATAGTCCAACTATGGTCTTACGT-TATATACAC
1 TGCCATAGTCCAACTATGGTCTTACATCTA-ATA-AC
* * *
43015 TGCCATGGTCCAACCATGGTCTTACATCTCAATAAT
1 TGCCATAGTCCAACTATGGTCTTACATCT-AATAAC
** *
43051 TGCCATAGTGTAGCTATGGTCTTAC
1 TGCCATAGTCCAACTATGGTCTTAC
43076 GTATAAATGC
Statistics
Matches: 214, Mismatches: 44, Indels: 33
0.74 0.15 0.11
Matches are distributed among these distances:
34 8 0.04
35 70 0.33
36 121 0.57
37 14 0.07
38 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (35 bp):
TGCCATAGTCCAACTATGGTCTTACATCTAATAAC
Found at i:44765 original size:25 final size:25
Alignment explanation
Indices: 44737--44796 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
44727 TTAACAATAA
**
44737 ATCATTCATATAAGTACAAAAAAAT
1 ATCATTCATATAAACACAAAAAAAT
*
44762 ATCATTCGA-ATAAACCCAAAAAAAT
1 ATCATTC-ATATAAACACAAAAAAAT
*
44787 AGCATTCATA
1 ATCATTCATA
44797 ATCATCTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 27 0.93
26 1 0.03
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (25 bp):
ATCATTCATATAAACACAAAAAAAT
Found at i:49050 original size:19 final size:19
Alignment explanation
Indices: 49026--49068 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
49016 GTCGAAAAAC
*
49026 GTCAAAGTCAACGATCAAA
1 GTCAAAGTCAACAATCAAA
*
49045 GTCAAAGTCAACAATCAAC
1 GTCAAAGTCAACAATCAAA
49064 GTCAA
1 GTCAA
49069 CGGTTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.16
Consensus pattern (19 bp):
GTCAAAGTCAACAATCAAA
Found at i:49069 original size:13 final size:12
Alignment explanation
Indices: 49023--49068 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
49013 TGCGTCGAAA
49023 AACGTCAAAGTC
1 AACGTCAAAGTC
49035 AACGATCAAAGTC
1 AACG-TCAAAGTC
* *
49048 AAAGTCAACAATC
1 AACGTCAA-AGTC
49061 AACGTCAA
1 AACGTCAA
49069 CGGTTCGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.15
Consensus pattern (12 bp):
AACGTCAAAGTC
Found at i:49783 original size:30 final size:30
Alignment explanation
Indices: 49749--49819 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
49739 AATTAAAGCT
49749 CAATTTAGTCCCTAAATTTCACTAAAATTC
1 CAATTTAGTCCCTAAATTTCACTAAAATTC
49779 CAATTTAGTCCCTAAATTTCACTAAAATTC
1 CAATTTAGTCCCTAAATTTCACTAAAATTC
49809 CAATTTAGTCC
1 CAATTTAGTCC
49820 TTAAGTCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (30 bp):
CAATTTAGTCCCTAAATTTCACTAAAATTC
Found at i:51984 original size:23 final size:22
Alignment explanation
Indices: 51958--52004 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
51948 GTTCATATTA
*
51958 TTTTATTCATTATTTATTGCTTT
1 TTTTATTCATTAATT-TTGCTTT
51981 TTTTATTCATTAATTTTGCTTT
1 TTTTATTCATTAATTTTGCTTT
52003 TT
1 TT
52005 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTTATTCATTAATTTTGCTTT
Found at i:52321 original size:22 final size:23
Alignment explanation
Indices: 52295--52362 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 23
52285 TTTTAGTGCC
*
52295 ATGATCCTTA-TTGTATTTTATT
1 ATGATCATTATTTGTATTTTATT
* *
52317 ATGATTATTATTTTTATTTTATT
1 ATGATCATTATTTGTATTTTATT
*
52340 -TG-T-GTTATTTGT-TATTTATT
1 ATGATCATTATTTGTAT-TTTATT
52360 ATG
1 ATG
52363 TATGCAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 13 0.34
21 3 0.08
22 10 0.26
23 11 0.29
ACGTcount: A:0.22, C:0.03, G:0.10, T:0.65
Consensus pattern (23 bp):
ATGATCATTATTTGTATTTTATT
Found at i:52338 original size:23 final size:22
Alignment explanation
Indices: 52308--52365 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
52298 ATCCTTATTG
52308 TATTTTATTATGATTATTATTT-T
1 TATTTTATTATG--TATTATTTGT
*
52331 TATTTTATT-TGTGTTATTTGT
1 TATTTTATTATGTATTATTTGT
52352 TA-TTTATTATGTAT
1 TATTTTATTATGTAT
52366 GCAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 13 0.42
21 7 0.23
22 2 0.06
23 9 0.29
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (22 bp):
TATTTTATTATGTATTATTTGT
Found at i:62554 original size:52 final size:52
Alignment explanation
Indices: 62476--62864 Score: 519
Period size: 52 Copynumber: 7.5 Consensus size: 52
62466 TTCCCATTTA
* * * * * *
62476 ATACTCATGATGACACAAAATCATCAGACCTTA-AATCTGTAATAGGATCCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAA-AGGATTCAT
* **
62528 ATACTCACGATGACACATACTCATCAGACCTCATAATTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* * *
62580 ATACTCACGATGAAAAATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* * * *
62632 ACACTCATGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
62684 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* * ** *
62736 ATACTCACGATGACACATAGTTATCGGACCTCATAATTTGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* * *
62788 ATACTTAAGATGACACGTAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
*
62840 ATACTCACGATTACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
62865 GGATCTTTTT
Statistics
Matches: 298, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 290 0.97
53 8 0.03
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:64533 original size:21 final size:21
Alignment explanation
Indices: 64508--64578 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
64498 TTTTTAAAAC
64508 CACTTGACTTTTGAACCAAAT
1 CACTTGACTTTTGAACCAAAT
* ***** *
64529 CACTTATACTATTTTTTTTAAAA
1 CACTT-GACT-TTTGAACCAAAT
64552 CCACTTGACTTTTGAACCAAAT
1 C-ACTTGACTTTTGAACCAAAT
64574 CACTT
1 CACTT
64579 ATACTAACTT
Statistics
Matches: 33, Mismatches: 14, Indels: 6
0.62 0.26 0.11
Matches are distributed among these distances:
21 9 0.27
22 10 0.30
23 10 0.30
24 4 0.12
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (21 bp):
CACTTGACTTTTGAACCAAAT
Found at i:64553 original size:45 final size:45
Alignment explanation
Indices: 64496--64584 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
64486 CAATACTTTA
64496 TTTTTTTAAAACCACTTGACTTTTGAACCAAATCACTTATACTAT
1 TTTTTTTAAAACCACTTGACTTTTGAACCAAATCACTTATACTAT
64541 TTTTTTTAAAACCACTTGACTTTTGAACCAAATCACTTATACTA
1 TTTTTTTAAAACCACTTGACTTTTGAACCAAATCACTTATACTA
64585 ACTTTTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (45 bp):
TTTTTTTAAAACCACTTGACTTTTGAACCAAATCACTTATACTAT
Found at i:67566 original size:21 final size:21
Alignment explanation
Indices: 67518--67566 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
67508 CTCACTTTAA
* **
67518 CAATTTTTTATTGATGTTTGC
1 CAATTTTTTACTGACATTTGC
*
67539 CATTTTTTTACTGACATTTGC
1 CAATTTTTTACTGACATTTGC
*
67560 TAATTTT
1 CAATTTT
67567 GACCAATGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (21 bp):
CAATTTTTTACTGACATTTGC
Done.