Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011000.1 Kokia drynarioides strain JFW-HI SEQ_125970, 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: 169102
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3171 original size:19 final size:20
Alignment explanation
Indices: 3147--3184 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3137 TAAACCCAAC
*
3147 CTAAAAGA-TATTGTCGAAT
1 CTAAAAGATTATTATCGAAT
3166 CTAAAAGATTATTATCGAA
1 CTAAAAGATTATTATCGAA
3185 ATTTTGCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
CTAAAAGATTATTATCGAAT
Found at i:13763 original size:23 final size:22
Alignment explanation
Indices: 13737--13802 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
13727 CGGTCAATTA
*
13737 TCAATGGTTTGGGTCTAGTTTGG
1 TCAATGGTTTGGGTC-AGGTTGG
* * *
13760 TCAATGGTTCGAGTCGGGTTGG
1 TCAATGGTTTGGGTCAGGTTGG
* *
13782 TCAATGGGTTGGGTCGGGTTG
1 TCAATGGTTTGGGTCAGGTTG
13803 ATGGGTCAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 23 0.64
23 13 0.36
ACGTcount: A:0.12, C:0.11, G:0.41, T:0.36
Consensus pattern (22 bp):
TCAATGGTTTGGGTCAGGTTGG
Found at i:16289 original size:9 final size:9
Alignment explanation
Indices: 16271--16312 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
16261 CTTCTAACTC
16271 TTACAAGCA
1 TTACAAGCA
*
16280 TTATAAGCA
1 TTACAAGCA
16289 TTACAAGCA
1 TTACAAGCA
16298 TTACAAGCA
1 TTACAAGCA
16307 TTACAA
1 TTACAA
16313 CCGGTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (9 bp):
TTACAAGCA
Found at i:16741 original size:52 final size:52
Alignment explanation
Indices: 16679--16820 Score: 180
Period size: 52 Copynumber: 2.7 Consensus size: 52
16669 ATTTGCAATG
16679 GATTCATATACTCACGATGACACATCA-CCATCAGACCTCATAAT-TCGTAAAA
1 GATTCATATACTCACGATGACACAT-AGCCATCAGACCTCATAATCT-GTAAAA
* * * * * * *
16731 GATTCATATACTCACGATGAGACGTAGTCACCGGAGCTCATAATCTGTAAAG
1 GATTCATATACTCACGATGACACATAGCCATCAGACCTCATAATCTGTAAAA
*
16783 GATTCATATACTCACGATGACCCATAGCCATCAGACCT
1 GATTCATATACTCACGATGACACATAGCCATCAGACCT
16821 TTTTCATTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
51 1 0.01
52 72 0.97
53 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (52 bp):
GATTCATATACTCACGATGACACATAGCCATCAGACCTCATAATCTGTAAAA
Found at i:18945 original size:15 final size:15
Alignment explanation
Indices: 18927--18955 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18917 TTTAATTCAA
18927 TAATTCAAAATTCCT
1 TAATTCAAAATTCCT
18942 TAATTCAAAATTCC
1 TAATTCAAAATTCC
18956 ATAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTCAAAATTCCT
Found at i:27974 original size:50 final size:50
Alignment explanation
Indices: 27842--28083 Score: 180
Period size: 50 Copynumber: 4.8 Consensus size: 50
27832 ATATTTATGT
* * **
27842 GTTTATGCTCATCAGCTTATTTATGTC-TTTACGCTTACCAACTTGCACAC
1 GTTTATGCTCGTCAGCTTATTTATG-CGTTTACACTCGCCAACTTGCACAC
* * * * *
27892 GTTTACGCTCGTTACCTTATTTATGTGATTACACTCGCCAACTTGCACAC
1 GTTTATGCTCGTCAGCTTATTTATGCGTTTACACTCGCCAACTTGCACAC
* * * ** ***
27942 GTTTATGCTGGTCAGCTTATTTATGCGTTTACATTCGCCAGCTTATTTATGT
1 GTTTATGCTCGTCAGCTTATTTATGCGTTTACACTCGCCAAC-T-TGCACAC
* ** * * * ** * * *
27994 GTTTACGCTCCCCAACTTATTTATACATTTATTCTCGCCAGCTTGCTCAT
1 GTTTATGCTCGTCAGCTTATTTATGCGTTTACACTCGCCAACTTGCACAC
* *
28044 GTTTATGCTCGTCAGCTTATTAATGCGTTTACATTCGCCA
1 GTTTATGCTCGTCAGCTTATTTATGCGTTTACACTCGCCA
28084 TCTTATTTAT
Statistics
Matches: 142, Mismatches: 47, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
50 106 0.75
51 2 0.01
52 34 0.24
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.40
Consensus pattern (50 bp):
GTTTATGCTCGTCAGCTTATTTATGCGTTTACACTCGCCAACTTGCACAC
Found at i:27983 original size:26 final size:26
Alignment explanation
Indices: 27954--28097 Score: 105
Period size: 26 Copynumber: 5.6 Consensus size: 26
27944 TTATGCTGGT
27954 CAGCTTATTTATGCGTTTACATTCGC
1 CAGCTTATTTATGCGTTTACATTCGC
* ** *
27980 CAGCTTATTTATGTGTTTACGCTCCC
1 CAGCTTATTTATGCGTTTACATTCGC
* * * *
28006 CAACTTATTTATACATTTA-TTCTCGC
1 CAGCTTATTTATGCGTTTACAT-TCGC
** * *** *
28032 CAGCTTGCTCAT--GTTTATGCTCGT
1 CAGCTTATTTATGCGTTTACATTCGC
*
28056 CAGCTTATTAATGCGTTTACATTCGC
1 CAGCTTATTTATGCGTTTACATTCGC
*
28082 CATCTTATTTATGCGT
1 CAGCTTATTTATGCGT
28098 ATATATATAT
Statistics
Matches: 86, Mismatches: 28, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
24 16 0.19
26 70 0.81
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (26 bp):
CAGCTTATTTATGCGTTTACATTCGC
Found at i:39276 original size:36 final size:35
Alignment explanation
Indices: 39236--39343 Score: 126
Period size: 36 Copynumber: 3.0 Consensus size: 35
39226 GCTTACGTGT
* **
39236 GTAATGCTAAGAGATTACTTACATCTCAGTTAGAGC
1 GTAATGCTAAGTGATTACTTATGTCTC-GTTAGAGC
* *
39272 GTAATGCTATGTGATTTCTTATGTCTCGATTAGAGC
1 GTAATGCTAAGTGATTACTTATGTCTCG-TTAGAGC
* *
39308 GTAATGTTAAGTTATTACTTATGTCTCGGTTAGAGC
1 GTAATGCTAAGTGATTACTTATGTCTC-GTTAGAGC
39344 ACAAGGCTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
35 1 0.02
36 59 0.97
37 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (35 bp):
GTAATGCTAAGTGATTACTTATGTCTCGTTAGAGC
Found at i:41078 original size:19 final size:19
Alignment explanation
Indices: 41054--41095 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41044 GGTCGTTTAT
* *
41054 CATTGACTTGACCATTGAC
1 CATTGACCTGACAATTGAC
*
41073 CATTGACCTGATAATTGAC
1 CATTGACCTGACAATTGAC
41092 CATT
1 CATT
41096 AACTGTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (19 bp):
CATTGACCTGACAATTGAC
Found at i:41149 original size:23 final size:23
Alignment explanation
Indices: 41119--41166 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
41109 TTGGGTTGAC
41119 TATTAACTTTTTTCGAGAAACCT
1 TATTAACTTTTTTCGAGAAACCT
41142 TATTAACTTTTTTCGAGAAACCT
1 TATTAACTTTTTTCGAGAAACCT
41165 TA
1 TA
41167 CCTGGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (23 bp):
TATTAACTTTTTTCGAGAAACCT
Found at i:54700 original size:36 final size:36
Alignment explanation
Indices: 54652--54816 Score: 204
Period size: 36 Copynumber: 4.6 Consensus size: 36
54642 TTCGATGGAA
* * *
54652 TGCTTACGTCTCGGTTAGAGCTTAATGCTAAGAGAT
1 TGCTTACGTCTCGATTAGAGCGTAATGCTAAGTGAT
* * * * *
54688 TGCTTACATCTCGGTTACAGCGTAATACTATGTGAT
1 TGCTTACGTCTCGATTAGAGCGTAATGCTAAGTGAT
* *
54724 TGATTACGTCTCGATTAGAGCGTAATGCTATGTGAT
1 TGCTTACGTCTCGATTAGAGCGTAATGCTAAGTGAT
* *
54760 TGCTTACGTCTCAATTAGAGCGTAATGCAAAGTGAT
1 TGCTTACGTCTCGATTAGAGCGTAATGCTAAGTGAT
* *
54796 TGTTTATGTCTCGATTAGAGC
1 TGCTTACGTCTCGATTAGAGC
54817 ATAAGGCCAT
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 111 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (36 bp):
TGCTTACGTCTCGATTAGAGCGTAATGCTAAGTGAT
Found at i:82488 original size:200 final size:194
Alignment explanation
Indices: 82064--82516 Score: 531
Period size: 195 Copynumber: 2.3 Consensus size: 194
82054 TACCAGTACT
* **
82064 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACGTATGTTGTACCAT-AGCCATCGATACGG
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACC-TCAGCCATCGATACGG
* *
82128 TGTCTGTATGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAAAGTATGCAA
65 TATCTG-ATGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAAAGTATGCAA
* * * *
82193 TAAGTAAAGTCCCACCCATCATAGGGCTTGTAATCTATTTAGGATCCATATCTCTTTCTCGAGTC
129 TAAGTAAAGTCCCAACCATCATAGGGCCTGTAATCCATTTAGGATCCATATCTCTTTCTCGACTC
82258 A
194 A
* *
82259 CGATGCTGCTCACACGAGCTATCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGT
* **
82324 ATCTG-TGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACACGAGTTGTCGAGAA-TATGCGCT
66 ATCTGATGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGA-AAGTATGC-AA
* * * *
82385 TATGCATAAA-TCTCAACCATCGTAGGGCCTGTAATCCATTTAGGATCCATTTTCTTTTCTCATT
129 TAAG--TAAAGTCCCAACCATCATAGGGCCTGTAATCCATTTAGGATCCA------TATCTC-TT
82449 TCTCGACTCA
185 TCTCGACTCA
** ** * *
82459 CGATTTTACTCGTACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAGCCATCG
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCG
82517 CGTCAGTTTC
Statistics
Matches: 220, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
191 42 0.19
192 8 0.04
193 37 0.17
194 5 0.02
195 62 0.28
199 5 0.02
200 61 0.28
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (194 bp):
CGATGCTACTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGATACGGT
ATCTGATGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAAAGTATGCAATA
AGTAAAGTCCCAACCATCATAGGGCCTGTAATCCATTTAGGATCCATATCTCTTTCTCGACTCA
Found at i:84194 original size:14 final size:15
Alignment explanation
Indices: 84177--84214 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
84167 TACTAATATT
84177 AATTCAATAATT-AA
1 AATTCAATAATTCAA
**
84191 AATTCTTTAATTCAA
1 AATTCAATAATTCAA
84206 AATTCAATA
1 AATTCAATA
84215 TAAATTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:87104 original size:109 final size:110
Alignment explanation
Indices: 86902--87121 Score: 406
Period size: 109 Copynumber: 2.0 Consensus size: 110
86892 GTCAATTCAT
*
86902 TACCAAACATATTTGCTTAATTACAATATCAAGCAAGCAAGAAAGTTTTTTTCAACAAAGAACCA
1 TACCAAACATATTTGCTTAATTACAACATCAAGCAAGCAAGAAAGTTTTTTTCAACAAAGAACCA
86967 ACAATCCAAAATCAAACATGTTAAGGGTAACATCATCCTAGTCCA
66 ACAATCCAAAATCAAACATGTTAAGGGTAACATCATCCTAGTCCA
* *
87012 TACCAAACATATTTGTTTAATTACAACATCAAGCAAGCAAGACAG-TTTTTTCAACAAAGAACCA
1 TACCAAACATATTTGCTTAATTACAACATCAAGCAAGCAAGAAAGTTTTTTTCAACAAAGAACCA
87076 ACAATCCAAAATCAAACATGTTAAGGGTAACATCATCCTAGTCCA
66 ACAATCCAAAATCAAACATGTTAAGGGTAACATCATCCTAGTCCA
87121 T
1 T
87122 GTCATATGAC
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
109 65 0.61
110 42 0.39
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.25
Consensus pattern (110 bp):
TACCAAACATATTTGCTTAATTACAACATCAAGCAAGCAAGAAAGTTTTTTTCAACAAAGAACCA
ACAATCCAAAATCAAACATGTTAAGGGTAACATCATCCTAGTCCA
Found at i:110235 original size:24 final size:24
Alignment explanation
Indices: 110203--110323 Score: 179
Period size: 24 Copynumber: 5.0 Consensus size: 24
110193 ATCTGGTTCA
*
110203 TAAGAGCTAACCATTTTGGGCTCG
1 TAAGAGCTAACCATTCTGGGCTCG
**
110227 TAAGAGCTAACCATTCTAAGCTCG
1 TAAGAGCTAACCATTCTGGGCTCG
**
110251 TAAGAGCTAACCATTCTAAGCTCG
1 TAAGAGCTAACCATTCTGGGCTCG
*
110275 TAAGAGTTAACCATTCTGGGCTCG
1 TAAGAGCTAACCATTCTGGGCTCG
*
110299 TAAGAGTTAACCATTCTGGGCTCG
1 TAAGAGCTAACCATTCTGGGCTCG
110323 T
1 T
110324 GTGGGCTAAG
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAGAGCTAACCATTCTGGGCTCG
Found at i:115159 original size:114 final size:114
Alignment explanation
Indices: 114959--115183 Score: 378
Period size: 114 Copynumber: 2.0 Consensus size: 114
114949 GCGATAGAGA
* * *
114959 GGGGTTTGTTCTTGGCGGGAGATTGCAGTATATGGAATTTGTGGTAAGCACGATTTGGCCTAAGG
1 GGGGTTTGTGCTCGGCGGGAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTAAGG
* * *
115024 ACGAGGCAATCAGTAAGGGTATTTCTTGGGCTTGTTCTACAAATATGTT
66 ACGAGACAATCAGTAAGGGTATATCTTGGGCTTGCTCTACAAATATGTT
*
115073 GGGGTTTGTGCTCGGCGGGAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTGAGG
1 GGGGTTTGTGCTCGGCGGGAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTAAGG
*
115138 ATGAGACAATCAGTAAGGGTATATCTTGGGCTTGCTCTACAAATAT
66 ACGAGACAATCAGTAAGGGTATATCTTGGGCTTGCTCTACAAATAT
115184 ATCCAAAGTT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (114 bp):
GGGGTTTGTGCTCGGCGGGAGATTGCAGTATATGAAATTTGTGGTAAGCACGATTTGGCCTAAGG
ACGAGACAATCAGTAAGGGTATATCTTGGGCTTGCTCTACAAATATGTT
Found at i:116921 original size:32 final size:31
Alignment explanation
Indices: 116885--116954 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
116875 TTTTAAGTTT
*
116885 CTTAAAAATTAGAAAAAAAAAATTTTAAATCC
1 CTTAAAAATCAGAAAAAAAAAATTTTAAAT-C
* * * *
116917 CTTAAAAGTCGGTAAAAAAAAATTTTGAATC
1 CTTAAAAATCAGAAAAAAAAAATTTTAAATC
116948 CTTAAAA
1 CTTAAAA
116955 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (31 bp):
CTTAAAAATCAGAAAAAAAAAATTTTAAATC
Found at i:117033 original size:26 final size:26
Alignment explanation
Indices: 116939--117042 Score: 79
Period size: 26 Copynumber: 3.9 Consensus size: 26
116929 TAAAAAAAAA
* *
116939 TTTTGAATCCTTAAAAGTT--ATTTT
1 TTTTGAACCCTTAAAAGTTAAAATTT
*
116963 TTTTGTAGCCCTTTAAAAGTTGATAAATTTTT
1 TTTTG-AACCC-TTAAAAGTT-A-AAA--TTT
**
116995 TTTTG-ACATTTAAAAGTTAAAATTT
1 TTTTGAACCCTTAAAAGTTAAAATTT
*
117020 TTTTGAACCCTTAAAAATTAAAA
1 TTTTGAACCCTTAAAAGTTAAAA
117043 AAAATATATT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
24 5 0.08
25 11 0.18
26 23 0.37
27 3 0.05
28 1 0.02
29 9 0.15
30 2 0.03
32 8 0.13
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (26 bp):
TTTTGAACCCTTAAAAGTTAAAATTT
Found at i:141829 original size:20 final size:20
Alignment explanation
Indices: 141786--141831 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
141776 TTGTACAAGT
* *
141786 TTGCACTTTAGTGTCTCTAT
1 TTGCACTCTAGTGTCTCTAA
141806 TTGCACTCTAGTG-CTCTTAA
1 TTGCACTCTAGTGTCTC-TAA
141826 TTGCAC
1 TTGCAC
141832 AATCATTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGCACTCTAGTGTCTCTAA
Found at i:142997 original size:21 final size:23
Alignment explanation
Indices: 142968--143029 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
142958 AAACTTTAAA
*
142968 AATAGATTTTAATATAATAATTTT
1 AATA-ATTTTAAAATAATAATTTT
* *
142992 -AT-ATTTCAAAAAAATAATTTT
1 AATAATTTTAAAATAATAATTTT
143013 AATAATTTTAAAATAAT
1 AATAATTTTAAAATAAT
143030 TTGCTGATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 16 0.52
22 2 0.06
23 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AATAATTTTAAAATAATAATTTT
Found at i:144655 original size:23 final size:23
Alignment explanation
Indices: 144635--144758 Score: 194
Period size: 23 Copynumber: 5.4 Consensus size: 23
144625 TAACCATATG
*
144635 AATATTTAAGCATAAATCATATT
1 AATATTTAAGCATAAATCACATT
*
144658 AATATTTAAGCATAAATCATATT
1 AATATTTAAGCATAAATCACATT
144681 AATATTTAAGCATAAATCACATT
1 AATATTTAAGCATAAATCACATT
* *
144704 AATATTTAAGTATAAACCACATT
1 AATATTTAAGCATAAATCACATT
* *
144727 AATATTTATGTATAAATCACATT
1 AATATTTAAGCATAAATCACATT
144750 AATATTTAA
1 AATATTTAA
144759 TACATTTAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 95 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.39
Consensus pattern (23 bp):
AATATTTAAGCATAAATCACATT
Found at i:145830 original size:21 final size:21
Alignment explanation
Indices: 145806--145853 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
145796 CTTTAGGGAT
145806 AGTTAAGAAACCTTCTAATCA
1 AGTTAAGAAACCTTCTAATCA
145827 AGTTAAGAAACCTTCTAATCA
1 AGTTAAGAAACCTTCTAATCA
*
145848 TGTTAA
1 AGTTAA
145854 AACAAGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (21 bp):
AGTTAAGAAACCTTCTAATCA
Found at i:154323 original size:3 final size:3
Alignment explanation
Indices: 154310--154340 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
154300 TTATTTCTAT
*
154310 TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
154341 TATTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:154345 original size:3 final size:3
Alignment explanation
Indices: 154339--154375 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
154329 CATCATCATC
154339 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
154376 AAGCTAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:155150 original size:22 final size:22
Alignment explanation
Indices: 155125--155166 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
155115 GCACCATCGT
* *
155125 GCCATCGTTGCACCGCCGTGTG
1 GCCATCATCGCACCGCCGTGTG
*
155147 GCCATCATCGCACCGTCGTG
1 GCCATCATCGCACCGCCGTG
155167 CCACCTCCTT
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:0.38, G:0.29, T:0.21
Consensus pattern (22 bp):
GCCATCATCGCACCGCCGTGTG
Found at i:156307 original size:49 final size:49
Alignment explanation
Indices: 156228--156345 Score: 155
Period size: 49 Copynumber: 2.4 Consensus size: 49
156218 ATTTACAAAT
** *
156228 TTTGGTGGCTTGTCCACAATTACATATATCTGGCAGCTTGATTGCATTA
1 TTTGGTGGCTTGTCCACAATTACATATATCTACCAACTTGATTGCATTA
* * *
156277 TTTGGTGGTTTGTCCACAATTACCTGTATCTACCAACTTGATTGCATTA
1 TTTGGTGGCTTGTCCACAATTACATATATCTACCAACTTGATTGCATTA
* * *
156326 TCTGGTGACTTATCCACAAT
1 TTTGGTGGCTTGTCCACAAT
156346 ATTGGTGTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (49 bp):
TTTGGTGGCTTGTCCACAATTACATATATCTACCAACTTGATTGCATTA
Found at i:159985 original size:9 final size:9
Alignment explanation
Indices: 159971--160066 Score: 81
Period size: 9 Copynumber: 10.6 Consensus size: 9
159961 AAATAACTCT
159971 TTTTTATAA
1 TTTTTATAA
*
159980 TTTTTAT-T
1 TTTTTATAA
159988 TTTTTATAA
1 TTTTTATAA
159997 TTTTTATAAA
1 TTTTTAT-AA
160007 TTTTTAT-A
1 TTTTTATAA
* *
160015 TGTTTAATGA
1 T-TTTTATAA
*
160025 TTCATTATAA
1 TT-TTTATAA
*
160035 TATTTATAAA
1 TTTTTAT-AA
*
160045 TTTTTGT-A
1 TTTTTATAA
160053 TTTTTATAA
1 TTTTTATAA
160062 TTTTT
1 TTTTT
160067 TAAATTTAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 16 0.23
9 30 0.43
10 23 0.33
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:159992 original size:17 final size:17
Alignment explanation
Indices: 159970--160003 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
159960 CAAATAACTC
159970 TTTTTTATAATTTTTAT
1 TTTTTTATAATTTTTAT
159987 TTTTTTATAATTTTTAT
1 TTTTTTATAATTTTTAT
160004 AAATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTATAATTTTTAT
Found at i:160612 original size:15 final size:15
Alignment explanation
Indices: 160560--160612 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
160550 TTTATTTATC
*
160560 TTATATTACATTTTAG
1 TTAT-TTACATTTTAA
* *
160576 TTATTTATATTTAAA
1 TTATTTACATTTTAA
*
160591 ATA-TTACATTTTAA
1 TTATTTACATTTTAA
160605 TTATTTAC
1 TTATTTAC
160613 GTAATCGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 11 0.38
15 14 0.48
16 4 0.14
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (15 bp):
TTATTTACATTTTAA
Found at i:160765 original size:18 final size:18
Alignment explanation
Indices: 160742--160784 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
160732 GAATAGATTT
160742 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
160760 TTAATTGAAAAGTTTAAA
1 TTAATTAAAAAATTTAAA
160778 TTAATTA
1 TTAATTA
160785 CATATTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:162603 original size:15 final size:15
Alignment explanation
Indices: 162583--162617 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
162573 ATCAAGAAAC
162583 AGAAAGAAGCTGAGA
1 AGAAAGAAGCTGAGA
162598 AGAAAGAAGCTGAGA
1 AGAAAGAAGCTGAGA
162613 A-AAAG
1 AGAAAG
162618 GCGAAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.57, C:0.06, G:0.31, T:0.06
Consensus pattern (15 bp):
AGAAAGAAGCTGAGA
Found at i:167491 original size:15 final size:15
Alignment explanation
Indices: 167471--167505 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
167461 TATTCTTTTA
167471 AATTATTTATCCTTT
1 AATTATTTATCCTTT
**
167486 AATTATTTATTTTTT
1 AATTATTTATCCTTT
167501 AATTA
1 AATTA
167506 AAATCGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTATTTATCCTTT
Found at i:167706 original size:31 final size:31
Alignment explanation
Indices: 167669--167735 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
167659 TTTGTGAATA
167669 AAATTAAATGATTTTAATTAAAAGATAAATG
1 AAATTAAATGATTTTAATTAAAAGATAAATG
* *
167700 AAATTAAATTATTTTAATTAAAGGATAAATG
1 AAATTAAATGATTTTAATTAAAAGATAAATG
167731 AAATT
1 AAATT
167736 CAAGTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (31 bp):
AAATTAAATGATTTTAATTAAAAGATAAATG
Done.