Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013554.1 Kokia drynarioides strain JFW-HI SEQ_128580, 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: 33104
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:790 original size:17 final size:17
Alignment explanation
Indices: 770--812 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
760 TCAGCTATAT
*
770 TTAAATTTAGAATAAAC
1 TTAAATTTAAAATAAAC
* *
787 TTAATTTTAAAATAAAT
1 TTAAATTTAAAATAAAC
*
804 TTAAGTTTA
1 TTAAATTTA
813 TTGGGCCCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAAATAAAC
Found at i:1821 original size:205 final size:206
Alignment explanation
Indices: 1200--2005 Score: 1026
Period size: 205 Copynumber: 3.9 Consensus size: 206
1190 GTGTTTCGTT
* * * * ** * *
1200 AGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGGAGCTAACCACTTCATTGCTTCGAC
1 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAATTAACCATTTTATTGCTTCGAC
* ** * ** * * *
1265 TTGCTTCTCAGCGTCTCATCAGGAAGTTG-GAGTTTAAAGATTTGCTCACATTGGGCGTGAGTTT
66 TTACTTCTCAGTATCTCATCAGGAAGCTGTG-GTTCGAAGATTTGCTCACATCGAGCGTGGGTTT
* * * *
1329 GATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCGTCGTTTGTTTCAATTCGTTTCT
130 GATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTTCT
*
1394 CTGTATCTCATT
195 CTGTATCTCATC
* *
1406 AGGAAAACGAATTTGGTCCACTTCTCCA-CATCTCATCAGGAAGATGGTCAGGAAGCTAACAATT
1 AGGAAGACGAATTTGGTCCACTTCT-CAGTATCTCATCAGGAA-AT--T----AA-C---C-ATT
* * *
1470 TTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACGTC
53 TTATTGCTTCGACTTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATC
*
1535 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATTTCATCAGGAAGATGACTGCGTCGTTTGTTT
118 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCGTCGTTTGTTT
*
1600 CAATCAGCTTCTCTGTATCTCATC
183 CAATCCGCTTCTCTGTATCTCATC
* * *
1624 AAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATAAGGAAATTAACC-TTTTATTGCTTCGTC
1 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAATTAACCATTTTATTGCTTCGAC
* *
1688 CTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTAGCTCACATCGAGCGTGGGTTTG
66 TTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTG
* * *
1753 ATTTGGTCTTCTTCTCAATATTTCATCAGGAAGAGGACTGCGTCGTTTGTTTCAATCCGCTACTC
131 ATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTTCTC
1818 TGTATCTCATC
196 TGTATCTCATC
* * *
1829 AGGAATACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGTTAACC-TTTTATTGCTTCGAC
1 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAATTAACCATTTTATTGCTTCGAC
* * * *
1893 TTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCACATCGAGCGTAGGTTTG
66 TTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTG
* * * *
1958 ACTTGGTCTTCTTCTCAGTATCTCATCAGGTAGATGACCGCGTCGTTT
131 ATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCGTCGTTT
2006 ATGGATAATC
Statistics
Matches: 527, Mismatches: 58, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
205 306 0.58
206 34 0.06
207 2 0.00
209 1 0.00
210 1 0.00
211 2 0.00
213 2 0.00
214 1 0.00
215 1 0.00
217 5 0.01
218 171 0.32
219 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (206 bp):
AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAATTAACCATTTTATTGCTTCGAC
TTACTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTG
ATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTTCTC
TGTATCTCATC
Found at i:13817 original size:30 final size:30
Alignment explanation
Indices: 13775--14091 Score: 227
Period size: 29 Copynumber: 10.7 Consensus size: 30
13765 ACCCGGGAGT
* * *
13775 AAATGGTAATTTTGGGAAATTTTGGGGTTAA
1 AAATGG-AATTTTTGGAAGTTTCGGGGTTAA
*
13806 AAATGGAATTTTTAGAAG-TTCAGGGG-TAA
1 AAATGGAATTTTTGGAAGTTTC-GGGGTTAA
**** * *
13835 AAGCAAAATTTTAGGAAGTTTCGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
* * *
13865 AAAT-GAGATCTTTGGAAGTTTAGGGGTCAA
1 AAATGGA-ATTTTTGGAAGTTTCGGGGTTAA
* * * *
13895 AAATGGGATTTTTGGAA-ATTCGAGGCTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
* *
13924 AAATGGAATTTTTGGAGGTTTTGGGGTTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
* ** *
13954 AAATGGGATTTTTGGAAGTTTTTGGG-TCA
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
* *
13983 AAATGGGATTTTTGGAAG-TTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
* * * *
14012 AAACGGAATTTTTGGAAGTTTC-GAGTCAG
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
* * * *
14041 AAATGGGATTTTTGGAAATTT-GAGGCTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTTAA
**
14070 AAACAGAATTTTTGGATAGTTT
1 AAATGGAATTTTTGGA-AGTTT
14092 AGGGACCTCA
Statistics
Matches: 221, Mismatches: 55, Indels: 21
0.74 0.19 0.07
Matches are distributed among these distances:
28 5 0.02
29 118 0.53
30 91 0.41
31 7 0.03
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTTAA
Found at i:13867 original size:59 final size:60
Alignment explanation
Indices: 13782--13896 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 60
13772 AGTAAATGGT
* * * *
13782 AATTTTGGGAAATTTTGGGGTTAAAAATG-GAATTTTTAGAAGTTCAGGGGT-AAAAGCAA
1 AATTTTAGGAAATTTCGGGGTCAAAAATGAG-ATCTTTAGAAGTTCAGGGGTCAAAAGCAA
* * *
13841 AATTTTAGGAAGTTTCGGGGTCAAAAATGAGATCTTTGGAAGTTTAGGGGTCAAAA
1 AATTTTAGGAAATTTCGGGGTCAAAAATGAGATCTTTAGAAGTTCAGGGGTCAAAA
13897 ATGGGATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 42 0.89
60 5 0.11
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (60 bp):
AATTTTAGGAAATTTCGGGGTCAAAAATGAGATCTTTAGAAGTTCAGGGGTCAAAAGCAA
Found at i:13926 original size:59 final size:57
Alignment explanation
Indices: 13863--14057 Score: 176
Period size: 59 Copynumber: 3.3 Consensus size: 57
13853 TTTCGGGGTC
*
13863 AAAAATGAGATCTTTGGAAGTTTAGGGGTCAAAAATGGGATTTTTGGAAATTCGAGGCT
1 AAAAATG-GATTTTTGGAAGTTTAGGGGT-AAAAATGGGATTTTTGGAAATTCGAGGCT
* * * *** *
13922 AAAAATGGAATTTTTGGAGGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTTGGGT
1 AAAAATGG-ATTTTTGGAAGTTTAGGGG-TAAAAATGGGATTTTTGGAAATTCGAGGCT
* ** * * * *
13981 CAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAACGGAATTTTTGGAAGTTTCGAGTC-
1 AAAAAT-GGATTTTTGGAAGTTTAGGGGTAAAAATGGGATTTTTGGAA-ATTCGAGGCT
*
14039 AGAAATGGGATTTTTGGAA
1 AAAAAT-GGATTTTTGGAA
14058 ATTTGAGGCT
Statistics
Matches: 110, Mismatches: 22, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
58 36 0.33
59 71 0.65
60 3 0.03
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.34
Consensus pattern (57 bp):
AAAAATGGATTTTTGGAAGTTTAGGGGTAAAAATGGGATTTTTGGAAATTCGAGGCT
Found at i:14871 original size:25 final size:25
Alignment explanation
Indices: 14825--14899 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
14815 GAAGGTAAAA
*
14825 AAACTTCCCTTTTCCCCTTTTTTTTTT
1 AAACTTCTCTTTT--CCTTTTTTTTTT
* **
14852 AAATTTCTCTTTTCCTTTTTCGTTT
1 AAACTTCTCTTTTCCTTTTTTTTTT
*
14877 AAACTTCTCTTTTCCCTTTTTTT
1 AAACTTCTCTTTTCCTTTTTTTT
14900 AAAAAAACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 29 0.73
27 11 0.28
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.61
Consensus pattern (25 bp):
AAACTTCTCTTTTCCTTTTTTTTTT
Found at i:15899 original size:17 final size:17
Alignment explanation
Indices: 15879--15926 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
15869 AAATAAATTT
*
15879 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
15896 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
15913 TAAATTTAAGTTTA
1 TAAATTTAAATTTA
15927 TTGGGCCTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:16376 original size:29 final size:29
Alignment explanation
Indices: 16320--16378 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
16310 CAATTTCTAC
* *
16320 TATTCATTTTAGGTCATTTAGGTGAATAT
1 TATTCAATTTAGGTCATTTAGGTAAATAT
16349 TATTCAATTTAGGTCATTT-GTGTAAATAT
1 TATTCAATTTAGGTCATTTAG-GTAAATAT
16378 T
1 T
16379 TTTTTCGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (29 bp):
TATTCAATTTAGGTCATTTAGGTAAATAT
Found at i:16521 original size:12 final size:12
Alignment explanation
Indices: 16504--16528 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16494 TTTTGATACA
16504 TTTTATAATTTT
1 TTTTATAATTTT
16516 TTTTATAATTTT
1 TTTTATAATTTT
16528 T
1 T
16529 ATAGAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:16603 original size:18 final size:18
Alignment explanation
Indices: 16582--16616 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16572 AAAAAATCTA
16582 ATTTTTAATAAAATTTAT
1 ATTTTTAATAAAATTTAT
*
16600 ATTTTTATTAAAATTTA
1 ATTTTTAATAAAATTTA
16617 ATAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTTAATAAAATTTAT
Found at i:20258 original size:23 final size:24
Alignment explanation
Indices: 20213--20278 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
20203 TTTCTATATT
**
20213 TTTTAAATTTACAGTAAAATTAAA
1 TTTTAAATTTACAAAAAAATTAAA
20237 TTTTAAATTTA-AAAAAAATTAAA
1 TTTTAAATTTACAAAAAAATTAAA
* *
20260 TTTCAAATTTAGAAAAAAA
1 TTTTAAATTTACAAAAAAA
20279 AAAATTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
TTTTAAATTTACAAAAAAATTAAA
Found at i:20279 original size:29 final size:29
Alignment explanation
Indices: 20247--20305 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
20237 TTTTAAATTT
20247 AAAAAAAATTAAATTTCAAATTTA-GAAA
1 AAAAAAAATTAAATTTCAAATTTATGAAA
20275 AAAAAAAATTAAATTTCAAATTTATGAAA
1 AAAAAAAATTAAATTTCAAATTTATGAAA
20304 AA
1 AA
20306 TATTAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAAAAATTAAATTTCAAATTTATGAAA
Found at i:20283 original size:23 final size:23
Alignment explanation
Indices: 20228--20284 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
20218 AATTTACAGT
* *
20228 AAAATTAAATTTTAAATTTAAAA
1 AAAATAAAATTTCAAATTTAAAA
*
20251 AAAATTAAATTTCAAATTTAGAAA
1 AAAATAAAATTTCAAATTTA-AAA
20275 AAAA-AAAATT
1 AAAATAAAATT
20285 AAATTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATAAAATTTCAAATTTAAAA
Found at i:27235 original size:44 final size:44
Alignment explanation
Indices: 27172--27259 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
27162 GTAGTAAGGA
* *
27172 AAGTTTGGAGTCTTAAGTGAAAACATTAATTTTTTTGGAACCCC
1 AAGTTGGGAGTCTCAAGTGAAAACATTAATTTTTTTGGAACCCC
27216 AAGTTGGGAGTCTCAAGTGAAAACATTAATTTTTTTGGAACCCC
1 AAGTTGGGAGTCTCAAGTGAAAACATTAATTTTTTTGGAACCCC
27260 TTTACGTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (44 bp):
AAGTTGGGAGTCTCAAGTGAAAACATTAATTTTTTTGGAACCCC
Found at i:30043 original size:13 final size:15
Alignment explanation
Indices: 30025--30057 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
30015 AAAAATTACG
30025 AAAAACA-CGAAT-C
1 AAAAACATCGAATAC
30038 AAAAACATCGAATAC
1 AAAAACATCGAATAC
30053 AAAAA
1 AAAAA
30058 AAAGGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 5 0.28
15 6 0.33
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAAACATCGAATAC
Found at i:30205 original size:30 final size:30
Alignment explanation
Indices: 30165--30319 Score: 165
Period size: 29 Copynumber: 5.3 Consensus size: 30
30155 GTCTCGGAGC
* *
30165 ATTT-AGGGTTAAAATGTAATTTTGGAAAA
1 ATTTGAGGGTCAATATGTAATTTTGGAAAA
* *
30194 ATTTGAGGGTTAATATGTAATTTTAG-AAA
1 ATTTGAGGGTCAATATGTAATTTTGGAAAA
* * *
30223 GTTTAAGGGTCAATGTGTAATTTT-GAAAA
1 ATTTGAGGGTCAATATGTAATTTTGGAAAA
30252 ATTTGAGGGTCAATATGTAATTTTGGAAAA
1 ATTTGAGGGTCAATATGTAATTTTGGAAAA
* * * * **
30282 GTTCGAGGGTCAAAATGTTATTTTTAAAAA
1 ATTTGAGGGTCAATATGTAATTTTGGAAAA
30312 ATTT-AGGG
1 ATTTGAGGG
30320 ATCTCTTAGC
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 55 0.52
30 50 0.47
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
ATTTGAGGGTCAATATGTAATTTTGGAAAA
Found at i:30232 original size:59 final size:59
Alignment explanation
Indices: 30169--30319 Score: 189
Period size: 59 Copynumber: 2.6 Consensus size: 59
30159 CGGAGCATTT
* * *
30169 AGGGTTAAAATGTAATTTTGGAAAAATTTGAGGGTTAATATGTAATTTTAG-AAAGTTTA
1 AGGGTCAAAATGTAATTTT-GAAAAATTTGAGGGTCAATATGTAATTTTAGAAAAGTTCA
** * *
30228 AGGGTCAATGTGTAATTTTGAAAAATTTGAGGGTCAATATGTAATTTTGGAAAAGTTCG
1 AGGGTCAAAATGTAATTTTGAAAAATTTGAGGGTCAATATGTAATTTTAGAAAAGTTCA
* *
30287 AGGGTCAAAATGTTATTTTTAAAAAATTT-AGGG
1 AGGGTCAAAATG-TAATTTTGAAAAATTTGAGGG
30320 ATCTCTTAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 29 0.37
59 36 0.46
60 14 0.18
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (59 bp):
AGGGTCAAAATGTAATTTTGAAAAATTTGAGGGTCAATATGTAATTTTAGAAAAGTTCA
Found at i:30756 original size:20 final size:20
Alignment explanation
Indices: 30727--30789 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
30717 ATCGCCACCA
* *
30727 TCGCTGTTCCCCATCGACCG
1 TCGCTATTCCCAATCGACCG
30747 TCGCTATTCCCAATCGACCG
1 TCGCTATTCCCAATCGACCG
30767 TCGCTATTCCCAATCGACCG
1 TCGCTATTCCCAATCGACCG
30787 TCG
1 TCG
30790 TTCACCGCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.41, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCTATTCCCAATCGACCG
Found at i:31003 original size:33 final size:33
Alignment explanation
Indices: 30930--31004 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 33
30920 AAGAAGTTTG
30930 TTTATTTGATGATTTTCGAATCTTTTCCTTGTTA
1 TTTATTT-ATGATTTTCGAATCTTTTCCTTGTTA
*
30964 GATTATTT-TGATTTTCGAATCTTTTCTCCTTGTT-
1 -TTTATTTATGATTTTCGAATC-TTT-TCCTTGTTA
30998 TTTATTT
1 TTTATTT
31005 CATTTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 19 0.53
34 3 0.08
35 14 0.39
ACGTcount: A:0.16, C:0.12, G:0.11, T:0.61
Consensus pattern (33 bp):
TTTATTTATGATTTTCGAATCTTTTCCTTGTTA
Found at i:31359 original size:15 final size:16
Alignment explanation
Indices: 31333--31362 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31323 TGCTATTGTT
31333 TTTCTCTTTTGTCTTA
1 TTTCTCTTTTGTCTTA
31349 TTTCT-TTTTGTCTT
1 TTTCTCTTTTGTCTT
31363 TGCAGGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.17, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTCTCTTTTGTCTTA
Found at i:32975 original size:46 final size:45
Alignment explanation
Indices: 32874--32975 Score: 152
Period size: 46 Copynumber: 2.3 Consensus size: 45
32864 TAATGCTGAC
*
32874 AAACTATCACA-TCAAATTGTGGACAAGCCACCACTTTTGTAGAT
1 AAACTATCACATTCAAATTGTGGACAAGCCACCACTTTTGCAGAT
* *
32918 ATACTACCACATTCAATATTGTGGACAAGCCACCACTTTTGCAGAT
1 AAACTATCACATTCAA-ATTGTGGACAAGCCACCACTTTTGCAGAT
*
32964 AAACTGTCACAT
1 AAACTATCACAT
32976 CTTCCACCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
44 9 0.18
45 4 0.08
46 37 0.74
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (45 bp):
AAACTATCACATTCAAATTGTGGACAAGCCACCACTTTTGCAGAT
Done.