Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015154.1 Kokia drynarioides strain JFW-HI SEQ_130198, 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: 822009
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 133 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:752865 original size:57 final size:58
Alignment explanation
Indices: 752735--752983 Score: 237
Period size: 57 Copynumber: 4.3 Consensus size: 58
752725 AAACTTTTCT
* *
752735 AAAATTACATTTTAACACCT-AAACTTCTCAAAAATTAC-TCTTTTACCCCTAATCTTCCA
1 AAAATTACATTTTTAC-CCTCAAACTTCTCAAAAATTACAT-TTTTACCCCGAA-CTTCCA
* * *
752794 AAAATTACATTTTTACCCTCAAACTTCT-AAAAATTTCATTTTTGCCTCGAACTTCCA
1 AAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCGAACTTCCA
* * * *
752851 AAAATTACATTTTTACCCCCGATCTTC-CAAAAATTACATTTTTACCCCCAAACTTCCA
1 AAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTA-CCCCGAACTTCCA
* * * * *
752909 AAACTCACATTTTGT---CTCAGACTTCTCAAAAA-TACATTTTTACCTCGAACTCTCCT
1 AAAATTACATTTT-TACCCTCAAACTTCTCAAAAATTACATTTTTACCCCGAACT-TCCA
752965 AAAATGT-CATTTTTTACCC
1 AAAAT-TACA-TTTTTACCC
752984 AAACTCTCCG
Statistics
Matches: 155, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
55 7 0.05
56 26 0.17
57 54 0.35
58 42 0.27
59 26 0.17
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCGAACTTCCA
Found at i:752876 original size:86 final size:85
Alignment explanation
Indices: 752756--752952 Score: 265
Period size: 86 Copynumber: 2.3 Consensus size: 85
752746 TTAACACCTA
* *
752756 AACTTCTCAAAAATTAC-TCTTTTACCCCTAATCTTCCAAAAATTACATTTTTACCCTCAAACTT
1 AACTTCTCAAAAATTACAT-TTTTACCCCCAATCTTCCAAAAATTACATTTTTACCCCCAAACTT
* **
752820 CTAAAAATTTCATTTTTGCCTC
65 CCAAAAATCACA-TTTTGCCTC
*
752842 GAACTTC-CAAAAATTACATTTTTACCCCCGATCTTCCAAAAATTACATTTTTACCCCCAAACTT
1 -AACTTCTCAAAAATTACATTTTTACCCCCAATCTTCCAAAAATTACATTTTTACCCCCAAACTT
* *
752906 CCAAAACTCACATTTTGTCTC
65 CCAAAAATCACATTTTGCCTC
752927 AGACTTCTCAAAAA-TACATTTTTACC
1 A-ACTTCTCAAAAATTACATTTTTACC
752953 TCGAACTCTC
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
84 1 0.01
85 25 0.25
86 66 0.67
87 7 0.07
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (85 bp):
AACTTCTCAAAAATTACATTTTTACCCCCAATCTTCCAAAAATTACATTTTTACCCCCAAACTTC
CAAAAATCACATTTTGCCTC
Found at i:752979 original size:86 final size:87
Alignment explanation
Indices: 752756--752983 Score: 256
Period size: 86 Copynumber: 2.6 Consensus size: 87
752746 TTAACACCTA
* *
752756 AACTTCTCAAAAATTAC-TCTTTTACCCCTAA-TCTTCCAAAAATTACATTTTTACCCTCAAACT
1 AACTTCTCAAAAATTACAT-TTTTACCCCGAACTC-TCCAAAAATTACATTTTTACCCCCAAACT
* **
752819 TCTAAAAATTTCATTTTTGCCTCG
64 TCCAAAAATCACATTTTTGCCTCG
*
752843 AACTTC-CAAAAATTACATTTTTACCCCCGATCT-TCCAAAAATTACATTTTTACCCCCAAACTT
1 AACTTCTCAAAAATTACATTTTTA-CCCCGAACTCTCCAAAAATTACATTTTTACCCCCAAACTT
* *
752906 CCAAAACTCACA-TTTTGTCTC-
65 CCAAAAATCACATTTTTGCCTCG
* *
752927 AGACTTCTCAAAAA-TACATTTTTACCTCGAACTCTCCTAAAATGT-CATTTTTTACCC
1 A-ACTTCTCAAAAATTACATTTTTACCCCGAACTCTCCAAAAAT-TACA-TTTTTACCC
752984 AAACTCTCCG
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
84 8 0.07
85 33 0.27
86 68 0.56
87 12 0.10
88 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (87 bp):
AACTTCTCAAAAATTACATTTTTACCCCGAACTCTCCAAAAATTACATTTTTACCCCCAAACTTC
CAAAAATCACATTTTTGCCTCG
Found at i:753137 original size:14 final size:14
Alignment explanation
Indices: 753101--753139 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
753091 TGATTCATAA
753101 TTTGTAT-TTTATT
1 TTTGTATATTTATT
*
753114 TTTCTCATATTTATT
1 TTTGT-ATATTTATT
753129 TTTGTATATTT
1 TTTGTATATTT
753140 GTTCATTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (14 bp):
TTTGTATATTTATT
Found at i:765046 original size:39 final size:39
Alignment explanation
Indices: 765003--765127 Score: 139
Period size: 39 Copynumber: 3.2 Consensus size: 39
764993 CTTGAGCTTA
765003 GGGCAGATTGCAGCCATTCGATCTCTTACCCCAATCATG
1 GGGCAGATTGCAGCCATTCGATCTCTTACCCCAATCATG
* * *
765042 GGGCAGA-T-CA-CCATTAGAAAATCTCTTACCCCAAGCCTG
1 GGGCAGATTGCAGCCATTCG---ATCTCTTACCCCAATCATG
** *
765081 GGATAGATTGTAGCCATTCGATCTCTTACCCCAATCATG
1 GGGCAGATTGCAGCCATTCGATCTCTTACCCCAATCATG
*
765120 GGGTAGAT
1 GGGCAGAT
765128 CACCATTAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
36 6 0.09
37 2 0.03
38 1 0.01
39 53 0.76
40 1 0.01
41 1 0.01
42 6 0.09
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
GGGCAGATTGCAGCCATTCGATCTCTTACCCCAATCATG
Found at i:765144 original size:39 final size:39
Alignment explanation
Indices: 765023--765149 Score: 152
Period size: 39 Copynumber: 3.3 Consensus size: 39
765013 CAGCCATTCG
*
765023 ATCTCTTACCCCAATCATGGGGCAGATCACCATTAGAAA
1 ATCTCTTACCCCAATCATGGGGTAGATCACCATTAGAAA
* * * * *
765062 ATCTCTTACCCCAAGCCTGGGATAGATTGTAGCCATTCG---
1 ATCTCTTACCCCAATCATGGGGTAGA-T-CA-CCATTAGAAA
765101 ATCTCTTACCCCAATCATGGGGTAGATCACCATTAGAAA
1 ATCTCTTACCCCAATCATGGGGTAGATCACCATTAGAAA
765140 ATCTCTTACC
1 ATCTCTTACC
765150 ACAAGCCTGG
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
36 6 0.08
37 1 0.01
38 1 0.01
39 55 0.77
40 1 0.01
41 1 0.01
42 6 0.08
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCAATCATGGGGTAGATCACCATTAGAAA
Found at i:765155 original size:78 final size:78
Alignment explanation
Indices: 764906--765174 Score: 317
Period size: 78 Copynumber: 3.4 Consensus size: 78
764896 GAAGATTTCG
* * ** * * * * *
764906 ATCTCTTACCTCGAGCCTGGGGCAGATTGTAGCCGTTTGATCTTTTACCCCAAGT-TTAGGGCAG
1 ATCTCTTACCACAAGCCTGGGATAGATTGTAGCCATTCGATCTCTTACCCCAA-TCATGGGGCAG
* **
764970 ATCACCATCAGCCA
65 ATCACCATTAGAAA
* *** * * *
764984 ATCTCTTCCCTTGAGCTTAGGG-CAGATTGCAGCCATTCGATCTCTTACCCCAATCATGGGGCAG
1 ATCTCTTACCACAAGCCT-GGGATAGATTGTAGCCATTCGATCTCTTACCCCAATCATGGGGCAG
765048 ATCACCATTAGAAA
65 ATCACCATTAGAAA
* *
765062 ATCTCTTACCCCAAGCCTGGGATAGATTGTAGCCATTCGATCTCTTACCCCAATCATGGGGTAGA
1 ATCTCTTACCACAAGCCTGGGATAGATTGTAGCCATTCGATCTCTTACCCCAATCATGGGGCAGA
765127 TCACCATTAGAAA
66 TCACCATTAGAAA
765140 ATCTCTTACCACAAGCCTGGGATAGATTGTAGCCA
1 ATCTCTTACCACAAGCCTGGGATAGATTGTAGCCA
765175 CTTACCCCGA
Statistics
Matches: 167, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
77 4 0.02
78 160 0.96
79 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCACAAGCCTGGGATAGATTGTAGCCATTCGATCTCTTACCCCAATCATGGGGCAGA
TCACCATTAGAAA
Found at i:765166 original size:39 final size:39
Alignment explanation
Indices: 765023--765166 Score: 150
Period size: 39 Copynumber: 3.7 Consensus size: 39
765013 CAGCCATTCG
* **
765023 ATCTCTTACCCCAATCATGGGGCAGATCACCATTAGAAA
1 ATCTCTTACCCCAAGCATGGGATAGATCACCATTAGAAA
* * *
765062 ATCTCTTACCCCAAGCCTGGGATAGATTGTAGCCATTCG---
1 ATCTCTTACCCCAAGCATGGGATAGA-T-CA-CCATTAGAAA
* *
765101 ATCTCTTACCCCAATCATGGGGTAGATCACCATTAGAAA
1 ATCTCTTACCCCAAGCATGGGATAGATCACCATTAGAAA
* *
765140 ATCTCTTACCACAAGCCTGGGATAGAT
1 ATCTCTTACCCCAAGCATGGGATAGAT
765167 TGTAGCCACT
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
36 6 0.07
37 1 0.01
38 1 0.01
39 68 0.81
40 1 0.01
41 1 0.01
42 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCAAGCATGGGATAGATCACCATTAGAAA
Found at i:765220 original size:39 final size:39
Alignment explanation
Indices: 765175--765352 Score: 184
Period size: 39 Copynumber: 4.6 Consensus size: 39
765165 ATTGTAGCCA
* * *
765175 CTTACCCCGAGCCTGGGGCAGATCACCGTCAGCCAATCT
1 CTTACCCCGAGCCTGGGGCAAATCACCATCAGCAAATCT
* * *
765214 CTTACCCCGAGCCTGGGACAAATCATCATTAGCAAATCT
1 CTTACCCCGAGCCTGGGGCAAATCACCATCAGCAAATCT
* * * *
765253 CTTACCCCGATCATGTGGCAAATTACAGCCAT--TC-AATCT
1 CTTACCCCGAGCCTGGGGCAAA-T-CA-CCATCAGCAAATCT
*
765292 CTTA-CCCGAGCCTGGGGCAGATCACCATCAGCAAATCT
1 CTTACCCCGAGCCTGGGGCAAATCACCATCAGCAAATCT
* *
765330 CTTACCCTGAGCTTGGGGCAAAT
1 CTTACCCCGAGCCTGGGGCAAAT
765353 TGCAATCTTC
Statistics
Matches: 112, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
35 4 0.04
36 2 0.02
37 2 0.02
38 22 0.20
39 75 0.67
40 2 0.02
41 2 0.02
42 3 0.03
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (39 bp):
CTTACCCCGAGCCTGGGGCAAATCACCATCAGCAAATCT
Found at i:765350 original size:77 final size:78
Alignment explanation
Indices: 765175--765353 Score: 216
Period size: 77 Copynumber: 2.3 Consensus size: 78
765165 ATTGTAGCCA
* * * * * ** *
765175 CTTACCCCGAGCCTGGGGCAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTGGGACAAATCAT
1 CTTACCCCGAGCATGGGGCAAATTACAGCCATTCAATCTCTTACCCCGAGCCTGGGACAAATCAC
*
765240 CATTAGCAAATCT
66 CATCAGCAAATCT
* * * *
765253 CTTACCCCGATCATGTGGCAAATTACAGCCATTCAATCTCTTA-CCCGAGCCTGGGGCAGATCAC
1 CTTACCCCGAGCATGGGGCAAATTACAGCCATTCAATCTCTTACCCCGAGCCTGGGACAAATCAC
765317 CATCAGCAAATCT
66 CATCAGCAAATCT
* *
765330 CTTACCCTGAGCTTGGGGCAAATT
1 CTTACCCCGAGCATGGGGCAAATT
765354 GCAATCTTCT
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
77 50 0.60
78 34 0.40
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (78 bp):
CTTACCCCGAGCATGGGGCAAATTACAGCCATTCAATCTCTTACCCCGAGCCTGGGACAAATCAC
CATCAGCAAATCT
Found at i:765561 original size:117 final size:117
Alignment explanation
Indices: 765355--765594 Score: 302
Period size: 117 Copynumber: 2.1 Consensus size: 117
765345 GGGCAAATTG
* * *
765355 CAATCTTCTACCCCAAGCTTAAGGCAGATCACCATCAGTTAATCTCTTACCTCAATCTTGAGGCA
1 CAATCTTCTACCCCAAGCTTAAGGCAGATCACCATCAATTAATCTCTTACCCCAATCTAGAGGCA
* * *
765420 GATTGCAACCGTTCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGT
66 GATTGCAACCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCACCATCAGC
* * * * * * *
765472 CAATCTTTTACCTCGAGCTTAGGGTAGATCACCATTAATTAATCTCTTACCCCGATCCTAG-GGC
1 CAATCTTCTACCCCAAGCTTAAGGCAGATCACCATCAATTAATCTCTTACCCCAAT-CTAGAGGC
* * * * *
765536 AGATTGCAGCCATTCGATCTCTTACCTCGATCTTGGGGCAGATCATCATCAGC
65 AGATTGCAACCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCACCATCAGC
765589 CAATCT
1 CAATCT
765595 CACCCCGATC
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
117 101 0.97
118 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (117 bp):
CAATCTTCTACCCCAAGCTTAAGGCAGATCACCATCAATTAATCTCTTACCCCAATCTAGAGGCA
GATTGCAACCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCACCATCAGC
Found at i:765595 original size:39 final size:39
Alignment explanation
Indices: 765372--765595 Score: 161
Period size: 39 Copynumber: 5.7 Consensus size: 39
765362 CTACCCCAAG
* * *
765372 CTTAAGGCAGATCACCATCAGTTAATCTCTTACCTCAAT
1 CTTAGGGCAGATCACCATCAGTCAATCTCTTACCTCGAT
** * * * * * *
765411 CTT-GAGGCAGAT-TGCAACCGTTCGATCTTTTACCCCGAG
1 CTTAG-GGCAGATCACCATCAG-TCAATCTCTTACCTCGAT
* *
765450 CTTAGGGCAGATCACCATCAGTCAATCTTTTACCTCGAG
1 CTTAGGGCAGATCACCATCAGTCAATCTCTTACCTCGAT
* * * * *
765489 CTTAGGGTAGATCACCATTAATTAATCTCTTACCCCGAT
1 CTTAGGGCAGATCACCATCAGTCAATCTCTTACCTCGAT
* *
765528 CCTAGGGCAGATTGCAGCCAT---TCGATCTCTTACCTCGAT
1 CTTAGGGCAGA-T-CA-CCATCAGTCAATCTCTTACCTCGAT
* * *
765567 CTTGGGGCAGATCATCATCAGCCAATCTC
1 CTTAGGGCAGATCACCATCAGTCAATCTC
765596 ACCCCGATCA
Statistics
Matches: 141, Mismatches: 34, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
36 3 0.02
37 2 0.01
38 5 0.04
39 119 0.84
40 6 0.04
41 2 0.01
42 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (39 bp):
CTTAGGGCAGATCACCATCAGTCAATCTCTTACCTCGAT
Found at i:766095 original size:17 final size:17
Alignment explanation
Indices: 766072--766182 Score: 141
Period size: 17 Copynumber: 6.5 Consensus size: 17
766062 AAACCCATTT
* *
766072 TTTAAATTTATTTTGAG
1 TTTAAATTTATTTTAAA
*
766089 GTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
766106 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* *
766123 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
766140 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
766158 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
766175 TTTAAATT
1 TTTAAATT
766183 AATAATGTCC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
17 66 0.82
18 14 0.17
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:766111 original size:6 final size:6
Alignment explanation
Indices: 766090--766182 Score: 79
Period size: 6 Copynumber: 16.2 Consensus size: 6
766080 TATTTTGAGG
* **
766090 TTAAAT TT-ATT TTAAAT TTAAAT TT-GTT TTAAAT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* ** *
766135 TTAAGT TTAAAT TTATTT TTAAAT TTAAAA TT--AT TCTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
766182 T
1 T
766183 AATAATGTCC
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 49 0.73
7 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:766130 original size:23 final size:23
Alignment explanation
Indices: 766100--766161 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
766090 TTAAATTTAT
766100 TTTAAATTTAAATTT-GTTTTAAA
1 TTTAAATTTAAATTTAG-TTTAAA
766123 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
**
766146 TTTATTTTTAAATTTA
1 TTTAAATTTAAATTTA
766162 AAATTATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.15
23 23 0.68
24 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:768068 original size:59 final size:57
Alignment explanation
Indices: 767970--768198 Score: 169
Period size: 59 Copynumber: 3.9 Consensus size: 57
767960 CCCAAAAGGT
* * ***
767970 CCCTAAACTTTCCAAAAATCACA-TTTTGACCCCTAAACTTCTTCAAATTACATTTTAAC
1 CCCTAAAC-TTCCAAAAATTACACTTTT-A-CCCTGAACTTCCAAAAATTACATTTTAAC
* * **
768029 CCTTGAACTTCTTC-AAAATTACACTTTTACCCTTGAACTTCCAAAAATTACATTTTTGC
1 CCCTAAACTTC--CAAAAATTACACTTTTACCC-TGAACTTCCAAAAATTACATTTTAAC
* * * * *
768088 CCCTAAACTTCCAAAAATTACATTTTTGCCCTGAACTTCCAAAAAATATAGTTTT-GC
1 CCCTAAACTTCCAAAAATTACACTTTTACCCTGAACTTCCAAAAATTACA-TTTTAAC
* ** * * * *
768145 CTC-AAACTTCCAAAAACCACATTTTTGCCCTTGAACTTTCAAAAATTATATTTT
1 CCCTAAACTTCCAAAAATTACACTTTTACCC-TGAACTTCCAAAAATTACATTTT
768199 TGCCCTCGAA
Statistics
Matches: 143, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
56 29 0.20
57 39 0.27
58 26 0.18
59 44 0.31
60 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTACACTTTTACCCTGAACTTCCAAAAATTACATTTTAAC
Found at i:768084 original size:28 final size:29
Alignment explanation
Indices: 767979--768319 Score: 230
Period size: 29 Copynumber: 11.8 Consensus size: 29
767969 TCCCTAAACT
* * * *
767979 TTCCAAAAATCACATTTTGACCCCTAAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
*** *
768008 TTCTTCAAATTACATTTTAACCCTTGAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
*
768037 TTCTTC-AAAATTACACTTTTACCCTTGAAC
1 TTC--CAAAAATTACATTTTTACCCTTGAAC
* * *
768067 TTCCAAAAATTACATTTTTGCCCCTAAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
*
768096 TTCCAAAAATTACATTTTTGCCC-TGAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
* * * * **
768124 TTCCAAAAAATATAGTTTT-GCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
** *
768152 TTCCAAAAACCACATTTTTGCCCTTGAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
* * * *
768181 TTTCAAAAATTATATTTTTGCCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTTGAAC
** * * *
768210 TTTTAAAAATCACATTTTTGTCCC--AAAC
1 TTCCAAAAATTACATTTTT-ACCCTTGAAC
*
768238 TTCTCAAAAA-TACATTTTTA-CCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTTGAAC
* * * *
768266 TCTCCCAAAATGACATTTTTATCCTTAAAAC
1 T-TCCAAAAATTACATTTTTACCCTT-GAAC
*
768297 TTTCC-AAAATTACATTTTAACCC
1 -TTCCAAAAATTACATTTTTACCC
768320 CAAACTCTTC
Statistics
Matches: 247, Mismatches: 51, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 61 0.25
29 130 0.53
30 45 0.18
31 6 0.02
32 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTTGAAC
Found at i:768266 original size:85 final size:84
Alignment explanation
Indices: 768064--768285 Score: 225
Period size: 85 Copynumber: 2.6 Consensus size: 84
768054 TTTACCCTTG
* * * *
768064 AACTTCCAAAAATTACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTTGCCCTGAACTTCCA
1 AACTTCCAAAAACTACATTTTTACCTC-GAACTTCCAAAAATTACATTTTTGCCCTGAACTTCCA
*
768129 AAAAATATAGTTTTGCCTCA
65 AAAAATACAGTTTTGCCTCA
* * * * * *
768149 AACTTCCAAAAACCACATTTTTGCCCTTGAACTTTCAAAAATTATATTTTTGCCCTCGAACTT-T
1 AACTTCCAAAAACTACATTTTT-ACCTCGAACTTCCAAAAATTACATTTTTGCCCT-GAACTTCC
* *
768213 TAAAAATCACATTTTTGTCC-CA
64 AAAAAAT-ACAGTTTTG-CCTCA
* *
768235 AACTTCTCAAAAA-TACATTTTTACCTCGAACTCTCCCAAAATGACATTTTT
1 AACTTC-CAAAAACTACATTTTTACCTCGAACT-TCCAAAAATTACATTTTT
768286 ATCCTTAAAA
Statistics
Matches: 112, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
85 59 0.53
86 45 0.40
87 8 0.07
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (84 bp):
AACTTCCAAAAACTACATTTTTACCTCGAACTTCCAAAAATTACATTTTTGCCCTGAACTTCCAA
AAAATACAGTTTTGCCTCA
Found at i:768282 original size:57 final size:56
Alignment explanation
Indices: 768043--768285 Score: 238
Period size: 57 Copynumber: 4.2 Consensus size: 56
768033 GAACTTCTTC
* * * *
768043 AAAATTACACTTTTACCCTTGAACTTCCAAAAATTACATTTTTGCCCCTAAACTTCCA
1 AAAATCACATTTTTGCCC-TGAACTTCCAAAAATTACATTTTTGCCTC-AAACTTCCA
* * * *
768101 AAAATTACATTTTTGCCCTGAACTTCCAAAAAATATAGTTTTGCCTCAAACTTCCA
1 AAAATCACATTTTTGCCCTGAACTTCCAAAAATTACATTTTTGCCTCAAACTTCCA
* * * * **
768157 AAAACCACATTTTTGCCCTTGAACTTTCAAAAATTATATTTTTGCCCTCGAACTTTTA
1 AAAATCACATTTTTGCCC-TGAACTTCCAAAAATTACATTTTTG-CCTCAAACTTCCA
* * * *
768215 AAAATCACATTTTTGTCCC-AAACTTCTCAAAAA-TACATTTTTACCTCGAACTCTCCC
1 AAAATCACATTTTTG-CCCTGAACTTC-CAAAAATTACATTTTTGCCTCAAACT-TCCA
*
768272 AAAATGACATTTTT
1 AAAATCACATTTTT
768286 ATCCTTAAAA
Statistics
Matches: 157, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
56 34 0.22
57 74 0.47
58 46 0.29
59 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (56 bp):
AAAATCACATTTTTGCCCTGAACTTCCAAAAATTACATTTTTGCCTCAAACTTCCA
Found at i:769124 original size:12 final size:12
Alignment explanation
Indices: 769107--769136 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
769097 ATTTCGAAGA
769107 CCAAAATGTTTT
1 CCAAAATGTTTT
769119 CCAAAATGTTTT
1 CCAAAATGTTTT
769131 CCAAAA
1 CCAAAA
769137 CGGATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (12 bp):
CCAAAATGTTTT
Found at i:793499 original size:14 final size:15
Alignment explanation
Indices: 793480--793508 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
793470 ATTTTGCTTG
793480 AAAATAA-AGAAATA
1 AAAATAATAGAAATA
793494 AAAATAATAGAAATA
1 AAAATAATAGAAATA
793509 GTGGATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAATAATAGAAATA
Found at i:794749 original size:52 final size:52
Alignment explanation
Indices: 794649--794751 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 52
794639 GTGGGGGGGT
* * * *
794649 GTGGGTGTGGGTGAGTGCGTGCGTACGTGCGTACATGCTTGTGTGTGCGTGG
1 GTGGGTGTGGGTGAGTGCGTGCGCACGTGCATACATGCTCGTGCGTGCGTGG
* *
794701 GTGGGTGTGGGTGTA-TGCGTGCGCATGTGCATGCATG-TGCGTGCGTGCGTG
1 GTGGGTGTGGGTG-AGTGCGTGCGCACGTGCATACATGCT-CGTGCGTGCGTG
794752 CGTGCGCATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
51 1 0.02
52 41 0.95
53 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.48, T:0.30
Consensus pattern (52 bp):
GTGGGTGTGGGTGAGTGCGTGCGCACGTGCATACATGCTCGTGCGTGCGTGG
Found at i:794897 original size:20 final size:20
Alignment explanation
Indices: 794873--794959 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
794863 TGCTCTTCAA
*
794873 TGCCCCTATTTGCATATCTA-
1 TGCCCCTATTTGCACATC-AG
794893 TGCCCCTATTTGCACATCAG
1 TGCCCCTATTTGCACATCAG
794913 TGCCCCTATTTGCACATCAG
1 TGCCCCTATTTGCACATCAG
*
794933 TGCCCCTATTTACACATCAG
1 TGCCCCTATTTGCACATCAG
794953 TGCCCCT
1 TGCCCCT
794960 GGTTGAACTC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 1 0.02
20 63 0.98
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.32
Consensus pattern (20 bp):
TGCCCCTATTTGCACATCAG
Found at i:795046 original size:20 final size:20
Alignment explanation
Indices: 794998--795058 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
794988 CTAGTGCCTT
* *
794998 TAATCGCACATTCGTGCCCT
1 TAATCGCACATTTGTGCCCC
*
795018 TGATCGCACATTTGTGCCCC
1 TAATCGCACATTTGTGCCCC
*
795038 TAATTGCAC-TTTGGTGCCCC
1 TAATCGCACATTT-GTGCCCC
795058 T
1 T
795059 GCTATGTGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (20 bp):
TAATCGCACATTTGTGCCCC
Found at i:808826 original size:2 final size:2
Alignment explanation
Indices: 808813--808860 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
808803 TTGTATAATA
*
808813 AT AT AC 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
808855 AT AT AT
1 AT AT AT
808861 TCTTTTTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:809951 original size:12 final size:13
Alignment explanation
Indices: 809931--809968 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
809921 ATTTCTTCTT
809931 CTTCTTCTTTTTC
1 CTTCTTCTTTTTC
809944 CTTC-TCTTTTTC
1 CTTCTTCTTTTTC
809956 TCATTCTTCTTTT
1 -C-TTCTTCTTTT
809969 CTTTTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 5 0.23
14 3 0.14
15 6 0.27
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTCTTCTTTTTC
Found at i:816164 original size:287 final size:289
Alignment explanation
Indices: 815645--816219 Score: 926
Period size: 287 Copynumber: 2.0 Consensus size: 289
815635 GTGACTACTG
* * *
815645 GTGGTTCCTCCTTATTTACTTTTGTTGTATCTTCTTCAAATGCAACTTCTCCTTATTGCTTTGGA
1 GTGGTTCCTCCTCATTTACTTCTGATGTATCTTCTTCAAATGCAACTTCTCCTTATTGCTTTGGA
* *
815710 TTATTTGTGTCGACAGGTGCTTGGTTAAAGCTGCGCTTTGTTCAGTAGTTTGCTTGTCACTCCGT
66 TCATTTGTGTCGACAGGTGCTTGGTTAAAGCTGCGCTTTGTTCAGTAGTTTGCTTGTCACTCCGC
*
815775 AATGTGATAGCCTTACAATGCTCCTTCCCTTTCTGATTTGGATTTTCAGTGTCACTGGGCAAAGC
131 AATGTGATAGCCTTACAATGCTCCTTCCCTTTCTGATTTGGATTTTCAGTGTCACTGGACAAAGC
* * * * *
815840 ACCTAGTGGTTGTGTGCTCATGTTATAAGCTAATTGTCCTAGTTGTGCTTCCAACACTCGGATGG
196 ACCTAATGGTCGTGTGCTCAAGTTAGAAGCCAATTGTCCTAGTTGTGCTTCCAACACTCGGATGG
815905 AAGAAGAATTTCCTTTATAATAGCTTCTA
261 AAGAAGAATTTCCTTTATAATAGCTTCTA
* *
815934 GTGGTTCCTCCTCATTTACTTCTGATGTATCTTCTTCAAATGCAACTTCTCTTTGTTGC-TTGGA
1 GTGGTTCCTCCTCATTTACTTCTGATGTATCTTCTTCAAATGCAACTTCTCCTTATTGCTTTGGA
*
815998 TCATTTGTGTCGACAGGTGCTTTGTTAAAGCTATG-GCTTTGTTC-GATAGTTTGCTT-TCACTC
66 TCATTTGTGTCGACAGGTGCTTGGTTAAAGC--TGCGCTTTGTTCAG-TAGTTTGCTTGTCACTC
* * *
816060 TGCAATGT-ATAGCCTTGCAATGCTCCTTCCCTTTCTGATTTTGATTTTCAGTGTCACTGGACAA
128 CGCAATGTGATAGCCTTACAATGCTCCTTCCCTTTCTGATTTGGATTTTCAGTGTCACTGGACAA
*
816124 AGCACCTAATGGTCGTGTGCTCAAGTTAGAAGCCAATTGTCCTAGTTGTGCTTCCAACGCTCGGA
193 AGCACCTAATGGTCGTGTGCTCAAGTTAGAAGCCAATTGTCCTAGTTGTGCTTCCAACACTCGGA
816189 TGGAAGAAGAATTTCCTTTATAATAGCTTCT
258 TGGAAGAAGAATTTCCTTTATAATAGCTTCT
816220 GTTCTGGTAA
Statistics
Matches: 265, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
287 143 0.54
288 47 0.18
289 73 0.28
290 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (289 bp):
GTGGTTCCTCCTCATTTACTTCTGATGTATCTTCTTCAAATGCAACTTCTCCTTATTGCTTTGGA
TCATTTGTGTCGACAGGTGCTTGGTTAAAGCTGCGCTTTGTTCAGTAGTTTGCTTGTCACTCCGC
AATGTGATAGCCTTACAATGCTCCTTCCCTTTCTGATTTGGATTTTCAGTGTCACTGGACAAAGC
ACCTAATGGTCGTGTGCTCAAGTTAGAAGCCAATTGTCCTAGTTGTGCTTCCAACACTCGGATGG
AAGAAGAATTTCCTTTATAATAGCTTCTA
Found at i:816385 original size:18 final size:18
Alignment explanation
Indices: 816364--816407 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
816354 AGAATGTGGT
*
816364 TGCATCTGATTATATGAC
1 TGCATCTGAGTATATGAC
*
816382 TGCATCTGAGTATGTGAC
1 TGCATCTGAGTATATGAC
*
816400 TACATCTG
1 TGCATCTG
816408 GTTAGGCTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (18 bp):
TGCATCTGAGTATATGAC
Found at i:818648 original size:52 final size:52
Alignment explanation
Indices: 818545--818985 Score: 609
Period size: 52 Copynumber: 8.4 Consensus size: 52
818535 TAATACTGAT
* * *
818545 GATGACACAAAGTCAATTCGAACCTTA-AATCCGTAAAAGGA-TCTATATACTCAC
1 GATGACACATAGTC-A-TCGGACCTCATAATCCGT-AAAGGATTC-ATATACTCAC
* * * *
818599 TATGACACATAGCCATCGGACCTCATAATCCGTAAAGGGTTCATATACTCAT
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* * *
818651 GATGACAAATAGCCATTGGACCTCATAATCCGTAAAGGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* *
818703 GATGACACATAGCCATCGGACCTCAAAATCCGTAAAGGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* * *
818755 GATGACACATAGTCATCGGACCTTATAATCCATAAAGGATTCAGATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* * *
818807 GATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTTAT
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
** *
818859 GATGACACATAGTCA-CTGGACCAAATAATCCGTAAAGGATTCATATACTCAT
1 GATGACACATAGTCATC-GGACCTCATAATCCGTAAAGGATTCATATACTCAC
*
818911 GATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
*
818963 GATGACACATAGTCATCGAACCT
1 GATGACACATAGTCATCGGACCT
818986 TTTTCATGTA
Statistics
Matches: 350, Mismatches: 33, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
51 1 0.00
52 327 0.93
53 11 0.03
54 11 0.03
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (52 bp):
GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
Done.