Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020806.1 Corchorus olitorius cultivar O-4 contig20839, 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: 10829
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3457 original size:13 final size:14
Alignment explanation
Indices: 3430--3462 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3420 TTTTTACCTT
*
3430 TAAAAAAAAATAAA
1 TAAAATAAAATAAA
3444 TAAAATAAAA-AAA
1 TAAAATAAAATAAA
3457 TAAAAT
1 TAAAAT
3463 TCCCTGGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:3798 original size:31 final size:27
Alignment explanation
Indices: 3760--5560 Score: 1925
Period size: 31 Copynumber: 64.1 Consensus size: 27
3750 ATTCAACTGC
3760 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
*
3791 GCATATTCAGTAGGGTCATATTCATACAGTT
1 GCATATTCAGTAGGG-C--A-TCATATAGTT
3822 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
*
3853 ACATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
* *
3884 GCATATTCAGTAGGG--TCTTACAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
3909 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
3940 GCATATTCAGTAGGGCCATAACCATATAGTT
1 GCATATTCAGTAGGG-CAT---CATATAGTT
*
3971 GCATATTCAGTAGGGTCATAACCATACAGTT
1 GCATATTCAGTAGGG-CAT---CATATAGTT
4002 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4033 GCATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4064 GCATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4095 GCATATTCAGTAGGGC--CATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4120 GCATATTCAGTAGGGC--CAT-TAAGTT
1 GCATATTCAGTAGGGCATCATAT-AGTT
*
4145 ACATATTCAGTAGGG--TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4170 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
*
4201 GCATATTCTGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4232 GCATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4263 GCATATTCAGTAGGGCCATAACCATATAGTT
1 GCATATTCAGTAGGG-CAT---CATATAGTT
4294 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
*
4325 GCATATTCCGTAGGG--TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4350 GCATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4381 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4412 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4443 GCATATTCAGTAGGGCCTTAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
4474 GCATATTCAGTAGGGCATCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4501 GCATATTCAGTAGGGCATCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4528 GCATATTCAGTAGGGC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4554 GCATATTCAGTAGGGCATCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
**
4581 GCATATTCAGTAGATC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4607 GCATATTCAGTAGGGC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4633 GCATATTCAGTAGGGGA-CATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4659 GCATATTCAGTAGGGGA-CATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4685 GCATATTCAGTAGGGGC--CATATAGTT
1 GCATATTCAGTA-GGGCATCATATAGTT
4711 GCATATTCAGTAGGGC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4737 GCATATTCAGTAGGGC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4763 GCATATTCAGTAGGGC-TCATATAATT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4789 GCATATTCAGTAGGGC-TCATATAATT
1 GCATATTCAGTAGGGCATCATATAGTT
4815 GCATATTCAGTAGGGGC--CATATAGTT
1 GCATATTCAGTA-GGGCATCATATAGTT
4841 GCATATTCAGTAGGGGC--CATATAGTT
1 GCATATTCAGTA-GGGCATCATATAGTT
4867 GCATATTCAGTAGGGC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4893 GCATATTCAGTAGGGC-TCATTTAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4919 GCAAATTCAGTAGGGGC--CATATAGTT
1 GCATATTCAGTA-GGGCATCATATAGTT
*
4945 GCATATTCAGTAGGGCCTCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
4972 GCATATTCAGTAGGGC-TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
4998 GCATATTTAGTAGGG-A-CATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
* * *
5023 GCATATTTAGTAGGGCCTCATATAGAT
1 GCATATTCAGTAGGGCATCATATAGTT
* *
5050 GCATATTCAGTAGGGCCTCATATAGAT
1 GCATATTCAGTAGGGCATCATATAGTT
5077 GCATATTCAGTAGGGC--CATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
5102 GCATATTCAGTAGGGCCTCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
5129 GCATATTCAGTAGGGGC--CATATAGTT
1 GCATATTCAGTA-GGGCATCATATAGTT
* *
5155 GCATATTTAGTAGGGC--CATATACTT
1 GCATATTCAGTAGGGCATCATATAGTT
5180 GCATATTCAGTAGGGC--CAT-TAAGTT
1 GCATATTCAGTAGGGCATCATAT-AGTT
*
5205 ACATATTCAGTAGGG--TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
*
5230 GCATATTCAGTAGGATCATAATCATATAGTT
1 GCATATTCAGTAGG-GC---ATCATATAGTT
5261 GCATATTCAGTAGGG--TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
5286 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
5317 GCATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
5348 GCATATTCAGTAGGGCCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
*
5379 ACATATTCAGTAGGG--TCATATAGTT
1 GCATATTCAGTAGGGCATCATATAGTT
5404 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
* *
5435 GCATATTCAGTCGGTCCATAATCATATAGTT
1 GCATATTCAGTAGG-GC---ATCATATAGTT
5466 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
5497 GCATATTCAGTAGGGTCATAATCATATAGTT
1 GCATATTCAGTAGGG-C---ATCATATAGTT
5528 GCATATTCAGTAGGGCATAATCATATAGTT
1 GCATATTCAGTAGGGC---ATCATATAGTT
5558 GCA
1 GCA
5561 ACTATTACGA
Statistics
Matches: 1636, Mismatches: 61, Indels: 147
0.89 0.03 0.08
Matches are distributed among these distances:
24 2 0.00
25 290 0.18
26 397 0.24
27 185 0.11
28 8 0.00
30 21 0.01
31 728 0.44
32 1 0.00
34 4 0.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (27 bp):
GCATATTCAGTAGGGCATCATATAGTT
Found at i:3828 original size:16 final size:15
Alignment explanation
Indices: 3776--3892 Score: 53
Period size: 16 Copynumber: 7.5 Consensus size: 15
3766 TCAGTAGGGT
*
3776 CATAATCATATAGTTG
1 CATATTCATA-AGTTG
* *
3792 CATATTCAGTAGGGT-
1 CATATTCA-TAAGTTG
3807 CATATTCATACAGTTG
1 CATATTCATA-AGTTG
* *
3823 CATATTCAGTAGGGT-
1 CATATTCA-TAAGTTG
* *
3838 CATAATCATATAGTTA
1 CATATTCATA-AGTTG
*
3854 CATATTCAGT-AG-GG
1 CATATTCA-TAAGTTG
*
3868 CCATAATCATATAGTTG
1 -CATATTCATA-AGTTG
3885 CATATTCA
1 CATATTCA
3893 GTAGGGTCTT
Statistics
Matches: 74, Mismatches: 16, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
14 5 0.07
15 28 0.38
16 35 0.47
17 6 0.08
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (15 bp):
CATATTCATAAGTTG
Found at i:3976 original size:118 final size:106
Alignment explanation
Indices: 3781--5560 Score: 1825
Period size: 118 Copynumber: 15.9 Consensus size: 106
3771 AGGGTCATAA
*
3781 TCATATAGTTGCATATTCAGTAGGGTCATATTCATACAGTTGCATATTCAGTAGGGTCATAATCA
1 TCATATAGTTGCATATTCAGTAGGG-C--A-TCATATAGTTGCATATTCAGTAGGG-C-T-A-CA
*
3846 TATAGTTACATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGG
58 TATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG
* *
3899 TCTTACAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCCATAACCA
1 TCATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG-C-T-A-CA
*
3964 TATAGTTGCATATTCAGTAGGGTCATAACCATACAGTTGCATATTCAGTAGGG
58 TATAGTTGCATATTCAGTAGGG-CAT---CATATAGTTGCATATTCAGTAGGG
4017 TCATAATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGCCA
1 ------TCATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG-C-
4082 TAATCATATAGTTGCATATTCAGTAGGGC--CATATAGTTGCATATTCAGTAGGG
54 T-A-CATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
* *
4135 CCAT-TAAGTTACATATTCAGTAGGG--TCATATAGTTGCATATTCAGTAGGGTCATAATCATAT
1 TCATAT-AGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG-C-T-A-CATAT
*
4197 AGTTGCATATTCTGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGG
61 AGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG
4247 CCATAATCATATAGTTGCATATTCAGTAGGGCCATAACCATATAGTTGCATATTCAGTAGGGTCA
1 ------TCATATAGTTGCATATTCAGTAGGG-CAT---CATATAGTTGCATATTCAGTAGGG-C-
*
4312 TAATCATATAGTTGCATATTCCGTAGGG--TCATATAGTTGCATATTCAGTAGGG
54 T-A-CATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
4365 CCATAATCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCA
1 ------TCATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG-C-
4430 TAATCATATAGTTGCATATTCAGTAGGGCCTTAATCATATAGTTGCATATTCAGTAGGG
54 T-A-CATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG
4489 CATCATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGGCT-CATATAGT
1 --TCATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGGCTACATATAGT
**
4553 TGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGATC
64 TGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAG-GG
*
4597 TCATATAGTTGCATATTCAGTAGGGC-TCATATAGTTGCATATTCAGTAGGG-GACATATAGTTG
1 TCATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGGCTACATATAGTTG
*
4660 CATATTCAGTAGGGGA-CATATAGTTGCATATTCAGTAGGGG
66 CATATTCAGTAGGGCATCATATAGTTGCATATTCAGTA-GGG
*
4701 CCATATAGTTGCATATTCAGTAGGGC-TCATATAGTTGCATATTCAGTAGGGCT-CATATAGTTG
1 TCATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGGCTACATATAGTTG
*
4764 CATATTCAGTAGGGC-TCATATAATTGCATATTCAGTAGGG
66 CATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
*
4804 CTCATATAATTGCATATTCAGTAGGGGC--CATATAGTTGCATATTCAGTAGGGGC--CATATAG
1 -TCATATAGTTGCATATTCAGTA-GGGCATCATATAGTTGCATATTCAGTA-GGGCTACATATAG
4865 TTGCATATTCAGTAGGGC-TCATATAGTTGCATATTCAGTAGGG
63 TTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
* *
4908 CTCATTTAGTTGCAAATTCAGTAGGGGC--CATATAGTTGCATATTCAGTAGGGCCT-CATATAG
1 -TCATATAGTTGCATATTCAGTA-GGGCATCATATAGTTGCATATTCAGTAGGG-CTACATATAG
*
4970 TTGCATATTCAGTAGGGC-TCATATAGTTGCATATTTAGTAGGG
63 TTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
* * * * *
5013 ACATATAGTTGCATATTTAGTAGGGCCTCATATAGATGCATATTCAGTAGGGCCT-CATATAGAT
1 TCATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG-CTACATATAGTT
5077 GCATATTCAGTAGGGC--CATATAGTTGCATATTCAGTAGGG
65 GCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
* *
5117 CCTCATATAGTTGCATATTCAGTAGGGGC--CATATAGTTGCATATTTAGTAGGGC--CATATAC
1 --TCATATAGTTGCATATTCAGTA-GGGCATCATATAGTTGCATATTCAGTAGGGCTACATATAG
*
5178 TTGCATATTCAGTAGGGC--CAT-TAAGTTACATATTCAGTAGGG
63 TTGCATATTCAGTAGGGCATCATAT-AGTTGCATATTCAGTAGGG
*
5220 TCATATAGTTGCATATTCAGTAGGATCATAATCATATAGTTGCATATTCAGTAGGG-T-CATATA
1 TCATATAGTTGCATATTCAGTAGG-GC---ATCATATAGTTGCATATTCAGTAGGGCTACATATA
5283 GTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGG
62 GTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG
*
5332 CCATAATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTACATATTCAGTAGGG-T-
1 ------TCATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGGCTA
* *
5395 CATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTCGGTCCATAA
56 CATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGG------G
5456 TCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCATAATCA
1 TCATATAGTTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGG-C-T-A-CA
5521 TATAGTTGCATATTCAGTAGGGCATAATCATATAGTTGCA
58 TATAGTTGCATATTCAGTAGGGC---ATCATATAGTTGCA
5561 ACTATTACGA
Statistics
Matches: 1508, Mismatches: 66, Indels: 171
0.86 0.04 0.10
Matches are distributed among these distances:
100 2 0.00
101 23 0.02
102 1 0.00
103 54 0.04
104 294 0.19
105 180 0.12
106 146 0.10
107 30 0.02
110 1 0.00
111 25 0.02
112 66 0.04
113 1 0.00
114 1 0.00
115 3 0.00
116 26 0.02
118 417 0.28
119 3 0.00
120 26 0.02
121 4 0.00
123 19 0.01
124 186 0.12
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (106 bp):
TCATATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGGCTACATATAGTTG
CATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG
Found at i:4030 original size:149 final size:140
Alignment explanation
Indices: 3760--5560 Score: 1960
Period size: 149 Copynumber: 12.8 Consensus size: 140
3750 ATTCAACTGC
*
3760 GCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCATATTCATACAGTTGCA
1 GCATATTCAGTAGGG-CATAATCATATAGTTGCATATTCAGTAGGG-CATA--CATATAGTTGCA
* *
3825 TATTCAGTAGGGTCATAATCATATAGTTACATATTCAGTAGGGCCATAATCATATAGTTGCATAT
62 TATTCAGTAGGG-CAT-ACCATATAGTTGCATATTCAGTAGGG-C-T-ATCATATAGTTGCATAT
* *
3890 TCAGTAGGGTCTTACAGTT
122 TCAGTAGGGTCATATAGTT
3909 GCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCCATAACCATATAGTTGCA
1 GCATATTCAGTAGGG-CATAATCATATAGTTGCATATTCAGTAGGG-CAT-A-CATATAGTTGCA
*
3974 TATTCAGTAGGGTCATAACCATACAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATAT
62 TATTCAGTAGGG-CAT-ACCATATAGTTGCATATTCAGTAGGG-C-T-ATCATATAGTTGCATAT
4039 TCAGTAGGGCCATAATCATATAGTT
122 TCAGTAGGG------TCATATAGTT
4064 GCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGC---CATATAGTTGCATAT
1 GCATATTCAGTAGGG-CATAATCATATAGTTGCATATTCAGTAGGGCATACATATAGTTGCATAT
*
4126 TCAGTAGGG----CCAT-TAAGTTACATATTCAGTAGGG---TCATATAGTTGCATATTCAGTAG
65 TCAGTAGGGCATACCATAT-AGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCAGTAG
4183 GGTCATAATCATATAGTT
129 GG------TCATATAGTT
*
4201 GCATATTCTGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCA
1 GCATATTCAGTAGGG-CATAATCATATAGTTGCATATTCAGTAGGG-CAT-A-CATATAGTTGCA
4266 TATTCAGTAGGGCCATAACCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATAT
62 TATTCAGTAGGG-CAT-ACCATATAGTTGCATATTCAGTAGGG-C-T-ATCATATAGTTGCATAT
*
4331 TCCGTAGGGTCATATAGTT
122 TCAGTAGGGTCATATAGTT
4350 GCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCA
1 GCATATTCAGTAGGG-CATAATCATATAGTTGCATATTCAGTAGGG-CAT-A-CATATAGTTGCA
*
4415 TATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCCTTAATCATATAGTTGCATAT
62 TATTCAGTAGGG-CAT-ACCATATAGTTGCATATTCAGTAGGG-C-T-ATCATATAGTTGCATAT
4480 TCAGTAGGGCATCATATAGTT
122 TCAGTAGGG--TCATATAGTT
4501 GCATATTCAGTAGGGC---ATCATATAGTTGCATATTCAGTAGGGC-T-CATATAGTTGCATATT
1 GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTAGGGCATACATATAGTTGCATATT
* *
4561 CAGTAGGGCAT--CATATAGTTGCATATTCAGTA--GATCTCATATAGTTGCATATTCAGTAGGG
66 CAGTAGGGCATACCATATAGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCAGTAGGG
4622 CTCATATAGTT
131 -TCATATAGTT
* *
4633 GCATATTCAGTAGGG---GA-CATATAGTTGCATATTCAGTAGGG--GACATATAGTTGCATATT
1 GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTAGGGCATACATATAGTTGCATATT
*
4692 CAGTAGGG---GCCATATAGTTGCATATTCAGTAGGGC--TCATATAGTTGCATATTCAGTAGGG
66 CAGTAGGGCATACCATATAGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCAGTAGGG
4752 CTCATATAGTT
131 -TCATATAGTT
* *
4763 GCATATTCAGTAGGGC----TCATATAATTGCATATTCAGTAGGGC-T-CATATAATTGCATATT
1 GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTAGGGCATACATATAGTTGCATATT
*
4822 CAGTAGGG---GCCATATAGTTGCATATTCAGTAGGGGC---CATATAGTTGCATATTCAGTAGG
66 CAGTAGGGCATACCATATAGTTGCATATTCAGTA-GGGCTATCATATAGTTGCATATTCAGTAGG
4881 GCTCATATAGTT
130 G-TCATATAGTT
* *
4893 GCATATTCAGTAGGGC----TCATTTAGTTGCAAATTCAGTAGGGGC---CATATAGTTGCATAT
1 GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTA-GGGCATACATATAGTTGCATAT
* *
4951 TCAGTAGGGCCT--CATATAGTTGCATATTCAGTAGGGC--TCATATAGTTGCATATTTAGTAGG
65 TCAGTAGGGCATACCATATAGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCAGTAGG
*
5012 GACATATAGTT
130 GTCATATAGTT
* * * * *
5023 GCATATTTAGTAGGGC---CTCATATAGATGCATATTCAGTAGGGCCT-CATATAGATGCATATT
1 GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTAGGGCATACATATAGTTGCATATT
*
5084 CAGTAGGG----CCATATAGTTGCATATTCAGTAGGGC-CTCATATAGTTGCATATTCAGTAGGG
66 CAGTAGGGCATACCATATAGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCAGTA-GG
*
5144 GCCATATAGTT
130 GTCATATAGTT
* * *
5155 GCATATTTAGTAGGGC-----CATATACTTGCATATTCAGTAGGGC---CAT-TAAGTTACATAT
1 GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTAGGGCATACATAT-AGTTGCATAT
*
5211 TCAGTAGGG--T--CATATAGTTGCATATTCAGTAGGATCATAATCATATAGTTGCATATTCAGT
65 TCAGTAGGGCATACCATATAGTTGCATATTCAGTAGG-GC-T-ATCATATAGTTGCATATTCAGT
5272 AGGGTCATATAGTT
127 AGGGTCATATAGTT
5286 GCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCA
1 GCATATTCAGTAGGG-CATAATCATATAGTTGCATATTCAGTAGGG-CAT-A-CATATAGTTGCA
* *
5351 TATTCAGTAGGGCCATAATCATATAGTTACATATTCAGTAGGG---TCATATAGTTGCATATTCA
62 TATTCAGTAGGG-CAT-ACCATATAGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCA
5413 GTAGGGTCATAATCATATAGTT
125 GTAGGG------TCATATAGTT
* *
5435 GCATATTCAGTCGGTCCATAATCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCA
1 GCATATTCAGTAGG-GCATAATCATATAGTTGCATATTCAGTAGGG-CAT-A-CATATAGTTGCA
*
5500 TATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCATAATCATATAGTTGCA
62 TATTCAGTAGGG-CAT-ACCATATAGTTGCATATTCAGTAGGGC-T-ATCATATAGTTGCA
5561 ACTATTACGA
Statistics
Matches: 1504, Mismatches: 61, Indels: 169
0.87 0.04 0.10
Matches are distributed among these distances:
127 1 0.00
128 43 0.03
129 1 0.00
130 314 0.21
131 166 0.11
132 101 0.07
133 25 0.02
134 1 0.00
136 1 0.00
137 108 0.07
138 23 0.02
141 3 0.00
142 24 0.02
143 92 0.06
144 1 0.00
145 1 0.00
146 2 0.00
147 26 0.02
149 452 0.30
150 3 0.00
151 25 0.02
154 14 0.01
155 77 0.05
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (140 bp):
GCATATTCAGTAGGGCATAATCATATAGTTGCATATTCAGTAGGGCATACATATAGTTGCATATT
CAGTAGGGCATACCATATAGTTGCATATTCAGTAGGGCTATCATATAGTTGCATATTCAGTAGGG
TCATATAGTT
Found at i:6622 original size:115 final size:115
Alignment explanation
Indices: 6419--6644 Score: 389
Period size: 115 Copynumber: 2.0 Consensus size: 115
6409 ATTTATAATT
* *
6419 AAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATCTCCAATGTGGCTGAGATTTGA
1 AAATCGAAATAAAATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGA
*
6484 CTCGATGAACATAGATATGTCAAGGAGTCTATGCACCAAAAATCATAGAG
66 CTCGATGAACATAGAGATGTCAAGGAGTCTATGCACCAAAAATCATAGAG
* * *
6534 AAATCGAAATAAAATTCAGATGCTCGTGAAAACAAATCCTTATATCCAATGTTGTTGAGATTTGA
1 AAATCGAAATAAAATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGA
*
6599 CTCGATGAACATAGAGATTTCAAGGAGTCTATGCACCAAAAATCAT
66 CTCGATGAACATAGAGATGTCAAGGAGTCTATGCACCAAAAATCAT
6645 GTAAAATTGA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 104 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (115 bp):
AAATCGAAATAAAATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGA
CTCGATGAACATAGAGATGTCAAGGAGTCTATGCACCAAAAATCATAGAG
Found at i:6965 original size:12 final size:12
Alignment explanation
Indices: 6948--6974 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6938 AATATAGATA
6948 TTTCAAGGAATC
1 TTTCAAGGAATC
6960 TTTCAAGGAATC
1 TTTCAAGGAATC
6972 TTT
1 TTT
6975 TTGCCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTCAAGGAATC
Found at i:8204 original size:657 final size:650
Alignment explanation
Indices: 6534--9561 Score: 3094
Period size: 657 Copynumber: 4.6 Consensus size: 650
6524 AATCATAGAG
* * * * * *
6534 AAATCGAAATAAAATTCAGATGCTCGTGAAAACAAATCCTTATATCCAATGTTGTTGAGATTTGA
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGCGATTTGA
* * * * * * * * * ***
6599 CTCGATGAACATAGAGATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAGGCA-GGAC
66 TTAGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAAAAAGGGAC
* * *
6663 TTCGAAACTCGTTTTTAGCAAAAACAGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
131 --CGCAACACGTTTTTAGCAAAAAC-CGTGATGGTTAGTACACGATTTCGGC--------T--AA
* * *** *
6728 AAACTGACCCGAAA-AG-TTTTCCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
183 AAACTCA-CCTAAACAGTTTTTTTATC-AATTTTTGCCACAATACTCAGAAAAAATATATAATTC
* * *
6791 AACGCCAACGAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATT
246 AACACCAA--AAGATTG-AGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-TCGAATT
* *
6855 TATTTCTT-ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
307 AATTT-TTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTG
* ** * * * * *
6919 TCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCAAGGAATCTTTTTGCCAAAA
371 GCTGAGATTTGACTCGATGAACATAGATATTTCAAGGAGTC--T--ATG---C-----ACC-AAA
* *** * * * * *
6984 AATCATG-CAAATCTGAATTGGGAC-CTCGAAACACGTTTTTAGCAAAAAACTGTGATGCTTAGT
423 AATCATGTAAAAT-TGAACCAGGACTC-CGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGT
* * * * * * *** * *
7047 AAATGATTTCGGC--------T--AAAAACTTATCTGAACAGTTTTTTTATCAATTATTTGCCAC
486 ACACGATTTCGGCTAAAATTTTACAAAAACTGACCCGAAAAG-TTTTCCCTCTATTTTTTGCCAC
* ** * * *
7102 AATACTCAGAAAAATTATATAATTCAACATCAAA-AAGATTG-AGGGCTTTTCATGCTTCTAATA
550 AATACTCAGAAAAAATATATAATTCAACGCCAAAGAA-ATTGAAGGGTTTTTCACGTTTCTAATA
* * *
7165 TCGTTTTTCCATTTTCTAT-CGAATTTATTT-TTAACT
614 TCGTTTTTCCATTTTTTTTCCGAATTTATTTCTT-ATT
* *
7201 AAATCGAAACAAGA-TCCGAATGCTCGT-AAAA-AAATCCTTATATCCAATGTGGTTGCGATTTG
1 AAATCGAAACAAGATTCAG-ATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGCGATTTG
* * * ****
7263 ATTCGATGAATGTAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCGGGGG
65 ATTAGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGA-AAAAGGG
* * * *
7328 TCCGGAACACGTTTTTAGCAGAAAACCGTGAT-G---GTACACGATTTCGGCTAAGAACTCACCC
129 ACCGCAACACGTTTTTAGCA-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTCACCT
* * * * *
7389 GAATA-ATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
193 AAACAGTTTTTTTATCAA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACC-AAAA
* * * * **
7453 GATTCACGAGCTTTACACGCTTCTAATATCGTTTTTCCATTTTTCT-GAACCAATTTTTAATTAA
256 GATTGA-GGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTTTTAATTAA
* * *
7517 ATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGCCTGACATTTGACT
320 ATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACT
* ** *
7582 CGATGAACATAGATATTTCAAGGTGTCTATGCACCAAAAATCATGTAAAATTGAGTCACGACTCC
385 CGATGAACATAGATATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAACCAGGACTCC
7647 GGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAA
450 GGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAA
* *
7712 CTGACCCGAAAGGTTTTCCCTCTAGTTTTTGCCACAATACTCAGAAAAAAATATATAATTCAACG
515 CTGACCCGAAAAGTTTTCCCTCTATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCAACG
7777 CCAAAGAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATATTTTTTTTCCCAGAATT
579 CCAAAGAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCC--ATTTTTTTT-CC-GAATT
*
7842 CATTTCTTATT
640 TATTTCTTATT
* * * * * * * *
7853 AAATCAAAACAAGATTCAGGTGCTCATAAAAGCAAATTCTTATTTCCAATGTGGCTGAGATTTGG
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGCGATTTGA
* *
7918 TTAGATGAATATAGATATTT-AATGGA-TCCTTT-CGGCCAAATATCATGC-AAATCT-AAAAAG
66 TTAGATGAATATAGATATTTGAA-GGAGT-CTTTGC-GCAAAAAATCATGCAAAAT-TGAAAAAG
* * * * *
7978 GGACCTCAACGCGTTTTTAGTCAAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAAACTGAC
127 GGACCGCAACACGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTCAC
*
8043 CTAAACAGTTTTTTTATCAACTTTTGCCACAATACTCAGAAAAAAGTATATAATTCAACACCTAA
191 CTAAACAGTTTTTTTATCAATTTTTGCCACAATACTCAGAAAAAA-TATATAATTCAACACC-AA
*
8108 AAGATTGAGGGCTTTTCACGCTTCTAATATCTTTTTTCCATTTTTTTCGAATTAATTTTTAATTA
254 AAGATTGAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTTTTAATTA
* * *
8173 AATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCATAATATCCAATGTGGCTGAGATTTCAC
319 AATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGAC
* *
8238 TCGATGAACATAGATATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAGCCTGGACTC
384 TCGATGAACATAGATATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAACCAGGACTC
* * *
8303 CGGAATTCTTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
449 CGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAA
*
8368 ACTGACCCGAAAAGTTTTCCCTCTATTTTTTG-CACAATACTCTAAAAAATATATATATAATTCA
514 ACTGACCCGAAAAGTTTTCCCTCTATTTTTTGCCACAATACTC-AGAAAA-A-ATATATAATTCA
*
8432 ACGCCAAAGAAATTGAAGGGTTTTTTACAC-TTT-TAATATCGTTTTTCCTTTTTTTTTTCCGAA
576 ACGCCAAAGAAATTGAAGGG-TTTTT-CACGTTTCTAATATCGTTTTTCC-ATTTTTTTTCCGAA
*
8495 TTTATTTCTAATT
638 TTTATTTCTTATT
* * *
8508 AAATCGAAACAAGATCCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTTCGATTTGA
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGCGATTTGA
* * * *** *
8573 TTCGATGAATGTAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCAGGGCT
66 TTAGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAAAAAGGG-A
* * * * *
8638 CCGGAACATG-TTTTAGCAAAAACCGTGATGGTTAGTATACGATTTCAGAT-AAAACTACACCGT
130 CCGCAACACGTTTTTAGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT-CACC-T
** * *
8701 AATTAGTTTTTTTTTTCAATTTTTACCACAA-ACTCAG-AAAAATATAGTAATTCAACGACCAAA
193 AAACAG-TTTTTTTATCAATTTTTGCCACAATACTCAGAAAAAATATA-TAATTCAAC-ACCAAA
* * *
8764 AGATTCACGGGCTTTACACACTTCTAATATCGTTTTTCCA--------G-------TTTTAATTA
255 AGATTGA-GGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTTTTAATTA
*
8814 AATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGAC
319 AATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGAC
* * * *
8879 TCGATGAACATAGATATTTCAAGGAGTTTATACACCAAAAGTCATGTAAAATTGAACCAAGACTC
384 TCGATGAACATAGATATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAACCAGGACTC
** *
8944 CGGAACTCGTTTTTAGCAAAAACAAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA
449 CGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAA
9009 ACTGACCCGAAAAGTTTTCCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACG
514 ACTGACCCGAAAAGTTTTCCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACG
*
9074 CCAAAGAAATTGAAGGGTTTTTCACGTTTCTAATATCATTTTTCCA--TTTTTTCCGAATTTATT
579 CCAAAGAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATT
9137 TCTTATT
644 TCTTATT
* *
9144 AAATCGAAATAAGATTCAGATGCCCGTAAAAACAAATCCTTATATCCAATGTGGCTG-GAATTTG
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGCG-ATTTG
* * * **
9208 GTCAGATG-A-ATAGATATTTCAAGGAGTCTTT-CTGCCAAAAAATCATGC-AAATCTG-AATTG
65 ATTAGATGAATATAGATATTTGAAGGAGTCTTTGC-G-CAAAAAATCATGCAAAAT-TGAAAAAG
* * * * * * *
9268 GGACCTCGAAAGATGTTTTTAGCCAAAAACCATTATGGTTAATACATGATTTCGGCTAAAAACAT
127 GGA-C-CGCAACACGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAAC-T
* * * * *
9333 -ATCTGAGCAGTTTTTTTATTAATTATTTGCCACAATACTCAGAAAAAGTATATAATTCAACACC
188 CACCTAAACAGTTTTTTTATCAATT-TTTGCCACAATACTCAGAAAAAATATATAATTCAACACC
* * * *
9397 AAAAAGATTGAGGGCTTTTTACGTTTCTAATATCATTTTTCCATTTTTTTTTCCAAATTAATTTC
252 -AAAAGATTGAGGGCTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTTT-CGAATTAATTT-
* * * * *
9462 TT-ATTAAATCGAAACAAGATTGAAATGCTCGTAAAAACAAATTCTTATATCCAATGTGACTGAG
312 TTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAG
** * *
9526 ATTTGGTTCGATGAATATAGATATTTGAAGGAGTCT
377 ATTTGACTCGATGAACATAGATATTTCAAGGAGTCT
9562 TTGCGCAAAA
Statistics
Matches: 2008, Mismatches: 253, Indels: 213
0.81 0.10 0.09
Matches are distributed among these distances:
633 1 0.00
634 29 0.01
635 35 0.02
636 194 0.10
637 63 0.03
638 21 0.01
639 47 0.02
640 1 0.00
641 227 0.11
642 11 0.01
644 1 0.00
645 27 0.01
646 39 0.02
647 32 0.02
648 3 0.00
649 101 0.05
650 8 0.00
651 94 0.05
652 59 0.03
653 21 0.01
654 163 0.08
655 162 0.08
656 164 0.08
657 299 0.15
658 47 0.02
659 8 0.00
660 3 0.00
661 15 0.01
664 1 0.00
665 97 0.05
666 12 0.01
667 23 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (650 bp):
AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGCGATTTGA
TTAGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAAAAAGGGAC
CGCAACACGTTTTTAGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTCACCTAAA
CAGTTTTTTTATCAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAGATTG
AGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAATTTTTAATTAAATCGAA
ATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTCGATGA
ACATAGATATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAACCAGGACTCCGGAACT
CGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAACTGACC
CGAAAAGTTTTCCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAGA
AATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTTATT
Found at i:9011 original size:972 final size:949
Alignment explanation
Indices: 6534--9581 Score: 2665
Period size: 972 Copynumber: 3.1 Consensus size: 949
6524 AATCATAGAG
* * * *
6534 AAATCGAAATAAAATTCAGATGCTCGTGAAAACAAATCCTTATATCCAATGTTG-TTGA-GATTT
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATG-TGACT-ACGATTT
* * * * * * * * * * *
6597 GACTCGATGAACATAGAGATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGAGGCAGGA
64 GATTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCACGA
* * *
6662 CTTCGAAACTCGTTTTTAGCAAAAACAGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
129 CTCCGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTT--GC-AAAA--TT--A
* * *
6727 AAAACTGACCCGAAAAGTTTTCCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAATTCA
187 AAAACTGACCCGAAAGGTTTTCCCTCTAATTTTTACCACAATACTCAGAAAAAATATATAATTCA
* * * * * *
6792 ACGCCAACGAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATTTA
252 ACGCCAAAGAAATTCAAGGGCTTTACACACTTCTAATATCG--------TTTTTTCCC--A--GA
* * * *
6857 TTTCTTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGTCT
305 TTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATATCCAATGTGGCT
** * *
6922 GAGATTTGGTTAGATGAATATAGATATTTCAA-GGAATCTTTCAAGGAATCTTTTTGCCAAAAAA
370 GAGATTTGACTAGATGAACATAGATATTT-AATGG-ATCTTTC---G-A--------CC-AAATA
* *** * * * * *
6986 TCATGCAAATCTGAATTGGGAC-CTCGAAACACGTTTTTAG-CAAAAAACTGTGATGCTTAGTAA
420 TCATGAAAATCT-AA-AAAGACAC-CGCAACGCGTTTTTAGTC-AAAAACAGTGATGGTTAGTAC
* * * *
7049 ATGATTTCGGCTAAAAACTTATCTG-AACAGTTTTTTTATCAATTATTTGCCACAATACTCAGAA
481 ACGATTTCGGCTAAAAACTGACCCGAAACAGTTTTTTTATCAATT-TTTGCCACAATACTCAGAA
* * * *
7113 AAATTATATAATTCAACATCAAAAAGATTGAGGGCTTTTCATGCTTCTAATATCGTTTTTCCATT
545 AAAATATATAATTCAACA-CCAAAAGATTGAGGGCTTTTCACGCTTCTAATATCATTTTTCCATT
* * * *
7178 TTCTATCGAATTTATTTTTAACTAAATCGAAACAAGA-TCCGAATGCTCGT-AAAA-AAATCCTT
609 TT-TTTCGAATTTATTTTTAATTAAATCGAAATAAGATTCAG-ATGCTCGTAAAAACAAATCCTT
* * * * *
7240 ATATCCAATGTGGTTGCGATTTGATTCGATGAATGTAGATATTTGAAGGAGTCTTTGCGCAAAAA
672 ATATCCAATGTGGCTG-GATTT-ACTCGATGAA-ATAGATATTTCAAGGAGTCTATGC-CAAAAA
* * **
7305 ATTATGCAAAATTGAGCCGGGGGTCCGGAACA-CGTTTTTAGCAGAAAACCGTGAT-G---GTAC
733 ATCATG-AAAATTGAGCCTGGACTCCGGAA-ATCGTTTTTAGCA-AAAACCGTGATGGTTAGTAC
* * *
7365 ACGATTTCGGCT--AAG--AACTCACCCGAATAATTTTTTCTCAATTTTTTGCCACAATACTCAG
795 ACGATTTCGGCTAAAAGCAAACTGACCCGAA-AAGTTTTTCTCTATTTTTTGCCACAATACTCAG
* * * ** *
7426 AAAAAATATATAATTCAACGCCAAAAAGATTCACGAGCTTTACACGCTTCTAATATCGTTTTTCC
859 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTAC-CTTTTAATATCGTTTTTCC
* ***
7491 ATTTTTCTGAACCAA--T-TTT-TAATT
923 -TTTTTTTTTTCCAATTTATTTCTAATT
* * *
7515 AAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGCCTGAC-ATTTG
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGACT-ACGATTTG
* * * * * * * * * *
7579 ACTCGATGAACATAGATATTTCAAGGTGTCTATGCACCAAAAATCATGTAAAATTGAGTCACGAC
65 ATTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCACGAC
7644 TCCGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAA
130 TCCGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTT--GC-AAAA--TT--AA
* *
7709 AAACTGACCCGAAAGGTTTTCCCTCTAGTTTTTGCCACAATACTCAGAAAAAAATATATAATTCA
188 AAACTGACCCGAAAGGTTTTCCCTCTAATTTTTACCACAATACTCAG-AAAAAATATATAATTCA
* * * **
7774 ACGCCAAAGAAATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATATTTTTTTTCCCAGA
252 ACGCCAAAGAAATTCAAGGGCTTTACACACTTCTAATATCG------------TTTTTTCCCAG-
* * * * *
7839 ATTCATTTCTTATTAAATCAAAACAAGATTCAGGTGCTCATAAAAGCAAATTCTTATTTCCAATG
304 ----ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATATCCAATG
** * * *
7904 TGGCTGAGATTTGGTTAGATGAATATAGATATTTAATGGATCCTTTCGGCCAAATATCATGCAAA
365 TGGCTGAGATTTGACTAGATGAACATAGATATTTAATGGAT-CTTTCGACCAAATATCATGAAAA
** * * *
7969 TCTAAAAAGGGACCTCAACGCGTTTTTAGTCAAAAACTGTGATGGTTAGTACATGATTTCGGCTA
429 TCTAAAAAGACACCGCAACGCGTTTTTAGTCAAAAACAGTGATGGTTAGTACACGATTTCGGCTA
* *
8034 AAAACTGA-CCTAAACAGTTTTTTTATCAACTTTTGCCACAATACTCAGAAAAAAGTATATAATT
494 AAAACTGACCCGAAACAGTTTTTTTATCAATTTTTGCCACAATACTCAGAAAAAA-TATATAATT
* *
8098 CAACACCTAAAAGATTGAGGGCTTTTCACGCTTCTAATATCTTTTTTCCATTTTTTTCGAATTAA
558 CAACACC-AAAAGATTGAGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTTA
* *
8163 TTTTTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCATAATATCCAATGTGGCT
622 TTTTTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCT
*
8228 GAGATTTCACTCGATGAACATAGATATTTCAAGGAGTCTATGCACCAAAAATCATGTAAAATTGA
687 G-GATTT-ACTCGATGAA-ATAGATATTTCAAGGAGTCTATGC-CAAAAAATCATG-AAAATTGA
* *
8293 GCCTGGACTCCGGAATTCTTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTCGGCTAAAA
747 GCCTGGACTCCGGAAATCGTTTTTAGCAAAAACC-GTGATGGTTAGTACACGATTTCGGCTAAAA
* *
8358 TTTTGCAAAAACTGACCCGAAAAGTTTTCCCTCTATTTTTTG-CACAATACTCTAAAAAATATAT
811 ----GC--AAACTGACCCGAAAAGTTTT-TCTCTATTTTTTGCCACAATACTC-AGAAAA-A-AT
*
8422 ATATAATTCAACGCCAAAGAA-ATTGAAGGGTTTTTTACACTTTTAATATCGTTTTTCCTTTTTT
866 ATATAATTCAACGCCAAA-AAGATTGAAGGGCTTTTTAC-CTTTTAATATCGTTTTTCCTTTTTT
8486 TTTTCCGAATTTATTTCTAATT
929 TTTTCC-AATTTATTTCTAATT
* * * *
8508 AAATCGAAACAAGATCCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTTCGATTTGA
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGACTACGATTTGA
* * *
8573 TTCGATGAATGTAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCAGGGCT
66 TTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCACGACT
* *
8638 CCGGAACAT-G-TTTTAGCAAAAACC-GTGATGGTTAGTATACGATTT-C-AGA-T-AAAACT-A
131 CCGGAAC-TCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTGCAAAATTAAAAACTGA
*** *
8695 CACCGTAATTA-GTTTTTTTTTTCAATTTTTACCACAA-ACTCAG-AAAAATATAGTAATTCAAC
195 C-CCG-AA--AGGTTTTCCCTCT-AATTTTTACCACAATACTCAGAAAAAATATA-TAATTCAAC
* *
8757 GACCAAA-AGATTCACGGGCTTTACACACTTCTAATATCG-TTTTT-CCAG-TTT-TAATTAAAT
254 G-CCAAAGAAATTCAAGGGCTTTACACACTTCTAATATCGTTTTTTCCCAGATTTCTAATTAAAT
* * *
8817 CAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTCG
318 CAAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTAG
*
8882 ATGAACATAGATATTTCAA-GGAGT-TTATAC-ACCAAA-AGTCATGTAAAAT-TGAACCAAGAC
383 ATGAACATAGATATTT-AATGGA-TCTT-T-CGACCAAATA-TCATG-AAAATCT-AA-AAAGAC
* * *
8942 TCCGGAACTCGTTTTTAG-CAAAAACAAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
440 ACCGCAACGCGTTTTTAGTCAAAAAC-AGTGATGGTTAGTACACGATTTCGGC--------T--A
*** *
9006 AAAACTGACCCGAAA-AG-TTTTCCCTCTATTTTTTGCCACAATACTCAGAAAAAATATATAATT
494 AAAACTGACCCGAAACAGTTTTTTTATC-AATTTTTGCCACAATACTCAGAAAAAATATATAATT
* * * * *
9069 CAACGCCAAAGAAATTGAAGGGTTTTTCACGTTTCTAATATCATTTTTCCATTTTTTCCGAATTT
558 CAACACCAAA-AGATTG-AGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTT
*
9134 ATTTCTT-ATTAAATCGAAATAAGATTCAGATGCCCGTAAAAACAAATCCTTATATCCAATGTGG
621 ATTT-TTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGG
** * *
9198 CTGGAATTTGGTCAGATG-AATAGATATTTCAAGGAGTCTTTCTGCCAAAAAATCATGCAAATCT
685 CTGG-ATTTACTC-GATGAAATAGATATTTCAAGGAGTC--TATGCCAAAAAATCATGAAAAT-T
** * * * * *
9262 GA-ATTGGGAC-CTCGAAAGAT-GTTTTTAGCCAAAAACCATTATGGTTAATACATGATTTCGGC
745 GAGCCT-GGACTC-CGGAA-ATCGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGC
* * * * * * *
9324 TAAAAACATATCTGA---G--CAGTTTTTTTATTAATTATTTGCCACAATACTCAGAAAAAGTAT
806 TAAAAGCA-AACTGACCCGAAAAGTTTTTCT-CT-ATTTTTTGCCACAATACTCAGAAAAAATAT
* * * *
9384 ATAATTCAACACCAAAAAGATTG-AGGGCTTTTTACGTTTCTAATATCATTTTTCCATTTTTTTT
868 ATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTACCTTT-TAATATCGTTTTTCCTTTTTTTTT
* *
9448 TCCAAATTAATTTCTTATT
932 TCC-AATTTATTTCTAATT
* * *
9467 AAATCGAAACAAGATTGAAATGCTCGTAAAAACAAATTCTTATATCCAATGTGACTGA-GATTTG
1 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGACT-ACGATTTG
*
9531 GTTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAA
65 ATTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAA
9582 TATAGAATTC
Statistics
Matches: 1767, Mismatches: 203, Indels: 216
0.81 0.09 0.10
Matches are distributed among these distances:
958 3 0.00
959 159 0.09
960 117 0.07
961 28 0.02
962 53 0.03
963 11 0.01
965 1 0.00
966 5 0.00
967 5 0.00
968 5 0.00
970 29 0.02
971 147 0.08
972 302 0.17
973 112 0.06
974 17 0.01
975 2 0.00
977 16 0.01
979 4 0.00
980 20 0.01
981 260 0.15
982 74 0.04
983 15 0.01
984 2 0.00
986 33 0.02
987 122 0.07
988 10 0.01
989 51 0.03
990 2 0.00
991 21 0.01
992 18 0.01
993 122 0.07
994 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (949 bp):
AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGACTACGATTTGA
TTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGCCACGACT
CCGGAACTCGTTTTTAGCAAAAACCGGTGATGGTTAGTACACGATTTGCAAAATTAAAAACTGAC
CCGAAAGGTTTTCCCTCTAATTTTTACCACAATACTCAGAAAAAATATATAATTCAACGCCAAAG
AAATTCAAGGGCTTTACACACTTCTAATATCGTTTTTTCCCAGATTTCTAATTAAATCAAAACAA
GATTCAGATGCTCATAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTAGATGAACAT
AGATATTTAATGGATCTTTCGACCAAATATCATGAAAATCTAAAAAGACACCGCAACGCGTTTTT
AGTCAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAACAGTTTTTTTAT
CAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAGATTGAGGGCTTTTCAC
GCTTCTAATATCATTTTTCCATTTTTTTCGAATTTATTTTTAATTAAATCGAAATAAGATTCAGA
TGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGGATTTACTCGATGAAATAGATATTTCAA
GGAGTCTATGCCAAAAAATCATGAAAATTGAGCCTGGACTCCGGAAATCGTTTTTAGCAAAAACC
GTGATGGTTAGTACACGATTTCGGCTAAAAGCAAACTGACCCGAAAAGTTTTTCTCTATTTTTTG
CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTTACCTTTTAA
TATCGTTTTTCCTTTTTTTTTTCCAATTTATTTCTAATT
Found at i:9730 original size:200 final size:199
Alignment explanation
Indices: 9381--9758 Score: 497
Period size: 200 Copynumber: 1.9 Consensus size: 199
9371 TCAGAAAAAG
* * * ** * *
9381 TATATAATTCAACACCAAAAAGATTGAGGGCTTTTTACGTTTCTAATATCATTTTTCCATTTTTT
1 TATAGAATTCAACACCAAAAAGATTCAGGACTTTACACGCTTCTAATATCATTTTTCCA-TTATT
** * * * *
9446 TTTCCAAATTAATTTCTTATTAAATCGAAACAAGATTGAAATGCTCGTAAAAACAAATTCTTATA
65 TTTCCAAATTAATTTCAAACTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAAATCCTTATA
**
9511 TCCAATGTGACTGAGATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCAAAAAATT
130 TCCAATGTGACTGAGATTTGACTCGATGAA-ATAGATATTTGAAGGAGTCTTTGCGCAAAAAATT
9576 ATGCAA
194 ATGCAA
*
9582 TATAGAATTCAACACCAAAAAGATTCACGGACTTTACACGCTTCTAATATCGTTTTTCCA-TATT
1 TATAGAATTCAACACCAAAAAGATTCA-GGACTTTACACGCTTCTAATATCATTTTTCCATTATT
** * *
9646 TTTCTGAATTAATTTCAAACTAAATCGAAATAAGATTCAGATGCTCGTAAAAAAAAATCCTTATA
65 TTTCCAAATTAATTTCAAACTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAAATCCTTATA
* ** * *
9711 TCCATTGTGGTTGAGATTTGACTCGATGAAATTGATATTTTAAGGAGT
130 TCCAATGTGACTGAGATTTGACTCGATGAAATAGATATTTGAAGGAGT
9759 ATATGCACCA
Statistics
Matches: 151, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
199 16 0.11
200 83 0.55
201 25 0.17
202 27 0.18
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (199 bp):
TATAGAATTCAACACCAAAAAGATTCAGGACTTTACACGCTTCTAATATCATTTTTCCATTATTT
TTCCAAATTAATTTCAAACTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAAATCCTTATAT
CCAATGTGACTGAGATTTGACTCGATGAAATAGATATTTGAAGGAGTCTTTGCGCAAAAAATTAT
GCAA
Done.