genome.fa.s6.2.7.7.80.10.50.1000.47.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  47  of  168  ( 20060 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13053509--13053591	42	2.0	43	83	7	107	26	13	24	36	1.92
13061111--13061145	18	2.0	17	88	5	52	42	0	2	54	1.15
13061333--13061379	16	2.9	16	93	0	85	21	36	4	38	1.73
13062533--13062645	43	2.6	43	84	5	140	26	18	24	30	1.98
13062536--13062645	42	2.6	42	84	4	141	26	19	24	30	1.98
13064977--13065036	30	1.9	32	83	6	79	1	13	18	66	1.32
13070648--13070697	18	2.8	18	84	0	64	32	12	16	40	1.84
13073508--13073613	49	2.2	49	94	0	185	43	20	4	31	1.73
13073531--13073610	25	3.2	25	62	28	62	43	23	5	27	1.74
13074863--13074905	22	2.0	22	90	9	70	27	13	11	46	1.78
13076241--13076293	3	17.7	3	92	0	88	32	3	0	64	1.12
13083547--13083782	45	5.3	45	68	11	180	28	23	25	22	1.99
13083535--13083810	89	3.1	89	86	2	394	27	24	23	24	2.00
13083799--13083999	44	4.6	44	73	8	176	27	19	26	26	1.99
13085482--13085537	3	18.7	3	96	0	103	33	30	0	35	1.58
13085485--13085597	9	12.2	9	86	5	82	31	19	1	46	1.60
13085536--13085576	3	13.7	3	100	0	82	34	0	0	65	0.93
13090133--13090174	22	1.9	22	90	0	66	45	9	7	38	1.64
13094333--13094829	70	7.1	71	84	5	579	42	15	15	26	1.87
13094333--13094829	210	2.4	209	86	4	660	42	15	15	26	1.87
13094344--13094814	23	20.2	24	70	12	241	41	15	16	26	1.88
13102149--13102274	28	4.5	28	88	0	180	30	25	12	31	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13104994--13105023	10	2.9	10	95	5	51	70	0	0	30	0.88
13106221--13106258	16	2.3	17	86	4	51	73	0	0	26	0.83
13109076--13109117	22	1.9	22	85	0	57	35	2	14	47	1.57
13109713--13109762	24	2.0	26	92	7	86	42	12	18	28	1.85
13120244--13120333	40	2.3	38	88	3	126	36	11	16	35	1.84
13120244--13120336	19	4.8	19	89	5	132	36	10	18	34	1.85
13122886--13122945	18	3.3	18	68	32	56	31	5	28	35	1.79
13122876--13122950	36	2.1	36	100	0	150	34	5	26	33	1.79
13123410--13123544	69	2.0	69	83	2	173	20	20	22	35	1.96
13123927--13124011	22	3.9	22	87	0	107	29	25	14	30	1.95
13134241--13134273	16	2.0	17	88	5	50	42	6	12	39	1.67
13136197--13136221	9	2.8	9	100	0	50	44	0	12	44	1.41
13145822--13145861	19	2.1	19	90	9	64	30	10	10	50	1.69
13148762--13148801	19	2.2	19	90	4	64	70	0	7	22	1.12
13159464--13159499	16	2.2	16	100	0	72	25	0	36	38	1.56
13159735--13159769	18	2.0	17	88	5	52	54	0	0	45	0.99
13159622--13159937	156	2.0	157	97	0	598	42	3	5	48	1.42
13159871--13159925	15	3.4	16	80	16	53	50	1	0	47	1.11
13159891--13159925	18	2.0	17	88	5	52	54	0	0	45	0.99
13159874--13160098	120	1.9	119	95	0	405	47	6	1	44	1.36
13160011--13160045	18	2.0	17	88	5	52	54	0	0	45	0.99
13160099--13160180	26	3.0	27	75	12	87	52	2	1	43	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13164510--13164558	21	2.3	22	85	3	64	40	26	12	20	1.87
13168599--13168624	13	2.0	13	100	0	52	30	15	15	38	1.88
13174158--13174201	13	3.4	13	80	0	52	31	22	2	43	1.66
13174703--13174735	17	2.1	16	88	11	50	45	12	0	42	1.41
13175839--13175935	50	1.9	50	95	4	178	49	13	2	35	1.54
13200349--13200376	2	14.0	2	100	0	56	50	0	0	50	1.00
13200462--13200510	21	2.3	21	85	0	62	32	8	10	48	1.66
13202722--13202773	19	2.9	18	78	10	63	30	1	3	63	1.23
13202761--13202825	26	2.6	25	81	9	71	58	0	1	40	1.07
13231221--13231258	19	2.0	19	85	10	51	21	42	0	36	1.53
13236798--13236855	29	2.0	29	100	0	116	20	24	13	41	1.89
13240410--13240546	50	2.7	50	85	0	184	21	27	24	27	1.99
13248708--13248732	13	1.9	13	100	0	50	80	0	4	16	0.87
13269989--13270079	29	3.1	29	87	0	137	40	30	7	20	1.81
13270458--13270518	26	2.3	26	77	5	70	31	14	6	47	1.70
13270497--13270546	16	3.3	15	81	10	57	34	18	4	44	1.68
13275475--13275695	29	7.6	29	78	5	205	36	13	25	24	1.92
13275500--13275907	58	7.2	58	76	8	342	35	13	26	23	1.93
13275475--13275907	87	5.1	87	80	8	489	35	14	26	24	1.93
13275702--13275895	29	6.7	29	75	3	194	35	12	28	23	1.92
13275598--13275793	106	1.8	106	91	0	320	35	13	27	23	1.92
13275698--13275907	86	2.4	87	93	2	361	35	13	27	23	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13282245--13282301	30	1.9	30	88	0	87	22	31	14	31	1.93
13282292--13282370	29	2.7	30	80	4	97	18	25	12	43	1.86
13282287--13282510	119	1.9	119	87	1	333	23	24	13	39	1.90
13289212--13289259	25	1.9	25	100	0	96	66	12	0	20	1.24
13289216--13289264	25	2.0	24	88	7	73	69	12	0	18	1.19
13289618--13289652	3	11.7	3	100	0	70	68	0	0	31	0.90
13292585--13292755	24	6.7	25	74	15	163	12	30	26	29	1.93
13292587--13292836	30	8.9	29	69	22	117	14	30	26	30	1.94
13292588--13292755	51	3.3	48	78	12	167	11	31	26	29	1.92
13292691--13292818	66	2.0	65	86	4	179	11	30	26	31	1.92
13292716--13292791	39	1.9	39	89	0	116	10	30	26	32	1.90
13292753--13292819	27	2.5	27	90	0	107	11	29	25	32	1.92
13297037--13297067	2	15.5	2	100	0	62	51	0	48	0	1.00
13304557--13304742	50	3.7	50	90	0	273	20	29	24	25	1.99
13308864--13308898	18	1.9	18	94	0	61	22	14	17	45	1.84
13311812--13312103	149	2.0	149	99	0	575	26	8	18	46	1.78
13312470--13312502	11	3.1	11	86	4	50	42	12	15	30	1.83
13316360--13316393	17	2.0	17	94	0	59	38	32	0	29	1.58
13318349--13318462	29	3.9	28	77	7	111	41	22	13	22	1.88
13319028--13319078	25	2.0	25	88	0	75	23	21	7	47	1.77
13321223--13321282	23	2.4	25	79	15	72	21	25	23	30	1.99
13321222--13321287	26	2.7	23	77	13	62	24	24	21	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13326630--13326737	52	2.1	53	89	1	164	28	20	7	43	1.78
13332688--13332732	19	2.4	19	82	10	56	31	22	2	44	1.65
13332701--13332740	20	2.0	20	85	9	55	32	20	5	42	1.73
13337054--13337262	104	2.0	104	100	0	418	34	31	11	22	1.89
13343775--13343844	18	3.8	18	81	9	88	38	2	0	58	1.13
13343793--13343843	9	5.6	9	79	11	59	41	1	0	56	1.10
13343764--13343856	11	9.4	11	72	26	59	40	2	0	56	1.11
13345873--13346136	58	4.6	58	80	2	273	25	13	21	39	1.90
13345873--13346136	29	9.1	29	83	5	243	25	13	21	39	1.90
13346086--13346154	29	2.4	29	83	7	79	33	10	17	39	1.83
13348303--13348344	14	3.1	13	78	21	50	59	4	0	35	1.19
13348311--13348348	16	2.4	16	82	4	51	60	5	0	34	1.19
13348600--13348722	3	41.0	3	93	0	201	65	1	1	31	1.12
13349615--13349663	23	2.1	22	85	14	64	30	0	6	63	1.19
13351677--13351906	51	4.6	51	84	5	310	23	20	26	29	1.99
13351682--13351863	101	1.8	101	95	0	328	23	19	26	29	1.98
13352010--13352189	74	2.4	74	85	4	234	23	18	25	31	1.98
13357433--13357493	20	3.1	19	80	15	61	26	27	11	34	1.91
13357980--13358035	12	4.8	12	80	10	71	75	3	7	14	1.16
13357983--13358035	11	4.6	11	80	4	61	77	3	5	13	1.09
13363416--13363463	20	2.4	21	80	19	66	25	33	12	29	1.92
13365329--13365595	138	1.9	137	96	0	498	29	8	13	48	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13365716--13365743	12	2.3	12	100	0	56	35	10	17	35	1.85
13365807--13365875	25	2.7	25	90	2	93	17	15	7	59	1.58
13365818--13365864	15	3.5	15	72	27	59	19	14	6	59	1.56
13373323--13373361	20	1.9	20	94	5	69	15	5	10	69	1.34
13373265--13373414	79	1.9	83	83	5	200	20	11	10	58	1.62
13373406--13373626	66	3.5	65	71	13	183	20	13	14	52	1.74
13373474--13373585	56	2.0	56	85	0	152	20	14	15	50	1.78
13373343--13373687	122	2.7	124	84	7	403	19	14	14	51	1.75
13377342--13377372	15	2.1	15	93	0	53	35	9	9	45	1.70
13379782--13379814	16	2.1	16	100	0	66	30	6	12	51	1.63

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168