genome.fa.s1.2.7.7.80.10.50.1000.143.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   

This is table  143  of  187  ( 22383 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)
42801344--42801411	7	9.4	7	73	12	57	25	0	39	35	1.56
42801376--42801429	22	2.4	23	87	3	74	25	0	42	31	1.55
42801595--42801641	14	3.3	15	82	8	62	27	0	31	40	1.57
42801625--42801677	21	2.5	22	81	9	65	20	0	39	39	1.53
42801660--42801698	7	5.4	7	81	6	51	17	0	46	35	1.49
42801656--42801698	15	2.9	15	86	3	61	18	0	46	34	1.50
42801643--42801707	22	3.0	22	77	4	62	20	0	46	33	1.51
42801660--42801707	14	3.4	13	83	13	51	20	0	45	33	1.52
42802279--42802436	83	1.9	83	93	0	271	51	9	10	28	1.66
42806641--42806809	85	2.0	85	82	4	207	22	17	31	28	1.96
42806663--42806825	43	3.8	43	86	3	204	22	19	30	28	1.98
42808756--42809008	40	6.3	39	79	5	247	16	31	18	33	1.94
42808745--42809002	81	3.2	79	81	4	277	17	31	18	33	1.94
42808745--42809020	20	13.8	21	64	12	89	16	31	18	33	1.93
42808978--42809033	20	2.8	20	75	0	58	10	30	21	37	1.87
42811403--42811438	18	2.1	18	90	10	58	44	16	13	25	1.85
42813694--42813718	13	1.9	13	100	0	50	24	4	8	64	1.38
42814142--42814189	20	2.3	21	79	13	55	20	20	4	54	1.61
42817102--42817132	16	1.9	16	100	0	62	25	29	6	38	1.81
42821716--42821748	17	1.9	17	100	0	66	24	27	6	42	1.78
42822387--42822428	22	1.9	22	90	0	66	28	9	26	35	1.88
42826529--42826578	2	24.5	2	79	4	55	50	4	2	44	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42827150--42827195	24	2.0	23	86	4	65	30	0	17	52	1.45
42828238--42828277	20	2.0	19	85	9	53	25	0	25	50	1.50
42828920--42829013	29	3.3	29	73	8	84	23	13	25	37	1.92
42834741--42834875	20	6.7	19	70	15	85	19	16	9	54	1.68
42834741--42834875	21	6.7	20	73	14	91	19	16	9	54	1.68
42835259--42835332	37	1.9	40	86	8	109	24	16	6	52	1.67
42835313--42835404	20	4.6	20	77	4	87	16	19	13	51	1.77
42837242--42837426	101	1.8	102	87	3	275	23	16	27	32	1.96
42837238--42837428	51	3.8	51	81	4	217	23	16	28	32	1.96
42837435--42837523	45	2.0	45	93	0	151	24	17	25	31	1.97
42837599--42837671	37	1.9	37	84	13	96	43	2	21	31	1.67
42840060--42840353	50	5.7	50	87	2	390	21	29	23	25	1.99
42844747--42844805	30	1.9	31	89	3	93	44	6	20	28	1.77
42845278--42845563	51	5.6	50	79	6	308	29	14	25	30	1.95
42845274--42845555	102	2.8	102	90	1	424	29	15	25	29	1.96
42845278--42845600	102	3.2	102	86	2	319	30	13	26	30	1.94
42848976--42849301	113	2.9	114	92	1	550	24	23	26	25	2.00
42849551--42849581	15	2.1	15	93	0	53	19	0	45	35	1.51
42849821--42849867	14	3.3	15	82	8	62	27	0	31	40	1.57
42849854--42849894	21	2.0	20	85	4	55	19	0	41	39	1.52
42851843--42851896	21	2.6	21	72	21	51	50	1	5	42	1.36
42851886--42851929	8	5.2	8	82	17	54	56	0	9	34	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42851891--42851939	9	5.4	9	88	9	73	61	0	8	30	1.25
42851908--42851967	9	6.2	10	83	9	54	71	0	3	25	1.01
42851927--42851967	21	2.0	21	90	9	66	78	0	0	21	0.76
42851916--42851977	10	6.4	9	76	12	52	75	0	3	20	0.94
42851935--42851977	21	2.2	20	83	8	52	81	0	2	16	0.79
42851972--42852070	47	2.1	48	86	1	137	45	10	1	43	1.44
42853714--42853764	26	2.0	26	88	0	75	27	11	17	43	1.84
42854993--42855018	13	2.0	13	100	0	52	30	15	0	53	1.42
42855906--42856032	50	2.5	50	98	0	245	31	7	31	29	1.86
42857423--42857693	43	6.3	43	83	3	314	25	16	26	31	1.96
42857436--42857687	85	3.0	83	85	4	310	26	16	26	30	1.97
42859948--42860100	10	16.1	10	72	18	73	41	2	0	56	1.13
42859940--42860100	36	4.5	36	84	12	199	40	2	0	56	1.13
42860018--42860100	32	2.7	31	83	9	109	45	1	0	53	1.08
42860075--42860099	8	3.1	8	100	0	50	48	0	0	52	1.00
42861212--42861313	32	3.4	32	69	20	103	6	15	4	72	1.23
42861207--42861313	56	1.9	56	94	0	187	6	16	4	71	1.24
42862397--42862433	17	2.4	17	86	13	53	43	0	2	54	1.14
42864093--42864176	21	4.0	21	82	4	98	36	25	21	16	1.94
42865193--42865224	16	2.1	16	94	5	57	40	0	0	59	0.97
42865180--42865232	27	2.1	26	86	10	74	43	0	0	56	0.99
42871159--42871440	43	6.6	42	75	9	232	33	26	18	21	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42871118--42871440	85	3.8	85	87	1	425	33	26	18	21	1.96
42876581--42876655	29	2.6	29	75	12	75	52	4	2	41	1.34
42879621--42879873	27	9.4	26	81	4	202	43	18	16	20	1.88
42879597--42879873	54	5.1	54	84	2	315	44	18	16	20	1.87
42879597--42879873	81	3.4	81	87	2	380	44	18	16	20	1.87
42880783--42880825	20	2.2	20	91	0	68	46	18	16	18	1.84
42891637--42891793	82	1.9	82	88	2	235	28	20	18	33	1.96
42891640--42891800	56	2.9	57	79	7	179	27	20	19	32	1.97
42891640--42891800	28	5.8	28	80	8	161	27	20	19	32	1.97
42892224--42892272	26	1.9	25	83	4	62	51	22	0	26	1.49
42898945--42898984	20	2.0	20	95	0	71	22	17	30	30	1.97
42899757--42899797	3	13.7	3	100	0	82	31	0	0	68	0.90
42899894--42899962	31	2.3	31	80	7	79	21	8	20	49	1.76
42901621--42901744	25	5.3	22	70	16	88	14	16	22	45	1.84
42901656--42901721	25	2.6	25	90	0	105	12	13	25	48	1.77
42908491--42908552	19	3.2	19	69	13	63	35	46	8	9	1.66
42908488--42908580	39	2.4	39	88	0	114	33	46	8	11	1.71
42918074--42918885	406	2.0	406	97	0	1516	31	19	15	33	1.93
42923482--42923526	13	3.5	13	78	3	56	31	20	6	42	1.77
42925728--42925773	22	2.1	22	87	0	65	60	26	10	2	1.41
42926146--42926260	62	1.9	59	89	5	176	41	3	3	51	1.36
42926240--42926655	148	2.8	148	97	0	787	40	12	9	38	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42927530--42927555	2	13.0	2	100	0	52	50	0	0	50	1.00
42928814--42928848	18	1.9	19	88	11	56	57	5	25	11	1.56
42931297--42931594	51	5.9	50	76	3	283	30	27	16	25	1.97
42931304--42931590	102	2.8	102	90	1	434	31	26	16	25	1.96
42937201--42937308	37	2.9	36	78	11	105	41	3	1	52	1.30
42937201--42937276	11	6.8	11	75	21	54	40	2	1	55	1.22
42937223--42937295	39	1.9	37	86	10	103	41	5	1	52	1.33
42937287--42937404	62	1.9	60	86	3	164	42	4	4	49	1.42
42941761--42941789	2	14.5	2	100	0	58	48	0	0	51	1.00
42943576--42943621	24	2.0	24	95	4	85	50	0	19	30	1.48
42944583--42944611	15	1.9	15	100	0	58	24	6	6	62	1.45
42950909--42950949	21	2.0	21	85	0	55	36	19	12	31	1.89
42958916--42959089	27	5.4	32	71	24	109	20	19	28	31	1.97
42958911--42959100	102	1.9	102	93	0	326	21	20	27	30	1.98
42963269--42963326	21	2.6	22	78	8	64	65	5	10	18	1.41
42963362--42963405	20	2.2	20	88	8	63	65	4	2	27	1.23
42964338--42964371	18	1.9	17	88	5	50	55	2	0	41	1.15
42972512--42972555	16	2.9	16	83	6	56	36	0	0	63	0.95
42974037--42974086	21	2.4	21	86	3	66	36	10	12	42	1.76
42983143--42983171	14	2.0	15	93	6	51	20	0	6	72	1.07
42983185--42983392	9	21.7	9	69	18	50	36	3	2	57	1.30
42983187--42983219	10	3.4	10	91	4	50	30	0	0	69	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42983262--42983402	9	15.0	9	70	16	65	34	3	2	59	1.29
42983359--42983401	19	2.3	19	88	4	61	32	2	0	65	1.06
42987441--42987491	24	2.0	25	85	14	70	17	17	3	60	1.50
42988541--42988588	10	4.9	10	75	14	55	58	2	8	31	1.39
42988528--42988603	29	2.7	29	78	17	95	59	1	9	30	1.37
42989014--42989056	16	2.6	17	81	3	52	79	2	2	16	0.95
42990477--42990959	50	9.7	50	71	5	285	22	19	25	32	1.97
42990452--42990989	100	5.4	100	87	2	713	22	21	24	31	1.98
42991085--42991177	44	2.1	44	87	0	132	26	20	20	32	1.97
42991051--42991260	44	4.5	44	67	18	122	29	19	17	33	1.95

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187