genome.fa.s6.2.7.7.80.10.50.1000.100.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  100  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)
29376638--29376965	51	6.8	49	67	18	172	31	18	20	29	1.96
29376783--29377093	50	6.4	49	68	15	150	31	20	19	27	1.97
29376650--29376920	94	2.9	93	78	9	293	32	17	21	29	1.96
29376781--29377093	145	2.2	145	91	0	502	32	20	19	27	1.97
29377771--29377822	2	26.5	2	92	3	79	44	1	0	53	1.11
29378870--29378919	21	2.2	23	83	16	61	22	12	6	60	1.53
29381972--29382008	20	2.0	20	84	10	51	27	0	5	67	1.12
29382318--29382358	21	1.9	22	85	5	57	39	17	2	41	1.62
29385481--29385557	35	2.2	36	79	11	88	23	11	33	31	1.91
29385528--29385572	21	2.1	21	84	8	56	28	6	33	31	1.83
29385533--29385588	21	2.7	21	81	8	53	32	10	26	30	1.90
29399062--29399130	25	2.8	24	78	6	75	15	26	18	39	1.91
29404733--29404776	21	2.1	21	86	0	61	15	20	47	15	1.82
29408562--29408634	37	1.9	38	83	2	94	28	13	19	38	1.90
29411669--29412269	31	19.6	31	71	11	348	45	15	5	32	1.71
29411672--29412361	92	7.5	92	93	0	1083	44	16	6	32	1.73
29415518--29415596	38	2.1	38	83	6	99	41	8	15	34	1.78
29416118--29416193	21	3.6	21	71	3	64	35	15	19	28	1.93
29418727--29418782	28	2.0	28	100	0	112	28	10	28	32	1.90
29420652--29420707	28	2.0	28	100	0	112	42	25	14	17	1.87
29425109--29425185	39	2.0	39	86	0	109	32	23	20	23	1.98
29425415--29425490	29	2.6	28	79	6	71	34	1	1	63	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29431490--29431689	27	7.3	27	82	1	202	43	22	15	19	1.88
29431490--29431689	54	3.7	54	83	1	238	43	22	15	19	1.88
29431864--29431917	26	2.1	26	92	0	90	18	20	24	37	1.94
29442777--29442815	18	2.1	18	90	4	60	38	7	5	48	1.54
29448192--29448218	11	2.5	11	100	0	54	51	0	0	48	1.00
29451465--29451509	20	2.2	20	88	0	63	31	6	8	53	1.58
29455205--29455413	72	2.9	73	91	1	339	34	17	18	29	1.94
29461957--29462498	50	10.9	50	71	4	394	26	19	21	33	1.97
29461957--29462492	100	5.4	100	88	0	741	26	19	21	33	1.97
29461955--29462523	299	1.9	300	85	1	791	26	19	20	32	1.97
29464277--29464317	20	2.0	21	86	13	59	36	4	0	58	1.20
29473444--29474035	45	13.5	45	74	10	424	31	19	21	27	1.98
29473572--29473943	134	2.8	132	79	7	310	30	19	22	26	1.98
29473486--29474044	174	3.2	171	74	10	472	31	19	22	26	1.98
29474853--29475335	50	9.7	50	76	2	425	26	18	21	33	1.96
29474872--29475185	150	2.1	149	91	0	502	27	18	21	33	1.96
29474904--29475349	100	4.5	100	84	3	488	26	19	21	33	1.97
29475110--29475872	361	2.1	361	93	0	1312	25	23	19	32	1.97
29475515--29475705	50	3.8	50	77	6	208	25	20	21	32	1.98
29475471--29475710	100	2.4	99	90	0	363	24	20	21	34	1.97
29475576--29475727	50	3.0	49	72	9	137	25	19	21	33	1.97
29489845--29490528	45	15.5	45	74	10	498	30	19	23	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29489879--29490528	89	7.4	90	77	9	423	30	19	23	26	1.98
29498784--29499063	72	3.9	72	94	0	488	34	18	19	27	1.95
29499538--29499567	10	3.0	10	95	0	51	36	0	13	50	1.42
29499716--29499752	19	2.0	18	89	5	56	56	0	8	35	1.29
29501658--29501730	23	3.2	23	92	1	121	35	0	15	49	1.44
29501665--29501731	13	5.6	13	73	20	74	34	0	16	49	1.46
29502484--29502547	30	2.1	31	91	2	103	57	14	3	25	1.51
29503330--29503355	6	4.3	6	100	0	52	19	0	0	80	0.71
29506430--29506487	20	3.0	19	82	9	64	39	32	15	12	1.84
29507760--29507814	13	4.5	13	73	13	62	40	1	10	47	1.49
29507773--29507817	23	2.0	23	90	0	72	42	2	11	44	1.52
29509873--29509935	30	2.1	30	85	5	83	19	20	34	25	1.96
29511512--29511547	18	2.1	17	89	5	54	58	0	0	41	0.98
29512341--29512427	30	2.9	30	85	0	111	17	20	39	22	1.92
29515644--29515698	26	2.1	27	86	10	78	21	3	5	69	1.25
29515652--29515729	29	2.7	30	80	15	92	19	3	3	73	1.15
29515677--29515735	14	4.1	14	78	8	57	16	3	3	76	1.06
29525872--29525942	35	2.0	35	97	0	133	15	26	11	46	1.79
29526300--29526389	29	3.1	29	64	20	78	34	14	12	38	1.83
29527705--29528270	44	12.6	44	76	9	396	31	18	20	29	1.96
29527656--29528270	227	2.7	223	78	6	603	31	18	20	29	1.96
29529093--29529144	26	2.0	27	85	11	72	21	3	5	69	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29530445--29530486	22	1.9	22	90	0	66	30	4	11	52	1.59
29531077--29531124	25	1.9	25	100	0	96	31	12	16	39	1.86
29532675--29532699	10	2.5	10	100	0	50	12	0	12	76	1.04
29532911--29533330	93	4.4	96	78	7	407	18	20	15	45	1.85
29533659--29533694	18	2.0	18	100	0	72	33	5	11	50	1.61
29539845--29539888	21	2.1	21	100	0	88	25	9	22	43	1.82
29542258--29542358	49	2.1	48	96	1	184	31	21	4	41	1.75
29544087--29544112	3	8.7	3	100	0	52	0	30	0	69	0.89
29551234--29551285	23	2.3	24	80	9	65	36	15	1	46	1.57
29552780--29552827	17	2.8	17	83	3	51	64	2	0	33	1.05
29559118--29559196	37	2.1	37	100	0	158	21	10	18	49	1.77
29569920--29569979	27	2.2	27	96	0	111	21	30	13	35	1.92
29570128--29570200	27	2.7	27	78	0	74	36	26	8	28	1.85
29575026--29575090	12	5.4	12	76	20	57	43	0	1	55	1.09
29575025--29575098	17	4.5	17	74	16	66	41	0	1	56	1.07
29575011--29575104	48	2.0	48	91	0	152	41	0	2	56	1.11
29575172--29575212	21	1.9	22	85	14	59	51	0	2	46	1.14
29575302--29575350	23	2.0	25	84	11	66	42	6	12	38	1.67
29578535--29579183	322	2.0	322	93	0	1118	35	18	17	28	1.94
29581163--29581204	16	2.5	17	84	11	59	33	2	11	52	1.51
29581260--29581321	27	2.3	27	80	5	63	27	4	16	51	1.64
29589575--29589736	46	3.6	46	90	2	249	29	22	16	32	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29609268--29609333	2	33.5	2	90	3	107	54	0	0	45	0.99
29612045--29612123	25	3.2	25	78	10	90	30	22	25	21	1.99
29614299--29614330	10	3.4	10	83	16	50	71	18	0	9	1.12
29615607--29615664	30	1.9	30	89	0	89	41	3	24	31	1.71
29619365--29619407	14	3.0	14	82	3	50	20	2	16	60	1.46
29623449--29623501	24	2.3	22	87	12	72	64	1	1	32	1.15
29625234--29625287	23	2.3	23	80	0	63	46	0	3	50	1.19
29628817--29628916	33	3.0	33	86	0	137	31	35	26	8	1.85
29628898--29629055	42	3.8	42	87	0	217	36	32	21	9	1.86
29630247--29630286	15	2.5	17	76	15	50	35	2	10	52	1.48
29646171--29646219	20	2.7	18	77	22	57	51	4	2	42	1.32
29647889--29647920	15	2.1	15	94	0	55	68	9	6	15	1.36
29652657--29652726	26	2.7	26	71	2	61	17	27	21	34	1.95
29655636--29655690	22	2.5	24	80	14	64	63	5	1	29	1.27
29657751--29657819	24	2.9	23	76	8	59	34	4	1	59	1.26
29667867--29667892	2	13.0	2	100	0	52	50	0	0	50	1.00
29674162--29674325	30	5.4	30	68	17	90	31	20	6	41	1.77
29674821--29674874	7	8.1	7	78	15	53	70	0	29	0	0.88
29674821--29674874	11	5.1	12	75	22	50	70	0	29	0	0.88
29674837--29674888	25	2.1	24	86	10	70	75	0	25	0	0.81
29674852--29674897	14	3.6	14	80	13	55	76	0	23	0	0.79
29674837--29674909	8	8.6	8	74	15	58	75	0	23	1	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29675021--29675076	23	2.3	23	81	6	67	60	14	23	1	1.43
29675186--29675238	7	7.7	7	83	8	65	84	0	15	0	0.61
29675186--29675239	10	5.8	9	81	14	65	83	0	16	0	0.65
29675186--29675238	17	3.2	16	84	7	70	84	0	15	0	0.61
29675556--29675591	19	1.9	18	88	5	54	30	8	13	47	1.73
29675796--29676061	17	15.3	16	71	17	176	30	14	10	44	1.78
29675796--29676013	18	12.5	17	78	15	214	30	14	9	44	1.77
29675796--29676061	35	7.6	35	76	12	212	30	14	10	44	1.78
29675796--29676061	53	5.1	51	78	13	233	30	14	10	44	1.78
29687802--29688486	75	9.0	75	84	6	754	29	17	20	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