genome.fa.s6.2.7.7.80.10.50.1000.19.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  19  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)
5088119--5088175	29	1.9	30	85	3	80	31	22	7	38	1.81
5089509--5089548	19	2.1	19	90	9	64	15	15	5	65	1.44
5090503--5090544	7	6.0	7	81	18	52	69	0	16	14	1.20
5090503--5090544	21	2.0	21	86	9	59	69	0	16	14	1.20
5091606--5091650	22	2.0	23	86	4	65	35	20	4	40	1.72
5091839--5092612	89	8.7	89	91	1	1221	31	17	23	27	1.97
5093225--5093281	17	3.4	17	77	0	60	15	50	14	19	1.77
5094431--5094525	18	5.3	19	70	22	71	29	8	0	62	1.25
5094444--5094518	14	5.5	14	68	17	50	32	6	0	61	1.22
5094425--5094539	54	2.1	54	96	0	212	28	6	0	64	1.19
5094444--5094536	26	3.5	26	64	14	64	32	6	0	61	1.21
5094446--5094559	54	2.1	54	81	3	131	35	7	0	56	1.35
5095534--5095582	19	2.6	19	83	3	55	28	4	2	65	1.22
5096916--5096949	16	2.1	16	89	10	52	58	2	2	35	1.28
5096994--5097035	18	2.4	18	80	15	52	38	2	2	57	1.25
5098269--5098558	144	2.0	144	91	1	474	27	20	18	34	1.96
5101993--5102667	46	14.0	47	80	7	599	29	18	24	28	1.98
5102035--5102654	97	6.4	97	88	1	756	28	18	24	28	1.98
5101993--5102654	148	4.6	139	81	6	653	28	18	24	28	1.98
5102689--5102852	44	3.7	44	76	3	114	29	21	22	25	1.99
5109432--5109472	18	2.2	18	86	8	55	78	0	21	0	0.76
5114670--5115242	46	11.9	46	72	9	374	30	18	22	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5114641--5115233	97	6.1	97	84	1	733	30	17	22	29	1.97
5115482--5115821	46	7.2	45	76	9	284	29	17	24	28	1.98
5115452--5115821	143	2.6	144	77	10	382	28	17	23	30	1.97
5115528--5115800	97	2.8	97	84	1	359	28	17	25	29	1.97
5116072--5116168	46	2.1	46	84	3	124	32	16	21	28	1.95
5116072--5125540	51	195.0	46	69	11	2740	30	17	22	28	1.96
5116043--5117491	143	10.1	142	71	14	491	29	17	23	29	1.97
5116165--5117460	46	26.9	51	72	12	676	29	17	23	28	1.97
5115248--5116372	591	1.9	591	87	1	1639	30	16	24	29	1.96
5116119--5116624	188	2.7	189	81	5	567	30	16	23	29	1.96
5116056--5124993	97	92.0	96	72	9	2775	30	17	22	28	1.96
5117600--5125540	148	54.4	148	72	9	3686	30	17	22	28	1.97
5118903--5119149	46	5.3	45	76	11	160	30	18	21	29	1.97
5121146--5121314	90	1.9	90	87	2	250	28	18	23	28	1.98
5121414--5121922	240	2.1	240	82	3	603	31	18	21	28	1.97
5117711--5125137	245	30.5	246	71	10	2027	30	17	22	28	1.97
5123289--5123457	90	1.9	90	85	2	232	29	18	22	28	1.98
5124824--5125139	143	2.2	142	83	8	419	31	15	22	30	1.95
5124867--5125542	97	7.0	97	76	5	584	31	16	22	29	1.96
5124235--5125527	194	6.7	193	75	9	608	31	17	21	29	1.96
5125569--5125743	44	4.0	44	85	3	226	32	26	19	22	1.97
5125993--5126035	17	2.5	17	77	7	52	67	11	2	18	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5126620--5127623	97	10.4	97	84	0	1175	29	17	23	28	1.97
5127658--5127837	44	4.1	44	77	5	193	30	21	21	26	1.98
5129477--5129533	27	2.1	28	83	3	71	21	7	15	56	1.63
5133320--5133355	17	2.1	17	89	5	54	19	2	11	66	1.35
5137659--5137856	94	2.1	94	84	3	274	30	16	20	32	1.95
5138073--5138840	89	8.6	89	86	1	1029	23	22	24	29	1.99
5140094--5140134	5	8.4	5	84	15	59	0	19	0	80	0.71
5140092--5140147	24	2.3	23	79	11	58	5	17	1	75	1.09
5146166--5146469	144	2.1	144	87	4	436	29	19	14	36	1.91
5156544--5156582	13	2.9	14	84	7	53	66	12	12	7	1.43
5157432--5157464	16	2.1	16	94	0	57	18	3	3	75	1.06
5158476--5158506	6	5.2	6	96	0	53	3	19	12	64	1.41
5159601--5159647	19	2.5	19	86	6	60	23	19	12	44	1.85
5162199--5162230	6	5.3	6	100	0	64	68	15	0	15	1.21
5162181--5162238	20	2.6	21	81	13	64	72	12	1	13	1.20
5163504--5164379	87	10.1	87	91	0	1261	30	22	22	24	1.99
5163651--5163787	43	3.2	43	64	17	111	29	24	21	24	1.99
5163781--5163917	42	3.2	43	67	13	109	26	21	24	27	1.99
5163911--5164047	43	3.2	43	64	17	111	29	25	21	23	1.99
5163997--5164134	43	3.2	43	64	20	106	29	23	21	25	1.99
5163504--5164379	434	2.0	434	92	0	1437	30	22	22	24	1.99
5163504--5164379	347	2.5	347	89	0	1322	30	22	22	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5165494--5165772	51	5.5	50	76	6	240	25	16	26	31	1.97
5165489--5165774	101	2.8	101	90	1	448	24	17	26	31	1.97
5165696--5165776	26	3.2	26	64	22	62	22	13	28	35	1.92
5165784--5165995	43	5.0	43	80	9	265	23	18	24	33	1.97
5165784--5165995	85	2.5	85	96	0	381	23	18	24	33	1.97
5168536--5168574	13	2.9	14	84	7	53	66	12	12	7	1.43
5170467--5170497	6	5.2	6	96	0	53	3	19	12	64	1.41
5171758--5171954	107	1.8	108	90	4	319	38	19	14	27	1.91
5172963--5173009	15	3.2	15	84	3	51	70	0	2	27	0.99
5175400--5175465	20	3.2	21	79	12	84	36	0	0	63	0.95
5175401--5175457	9	5.9	9	80	15	69	36	0	0	63	0.95
5175407--5175465	10	5.6	11	71	17	54	35	0	0	64	0.94
5175401--5175482	30	2.8	29	78	9	76	37	0	0	62	0.96
5183624--5183653	15	2.0	15	100	0	60	26	6	40	26	1.81
5185603--5185632	11	2.6	11	94	5	51	10	0	0	90	0.47
5187081--5187587	144	3.5	144	95	0	915	28	20	17	34	1.95
5187659--5187969	144	2.2	144	95	1	561	30	20	14	35	1.92
5195440--5195540	27	3.7	27	79	10	82	58	1	4	34	1.31
5195406--5195507	27	3.6	27	76	19	93	59	0	4	34	1.25
5205378--5205414	17	2.1	18	95	5	67	27	10	2	59	1.44
5205513--5205590	27	2.9	27	86	0	111	28	25	30	15	1.96
5205675--5205714	11	3.7	11	86	6	64	70	0	30	0	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5205674--5205712	21	1.9	20	94	5	69	69	0	30	0	0.89
5205827--5205859	15	2.2	15	94	0	57	24	0	12	63	1.28
5206729--5206766	18	2.1	18	95	0	67	34	7	47	10	1.67
5213299--5213406	22	5.0	22	68	22	68	0	29	0	70	0.88
5213280--5213423	29	5.2	29	70	15	74	0	31	0	68	0.90
5213304--5213489	39	4.7	42	79	16	202	0	31	0	67	0.95
5213300--5213475	81	2.2	79	88	9	252	0	30	0	69	0.93
5213336--5213480	4	35.0	4	76	18	104	0	30	0	68	0.94
5213618--5213681	24	2.5	25	90	10	94	46	0	12	40	1.42
5219038--5220188	144	8.0	144	94	0	1779	31	16	24	27	1.96
5222869--5222904	18	2.0	18	100	0	72	44	5	22	27	1.75
5223227--5223303	29	2.6	29	83	4	91	48	14	12	24	1.79
5223427--5223459	17	2.0	17	94	5	59	45	36	6	12	1.66
5227946--5227995	3	15.3	3	80	15	55	4	34	2	60	1.27
5229850--5229890	6	7.0	6	83	5	57	70	0	0	29	0.87
5229849--5229890	17	2.4	17	84	4	57	71	0	0	28	0.86
5230990--5231070	25	3.2	25	78	13	76	50	0	8	40	1.33
5231331--5231398	3	22.7	3	100	0	136	66	0	0	33	0.92
5235199--5235355	56	2.8	56	88	0	233	47	15	6	31	1.70
5237369--5237440	29	2.4	29	86	6	92	51	0	2	45	1.15
5238600--5238643	21	2.1	21	87	8	63	40	15	6	36	1.74
5250589--5250631	20	2.3	18	88	8	59	76	4	0	18	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5252207--5252255	9	5.3	9	86	11	55	75	0	6	18	1.00
5252212--5252277	30	2.2	29	83	2	78	74	1	6	18	1.10
5253304--5253445	64	2.2	64	82	7	164	19	28	23	28	1.98
5253449--5253673	76	3.0	76	96	1	411	44	8	8	38	1.66
5266336--5266369	17	2.0	17	88	0	50	29	5	8	55	1.54
5266370--5266412	22	2.0	22	85	0	59	37	4	2	55	1.33
5266525--5266579	24	2.2	24	83	3	74	41	5	1	50	1.36
5269810--5269846	7	5.1	7	93	3	56	10	16	2	70	1.27
5273117--5273168	4	13.2	4	84	8	63	25	1	1	71	1.07
5277455--5277636	45	4.1	45	89	2	262	34	24	17	23	1.96

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