genome.fa.s5.2.7.7.80.10.50.1000.17.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   

This is table  17  of  208  ( 24913 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)
5108830--5108871	21	2.0	21	85	0	57	59	2	4	33	1.31
5108838--5108879	21	2.0	21	86	9	59	54	2	4	38	1.34
5110642--5110790	40	3.8	40	82	5	178	32	21	22	23	1.98
5111422--5111695	7	38.7	7	70	7	88	21	1	32	44	1.61
5111547--5111619	23	3.3	22	78	14	78	24	2	38	34	1.70
5112183--5112249	23	2.9	24	76	14	77	19	35	1	43	1.60
5112183--5112258	23	3.3	23	75	14	75	21	35	1	42	1.61
5112348--5112422	22	3.3	22	72	17	64	18	36	2	42	1.65
5112164--5112490	164	2.0	165	89	1	496	18	37	9	34	1.84
5114104--5114186	21	4.3	20	70	22	70	45	16	0	37	1.48
5114134--5114376	52	4.6	52	81	13	248	46	18	1	33	1.57
5114111--5114422	61	5.6	52	81	10	286	46	17	1	34	1.57
5114097--5114422	9	36.8	9	71	14	155	46	17	1	34	1.56
5114111--5114422	112	2.8	107	81	12	360	46	17	1	34	1.57
5114320--5114357	17	2.2	17	86	9	51	55	7	0	36	1.29
5116130--5116155	12	2.2	12	100	0	52	34	7	26	30	1.85
5118763--5118802	16	2.5	16	91	0	62	47	2	7	42	1.45
5118875--5118918	9	5.1	9	83	10	65	29	0	13	56	1.38
5118872--5118909	16	2.4	16	90	0	58	31	0	13	55	1.38
5120244--5120300	29	2.0	29	90	6	91	56	5	0	38	1.22
5121374--5121402	13	2.1	14	93	6	51	37	0	6	55	1.27
5122175--5122305	43	3.2	42	77	12	146	25	16	27	31	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5122214--5122289	38	2.0	38	86	0	107	26	15	27	30	1.96
5127812--5127867	29	1.9	29	88	0	85	33	14	7	44	1.72
5129444--5129492	12	4.3	12	72	15	50	22	12	42	22	1.86
5129603--5129682	6	13.8	6	79	7	67	28	11	38	21	1.88
5129810--5129844	18	1.9	18	88	0	52	28	5	42	22	1.76
5134605--5134645	18	2.3	18	87	8	57	34	2	2	60	1.23
5137827--5137887	20	3.0	20	70	15	54	68	3	1	26	1.14
5139260--5139304	23	2.0	23	90	0	72	53	28	2	15	1.54
5139262--5139304	12	3.7	12	81	6	52	51	30	2	16	1.57
5145651--5145756	30	3.5	29	75	10	88	22	2	50	23	1.62
5145671--5145960	78	3.7	78	93	1	458	25	4	51	18	1.65
5145905--5145990	30	2.7	30	76	10	82	24	4	51	19	1.66
5146001--5146041	18	2.3	18	86	0	55	26	2	53	17	1.56
5146076--5146140	24	2.7	24	73	7	78	15	1	55	27	1.49
5146642--5146691	21	2.3	23	82	6	59	14	12	2	72	1.22
5147020--5147086	31	2.2	29	82	15	75	22	5	7	64	1.42
5153675--5153717	18	2.4	18	88	7	61	53	0	0	46	1.00
5155603--5155728	63	2.1	59	84	11	157	20	11	11	57	1.64
5157192--5157251	28	2.1	28	84	6	77	60	8	0	31	1.27
5157262--5157295	17	2.0	17	88	0	50	35	0	5	58	1.22
5168601--5168638	19	1.9	20	84	10	51	42	7	2	47	1.46
5169119--5169203	40	2.1	41	93	2	145	5	15	17	61	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5171056--5171122	34	1.9	35	87	3	100	44	14	8	31	1.76
5175416--5175468	24	2.2	23	83	6	61	43	22	0	33	1.54
5177937--5177979	18	2.4	18	84	7	52	41	41	2	13	1.57
5178068--5178126	9	6.6	9	90	0	82	25	10	23	40	1.86
5178067--5178126	18	3.3	18	85	0	93	25	10	23	41	1.85
5178067--5178126	27	2.2	27	93	0	102	25	10	23	41	1.85
5178193--5178247	28	2.0	28	88	0	83	32	7	14	45	1.72
5182455--5182512	27	2.1	27	84	12	75	46	0	6	46	1.29
5199467--5199526	26	2.3	26	97	2	113	63	0	3	33	1.11
5200761--5200816	3	18.7	3	88	0	85	37	0	0	62	0.95
5200761--5200816	18	3.1	18	94	0	94	37	0	0	62	0.95
5204380--5204429	21	2.4	21	82	0	64	38	18	42	2	1.61
5204801--5204901	42	2.4	42	96	0	184	30	19	22	26	1.98
5204830--5205075	42	5.8	42	87	0	330	24	21	21	32	1.98
5210380--5210404	8	3.1	8	100	0	50	24	24	0	52	1.48
5211962--5212050	13	6.8	13	89	0	133	24	11	24	39	1.88
5211962--5212046	39	2.2	39	97	0	161	23	11	23	41	1.87
5213207--5213251	21	2.1	21	100	0	90	40	24	13	22	1.90
5216577--5216632	3	18.7	3	100	0	112	32	0	0	67	0.91
5216837--5216882	24	1.9	24	86	8	67	43	4	2	50	1.34
5218429--5218463	16	2.2	16	94	0	61	17	17	20	45	1.85
5222936--5223334	45	8.9	45	87	0	555	30	16	22	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5225169--5225215	3	15.7	3	100	0	94	31	0	0	68	0.90
5225419--5225464	24	1.9	24	86	8	67	43	4	2	50	1.34
5226169--5226232	18	3.4	18	76	19	76	32	3	0	64	1.10
5226186--5226281	29	3.2	30	76	8	90	28	4	0	67	1.09
5226167--5226288	39	3.1	38	86	8	142	29	3	0	67	1.07
5226167--5226288	9	12.6	9	66	20	52	29	3	0	67	1.07
5226251--5226398	11	13.8	11	73	22	79	41	2	0	56	1.11
5226303--5226413	40	2.7	39	82	13	118	43	1	0	54	1.10
5226297--5226416	49	2.4	48	75	20	131	44	1	0	54	1.10
5226682--5226721	20	2.0	20	90	0	62	27	10	12	50	1.72
5226667--5226733	34	1.9	35	84	3	91	34	8	10	46	1.70
5231373--5231415	9	4.6	9	85	8	50	25	0	0	74	0.82
5231372--5231415	19	2.2	20	88	4	63	25	0	0	75	0.81
5233218--5233277	32	1.9	33	86	10	90	43	0	0	56	0.99
5235483--5235553	30	2.4	29	83	6	81	33	8	2	54	1.45
5235722--5235760	19	2.1	19	85	4	53	35	7	0	56	1.28
5235915--5235973	19	3.2	19	80	4	84	38	11	0	49	1.40
5235970--5236016	18	2.6	19	83	6	53	53	0	10	36	1.36
5235985--5236025	19	2.1	19	86	4	55	53	0	9	36	1.34
5236235--5236305	37	1.9	37	97	0	133	49	0	9	40	1.36
5236235--5236309	18	4.1	18	76	6	71	52	0	9	38	1.34
5236241--5236309	19	3.7	19	78	5	88	52	0	8	39	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5236525--5236567	16	2.9	14	74	12	50	25	0	6	67	1.15
5257373--5257402	12	2.5	12	100	0	60	40	6	0	53	1.27
5257364--5257443	20	4.0	21	71	19	80	35	3	0	61	1.14
5257406--5257450	21	2.2	20	84	4	54	35	2	2	60	1.22
5259109--5259153	18	2.5	18	85	7	56	31	11	24	33	1.90
5262494--5262533	20	2.0	20	85	0	53	5	2	32	60	1.32
5263233--5263349	56	2.1	56	100	0	234	48	5	1	44	1.35
5263264--5263366	31	3.5	31	67	20	87	50	2	1	44	1.28
5265186--5265237	26	2.0	26	85	3	70	26	0	3	69	1.06
5272551--5272631	22	3.7	22	80	9	94	22	18	48	11	1.79
5276169--5276208	20	2.0	20	90	0	62	72	12	5	10	1.26
5279174--5279211	6	6.3	6	93	0	58	50	18	5	26	1.68
5279163--5279215	18	2.9	18	85	0	70	47	15	11	26	1.79
5279163--5279215	12	4.4	12	85	0	61	47	15	11	26	1.79
5287297--5287373	31	2.5	31	87	4	102	58	3	6	31	1.42
5287586--5287658	37	2.0	37	89	5	112	60	2	6	30	1.37
5287738--5287767	10	2.9	10	95	5	51	53	0	0	46	1.00
5288270--5288327	18	3.3	17	80	11	55	32	0	5	62	1.18
5290242--5290266	2	12.5	2	100	0	50	48	0	0	52	1.00
5303662--5303848	60	3.2	60	87	4	290	20	20	18	39	1.93
5303674--5303847	57	3.0	57	89	2	267	18	21	19	40	1.91
5305559--5305600	20	2.2	20	83	12	52	21	0	9	69	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5318038--5318062	10	2.5	10	100	0	50	24	8	0	68	1.16
5318363--5318406	23	1.9	22	82	17	54	36	25	0	38	1.56
5319045--5319093	2	24.5	2	100	0	98	51	0	0	48	1.00
5319579--5319724	41	3.6	40	77	12	138	28	28	19	23	1.99
5319579--5319734	82	1.9	82	82	10	194	28	26	19	24	1.99
5321609--5321798	51	3.7	51	76	5	188	31	28	16	23	1.96
5321607--5321794	101	1.9	101	86	3	261	31	27	16	24	1.96
5325090--5325134	18	2.4	19	81	3	56	35	0	4	60	1.17
5325239--5325355	62	1.9	62	82	3	146	39	3	0	56	1.22
5325277--5325342	28	2.5	24	79	13	69	36	3	1	59	1.22

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   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208