genome.fa.s4.2.7.7.80.10.50.1000.20.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: A04
Parameters: 2 7 7 80 10 50 1000
Length:  82679320

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   

This is table  20  of  255  ( 30512 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)
5348781--5348814	18	1.9	18	88	5	52	11	26	44	17	1.83
5353831--5353856	13	2.0	13	100	0	52	92	7	0	0	0.39
5353836--5353873	11	3.4	11	89	7	58	86	10	2	0	0.66
5353835--5353873	12	3.3	12	85	7	53	87	10	2	0	0.65
5353834--5353873	17	2.3	17	86	4	53	87	10	2	0	0.63
5354427--5354457	15	2.1	15	100	0	62	22	32	6	38	1.80
5357819--5357848	15	2.0	15	93	0	51	23	46	6	23	1.75
5358590--5358628	18	2.3	18	86	8	55	43	12	5	38	1.65
5358785--5358815	15	2.1	15	100	0	62	22	32	6	38	1.80
5365634--5365677	21	2.1	21	100	0	88	13	4	22	59	1.53
5369450--5369492	22	1.9	23	85	4	61	44	6	2	46	1.43
5369451--5369499	22	2.2	23	81	3	55	46	8	4	40	1.52
5374685--5374950	46	6.0	46	84	7	325	21	23	15	39	1.91
5374864--5374939	38	2.0	38	97	0	143	23	25	18	32	1.97
5376804--5376838	17	2.1	17	100	0	70	28	11	11	48	1.74
5377096--5377175	31	2.6	32	76	13	87	57	3	1	37	1.25
5380616--5380669	28	2.0	27	85	10	74	81	1	11	5	0.93
5380637--5380669	11	3.1	11	86	8	50	84	0	12	3	0.72
5384070--5384182	29	3.9	29	77	7	88	27	32	12	27	1.92
5384256--5384293	19	2.1	19	90	5	60	18	39	15	26	1.91
5384266--5384302	19	1.9	19	88	0	56	16	37	18	27	1.92
5385674--5385705	16	2.0	16	93	0	55	9	6	34	50	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5387412--5387452	18	2.3	19	87	8	59	60	12	4	21	1.50
5388986--5389029	6	7.2	6	82	5	52	31	13	13	40	1.84
5389542--5389618	31	2.5	31	89	0	118	15	37	28	18	1.91
5396032--5396105	33	2.3	33	80	2	87	41	10	20	27	1.85
5396089--5396169	33	2.5	33	83	2	92	33	17	23	25	1.96
5398450--5398486	14	2.6	15	83	12	51	67	0	5	27	1.12
5398731--5398766	17	2.1	18	89	5	56	33	0	0	66	0.92
5402941--5402982	22	1.9	22	95	0	75	61	4	2	30	1.29
5402998--5403133	25	5.6	25	71	13	95	55	2	5	36	1.39
5403101--5403140	20	2.1	19	90	4	62	67	0	0	32	0.91
5403103--5403136	14	2.4	14	85	0	50	64	0	0	35	0.94
5404761--5404798	19	2.0	19	94	0	67	26	23	10	39	1.87
5405988--5406104	58	2.0	58	98	0	225	13	29	14	41	1.84
5408553--5408596	23	2.0	22	86	4	61	40	2	15	40	1.60
5408625--5408677	25	2.1	26	86	10	74	58	7	1	32	1.37
5408642--5408683	22	1.9	22	90	0	66	64	7	0	28	1.20
5408694--5408754	15	4.1	14	72	19	52	57	1	4	36	1.30
5408702--5408825	23	5.2	25	75	10	100	54	3	6	35	1.42
5408700--5408825	48	2.7	48	75	7	123	54	3	6	35	1.42
5409108--5409146	16	2.4	16	91	0	60	46	28	5	20	1.72
5415327--5415351	2	12.5	2	100	0	50	48	0	0	52	1.00
5417792--5417825	3	11.3	3	100	0	68	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5419900--5419957	30	1.9	30	85	0	80	53	8	8	29	1.61
5419939--5419967	12	2.5	12	94	5	51	68	0	0	31	0.89
5419991--5420033	22	2.0	22	85	0	59	58	11	11	18	1.63
5419998--5420038	11	3.7	11	80	0	55	56	9	14	19	1.66
5427300--5427345	18	2.6	18	75	0	56	60	32	0	6	1.22
5431336--5431371	12	3.0	12	83	0	54	30	22	2	44	1.67
5439652--5439957	116	2.6	116	94	0	524	25	13	23	38	1.91
5439888--5440077	72	2.6	73	82	4	233	25	13	25	36	1.92
5440317--5440437	56	2.2	56	86	4	165	28	11	17	42	1.84
5440410--5440467	30	1.9	30	89	6	91	20	8	27	43	1.81
5443211--5443235	12	2.1	12	100	0	50	36	0	0	64	0.94
5444349--5444448	49	2.0	49	98	0	191	33	10	22	35	1.87
5448440--5448475	3	12.0	3	87	0	54	66	0	2	30	1.06
5448764--5448821	21	2.7	22	78	5	64	65	6	6	20	1.40
5449200--5449261	28	2.2	28	82	5	72	58	1	6	33	1.34
5460391--5460433	20	2.2	20	100	0	86	37	9	0	53	1.33
5460862--5461024	82	2.0	81	91	3	265	34	15	10	39	1.81
5462568--5462629	25	2.5	25	89	2	99	33	4	4	56	1.42
5466516--5466580	33	2.0	33	96	0	121	20	35	24	20	1.96
5468409--5468567	62	2.6	60	71	11	142	46	1	3	48	1.28
5470285--5470335	23	2.2	23	96	0	93	50	3	5	39	1.45
5471551--5471613	33	1.9	33	83	6	83	49	1	9	39	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5472150--5472214	26	2.5	26	90	2	96	4	6	20	69	1.28
5473073--5473766	72	9.5	72	90	3	1037	30	21	16	30	1.96
5473073--5473785	293	2.4	295	90	3	1102	31	21	16	30	1.95
5482063--5482098	12	3.0	12	95	0	63	41	5	25	27	1.77
5484615--5484673	22	2.8	21	90	10	93	5	5	20	69	1.27
5487006--5487032	14	1.9	14	100	0	54	0	70	0	29	0.88
5490596--5490665	31	2.3	31	85	5	88	47	5	5	41	1.51
5490799--5491082	143	2.0	143	88	2	428	42	14	11	31	1.81
5495315--5495354	21	1.9	21	94	0	71	37	27	15	20	1.92
5503487--5503564	40	2.0	40	92	5	131	14	11	34	39	1.82
5503489--5503582	40	2.4	39	84	8	120	12	10	38	38	1.78
5512219--5512269	17	3.0	17	80	8	59	41	5	1	50	1.37
5512778--5512869	47	2.0	47	97	0	175	41	13	4	41	1.63
5514993--5515033	21	2.0	21	90	0	64	60	4	0	34	1.18
5516545--5516579	18	1.9	18	94	0	61	60	2	0	37	1.12
5537414--5537443	15	2.0	15	93	0	51	90	0	10	0	0.47
5538338--5538373	17	2.1	17	94	0	63	30	8	25	36	1.85
5541945--5542051	27	4.0	27	93	2	171	37	11	25	26	1.89
5544591--5544656	6	11.2	6	96	3	125	81	0	0	18	0.68
5552301--5552422	42	2.9	42	86	7	124	23	34	9	31	1.88
5552543--5552643	42	2.4	44	78	9	120	21	40	10	26	1.86
5552585--5552703	54	2.2	54	84	0	166	21	36	13	28	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5552925--5552957	16	2.1	17	88	11	52	27	39	18	15	1.90
5557669--5557752	38	2.2	38	84	0	114	21	17	26	34	1.96
5576820--5576856	3	12.3	3	100	0	74	32	0	0	67	0.91
5576847--5577251	170	2.4	167	82	5	467	33	20	11	34	1.89
5587096--5587152	25	2.3	25	90	0	87	29	14	17	38	1.89
5587116--5587164	25	2.0	25	83	0	62	32	14	14	38	1.86
5587905--5587970	34	1.9	34	90	0	105	19	24	27	28	1.99
5591836--5591865	6	5.0	6	91	0	51	70	0	0	30	0.88
5599827--5599865	20	1.9	21	84	5	53	17	23	5	53	1.63
5604137--5604193	6	8.8	6	74	14	51	75	3	8	12	1.16
5605072--5605165	23	4.1	23	85	0	134	22	25	4	47	1.69
5609579--5609671	23	4.0	23	85	0	132	22	25	4	47	1.70
5614198--5614222	6	4.2	6	100	0	50	80	0	0	20	0.72
5631265--5631548	43	6.6	43	95	0	505	30	32	25	10	1.90
5631546--5631648	38	2.7	38	87	0	143	29	26	22	22	1.99
5635276--5635398	12	10.5	12	69	19	82	62	1	4	31	1.23
5635271--5635380	7	14.4	7	69	19	51	61	1	3	32	1.24
5635278--5635395	38	3.2	38	74	21	92	62	1	4	31	1.24
5635285--5635379	16	6.3	15	72	27	69	61	2	4	32	1.27
5635348--5635397	17	2.8	17	80	14	57	68	0	4	28	1.08
5635338--5635398	33	1.9	31	83	6	77	63	0	4	31	1.15
5635369--5635425	17	3.6	17	71	20	52	63	3	3	29	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5635475--5635519	24	1.9	24	82	13	58	51	0	4	44	1.21
5635503--5635553	20	2.7	18	84	9	57	74	0	1	23	0.92
5643758--5643859	51	2.0	52	84	9	138	37	17	16	28	1.92
5644231--5644392	82	2.0	81	86	1	225	22	25	9	41	1.85
5644696--5644943	103	2.4	103	82	7	297	32	17	21	28	1.96
5647957--5648167	76	2.8	76	84	6	266	55	2	14	27	1.51
5648157--5648262	48	2.2	47	78	6	124	62	1	10	25	1.38
5648243--5648332	22	4.2	21	70	9	65	63	0	8	27	1.24
5648291--5648327	17	2.2	18	85	9	51	64	0	5	29	1.15
5648197--5648328	44	2.9	44	77	5	131	62	0	8	28	1.30

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255