genome.fa.s23.2.7.7.80.10.50.1000.18.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: At_chr5
Parameters: 2 7 7 80 10 50 1000
Length:  55438857

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   

This is table  18  of  167  ( 19959 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)
5347929--5348057	22	6.0	21	72	8	84	25	0	27	47	1.52
5347917--5348082	64	2.6	63	86	8	203	24	0	29	45	1.57
5348385--5348477	40	2.3	40	86	0	132	23	20	23	32	1.98
5353044--5353081	18	2.2	18	86	9	53	55	15	2	26	1.54
5353625--5353675	26	1.9	27	88	4	77	25	7	9	56	1.58
5354677--5354716	20	2.0	20	85	0	53	25	10	15	50	1.74
5355925--5355958	11	3.1	11	100	0	68	44	8	11	35	1.72
5356827--5356860	16	2.1	16	94	0	59	52	0	35	11	1.38
5359176--5359206	16	1.9	16	100	0	62	35	0	0	64	0.94
5365822--5365853	5	6.6	5	92	7	57	81	0	0	18	0.70
5365823--5365853	9	3.3	9	95	4	53	80	0	0	19	0.71
5373718--5373814	31	3.2	31	72	11	92	40	16	12	30	1.85
5378565--5378618	25	2.1	26	82	3	65	5	3	16	74	1.16
5380411--5380456	6	7.8	6	92	2	76	50	0	34	15	1.44
5385753--5385848	31	3.1	31	100	0	192	26	19	12	41	1.87
5389187--5389211	11	2.3	11	100	0	50	44	16	20	20	1.87
5394714--5394819	37	2.9	37	90	2	162	25	22	16	35	1.94
5394782--5394946	46	3.2	52	84	11	243	27	23	14	35	1.93
5402665--5402705	21	2.0	21	90	0	64	19	29	21	29	1.98
5405931--5405971	20	2.0	20	86	9	57	39	0	0	60	0.96
5405940--5405972	10	3.3	10	84	16	50	36	0	0	63	0.95
5406508--5406578	35	2.0	35	86	0	97	36	9	23	29	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5413168--5413437	3	91.3	3	71	9	180	28	7	1	62	1.33
5413197--5413224	11	2.5	11	100	0	56	28	7	0	64	1.20
5413233--5413306	32	2.3	32	88	4	105	25	8	1	64	1.29
5413306--5413330	13	1.9	13	100	0	50	36	8	0	56	1.29
5413367--5413412	13	3.6	13	82	8	51	28	8	0	63	1.24
5413252--5413403	32	4.7	32	71	11	105	28	7	1	63	1.29
5419251--5419310	28	2.2	26	77	11	66	26	26	11	35	1.91
5419265--5419336	28	2.6	28	88	0	99	29	27	12	30	1.93
5423624--5423905	141	2.0	143	90	2	453	31	20	21	26	1.98
5425677--5425984	3	101.3	3	72	9	205	27	7	1	62	1.33
5426305--5426614	3	102.3	3	71	9	184	27	7	2	62	1.34
5425421--5427326	630	3.0	630	96	2	3470	24	11	6	57	1.56
5426935--5427241	3	101.3	3	72	10	196	27	8	1	62	1.34
5427398--5427627	116	2.0	116	98	0	442	32	18	12	36	1.89
5429221--5430036	407	2.0	407	100	0	1632	36	15	11	37	1.82
5432125--5432186	30	2.1	30	87	0	88	25	3	11	59	1.46
5438801--5438840	7	5.7	7	90	0	53	40	7	27	25	1.82
5438762--5438874	58	1.9	58	92	0	190	33	15	23	28	1.94
5438831--5438914	37	2.3	37	89	0	132	30	16	19	33	1.94
5445062--5445099	19	2.0	19	94	0	67	36	13	36	13	1.83
5446274--5446434	44	3.5	44	83	11	214	33	15	21	29	1.94
5446331--5446434	51	2.0	51	94	0	181	35	12	21	30	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5449171--5449225	19	3.3	19	63	36	54	32	0	10	56	1.34
5449165--5449226	30	2.1	30	100	0	124	32	0	9	58	1.31
5449388--5449434	24	1.9	25	82	4	60	65	4	17	12	1.40
5450622--5450665	17	2.4	20	78	21	60	56	0	9	34	1.31
5451678--5451727	21	2.5	20	77	6	64	46	6	6	42	1.53
5452042--5452076	7	5.0	7	89	10	54	71	0	2	25	1.00
5454923--5454985	28	2.2	29	85	2	83	17	14	9	58	1.61
5455026--5455095	35	2.0	35	100	0	140	25	17	17	40	1.90
5457116--5457434	48	6.7	48	79	2	284	24	30	17	26	1.97
5457116--5457447	96	3.5	94	82	3	360	25	30	17	26	1.97
5466224--5466498	48	5.7	48	78	2	259	24	29	18	27	1.98
5466223--5466508	96	3.0	96	82	1	313	25	29	17	27	1.98
5466224--5466495	144	1.9	144	83	3	359	24	29	18	27	1.98
5467673--5467698	12	2.2	12	100	0	52	30	30	30	7	1.85
5469629--5469666	18	2.1	18	85	9	51	57	0	18	23	1.40
5470591--5470626	18	2.0	18	100	0	72	44	5	22	27	1.75
5473122--5473170	19	2.6	19	87	3	73	71	0	2	26	0.97
5473247--5473293	20	2.3	20	85	0	67	61	0	0	38	0.96
5473253--5473316	28	2.3	28	82	12	71	59	1	0	39	1.07
5473384--5473434	19	2.7	19	77	14	52	29	1	1	66	1.13
5473378--5473426	19	2.5	20	77	16	57	24	4	2	69	1.17
5473631--5473675	19	2.4	19	85	14	58	28	0	4	66	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5473632--5473675	20	2.3	19	84	11	54	27	0	4	68	1.09
5473675--5473726	27	2.0	27	85	11	72	53	0	0	46	1.00
5474003--5474055	27	2.0	27	88	0	79	56	1	15	26	1.49
5476476--5476502	12	2.2	12	100	0	54	51	0	7	40	1.30
5484152--5484218	25	2.7	26	76	6	84	22	20	20	35	1.96
5484152--5484233	25	3.3	25	70	11	69	21	25	18	34	1.96
5484185--5484240	25	2.2	25	78	6	60	23	28	17	30	1.97
5484152--5484265	50	2.3	49	81	1	120	22	24	19	33	1.97
5489157--5489190	5	6.8	5	100	0	68	61	0	0	38	0.96
5492904--5492947	13	3.2	13	80	20	54	22	4	0	72	1.02
5493417--5493453	18	2.2	18	85	9	51	45	5	0	48	1.25
5493658--5493699	22	1.9	22	85	0	57	14	11	14	59	1.61
5493666--5493723	22	2.6	22	83	0	62	20	6	8	63	1.45
5494442--5494474	3	11.0	3	100	0	66	33	0	0	66	0.92
5499181--5499227	18	2.6	18	100	0	94	31	25	10	31	1.90
5499285--5499392	22	4.8	22	82	10	137	32	8	21	37	1.83
5499285--5499407	47	2.7	46	78	10	144	31	9	20	38	1.85
5499659--5499747	18	5.1	18	71	14	69	26	32	16	23	1.96
5499698--5499781	34	2.5	34	84	3	98	26	25	21	27	1.99
5499701--5499795	34	2.8	34	80	6	86	25	24	24	26	2.00
5500130--5500174	14	3.1	14	84	6	63	31	4	24	40	1.75
5500582--5500644	17	3.8	16	82	4	72	33	6	14	46	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5500576--5500644	34	2.0	34	88	5	104	33	5	14	46	1.68
5502078--5502125	25	2.0	24	84	12	62	66	2	0	31	1.03
5502594--5502623	12	2.6	12	94	5	53	26	6	6	60	1.47
5517069--5517109	17	2.5	17	92	4	66	43	19	12	24	1.85
5518531--5518684	77	2.0	77	100	0	308	46	7	10	35	1.67
5520519--5520628	55	2.0	55	96	0	202	38	10	12	38	1.79
5520839--5520878	21	2.0	21	90	5	64	20	22	40	17	1.92
5522061--5522289	96	2.4	96	82	1	262	23	27	20	28	1.99
5522061--5522292	48	4.8	48	77	8	202	23	27	20	28	1.99
5525999--5526033	19	1.9	18	88	11	54	45	28	8	17	1.77
5537721--5537765	22	2.0	22	100	0	90	44	13	22	20	1.85
5541988--5542110	25	5.0	26	64	17	73	39	20	20	19	1.92
5544100--5544130	16	1.9	16	100	0	62	16	25	0	58	1.38
5550659--5550843	79	2.3	82	83	7	229	24	28	22	24	2.00
5550640--5550843	40	5.1	40	81	8	229	24	27	22	25	2.00
5555862--5555920	31	1.9	31	89	0	91	10	37	15	37	1.81
5565983--5566039	22	2.7	21	76	12	55	66	3	8	21	1.34
5570968--5571006	16	2.5	16	87	4	53	17	2	0	79	0.84
5587233--5587267	17	2.0	18	88	5	54	11	2	5	80	1.00
5588888--5588928	17	2.5	17	77	18	50	17	4	0	78	0.93
5589860--5590159	4	75.0	4	98	0	564	49	24	0	26	1.51
5591048--5591085	19	2.0	19	85	10	51	26	26	23	23	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5592676--5592737	28	2.3	28	81	10	76	22	20	9	46	1.80
5596388--5596478	44	2.1	44	91	0	146	48	9	12	29	1.73
5597754--5597780	13	2.1	13	100	0	54	22	0	33	44	1.53
5607814--5608387	287	2.0	287	100	0	1148	35	21	17	25	1.95
5611075--5611196	55	2.2	55	79	4	131	27	24	29	18	1.98
5622518--5622576	10	6.0	10	82	11	68	66	1	6	25	1.26
5627931--5627970	10	4.0	10	84	12	55	70	2	5	22	1.19
5627931--5627970	20	2.0	20	90	9	64	70	2	5	22	1.19
5630507--5630555	22	2.2	22	82	10	55	63	10	10	16	1.52
5631742--5631777	18	1.9	19	88	5	56	69	0	0	30	0.89

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