genome.fa.s1.2.7.7.80.10.50.1000.18.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  18  of  187  ( 22383 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)
6161958--6161982	7	3.6	7	100	0	50	56	16	0	28	1.41
6163080--6163109	15	2.1	15	93	6	53	76	6	0	16	0.99
6163099--6163154	28	2.0	29	92	3	96	53	5	1	39	1.34
6163151--6163227	11	7.2	10	87	10	100	41	0	31	27	1.56
6165335--6165465	60	2.2	59	82	8	149	38	11	16	32	1.85
6165939--6166244	153	2.0	153	99	0	603	38	9	10	41	1.71
6171272--6171306	2	17.5	2	100	0	70	51	0	0	48	1.00
6172913--6172954	3	14.0	3	100	0	84	66	0	0	33	0.92
6179308--6181412	265	8.0	263	77	8	1474	37	25	13	23	1.92
6179486--6180906	523	2.7	523	84	6	1755	38	25	12	23	1.90
6179316--6180861	788	2.0	781	79	6	1705	37	25	13	23	1.91
6180538--6181413	272	3.2	272	79	8	787	37	24	13	23	1.92
6183842--6183912	19	3.6	19	71	17	56	38	1	2	57	1.22
6183901--6183957	19	3.1	19	73	12	55	22	0	3	73	0.98
6183899--6183980	27	3.0	28	76	15	82	26	0	4	68	1.10
6183920--6183986	36	1.9	34	85	11	91	23	0	5	70	1.09
6195398--6195430	8	4.1	8	96	0	57	39	33	15	12	1.84
6196300--6197142	254	3.2	253	83	8	873	46	14	13	25	1.82
6196518--6197142	134	4.6	137	85	5	793	46	14	13	25	1.81
6208867--6208914	16	2.9	17	78	6	62	37	0	10	52	1.36
6209104--6209177	29	2.5	29	82	4	85	25	14	13	45	1.82
6220719--6220761	23	1.9	23	85	4	61	27	2	2	67	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6229095--6229647	9	66.0	9	66	17	244	32	2	18	45	1.64
6229117--6229587	16	28.8	16	67	16	125	33	2	18	45	1.63
6229155--6229306	25	6.1	25	79	6	139	33	1	19	45	1.59
6229155--6229531	50	7.7	50	74	11	291	34	2	18	45	1.62
6229153--6229648	75	6.5	75	78	12	276	33	2	18	45	1.63
6229131--6229417	116	2.5	116	94	2	495	33	2	18	46	1.61
6229268--6229531	25	10.6	25	78	7	243	34	2	17	45	1.63
6229328--6229647	25	12.7	25	70	10	81	32	3	18	45	1.65
6234326--6234369	19	2.3	19	92	0	70	15	2	2	79	0.93
6235702--6235940	41	5.8	41	85	2	286	31	26	21	20	1.98
6235702--6235937	82	2.9	81	85	3	321	32	25	21	20	1.98
6235702--6235936	123	1.9	123	86	3	339	32	25	21	20	1.97
6236638--6236754	60	1.9	62	82	5	148	36	13	4	45	1.64
6236806--6236866	21	2.7	22	75	12	61	54	4	3	37	1.39
6237954--6238013	31	1.9	31	86	6	86	36	11	8	43	1.71
6250917--6250962	14	3.3	14	76	17	51	34	4	8	52	1.52
6257720--6257745	7	3.7	7	100	0	52	30	38	15	15	1.88
6265526--6265595	31	2.2	33	82	12	83	34	15	31	18	1.92
6269657--6269887	46	5.0	46	93	2	374	41	10	20	26	1.85
6273273--6273343	30	2.4	30	95	0	124	7	26	21	45	1.77
6273273--6273360	30	2.9	30	86	6	99	5	28	21	44	1.75
6274097--6274135	4	9.8	4	100	0	78	51	23	0	25	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6274251--6274388	43	3.2	43	63	19	106	31	13	14	40	1.85
6274245--6274489	86	2.9	86	95	0	429	32	13	13	40	1.84
6277365--6277449	43	2.0	43	90	0	134	28	20	7	44	1.77
6279062--6279109	18	2.6	19	74	9	55	52	0	2	45	1.12
6282458--6282511	20	2.7	21	77	13	60	55	3	0	40	1.17
6293123--6293166	18	2.4	18	92	0	70	15	2	40	40	1.60
6293566--6293634	19	3.6	19	76	7	77	50	5	31	11	1.62
6294433--6294546	23	5.0	23	75	14	94	32	5	4	57	1.40
6294407--6294546	47	3.1	45	75	7	140	32	5	5	56	1.45
6295802--6295839	19	2.0	19	85	10	51	71	2	0	26	1.00
6296788--6296813	6	4.3	6	100	0	52	30	50	0	19	1.48
6299497--6299535	13	2.9	13	82	17	53	82	0	15	2	0.79
6299497--6299535	6	6.0	6	88	11	51	82	0	15	2	0.79
6300627--6300657	16	1.9	16	100	0	62	6	41	25	25	1.79
6304230--6304292	3	21.0	3	96	0	117	31	0	1	66	1.01
6304433--6304463	13	2.4	13	88	0	53	32	0	3	64	1.09
6304919--6305156	110	2.2	109	92	3	388	33	16	17	32	1.93
6306673--6306716	19	2.3	20	84	7	56	27	20	11	40	1.86
6309083--6309114	16	1.9	16	93	6	55	81	0	18	0	0.70
6309084--6309130	6	8.0	6	79	11	53	80	0	17	2	0.80
6311851--6311900	25	2.0	25	84	0	64	36	20	18	26	1.95
6311976--6312025	25	2.0	25	84	0	64	36	20	18	26	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6312102--6312151	25	2.0	25	84	0	64	36	20	18	26	1.95
6311601--6312239	125	5.1	125	97	0	1179	35	20	18	25	1.95
6311601--6312239	251	2.6	250	96	0	1179	35	20	18	25	1.95
6313654--6313728	3	25.0	3	97	0	141	32	0	1	66	1.00
6313870--6313900	13	2.4	13	88	0	53	32	0	3	64	1.09
6314354--6314648	110	2.7	109	92	2	477	30	16	20	32	1.95
6317368--6317448	24	3.4	24	91	3	137	22	18	20	38	1.94
6317458--6317512	25	2.2	25	77	6	58	18	25	25	30	1.98
6320180--6320356	41	4.3	43	81	10	185	28	18	27	25	1.98
6322253--6322345	43	2.1	44	80	9	102	50	9	4	35	1.55
6325322--6325414	31	3.0	31	83	0	123	37	11	8	41	1.73
6342143--6342237	47	2.0	47	87	4	138	31	17	4	46	1.68
6342833--6343043	105	2.0	105	99	0	413	46	14	7	32	1.71
6346529--6346631	51	2.0	51	100	0	206	33	9	27	30	1.89
6349559--6349644	45	1.9	45	90	0	136	36	23	13	26	1.93
6349646--6349837	50	3.9	48	79	6	195	30	28	17	24	1.97
6349653--6349836	100	1.8	100	88	3	280	30	27	16	24	1.97
6349981--6350017	9	4.1	9	92	0	65	45	13	10	29	1.77
6351105--6351130	5	5.2	5	100	0	52	19	19	19	42	1.90
6355771--6355812	15	2.8	16	82	10	52	4	7	14	73	1.21
6356522--6356551	2	15.0	2	92	0	51	50	3	0	46	1.18
6357750--6357835	40	2.2	40	85	8	113	50	6	2	40	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6357936--6357991	13	4.6	12	77	16	53	46	0	1	51	1.11
6358085--6358121	19	1.9	19	88	0	56	35	0	0	64	0.94
6364740--6364788	25	2.0	26	84	8	66	20	12	0	67	1.22
6377899--6378005	24	4.5	24	86	5	139	39	21	23	15	1.92
6378836--6378867	12	2.6	13	85	14	50	40	25	0	34	1.56
6379013--6379052	12	3.0	14	82	17	50	2	22	0	75	0.93
6379028--6379052	4	6.2	4	100	0	50	0	24	0	76	0.80
6379048--6379073	11	2.4	11	100	0	52	0	42	7	50	1.31
6382138--6382189	19	2.9	17	71	20	52	63	0	0	36	0.95
6382107--6382195	33	2.8	33	74	19	80	53	0	1	44	1.07
6387484--6387546	21	3.0	21	73	0	72	39	17	25	17	1.91
6387461--6387590	42	3.1	42	82	2	145	43	16	21	18	1.88
6389904--6389947	23	2.0	23	86	4	63	27	13	2	56	1.49
6390620--6390663	21	2.1	21	86	0	61	34	9	20	36	1.84
6392467--6392503	9	4.1	9	85	0	56	29	8	13	48	1.71
6392601--6392627	9	3.0	9	100	0	54	11	11	11	66	1.45
6392905--6392974	29	2.3	29	83	9	79	22	14	15	47	1.82
6393989--6394045	23	2.5	23	85	5	71	15	3	5	75	1.12
6399578--6399651	31	2.4	31	76	0	76	25	24	24	25	2.00
6399540--6399710	89	1.9	90	80	1	200	35	21	21	22	1.96
6406639--6406673	16	2.1	17	89	5	54	42	8	0	48	1.33
6415552--6415589	19	2.0	19	85	10	51	34	34	10	21	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6427913--6428011	49	2.0	49	92	3	164	37	22	15	25	1.93
6429811--6430058	121	2.0	121	98	0	478	32	27	18	20	1.97
6444874--6444904	3	10.3	3	100	0	62	35	32	0	32	1.58
6445470--6445621	76	2.0	76	100	0	304	38	19	14	27	1.91
6450081--6450166	43	2.0	43	100	0	172	39	13	16	30	1.87
6451405--6451439	16	2.2	16	90	10	54	57	0	0	42	0.99
6451950--6452514	125	4.5	126	84	2	726	30	18	21	29	1.97
6451950--6452514	251	2.3	250	90	0	889	30	18	21	29	1.97
6454951--6455012	28	2.3	27	81	10	74	43	6	0	50	1.28
6454961--6455018	28	2.1	28	93	0	98	37	8	0	53	1.32

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