genome.fa.s11.2.7.7.80.10.50.1000.29.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   

This is table  29  of  210  ( 25152 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)
9336975--9337051	23	3.4	22	77	12	75	16	2	5	75	1.10
9337084--9337123	14	2.7	15	84	7	55	30	0	0	70	0.88
9337638--9337741	53	2.0	52	83	5	129	33	4	14	47	1.65
9338302--9338336	14	2.5	14	85	0	52	25	0	8	65	1.21
9339580--9339640	7	8.6	7	73	22	56	44	0	3	52	1.17
9339556--9339633	36	2.2	36	86	6	106	47	0	3	48	1.20
9339652--9339723	15	4.7	15	74	16	51	75	5	18	1	1.07
9339652--9339723	16	4.7	15	73	13	51	75	5	18	1	1.07
9339652--9339732	41	2.0	39	81	11	92	72	4	20	1	1.10
9343567--9343726	25	6.6	25	84	5	181	37	19	24	18	1.94
9344679--9344707	5	5.8	5	100	0	58	58	0	0	41	0.98
9348548--9348660	37	3.2	36	70	19	112	60	5	2	31	1.33
9348571--9348671	10	10.4	10	65	25	56	61	3	1	32	1.26
9348581--9348691	31	3.4	31	71	23	102	62	4	2	30	1.29
9348550--9348694	68	2.1	68	92	3	247	60	5	2	31	1.33
9355841--9355900	3	20.0	3	100	0	120	66	0	0	33	0.92
9356802--9356859	15	3.6	15	72	17	53	50	1	1	46	1.22
9357214--9357286	33	2.2	34	80	9	89	50	16	6	26	1.70
9361821--9361938	41	2.9	41	94	0	209	31	22	21	24	1.98
9364079--9364121	18	2.3	19	88	4	61	72	0	23	4	1.04
9372940--9373014	3	25.0	3	81	0	60	57	2	1	38	1.21
9372940--9373005	27	2.4	27	92	0	114	56	3	1	39	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9373762--9373806	5	9.2	5	90	4	74	60	2	0	37	1.09
9377159--9377592	41	10.6	41	93	0	679	29	20	27	21	1.98
9381414--9381468	25	2.2	24	87	3	74	27	29	12	30	1.93
9381431--9381511	25	3.3	25	77	5	76	23	23	22	30	1.99
9387643--9387667	8	3.1	8	100	0	50	64	0	0	36	0.94
9393315--9393350	2	18.0	2	100	0	72	50	0	0	50	1.00
9395129--9395212	38	2.2	37	87	8	116	53	3	7	35	1.46
9397204--9397258	18	3.1	18	94	0	92	29	14	14	41	1.85
9401068--9401092	7	3.6	7	100	0	50	76	0	0	24	0.80
9401554--9401619	32	2.1	32	97	0	123	24	10	15	50	1.75
9402981--9403039	31	1.9	31	93	6	102	27	13	27	32	1.94
9407593--9407671	30	2.7	29	80	7	88	56	7	7	27	1.54
9410891--9410928	7	5.4	7	96	0	67	28	42	10	18	1.83
9417320--9417347	11	2.5	11	100	0	56	35	35	17	10	1.85
9417905--9417977	31	2.4	30	81	4	74	45	16	20	17	1.86
9420922--9420975	25	2.2	25	93	0	90	46	22	9	22	1.80
9421400--9421441	17	2.5	17	88	0	57	21	16	28	33	1.95
9421434--9421479	17	2.6	18	79	10	58	34	19	17	28	1.94
9421417--9421474	17	3.3	17	79	13	64	29	17	20	32	1.95
9421468--9421500	17	1.9	17	93	0	57	21	18	30	30	1.97
9421540--9421611	23	3.2	23	82	2	83	36	15	15	33	1.89
9428376--9428436	20	3.1	18	88	6	59	24	13	16	45	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9428392--9428436	20	2.2	20	100	0	90	28	15	15	40	1.88
9431745--9431777	14	2.3	15	89	5	50	72	9	0	18	1.10
9432671--9432723	3	17.7	3	100	0	106	33	0	0	66	0.92
9433347--9433398	24	2.2	24	100	0	104	38	7	21	32	1.82
9437963--9438002	16	2.8	14	82	17	55	80	7	0	12	0.91
9437968--9438002	16	2.3	15	95	5	61	82	5	0	11	0.82
9438055--9438098	16	2.8	16	82	0	61	72	0	27	0	0.85
9438908--9438971	6	9.3	7	79	20	73	68	0	15	15	1.21
9438910--9438971	27	2.2	28	88	2	99	70	0	14	14	1.16
9438911--9438962	14	3.8	14	94	5	97	73	0	13	13	1.11
9440268--9440404	43	3.2	42	64	20	102	29	24	21	24	1.99
9440209--9440598	87	4.5	87	91	0	602	28	22	24	24	2.00
9440209--9440598	175	2.2	173	90	0	627	28	22	24	24	2.00
9442156--9442214	3	19.7	3	92	0	100	33	0	1	64	1.04
9450565--9450597	10	3.7	9	88	11	50	21	0	9	69	1.15
9456887--9457053	40	4.2	40	74	13	155	16	29	17	35	1.93
9456883--9457033	80	1.9	80	86	5	216	16	29	17	36	1.92
9456959--9457023	20	3.3	19	68	12	51	13	36	16	32	1.89
9457030--9457067	20	1.9	20	88	0	58	21	28	21	28	1.98
9472474--9472520	22	2.1	23	84	11	62	38	0	0	61	0.96
9472461--9472527	28	2.4	28	80	11	75	43	1	0	55	1.09
9472719--9472796	37	2.1	37	92	0	129	62	6	8	21	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9472952--9472991	20	2.0	20	90	0	62	27	10	12	50	1.72
9472937--9473003	34	1.9	35	90	3	109	31	8	13	46	1.74
9473857--9473909	19	3.0	17	78	10	61	35	9	18	35	1.84
9473881--9473925	23	2.0	23	91	4	74	37	4	17	40	1.70
9473891--9473935	23	2.0	23	86	4	65	33	4	15	46	1.66
9474315--9474343	15	1.9	15	100	0	58	27	0	6	65	1.18
9480337--9480420	35	2.4	35	83	0	105	30	14	23	30	1.94
9488644--9488676	17	1.9	18	88	11	52	39	12	0	48	1.40
9493214--9493246	17	2.0	16	94	5	57	30	21	6	42	1.77
9500138--9500166	4	7.2	4	100	0	58	48	0	24	27	1.51
9503420--9503452	16	2.1	16	94	0	57	15	0	12	72	1.12
9506467--9506730	85	3.1	86	84	1	343	32	17	19	30	1.95
9508919--9509048	43	3.0	43	72	12	122	21	20	26	31	1.98
9522158--9522301	69	2.1	69	93	0	243	29	25	8	37	1.85
9524743--9524807	30	2.1	31	91	8	107	38	15	3	43	1.62
9525967--9526010	20	2.1	21	87	4	63	15	6	9	68	1.38
9527374--9527406	17	1.9	17	93	0	57	21	15	18	45	1.85
9528944--9528984	20	2.0	20	100	0	82	4	24	4	65	1.32
9529928--9529973	2	23.5	2	86	4	67	47	2	2	47	1.26
9533502--9533544	22	2.0	22	86	4	61	34	0	11	53	1.37
9538235--9538326	33	2.8	33	83	1	121	45	10	9	33	1.72
9542171--9542348	67	2.6	67	80	5	180	43	14	13	28	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9542171--9542348	33	5.3	34	73	11	116	43	14	13	28	1.83
9542263--9542348	35	2.5	34	81	10	104	44	16	11	27	1.82
9547744--9547781	2	19.0	2	100	0	76	50	50	0	0	1.00
9547779--9547823	4	11.2	4	100	0	90	51	24	0	24	1.49
9548380--9548441	22	2.8	22	92	0	97	35	14	25	24	1.93
9561247--9561271	5	5.0	5	100	0	50	0	80	0	20	0.72
9564674--9564717	19	2.4	19	84	3	63	31	0	2	65	1.05
9564674--9564721	9	5.2	9	77	5	51	37	0	2	60	1.09
9585239--9585279	20	2.0	20	86	9	57	68	0	7	24	1.15
9587114--9587155	17	2.4	19	77	22	56	28	7	0	64	1.20
9588768--9588800	2	16.5	2	100	0	66	51	0	0	48	1.00
9589647--9589695	25	2.0	25	100	0	98	38	4	0	57	1.18
9599677--9599714	17	2.2	17	90	9	60	36	2	15	44	1.61
9600553--9600746	97	2.0	97	92	0	325	32	21	17	28	1.95
9604147--9604188	17	2.4	18	84	11	61	30	4	23	40	1.75
9605221--9605270	20	2.5	20	87	6	66	36	2	2	60	1.20
9605260--9605308	20	2.2	24	79	17	61	34	0	8	57	1.29
9605263--9605314	23	2.5	20	84	9	59	40	0	7	51	1.30
9606468--9606499	2	16.0	2	100	0	64	50	0	0	50	1.00
9612543--9612576	9	3.8	9	100	0	68	20	11	11	55	1.67
9624478--9624527	17	3.0	16	80	8	64	46	6	20	28	1.74
9628014--9628063	17	2.9	17	100	0	100	42	6	28	24	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9629555--9629627	38	1.9	38	100	0	146	56	8	2	32	1.43
9630975--9631000	11	2.4	11	100	0	52	65	0	7	26	1.20
9633095--9633182	41	2.1	41	100	0	176	35	18	15	30	1.92
9635143--9635239	21	4.6	21	71	5	79	46	18	21	13	1.83
9635151--9635300	42	3.6	42	80	3	149	45	17	22	15	1.85
9635172--9635322	21	7.2	21	73	0	104	43	17	23	15	1.87
9644845--9644905	7	8.7	7	100	0	122	27	0	14	57	1.38
9645806--9645861	21	2.7	21	83	5	69	30	41	17	10	1.84
9645821--9645865	21	2.1	21	91	0	72	26	37	24	11	1.89
9649623--9649722	37	2.6	38	74	6	94	29	29	19	23	1.98

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