genome.fa.s9.2.7.7.80.10.50.1000.121.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   

This is table  121  of  226  ( 27023 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)
40956741--40956894	39	3.8	40	78	15	158	70	0	29	0	0.87
40956740--40956889	18	8.8	17	74	17	116	70	0	29	0	0.87
40963555--40963580	3	8.7	3	100	0	52	69	30	0	0	0.89
40963839--40963896	27	2.1	27	87	0	80	13	29	29	27	1.94
40963944--40964014	28	2.6	29	93	6	121	49	0	9	40	1.36
40966710--40966880	41	4.2	41	81	4	211	21	21	28	28	1.98
40966706--40966856	82	1.8	82	94	0	266	23	21	27	27	1.99
40967190--40967240	14	3.5	15	79	12	54	23	0	39	37	1.55
40967248--40967290	16	2.7	16	85	10	61	20	0	44	34	1.52
40967474--40967505	15	2.1	15	94	0	55	25	0	34	40	1.56
40970506--40970543	15	2.4	17	86	8	53	28	0	2	68	1.03
40971626--40971681	27	2.1	27	83	6	69	26	8	1	62	1.35
40974705--40974745	21	2.0	21	85	9	57	58	2	2	36	1.24
40975801--40975828	14	2.0	14	100	0	56	42	21	0	35	1.53
40977929--40978207	148	1.9	148	91	1	461	48	18	7	25	1.75
40985740--40985815	29	2.6	29	82	2	89	32	6	15	44	1.73
40986779--40986830	17	3.1	17	83	8	61	34	5	15	44	1.70
40987884--40987977	29	3.3	29	95	1	172	20	21	10	47	1.79
40998751--40998939	41	4.6	41	89	0	252	28	18	24	29	1.98
41011275--41011304	15	1.9	16	93	6	53	53	3	23	20	1.60
41012334--41012380	13	3.5	13	77	11	58	25	4	12	57	1.54
41012338--41012394	28	2.0	28	96	0	105	28	8	10	52	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41018573--41018601	12	2.4	12	100	0	58	34	27	10	27	1.89
41019828--41019873	23	2.0	23	100	0	92	30	26	4	39	1.75
41020370--41020458	21	4.2	21	69	0	61	40	16	26	15	1.89
41020370--41020505	42	3.2	42	82	2	139	43	16	23	16	1.87
41020433--41020500	21	3.2	21	70	0	64	47	17	20	14	1.83
41034838--41034926	29	3.2	27	70	10	74	40	21	22	15	1.91
41040098--41040146	20	2.3	21	89	6	73	61	0	2	36	1.08
41042935--41043106	75	2.3	74	82	5	202	28	23	24	23	2.00
41045016--41045046	16	1.9	16	93	0	53	41	0	3	54	1.16
41047828--41048069	129	1.9	128	83	2	315	34	14	27	24	1.93
41050722--41050859	56	2.5	56	80	4	145	31	27	18	22	1.97
41051754--41051800	17	2.7	17	77	9	51	36	17	10	36	1.84
41052449--41052546	36	2.7	36	91	0	160	19	20	18	41	1.90
41066121--41066162	21	2.0	21	86	13	61	26	16	19	38	1.92
41067935--41067986	25	2.1	24	85	3	68	44	1	1	51	1.23
41081029--41081079	23	2.2	23	89	0	75	43	17	7	31	1.78
41083798--41083823	13	2.0	13	100	0	52	23	23	15	38	1.92
41083285--41084323	524	2.0	524	95	0	1862	30	19	21	28	1.97
41084835--41084871	15	2.4	16	82	17	51	40	0	0	59	0.97
41091333--41091520	69	2.7	69	94	0	322	43	16	13	26	1.85
41091400--41091507	34	3.1	34	63	25	82	40	15	14	28	1.87
41092380--41092465	42	2.0	43	90	2	138	32	25	17	24	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41095036--41095131	28	3.4	27	75	11	77	34	22	22	19	1.97
41095457--41095544	27	3.3	27	81	0	104	19	13	20	46	1.83
41102817--41102871	28	2.0	28	88	0	83	32	16	25	25	1.96
41118474--41118573	36	2.9	34	74	14	96	43	20	13	24	1.86
41119326--41119416	42	2.1	43	85	2	121	28	23	17	30	1.97
41123728--41123766	10	3.8	10	82	3	51	58	10	0	30	1.31
41125642--41125696	25	2.2	25	77	6	58	18	9	7	65	1.44
41136234--41136272	20	2.0	20	90	10	62	56	5	23	15	1.59
41142747--41142774	12	2.3	12	100	0	56	17	17	7	57	1.62
41143063--41143260	50	3.9	49	83	5	198	22	32	19	25	1.98
41143821--41143878	27	2.1	27	100	0	116	37	13	13	34	1.85
41145686--41145752	21	3.3	21	77	8	59	49	7	23	19	1.74
41146244--41147822	790	2.0	792	90	2	2472	31	13	18	36	1.90
41154496--41154566	29	2.4	30	88	2	99	42	14	25	18	1.87
41156581--41156609	14	2.1	14	100	0	58	51	13	6	27	1.66
41160524--41160568	18	2.5	18	100	0	90	53	15	0	31	1.43
41161506--41161539	17	1.9	18	88	5	52	47	11	11	29	1.76
41165447--41165493	17	2.6	17	83	6	58	42	2	2	53	1.25
41165447--41165490	19	2.4	19	85	7	56	43	2	2	52	1.26
41167519--41167568	24	2.1	24	85	7	66	54	0	2	44	1.11
41170691--41170849	44	3.6	45	77	3	153	25	23	22	28	1.99
41171095--41171339	87	2.8	87	92	0	409	24	23	22	29	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41172608--41172679	12	6.1	12	67	15	51	9	5	5	79	1.06
41172603--41172676	29	2.5	29	78	8	78	10	4	6	78	1.07
41175873--41176064	98	2.0	98	90	0	303	36	23	10	29	1.89
41179479--41179570	40	2.7	30	69	27	85	57	6	7	28	1.51
41189412--41189460	25	2.0	25	83	0	62	30	18	14	36	1.90
41189794--41189838	18	2.5	18	78	7	56	40	20	2	37	1.65
41197021--41197091	26	2.7	26	86	0	97	30	18	9	40	1.83
41197257--41197296	6	6.8	6	94	2	64	15	20	0	65	1.28
41197251--41197294	18	2.5	19	82	14	58	15	18	0	65	1.27
41197242--41197296	12	4.6	12	86	8	58	18	18	0	63	1.31
41203090--41203150	25	2.4	26	88	2	88	32	13	16	37	1.87
41213575--41213613	14	2.7	14	84	4	51	58	2	2	35	1.25
41214059--41214120	31	2.0	31	81	6	72	58	4	9	27	1.50
41215517--41215569	18	3.0	18	86	2	81	9	15	5	69	1.33
41217528--41217759	50	4.6	50	89	0	338	26	22	30	20	1.98
41220538--41220791	63	4.1	63	75	8	184	27	22	25	24	2.00
41221387--41221433	22	2.1	22	88	0	67	17	17	17	48	1.81
41227265--41227489	109	2.1	109	98	1	436	40	16	19	23	1.91
41230473--41230525	23	2.3	23	93	3	90	32	43	7	16	1.76
41239099--41239269	63	2.7	62	83	3	200	22	20	28	29	1.98
41244214--41244244	13	2.3	14	94	5	55	41	0	12	45	1.42
41244532--41244609	22	3.6	21	81	8	93	33	8	14	43	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41244848--41244898	27	2.0	26	84	7	68	27	31	23	17	1.97
41244931--41244959	14	2.1	14	100	0	58	31	34	13	20	1.92
41244933--41244963	14	2.2	14	94	0	53	25	32	22	19	1.97
41245272--41245303	11	2.8	12	95	4	57	18	9	15	56	1.66
41245527--41245585	23	2.5	24	86	2	84	32	13	13	40	1.84
41247068--41247100	14	2.5	14	90	9	52	72	0	15	12	1.12
41247394--41247447	21	2.7	19	83	10	81	48	3	11	37	1.57
41253459--41253500	14	2.9	14	92	3	66	35	0	23	40	1.55
41254091--41254148	27	2.1	27	90	0	89	17	12	43	27	1.84
41268539--41268784	134	1.8	135	80	6	302	40	14	13	31	1.85
41270118--41270164	24	1.9	25	86	4	69	65	8	2	23	1.31
41274066--41274118	26	2.0	26	89	7	81	58	13	7	20	1.59
41284111--41284182	30	2.4	30	100	0	144	45	22	9	22	1.81
41295605--41295661	22	2.6	21	76	13	62	40	0	1	57	1.09
41295934--41295971	12	3.2	12	78	14	51	34	5	0	60	1.19
41295921--41295971	24	2.1	25	92	3	86	35	3	0	60	1.15
41295920--41295967	13	3.8	13	78	10	55	37	2	0	60	1.09
41298318--41298365	21	2.3	21	77	0	51	10	22	8	58	1.58
41301524--41302028	51	10.6	46	84	9	594	32	15	23	28	1.95
41301546--41301684	46	3.2	39	71	24	134	35	13	20	30	1.91
41301538--41302028	96	5.1	97	91	4	705	32	14	23	28	1.94
41301538--41302028	147	3.4	146	83	11	615	32	14	23	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41305444--41305479	11	3.3	11	84	0	54	0	13	0	86	0.58
41305776--41305819	21	2.1	21	82	0	52	47	0	11	40	1.39
41305647--41305922	147	1.9	147	88	3	421	43	5	9	42	1.59
41307473--41307548	23	3.3	23	89	7	127	28	26	22	22	1.99
41308341--41308376	16	2.2	16	90	0	54	58	13	13	13	1.64
41309496--41309551	30	1.9	30	86	13	82	16	14	8	60	1.57
41318833--41319074	70	3.5	72	81	14	260	48	12	0	38	1.47
41318903--41319030	25	5.3	25	75	12	133	47	13	0	39	1.43
41319011--41319096	44	2.0	43	93	2	145	50	9	0	40	1.35
41320193--41320218	7	3.7	7	100	0	52	57	15	0	26	1.38

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