genome.fa.s4.2.7.7.80.10.50.1000.130.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  130  of  198  ( 23681 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)
41371793--41371819	6	4.5	6	100	0	54	14	18	0	66	1.25
41372142--41372177	17	2.1	17	94	0	63	47	0	16	36	1.47
41378311--41378549	50	4.7	50	79	6	214	22	27	20	29	1.98
41380267--41380300	12	2.9	12	91	4	52	61	8	5	23	1.47
41388691--41388870	87	2.1	87	95	0	324	45	10	6	38	1.63
41397712--41397827	43	2.7	43	85	1	153	29	26	18	25	1.98
41399254--41399348	33	2.9	34	72	12	108	18	42	13	25	1.87
41399618--41399752	48	2.8	48	92	3	218	48	13	7	30	1.69
41405106--41405136	16	1.9	16	93	0	53	80	3	0	16	0.83
41406058--41406100	14	3.3	13	84	9	52	69	0	23	6	1.12
41406064--41406106	12	3.3	13	87	6	52	65	0	23	11	1.25
41406058--41406132	33	2.3	33	81	11	91	70	0	20	9	1.14
41406091--41406135	21	2.1	21	84	8	56	73	0	17	8	1.08
41406078--41406132	12	4.8	12	76	15	53	70	0	18	10	1.15
41411677--41411716	4	9.8	4	89	5	62	2	25	0	72	0.97
41411975--41412013	13	3.2	13	85	7	55	56	7	0	35	1.28
41411994--41412037	17	2.6	17	75	13	54	63	2	0	34	1.07
41412005--41412052	23	2.0	25	84	8	64	64	0	0	35	0.94
41413545--41413575	3	10.3	3	100	0	62	67	0	32	0	0.91
41422774--41422820	21	2.2	22	92	3	78	21	19	38	21	1.94
41426227--41426256	10	3.0	10	95	0	51	36	23	10	30	1.87
41434915--41434972	28	2.1	28	100	0	116	65	10	10	13	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41440596--41440855	92	2.9	89	82	6	285	39	16	11	32	1.84
41440597--41440855	89	2.9	88	83	4	297	39	16	11	32	1.84
41440883--41441104	88	2.6	84	77	10	243	32	10	18	37	1.86
41448171--41448198	6	4.7	6	100	0	56	50	0	0	50	1.00
41448299--41448353	23	2.4	22	75	16	58	32	1	1	63	1.15
41453682--41453744	28	2.2	28	97	0	117	36	19	17	26	1.94
41454808--41454961	57	2.7	57	85	2	202	37	16	11	33	1.85
41454808--41454986	57	3.1	57	83	3	173	36	15	12	35	1.85
41472335--41472375	2	20.5	2	100	0	82	51	0	0	48	1.00
41473477--41473503	14	1.9	14	100	0	54	37	25	7	29	1.83
41477385--41477459	37	2.0	37	100	0	150	24	42	12	21	1.86
41483804--41483878	37	2.0	37	100	0	150	41	10	18	29	1.84
41483959--41484000	15	2.8	16	86	13	63	71	14	0	14	1.15
41484907--41484936	13	2.3	13	100	0	60	73	0	13	13	1.10
41484906--41484945	7	5.7	7	88	11	64	75	0	12	12	1.06
41486207--41486693	129	3.8	129	93	1	823	31	19	23	25	1.98
41486854--41487224	44	8.6	43	74	5	273	28	16	23	31	1.96
41486855--41487270	85	4.8	85	71	7	264	26	17	24	31	1.97
41486853--41487273	129	3.3	129	92	0	698	27	17	24	31	1.97
41494619--41494654	15	2.5	14	86	8	54	44	8	0	47	1.33
41499140--41499171	15	2.0	17	88	11	50	62	9	0	28	1.26
41499338--41499382	19	2.2	20	84	7	56	44	2	11	42	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41509820--41509863	16	2.8	16	75	0	52	54	2	2	40	1.25
41511370--41511452	33	2.5	33	75	5	78	38	15	18	27	1.91
41516641--41516683	21	2.0	21	90	0	68	16	32	16	34	1.91
41523110--41523194	21	4.0	21	90	0	125	17	27	16	38	1.91
41524040--41524109	29	2.4	30	87	4	106	28	25	28	17	1.97
41524823--41524880	19	3.1	18	77	15	64	39	6	10	43	1.66
41525377--41525471	31	3.1	31	80	6	122	41	16	21	21	1.91
41538378--41538423	2	23.0	2	95	0	83	52	0	0	47	1.00
41547452--41547528	33	2.4	33	84	6	95	19	29	36	14	1.91
41547955--41547995	13	3.1	14	75	10	50	19	14	17	48	1.81
41548193--41548234	20	2.2	20	87	8	61	28	0	11	59	1.33
41548343--41548372	14	2.1	15	93	6	53	40	6	13	40	1.71
41554002--41554026	12	2.1	12	100	0	50	0	24	0	76	0.80
41554533--41554557	13	1.9	13	100	0	50	24	32	28	16	1.96
41555212--41555236	13	1.9	13	100	0	50	24	40	28	8	1.83
41556097--41556125	14	2.0	15	93	6	51	34	6	17	41	1.76
41557251--41557301	19	2.6	19	81	12	59	37	0	1	60	1.08
41557251--41557318	20	3.5	20	82	8	68	36	0	4	58	1.18
41557257--41557329	20	3.7	19	78	12	60	38	0	2	58	1.12
41566688--41566855	30	5.7	30	75	11	134	32	22	4	41	1.73
41566688--41566843	59	2.6	58	75	16	149	32	21	4	41	1.73
41567380--41567420	10	3.7	11	84	12	57	80	0	17	2	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41567380--41567420	6	7.3	6	78	15	52	80	0	17	2	0.82
41567380--41567420	16	2.5	17	92	4	66	80	0	17	2	0.82
41567544--41567582	13	2.9	14	88	7	62	71	0	28	0	0.86
41567551--41567615	14	4.6	14	73	5	60	75	0	24	0	0.81
41567770--41567796	14	1.9	14	100	0	54	29	44	22	3	1.70
41568422--41568724	18	16.8	17	74	15	193	31	10	10	47	1.72
41568422--41568657	36	6.6	35	77	13	216	31	10	11	47	1.72
41568567--41568724	33	4.5	35	74	12	108	31	11	11	46	1.75
41579573--41579624	25	2.1	24	82	10	61	17	21	21	40	1.91
41582865--41582921	25	2.3	25	84	0	69	22	21	24	31	1.98
41586665--41586708	23	1.9	23	95	0	79	27	4	25	43	1.74
41592571--41592652	38	2.1	40	84	4	105	14	20	29	35	1.93
41610395--41610678	80	3.4	80	70	15	234	29	23	17	29	1.97
41610312--41610854	44	12.6	44	70	14	262	27	22	19	30	1.98
41610484--41610854	46	8.5	45	74	12	251	26	22	19	30	1.98
41610247--41610768	170	3.1	170	89	3	723	28	22	19	29	1.98
41610574--41610678	39	2.6	40	73	11	108	32	23	16	27	1.96
41620257--41620299	20	2.2	20	91	0	68	39	20	9	30	1.84
41620376--41620417	21	2.0	21	90	9	68	38	19	9	33	1.84
41620392--41620960	285	2.0	285	94	0	996	36	16	14	32	1.90
41623124--41623172	20	2.7	18	77	22	57	51	4	2	42	1.32
41623642--41623681	19	2.1	19	85	0	53	37	2	5	55	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41626963--41627002	21	2.0	20	85	14	55	65	0	0	35	0.93
41628130--41628210	36	2.2	36	82	6	92	22	8	3	65	1.36
41629369--41629574	51	4.3	46	70	14	141	39	18	14	27	1.89
41629368--41629570	97	2.1	95	81	5	230	39	18	14	27	1.89
41630297--41630452	28	5.5	28	92	1	231	32	25	10	31	1.90
41630297--41630452	57	2.7	57	90	2	233	32	25	10	31	1.90
41636827--41637066	46	5.1	46	74	6	248	41	19	12	26	1.88
41636835--41637089	23	10.9	23	66	15	112	41	18	13	26	1.88
41636745--41637116	94	3.9	94	90	2	564	40	18	13	27	1.89
41637863--41637989	28	4.5	28	92	2	182	31	25	11	31	1.92
41637863--41637989	57	2.2	56	91	4	202	31	25	11	31	1.92
41638042--41638077	2	18.0	2	100	0	72	50	0	0	50	1.00
41652922--41652959	16	2.4	16	90	0	58	31	0	34	34	1.58
41653271--41653312	15	2.7	16	82	14	52	52	2	0	45	1.13
41653280--41653321	15	2.9	15	82	10	52	52	0	0	47	1.00
41656828--41656933	43	2.5	41	86	9	142	44	2	4	48	1.38
41656855--41656927	23	3.3	23	66	11	71	47	4	2	45	1.36
41657939--41658040	50	2.0	50	100	0	204	35	13	13	37	1.85
41665501--41665528	2	14.0	2	100	0	56	50	0	0	50	1.00
41666939--41666963	12	2.1	12	100	0	50	32	8	36	24	1.84
41669412--41669505	9	10.4	9	91	0	134	42	24	8	24	1.82
41675499--41675559	31	2.0	30	82	17	74	29	18	6	45	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41675550--41675581	9	3.4	10	83	16	50	21	15	9	53	1.70
41675747--41675858	25	4.5	26	83	10	137	32	25	22	20	1.98
41686212--41686254	16	2.8	16	92	3	70	41	0	16	41	1.48
41686253--41686287	18	2.0	17	88	5	52	45	0	0	54	0.99
41686312--41686739	61	7.1	59	68	15	286	41	1	6	50	1.36
41686228--41686787	120	4.7	120	97	0	1043	42	1	5	50	1.33
41686613--41686647	18	2.0	17	88	5	52	45	0	0	54	0.99
41686228--41686752	59	8.7	58	66	18	256	42	1	6	50	1.34
41686987--41687019	16	2.1	16	94	0	57	21	39	6	33	1.78
41687064--41687088	13	1.9	13	100	0	50	48	0	20	32	1.50

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