genome.fa.s4.2.7.7.80.10.50.1000.145.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  145  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)
46101536--46101568	13	2.5	14	85	14	52	75	0	24	0	0.80
46101756--46101832	29	2.5	30	83	6	93	49	16	14	19	1.80
46112171--46112207	2	18.5	2	100	0	74	51	0	48	0	1.00
46113042--46113087	24	1.9	24	81	0	56	41	23	17	17	1.90
46114890--46114936	18	2.8	16	73	20	51	42	2	0	55	1.12
46115200--46115324	60	2.1	59	90	1	196	39	16	4	40	1.69
46119716--46119960	83	2.9	84	93	1	438	46	23	4	24	1.71
46124960--46126336	690	2.0	690	89	2	2093	39	11	21	28	1.87
46131439--46131483	19	2.2	20	80	11	56	40	15	17	26	1.90
46134278--46134334	30	1.9	30	96	0	105	47	5	7	40	1.53
46136838--46136901	3	21.7	3	93	3	112	65	1	0	32	1.02
46137006--46137031	12	2.2	12	100	0	52	76	0	0	23	0.78
46139704--46139842	44	3.2	43	67	8	109	22	25	27	25	2.00
46139577--46139891	88	3.6	88	90	0	452	20	23	28	27	1.99
46141176--46141214	20	1.9	21	84	5	53	23	5	10	61	1.48
46144594--46144842	50	4.8	50	84	4	291	20	28	23	26	1.99
46144593--46144842	100	2.4	104	87	5	346	20	28	23	26	1.99
46144937--46144968	13	2.5	13	94	0	55	56	12	0	31	1.37
46145180--46145237	30	1.9	30	92	0	98	32	24	3	39	1.72
46148646--46148750	51	2.0	51	81	5	122	55	5	6	32	1.50
46149480--46149577	21	4.7	21	88	8	130	39	15	9	35	1.79
46149506--46149589	21	4.3	18	85	11	62	38	15	11	34	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46149730--46149771	21	2.0	22	85	4	59	21	2	14	61	1.43
46156692--46156888	98	2.0	98	91	0	322	37	24	10	27	1.88
46158828--46159554	44	16.5	44	64	11	245	24	25	20	29	1.99
46158828--46159628	132	6.1	132	95	0	1415	24	25	20	29	1.99
46171041--46171237	98	2.0	98	90	0	313	38	25	9	26	1.86
46174062--46174265	109	1.9	108	85	5	286	21	25	24	27	1.99
46175439--46175513	34	2.2	35	78	7	82	34	24	18	22	1.96
46182502--46182537	18	2.1	16	90	10	54	30	5	2	61	1.33
46182608--46182645	3	12.7	3	94	0	67	28	0	0	71	0.87
46189319--46189347	6	4.8	6	100	0	58	0	51	13	34	1.42
46197933--46197996	17	3.5	17	69	19	56	29	9	14	46	1.75
46197920--46197995	39	1.9	39	100	0	152	28	10	14	46	1.78
46203661--46203734	39	2.0	37	89	10	116	25	21	13	39	1.90
46206092--46206151	29	2.1	29	100	0	120	61	11	3	23	1.45
46206904--46206938	16	2.1	17	94	5	63	11	0	2	85	0.69
46210408--46210462	25	2.3	24	81	12	60	23	3	7	65	1.34
46215530--46215560	12	2.6	12	89	0	53	12	38	19	29	1.89
46215649--46215729	42	1.9	42	82	9	103	18	39	27	14	1.90
46219790--46219851	25	2.5	25	83	0	79	20	16	24	38	1.92
46228571--46228664	25	3.6	25	76	19	95	32	23	22	21	1.98
46239492--46239598	50	2.1	50	78	10	112	35	17	25	21	1.95
46246464--46246544	35	2.3	35	91	0	126	35	6	13	44	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46262239--46262274	7	5.1	7	100	0	72	16	41	13	27	1.87
46271755--46271790	18	2.0	18	94	0	63	58	5	22	13	1.56
46276610--46276980	69	5.4	68	76	7	284	24	20	25	29	1.99
46280878--46281055	21	8.5	21	73	4	144	19	17	15	47	1.82
46280877--46281055	42	4.3	41	81	8	175	18	17	15	48	1.82
46280886--46281049	84	2.0	84	82	4	206	20	18	14	46	1.84
46288540--46288617	21	3.7	21	83	6	95	17	21	16	43	1.88
46288535--46288622	21	4.2	21	79	5	88	18	22	17	42	1.89
46309908--46310056	37	4.0	37	93	0	253	26	21	14	36	1.92
46318259--46318292	17	2.0	17	88	0	50	32	20	2	44	1.67
46319027--46319074	20	2.3	21	78	7	62	52	2	2	43	1.24
46319194--46319235	18	2.2	20	84	12	54	35	7	0	57	1.26
46322270--46322337	33	2.1	33	100	0	136	35	17	20	26	1.95
46330671--46330725	3	18.3	3	81	7	67	36	1	1	60	1.18
46330909--46330939	2	15.5	2	100	0	62	48	0	0	51	1.00
46337108--46337193	22	3.9	22	90	0	118	27	15	27	29	1.96
46343341--46343898	50	11.2	50	70	6	362	32	23	20	22	1.98
46343332--46343898	100	5.7	99	86	3	712	32	23	20	23	1.98
46345564--46345621	3	19.3	3	85	7	82	34	1	1	62	1.16
46345720--46345754	2	17.5	2	93	0	61	45	0	0	54	0.99
46348445--46348654	91	2.3	91	81	8	257	32	13	24	29	1.94
46350204--46350282	37	2.1	37	81	4	88	53	2	5	39	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46353656--46353709	18	3.0	18	86	10	67	33	0	5	61	1.19
46353656--46353709	19	2.9	19	84	10	60	33	0	5	61	1.19
46354150--46354206	29	1.9	30	82	10	73	43	0	14	42	1.44
46355525--46355557	2	16.5	2	93	0	57	48	0	3	48	1.17
46356187--46356213	4	6.8	4	100	0	54	25	0	22	51	1.48
46359408--46359437	14	2.1	14	93	0	51	3	13	0	83	0.77
46362535--46362577	20	2.0	20	86	8	59	65	4	0	30	1.13
46377742--46377829	43	2.0	43	100	0	176	21	20	6	51	1.70
46384522--46384553	5	6.4	5	100	0	64	40	18	18	21	1.91
46385465--46385525	30	2.0	31	93	3	106	37	0	42	19	1.52
46385574--46385610	9	4.1	9	92	0	65	29	10	13	45	1.77
46385663--46385693	9	3.4	9	90	0	53	38	22	12	25	1.90
46386866--46386926	9	6.6	9	83	7	77	24	8	26	40	1.83
46386866--46386917	20	2.7	20	82	5	63	25	7	25	42	1.81
46388295--46388325	3	10.3	3	100	0	62	67	0	0	32	0.91
46388387--46388423	3	12.3	3	100	0	74	67	0	0	32	0.91
46390022--46390276	129	2.0	127	82	3	314	29	21	17	31	1.96
46390067--46390450	44	9.0	41	72	13	242	27	20	20	32	1.97
46390071--46390407	173	2.0	172	86	1	469	28	20	20	30	1.98
46390086--46390401	85	3.7	84	72	9	282	29	20	19	30	1.98
46390206--46390448	128	1.9	128	82	9	307	28	19	20	30	1.97
46390067--46390450	172	2.2	173	83	2	504	27	20	20	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46390467--46390988	210	2.5	210	91	2	818	26	22	18	32	1.97
46390474--46390822	102	3.4	102	66	19	268	26	23	17	32	1.97
46397230--46397281	3	17.3	3	100	0	104	67	0	0	32	0.91
46397355--46397403	3	16.3	3	95	0	89	67	2	0	30	1.02
46397415--46397473	20	3.2	20	68	26	67	67	6	10	15	1.39
46397410--46397487	34	2.3	34	97	2	149	67	5	11	15	1.37
46399872--46399921	20	2.6	19	81	9	57	22	4	2	72	1.12
46400169--46400193	2	12.5	2	100	0	50	52	0	0	48	1.00
46400294--46400332	2	19.0	2	94	5	69	48	2	0	48	1.15
46406709--46406733	10	2.5	10	100	0	50	72	0	0	28	0.86
46408265--46408313	25	2.0	25	83	0	62	38	0	16	44	1.48
46408286--46408328	16	2.6	17	78	17	54	44	0	13	41	1.44
46408710--46408795	43	2.0	43	86	8	122	53	1	18	26	1.52
46409360--46409386	13	2.1	13	100	0	54	37	14	14	33	1.88
46412749--46412789	21	2.0	20	85	4	55	53	0	0	46	1.00
46412758--46412792	18	1.9	18	88	0	52	51	0	0	48	1.00
46415617--46415643	7	3.9	7	100	0	54	29	11	29	29	1.91
46421376--46421400	7	3.6	7	100	0	50	32	56	0	12	1.36
46434161--46434766	43	14.0	43	81	6	676	24	0	30	43	1.61
46434164--46434737	65	9.0	63	82	8	467	25	1	30	43	1.61
46434161--46434737	21	27.0	21	82	4	651	24	1	30	43	1.61
46434161--46434766	22	28.0	22	81	6	681	24	0	30	43	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46437139--46437238	51	2.0	51	88	4	148	45	3	26	26	1.68
46437216--46437262	11	4.2	11	88	2	67	42	2	34	21	1.65
46437203--46437262	22	2.7	23	82	12	72	43	1	33	21	1.63
46451757--46451787	7	4.3	7	92	8	53	87	0	12	0	0.55
46451757--46451787	15	2.1	15	94	5	55	87	0	12	0	0.55
46452583--46452617	18	1.9	19	88	11	56	68	5	8	17	1.35
46452932--46453007	38	2.0	38	94	0	134	3	28	10	56	1.51
46455584--46455616	16	2.1	16	100	0	66	21	36	6	36	1.78
46456481--46456536	22	2.5	22	85	0	67	21	50	12	16	1.78
46456625--46456671	22	2.1	22	96	0	85	14	51	19	14	1.77

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