genome.fa.s4.2.7.7.80.10.50.1000.171.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  171  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)
53729423--53729498	23	3.3	23	98	0	143	19	21	28	30	1.97
53732365--53732395	9	3.4	9	90	0	53	25	12	22	38	1.90
53732449--53732485	9	4.1	9	92	0	65	45	13	10	29	1.77
53738023--53738064	13	2.9	14	80	13	50	52	0	0	47	1.00
53738027--53738063	15	2.3	17	86	13	60	56	0	0	43	0.99
53739842--53740062	114	1.9	114	90	0	352	29	16	21	32	1.96
53740544--53740617	29	2.5	29	82	4	85	25	14	13	45	1.82
53741172--53741240	29	2.3	29	85	5	84	47	15	14	21	1.81
53741257--53741343	38	2.3	38	75	15	90	41	3	4	50	1.40
53751412--53751446	16	2.2	16	90	10	54	25	11	11	51	1.71
53751414--53751458	12	3.4	12	78	21	54	26	8	13	51	1.70
53754523--53754555	2	16.5	2	100	0	66	51	0	0	48	1.00
53755638--53755731	41	2.3	40	80	12	102	30	15	21	31	1.95
53755845--53755907	22	2.8	22	69	19	58	26	0	3	69	1.03
53759350--53759573	57	4.0	57	84	2	292	30	9	16	42	1.81
53759350--53759603	57	4.5	57	81	6	277	31	9	15	42	1.79
53759839--53759906	33	2.1	33	97	2	129	38	22	2	36	1.69
53762367--53762421	26	2.1	27	75	21	64	32	7	18	41	1.78
53762450--53762499	9	5.6	9	90	0	82	24	10	24	42	1.85
53762442--53762499	18	3.2	18	90	0	89	24	8	25	41	1.83
53763833--53763938	43	2.5	42	85	1	149	28	21	2	47	1.65
53770280--53770489	41	5.1	40	78	5	197	16	23	22	37	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53770280--53770466	82	2.3	82	89	0	284	16	24	23	35	1.95
53770284--53770489	82	2.5	82	86	3	254	16	23	23	36	1.94
53771023--53771060	15	2.5	15	86	0	58	21	0	42	36	1.53
53770996--53771063	15	4.9	14	74	13	52	23	0	35	41	1.55
53771725--53771749	2	12.5	2	100	0	50	52	0	0	48	1.00
53780119--53780500	43	8.9	43	79	5	150	28	21	25	24	1.99
53780119--53780500	86	4.5	84	77	8	294	28	21	25	24	1.99
53780188--53780500	129	2.4	127	82	6	364	26	20	26	25	1.99
53782496--53782584	40	2.3	39	80	7	99	33	6	7	51	1.57
53787944--53787985	22	2.0	21	90	4	66	23	0	11	64	1.27
53787856--53788756	163	5.5	164	70	14	629	29	11	7	50	1.67
53787833--53788913	327	3.3	324	90	3	1693	29	12	8	50	1.68
53790370--53790436	33	2.1	32	91	2	107	19	4	40	35	1.72
53791248--53791325	41	1.9	41	94	0	138	17	7	17	56	1.64
53791644--53791913	43	6.3	43	87	0	344	21	18	31	28	1.97
53792043--53792101	31	1.9	31	86	6	84	0	35	0	64	0.94
53792080--53792192	5	23.4	5	70	15	69	0	31	0	68	0.90
53792082--53792188	10	10.5	10	76	11	85	0	31	0	68	0.90
53792044--53792194	44	3.5	43	83	13	179	0	31	0	68	0.90
53792092--53792203	34	3.2	35	80	12	131	0	32	0	67	0.91
53792052--53792201	10	15.0	10	71	12	76	0	30	0	69	0.89
53792052--53792211	44	3.8	41	77	15	148	0	32	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53792260--53792318	27	2.2	27	93	0	100	15	35	32	16	1.90
53800314--53800365	2	26.5	2	88	3	79	44	3	0	51	1.19
53801704--53801833	63	2.1	63	100	0	260	39	9	7	43	1.65
53802647--53802674	6	4.7	6	100	0	56	82	0	17	0	0.68
53807432--53807476	20	2.3	19	82	14	56	62	0	4	33	1.15
53808331--53808377	2	23.5	2	100	0	94	48	0	0	51	1.00
53808497--53808522	6	4.3	6	100	0	52	30	0	19	50	1.48
53809810--53809863	11	4.8	12	75	11	60	25	27	1	44	1.64
53809809--53809863	23	2.5	22	80	11	67	25	27	1	45	1.64
53809823--53809922	51	2.0	51	84	4	130	27	25	1	47	1.59
53811069--53811094	7	3.7	7	100	0	52	26	0	15	57	1.38
53811743--53811782	18	2.2	18	86	0	53	15	30	10	45	1.78
53812711--53812762	13	4.0	13	78	9	61	36	7	21	34	1.82
53812952--53812997	24	1.9	24	86	0	65	52	2	0	45	1.13
53828257--53828305	21	2.3	20	76	10	53	28	16	12	42	1.84
53829447--53829492	23	2.0	23	100	0	92	39	17	8	34	1.80
53847405--53847440	15	2.5	14	91	8	63	50	0	5	44	1.25
53851686--53851932	43	5.7	43	84	1	271	27	28	21	22	1.99
53851693--53851932	129	1.9	129	82	1	302	27	28	21	22	1.99
53851675--53851953	129	2.2	127	76	7	292	29	27	20	23	1.99
53851698--53852058	43	8.4	43	78	7	229	27	28	19	24	1.99
53852392--53852559	66	2.5	66	83	5	207	13	27	18	40	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53856681--53856741	23	2.8	22	83	9	81	34	8	0	57	1.29
53857035--53857077	23	1.9	23	85	4	61	46	4	0	48	1.22
53861772--53861942	41	4.2	41	96	0	297	20	27	21	30	1.98
53861795--53861970	82	2.1	82	91	0	289	22	27	21	29	1.99
53863527--53863572	25	1.9	23	83	16	58	39	13	0	47	1.42
53871259--53871304	25	1.9	23	83	16	58	39	13	0	47	1.42
53874377--53874451	20	3.8	20	81	0	96	36	22	32	9	1.86
53875806--53875839	11	3.1	11	86	0	50	50	11	2	35	1.54
53878987--53879212	105	2.2	105	80	6	244	20	28	24	26	1.99
53881596--53882056	90	5.2	88	83	4	536	52	12	7	27	1.66
53881596--53882056	175	2.6	175	82	6	534	52	12	7	27	1.66
53882469--53882593	58	2.2	58	80	7	139	27	19	20	33	1.96
53884865--53884892	2	14.0	2	100	0	56	50	0	0	50	1.00
53890235--53890291	27	2.2	26	83	3	69	24	15	28	31	1.96
53896008--53896052	17	2.5	18	85	7	56	71	2	2	24	1.09
53896079--53896103	12	2.1	12	100	0	50	68	0	16	16	1.22
53902736--53902795	31	1.9	31	83	6	77	43	13	10	33	1.77
53904130--53904475	43	8.1	42	85	4	377	26	26	19	27	1.99
53904172--53904475	43	7.1	43	88	1	396	24	26	20	28	1.99
53904836--53905006	87	2.0	87	90	0	270	12	29	18	39	1.87
53904921--53904967	21	2.2	21	88	0	67	2	42	19	36	1.63
53908788--53908833	22	2.1	22	88	8	67	34	39	4	21	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53908794--53908846	22	2.4	21	81	9	61	39	39	3	16	1.67
53909054--53909098	21	2.1	22	83	4	56	37	37	2	22	1.67
53909174--53909206	14	2.4	14	89	0	57	51	27	0	21	1.48
53909146--53909233	39	2.2	40	84	6	117	47	26	2	23	1.63
53909623--53910280	208	3.2	207	91	1	996	29	23	18	28	1.98
53912259--53912350	9	10.2	9	83	4	96	22	8	26	42	1.82
53914469--53914505	16	2.2	16	90	4	56	40	5	8	45	1.56
53920310--53920409	42	2.4	42	94	0	173	36	10	28	26	1.88
53921244--53921326	23	3.5	24	85	3	98	21	15	21	40	1.90
53929458--53929745	17	16.5	17	69	18	130	45	11	13	29	1.78
53929458--53929745	35	8.2	33	71	16	131	45	11	13	29	1.78
53929507--53929638	68	1.9	67	79	11	144	43	11	14	30	1.80
53929448--53929747	18	16.9	19	68	15	123	46	11	13	29	1.78
53929614--53929749	72	1.9	72	89	3	211	43	9	13	33	1.77
53929927--53929965	20	2.0	20	94	0	69	38	10	12	38	1.78
53930578--53930628	10	5.1	11	80	20	58	5	17	0	76	0.98
53930580--53930630	20	2.6	19	85	14	68	3	17	0	78	0.90
53930729--53930791	21	2.9	21	80	4	72	0	26	1	71	0.95
53931202--53931288	30	2.9	30	79	5	95	35	1	27	35	1.65
53931173--53931299	30	4.3	30	73	10	93	38	3	24	33	1.74
53932298--53932330	16	2.1	16	94	0	57	51	6	18	24	1.68
53934398--53934541	46	3.2	45	75	8	150	14	17	22	45	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53934411--53934527	22	5.3	22	71	6	83	14	16	23	46	1.83
53934342--53934495	68	2.3	68	82	0	191	15	18	21	44	1.86
53934411--53934574	89	1.8	90	88	1	249	15	17	21	45	1.85
53940263--53940311	22	2.2	22	88	0	71	30	28	14	26	1.95
53942690--53942759	25	2.8	24	84	4	86	27	28	15	28	1.96
53945367--53945472	52	2.0	52	92	0	176	43	16	12	28	1.83
53946265--53946333	30	2.3	30	94	0	120	26	18	20	34	1.96
53948370--53948444	37	2.0	37	100	0	150	26	18	14	40	1.90
53949436--53949487	27	1.9	27	81	14	63	32	5	1	59	1.32
53950886--53950941	27	2.1	27	100	0	112	37	0	35	26	1.57

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