genome.fa.s1.2.7.7.80.10.50.1000.102.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  102  of  187  ( 22383 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)
30084440--30084681	84	2.9	84	84	4	310	24	18	14	42	1.88
30088621--30088654	18	1.9	17	88	5	50	58	0	5	35	1.22
30095944--30096010	27	2.5	27	82	0	89	19	25	32	22	1.97
30097035--30097077	19	2.2	20	84	12	63	32	18	0	48	1.48
30097198--30097278	38	2.2	38	82	6	94	28	27	23	20	1.99
30098680--30098736	29	2.0	29	86	6	80	52	3	1	42	1.28
30105162--30105216	2	27.5	2	100	0	110	0	49	0	50	1.00
30106221--30106253	12	2.8	12	95	0	57	0	42	0	57	0.98
30106549--30106792	124	2.0	124	88	1	364	22	18	20	38	1.93
30108033--30108078	17	2.6	18	82	6	67	39	4	0	56	1.19
30114468--30114680	84	2.5	82	89	6	313	20	8	19	51	1.72
30114478--30114680	81	2.5	81	91	3	316	20	8	18	51	1.72
30117486--30117516	16	1.9	16	93	0	53	9	9	9	70	1.33
30132311--30132357	18	2.5	18	80	16	51	48	0	4	46	1.21
30134075--30134107	16	2.1	16	100	0	66	36	6	36	21	1.78
30134089--30134183	44	2.1	45	86	5	131	32	5	29	32	1.80
30134340--30134374	18	2.0	17	88	5	52	54	0	0	45	0.99
30134458--30134494	16	2.2	17	86	13	51	54	0	2	43	1.14
30134326--30134739	120	3.5	120	96	1	742	48	3	3	44	1.37
30134578--30134614	16	2.2	17	86	13	51	54	0	2	43	1.14
30134698--30134734	16	2.2	17	86	13	51	54	0	2	43	1.14
30134326--30134734	59	6.8	60	68	11	275	48	3	3	44	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30134802--30134836	18	2.0	17	88	5	52	48	2	0	48	1.16
30134751--30135139	91	4.3	91	96	0	697	46	3	2	47	1.32
30134960--30135008	17	3.1	16	83	13	57	55	0	0	44	0.99
30134965--30135014	18	3.0	17	85	8	59	56	2	0	42	1.11
30141670--30141717	2	24.0	2	91	0	78	50	0	50	0	1.00
30143978--30144020	22	2.0	22	81	9	52	60	9	0	30	1.28
30145423--30145663	120	2.0	120	96	0	446	24	15	17	42	1.88
30154569--30155107	69	7.8	69	85	0	648	35	25	19	19	1.96
30154571--30155107	207	2.6	207	86	0	741	35	25	19	19	1.95
30161055--30161087	11	2.9	12	91	8	52	42	9	0	48	1.35
30169997--30170109	57	2.0	57	85	3	156	36	12	22	29	1.90
30178198--30178373	50	3.6	48	83	3	203	23	30	21	25	1.99
30178198--30178383	96	1.9	98	85	4	259	22	30	21	25	1.99
30178543--30178613	23	3.2	23	61	15	58	40	9	5	43	1.61
30178529--30178616	44	2.0	44	100	0	176	40	9	4	45	1.56
30185429--30185515	43	2.0	43	97	0	165	25	31	9	34	1.87
30186357--30186381	8	3.1	8	100	0	50	76	0	0	24	0.80
30187798--30187898	49	2.1	49	83	10	127	30	27	14	26	1.95
30188676--30188798	33	3.4	33	74	20	111	34	28	17	19	1.95
30188922--30189107	101	1.8	102	88	3	286	32	27	17	23	1.96
30191500--30191524	8	3.1	8	100	0	50	76	0	0	24	0.80
30193426--30193647	50	4.4	50	87	0	273	21	27	21	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30196500--30196910	203	2.0	203	83	2	531	34	16	16	33	1.91
30204765--30204840	36	2.1	36	95	0	134	28	14	21	35	1.92
30205499--30205545	15	3.1	15	84	0	67	55	2	0	42	1.12
30205484--30205536	23	2.3	23	81	12	65	50	1	0	47	1.12
30205779--30205824	21	2.1	23	84	8	60	23	2	4	69	1.17
30223161--30223289	40	3.3	39	76	6	127	31	23	20	24	1.98
30223325--30223618	40	7.7	40	70	12	152	29	20	22	28	1.98
30223184--30223580	147	2.7	143	82	5	426	30	20	22	27	1.98
30228431--30228512	9	9.1	9	73	5	67	43	17	1	37	1.56
30228416--30228476	18	3.0	21	70	18	58	47	13	1	37	1.52
30228544--30228687	47	3.1	47	87	6	195	45	16	0	37	1.48
30228571--30228687	56	2.1	56	91	3	191	46	17	0	35	1.49
30234480--30234698	43	5.1	42	76	5	190	26	20	23	29	1.98
30236115--30236382	92	2.9	93	82	5	305	27	20	21	30	1.98
30236115--30236382	46	5.8	46	77	5	227	27	20	21	30	1.98
30236116--30236382	138	1.9	138	81	1	320	28	20	20	30	1.98
30238809--30238877	33	2.1	33	91	0	111	46	23	10	20	1.80
30246958--30246997	20	2.0	20	85	9	55	22	30	0	47	1.52
30254391--30254439	24	2.0	24	92	0	80	14	26	10	48	1.75
30254408--30254512	41	2.6	40	90	3	165	20	22	9	47	1.78
30256352--30256470	37	3.2	36	74	9	123	43	24	15	16	1.86
30273790--30273814	2	12.5	2	100	0	50	0	0	48	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30275411--30275454	6	7.3	6	92	0	52	22	2	9	65	1.32
30276051--30276119	24	2.8	25	75	18	72	39	2	1	56	1.23
30276031--30276099	25	2.7	25	75	20	72	39	2	0	57	1.13
30276311--30276360	2	25.0	2	100	0	100	50	0	0	50	1.00
30279077--30279137	25	2.4	25	72	22	63	67	3	0	29	1.07
30279268--30279330	21	3.0	21	83	2	72	58	14	14	12	1.63
30279516--30279548	2	16.5	2	100	0	66	51	0	0	48	1.00
30280370--30280400	8	3.9	8	100	0	62	38	0	0	61	0.96
30292930--30294047	100	11.2	99	83	4	1300	31	21	21	25	1.98
30292915--30294007	199	5.5	199	85	2	1401	30	21	21	25	1.98
30294009--30294165	44	3.6	44	74	13	144	34	19	22	23	1.97
30294188--30294767	289	2.0	289	99	0	1142	34	20	21	22	1.96
30302850--30302890	12	3.5	12	90	6	66	41	0	0	58	0.98
30302839--30302890	23	2.2	22	86	10	68	40	1	1	55	1.22
30303347--30303406	30	2.0	30	100	0	120	36	6	16	40	1.75
30303602--30303634	2	16.5	2	93	0	57	48	3	0	48	1.17
30310479--30310612	61	2.2	59	85	7	182	52	2	0	44	1.21
30310609--30310639	16	1.9	16	100	0	62	41	0	0	58	0.98
30314417--30314456	2	20.0	2	100	0	80	50	0	0	50	1.00
30314818--30314848	16	2.0	16	93	6	55	6	25	0	67	1.14
30315654--30315704	22	2.3	22	79	0	66	39	17	7	35	1.79
30316838--30316876	12	3.5	11	86	10	53	74	0	23	2	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30322912--30322962	22	2.3	22	77	12	59	37	17	7	37	1.79
30322970--30323064	44	2.2	44	81	3	113	31	17	7	43	1.77
30322992--30323064	22	3.4	21	81	7	85	34	19	4	42	1.70
30322992--30323067	5	14.4	5	78	10	71	34	19	3	42	1.70
30324146--30324182	6	6.0	6	87	6	56	81	2	16	0	0.81
30324852--30324882	15	2.1	15	100	0	62	41	12	12	32	1.81
30326187--30326231	19	2.3	20	88	3	65	28	6	17	46	1.73
30327821--30327872	25	2.1	25	88	0	77	51	7	19	21	1.71
30334104--30334759	179	3.7	179	88	0	952	27	17	22	32	1.96
30334238--30334755	44	11.6	44	67	11	189	27	16	23	32	1.96
30334788--30334895	44	2.4	45	84	1	137	30	23	20	25	1.98
30334798--30335237	143	3.1	143	89	0	664	29	21	19	29	1.98
30336067--30336116	14	3.6	14	77	17	50	0	18	2	80	0.82
30336071--30336124	15	3.5	15	82	12	65	0	14	3	81	0.82
30336072--30336109	20	2.0	20	94	5	69	0	13	2	84	0.73
30336073--30336122	5	9.8	5	81	14	50	0	14	4	82	0.82
30336560--30336597	15	2.5	15	91	4	58	0	2	13	84	0.73
30336560--30336597	8	4.9	8	80	6	51	0	2	13	84	0.73
30353779--30354035	129	2.0	129	90	1	408	31	13	24	31	1.93
30355774--30355798	11	2.3	11	100	0	50	56	16	0	28	1.41
30358543--30358582	20	2.0	21	85	14	57	32	10	17	40	1.83
30359435--30360103	334	2.0	334	100	0	1338	28	18	14	39	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30365634--30365947	157	2.0	157	93	0	538	28	12	24	35	1.91
30367116--30368098	493	2.0	492	95	0	1750	27	17	24	30	1.97
30371714--30371752	17	2.2	18	86	4	53	61	0	12	25	1.31
30371879--30371909	16	1.9	16	93	0	53	32	6	35	25	1.82
30373229--30373262	11	3.2	10	91	4	50	35	2	0	61	1.11
30375622--30375709	23	3.8	23	77	7	72	39	20	10	29	1.85
30376184--30376235	2	26.0	2	96	0	95	51	0	0	48	1.00
30377914--30379018	281	3.8	286	86	6	1447	37	10	18	34	1.84
30379120--30379169	20	2.5	19	81	12	55	26	2	8	64	1.32
30379134--30379170	20	1.9	20	94	5	67	27	0	5	67	1.12

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