genome.fa.s1.2.7.7.80.10.50.1000.13.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  13  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)
4708300--4708354	24	2.3	24	96	3	103	25	30	0	43	1.55
4710168--4710218	21	2.5	19	75	12	57	45	5	0	49	1.26
4716740--4716779	3	13.3	3	100	0	80	0	32	0	67	0.91
4722730--4722770	10	4.3	10	87	9	59	36	0	0	63	0.95
4722744--4722786	19	2.3	18	84	4	50	44	0	0	55	0.99
4722806--4722851	19	2.4	19	88	0	65	63	2	0	34	1.07
4724509--4724535	6	4.5	6	100	0	54	48	14	18	18	1.82
4726891--4726933	11	3.8	11	80	17	52	30	2	2	65	1.18
4726894--4726937	23	1.9	23	90	0	70	31	2	4	61	1.28
4731145--4731210	29	2.2	31	83	5	82	56	3	6	34	1.40
4731504--4731587	7	11.9	7	78	12	82	23	2	0	73	0.94
4733252--4733278	5	5.4	5	100	0	54	18	0	0	81	0.69
4739958--4740011	21	2.5	22	80	14	60	29	1	1	66	1.12
4752984--4753118	46	2.9	46	88	2	191	31	25	7	35	1.84
4774695--4774746	24	2.2	24	89	0	77	50	9	3	36	1.54
4779108--4779157	24	2.1	24	84	0	64	46	10	4	40	1.56
4782222--4782282	27	2.3	27	100	0	122	24	3	18	54	1.58
4788247--4788280	3	12.0	3	87	12	54	0	32	0	67	0.91
4790840--4790883	3	14.7	3	100	0	88	68	0	0	31	0.90
4812295--4812333	2	19.5	2	100	0	78	48	0	0	51	1.00
4816959--4816988	15	2.0	15	100	0	60	33	20	13	33	1.91
4828303--4828371	34	2.1	33	91	2	111	62	14	10	13	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4845967--4846003	14	2.6	14	91	0	56	18	5	10	64	1.43
4846214--4846246	11	2.9	12	86	13	52	66	0	0	33	0.92
4851310--4851360	25	2.0	25	100	0	102	35	7	37	19	1.81
4851855--4851885	15	2.1	15	100	0	62	19	19	0	61	1.35
4853705--4853752	19	2.5	20	86	6	64	39	10	4	45	1.58
4854897--4854945	25	2.0	25	92	4	82	65	6	6	22	1.38
4855546--4855596	26	2.0	26	88	3	77	60	5	0	33	1.21
4855649--4855681	11	3.0	11	90	0	57	39	0	9	51	1.34
4862785--4862840	16	3.4	17	75	9	71	28	0	5	66	1.14
4864983--4865031	17	2.6	20	71	18	59	36	16	18	28	1.92
4869161--4869218	30	1.9	30	82	10	73	43	0	6	50	1.29
4869402--4869427	11	2.4	11	100	0	52	84	15	0	0	0.62
4869721--4869762	3	14.0	3	100	0	84	33	0	0	66	0.92
4870599--4870636	18	2.1	18	95	0	67	34	7	47	10	1.67
4876159--4876314	38	4.1	36	77	15	147	1	32	0	66	1.00
4876169--4876305	38	3.4	42	82	10	185	1	28	0	70	0.96
4876272--4876365	5	20.6	5	79	10	80	0	36	0	63	0.94
4876274--4876365	8	10.7	9	75	20	74	0	35	0	64	0.94
4876155--4876324	79	2.2	77	87	4	261	1	33	0	65	1.01
4876298--4876367	14	4.9	14	75	16	63	0	38	0	61	0.96
4879975--4880022	23	2.1	23	100	0	96	33	4	6	56	1.44
4880090--4880123	17	2.0	17	94	0	59	55	0	14	29	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4880545--4880611	34	1.9	35	84	3	91	46	13	8	31	1.74
4880580--4880619	14	2.9	14	84	0	53	42	17	7	32	1.77
4888597--4888623	4	6.8	4	100	0	54	0	0	22	77	0.76
4894280--4894341	28	2.2	29	97	2	117	30	4	24	40	1.76
4914637--4914688	26	2.0	26	96	0	95	32	11	7	48	1.68
4915128--4915984	150	5.7	150	90	1	1227	38	16	7	37	1.77
4915128--4915988	301	2.9	299	88	2	1235	39	16	7	37	1.76
4915885--4916089	109	1.9	107	85	4	286	37	18	7	37	1.79
4920683--4920750	21	3.2	21	74	0	64	42	22	20	14	1.88
4920676--4920854	42	4.3	42	78	0	133	43	17	18	19	1.88
4920762--4920867	42	2.5	41	79	10	99	44	16	17	21	1.87
4932383--4932417	16	2.2	16	89	0	52	34	2	0	62	1.10
4936099--4936149	6	8.7	6	78	4	50	5	11	39	43	1.66
4936181--4936232	18	2.9	18	73	0	50	11	7	51	28	1.65
4936697--4936744	24	2.0	24	100	0	96	33	12	16	37	1.86
4938521--4938561	16	2.6	16	84	7	57	21	7	14	56	1.63
4958298--4958336	21	1.9	20	84	5	51	53	2	28	15	1.55
4962964--4962997	17	1.9	18	94	5	61	38	26	0	35	1.57
4973240--4973289	23	2.2	23	82	7	57	66	2	2	30	1.14
4976282--4976322	17	2.4	17	87	0	55	43	14	9	31	1.78
4981893--4982099	42	4.9	42	87	0	315	34	21	20	23	1.96
4982418--4982467	21	2.4	21	82	0	64	2	42	18	38	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4984967--4985005	18	2.2	17	86	13	53	33	0	20	46	1.51
4985231--4985306	23	3.3	23	86	0	107	21	18	27	32	1.96
4990671--4990716	7	6.0	7	90	9	56	30	0	17	52	1.45
4990678--4991633	9	107.2	9	78	3	943	31	1	18	48	1.56
4991740--4991785	7	6.6	7	78	16	51	28	0	10	60	1.30
4991727--4991800	27	2.8	26	77	6	85	33	1	10	54	1.44
4991740--4991785	15	3.3	15	79	17	62	28	0	10	60	1.30
4991922--4992069	61	2.4	61	81	8	176	47	8	4	40	1.52
4992000--4992039	16	2.6	15	76	7	53	47	7	0	45	1.31
4992048--4992080	17	1.9	17	93	0	57	51	9	3	36	1.49
4993729--4993806	39	2.0	39	97	0	147	37	6	38	17	1.76
4995802--4996026	115	2.0	113	81	8	260	26	21	18	33	1.97
4999935--4999969	6	5.8	6	100	0	70	82	0	0	17	0.66
5000332--5000365	11	3.2	11	91	4	52	52	14	0	32	1.42
5001845--5002423	189	2.9	193	82	6	603	31	13	19	34	1.91
5003307--5003355	17	2.8	18	81	3	64	51	0	4	44	1.20
5004495--5004542	23	2.1	23	96	0	87	25	12	22	39	1.89
5011915--5011949	10	3.7	10	85	14	56	91	0	0	8	0.42
5011915--5011949	18	1.9	18	100	0	70	91	0	0	8	0.42
5014778--5014812	13	2.7	13	90	0	61	85	5	8	0	0.73
5017720--5017753	7	4.9	7	100	0	68	29	0	0	70	0.87
5023048--5023091	2	22.0	2	100	0	88	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5025437--5025504	31	2.2	32	86	5	95	42	7	8	41	1.64
5027516--5027628	38	3.3	37	71	28	131	61	8	8	21	1.53
5027552--5027610	26	2.2	27	81	6	84	62	6	10	20	1.49
5028709--5028866	45	3.5	45	80	1	210	25	25	17	31	1.97
5028709--5028889	45	4.1	45	78	2	195	28	24	17	29	1.97
5028709--5028889	89	2.0	89	97	0	344	28	24	17	29	1.97
5028990--5029504	45	11.5	44	74	6	273	27	23	17	31	1.97
5028990--5029235	89	2.7	90	89	4	377	28	23	17	30	1.97
5029161--5029548	89	4.4	89	85	1	474	27	22	18	31	1.97
5029044--5029458	223	1.8	226	90	1	665	27	22	18	31	1.97
5028995--5029576	134	4.3	133	76	6	451	28	23	18	30	1.97
5029094--5029575	89	5.4	89	83	2	448	27	22	18	30	1.97
5035263--5035294	13	2.5	13	94	0	55	31	0	12	56	1.37
5035399--5035588	50	3.7	50	87	4	245	25	23	30	21	1.99
5035389--5035588	100	1.9	103	87	6	289	26	23	30	21	1.99
5050983--5051028	16	2.9	15	81	9	56	47	0	2	50	1.13
5054079--5054113	16	2.1	17	89	5	54	60	0	0	40	0.97
5059568--5059723	33	4.6	32	67	24	106	17	21	27	33	1.96
5059640--5059691	27	1.9	27	92	7	88	21	23	30	25	1.99
5059563--5059767	103	2.0	103	96	0	374	20	20	27	31	1.97
5059704--5059843	33	3.5	42	71	26	140	22	19	26	32	1.97
5059667--5059879	76	2.8	76	92	0	345	21	21	26	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5062997--5063131	33	3.7	34	71	23	114	28	25	21	24	1.99
5062999--5063211	76	2.8	77	89	1	320	30	25	20	23	1.99
5063187--5063238	27	1.9	27	96	0	95	26	30	21	21	1.98
5064972--5065031	29	2.0	30	84	9	79	60	3	1	35	1.23
5069511--5069546	2	18.0	2	94	0	63	52	0	0	47	1.00
5072048--5072073	12	2.2	12	100	0	52	46	0	0	53	1.00
5079895--5079953	31	1.9	31	85	0	82	28	23	15	32	1.95
5083461--5083489	3	9.7	3	100	0	58	0	34	0	65	0.93
5084445--5084479	18	2.0	17	88	5	52	20	37	11	31	1.88
5087588--5087622	12	2.9	12	100	0	70	34	0	14	51	1.42

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