genome.fa.s1.2.7.7.80.10.50.1000.28.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  28  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)
9167907--9167946	3	13.3	3	100	0	80	67	0	0	32	0.91
9169078--9169321	45	5.4	45	79	7	233	31	20	16	31	1.95
9169018--9169321	94	3.3	93	81	5	312	29	20	17	32	1.95
9176756--9176810	3	18.3	3	100	0	110	65	0	0	34	0.93
9176826--9176855	15	2.0	15	100	0	60	60	13	6	20	1.55
9176903--9176947	23	2.0	23	100	0	90	57	2	8	31	1.41
9177141--9177175	3	11.7	3	87	0	52	62	2	0	34	1.10
9178326--9178359	17	2.0	17	94	0	59	11	8	41	38	1.73
9178968--9179081	44	2.6	44	81	2	131	28	25	21	25	1.99
9178968--9179110	44	3.3	43	72	11	121	26	26	19	27	1.99
9179104--9179706	50	12.1	50	72	1	445	25	20	21	32	1.97
9179122--9179704	100	5.8	100	86	0	770	24	20	21	33	1.97
9181097--9181236	49	2.9	48	82	6	158	13	20	20	45	1.84
9185893--9185938	3	15.3	3	100	0	92	67	0	0	32	0.91
9186071--9186126	11	5.1	11	76	6	51	51	1	3	42	1.29
9186247--9186329	3	27.7	3	100	0	166	67	0	0	32	0.91
9187623--9187754	26	5.3	25	72	14	94	36	22	21	18	1.95
9187623--9187729	25	4.3	23	75	12	72	37	22	21	18	1.94
9189111--9189162	24	2.2	24	85	0	68	53	9	3	32	1.51
9192310--9192350	3	13.7	3	94	0	73	31	2	0	65	1.05
9192346--9192372	14	1.9	14	100	0	54	14	0	7	77	0.97
9201980--9202012	8	4.1	8	85	14	50	87	3	9	0	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9201981--9202012	16	1.9	17	93	6	57	87	3	9	0	0.64
9213108--9213190	3	27.7	3	83	9	98	31	1	1	66	1.07
9222685--9222717	16	2.1	16	88	5	50	75	9	6	9	1.18
9228389--9228462	28	2.7	26	77	10	76	72	5	9	12	1.25
9228828--9228861	13	2.7	13	86	4	52	73	0	11	14	1.10
9230131--9230229	49	2.0	49	88	0	144	29	18	25	27	1.98
9230663--9230711	25	1.9	26	83	4	64	40	36	8	14	1.75
9233377--9233410	2	17.0	2	100	0	68	50	0	0	50	1.00
9235747--9235775	2	14.5	2	100	0	58	51	0	0	48	1.00
9246006--9246043	3	12.7	3	100	0	76	68	0	31	0	0.90
9246758--9246798	20	2.0	20	85	4	55	39	4	2	53	1.35
9252385--9252419	15	2.3	15	90	0	52	5	42	42	8	1.59
9252386--9252424	15	2.6	15	87	0	51	5	43	41	10	1.61
9253655--9253684	3	10.0	3	100	0	60	66	0	0	33	0.92
9254567--9254625	24	2.6	23	81	7	59	54	6	3	35	1.44
9261385--9261435	24	2.2	24	85	3	68	33	41	1	23	1.66
9264486--9264528	21	2.0	21	82	8	52	37	11	4	46	1.61
9265682--9265714	16	2.0	17	88	5	50	42	0	9	48	1.35
9268501--9268549	12	4.3	12	82	12	59	61	0	0	38	0.96
9268513--9268543	16	1.9	16	93	0	53	64	0	0	35	0.94
9268506--9268549	6	7.3	6	87	10	54	61	0	0	38	0.96
9270276--9270369	47	2.0	47	97	0	179	41	6	9	42	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9277633--9277689	23	2.6	21	81	8	62	57	1	1	38	1.19
9277633--9277677	20	2.1	21	84	12	56	62	0	0	37	0.96
9279569--9279621	20	2.7	20	81	0	70	56	15	22	5	1.60
9279560--9279628	5	13.8	5	75	6	50	55	15	21	7	1.65
9279596--9279648	15	3.5	15	76	0	52	56	16	20	5	1.60
9280757--9280836	41	2.0	41	82	0	97	28	32	20	18	1.96
9292809--9292846	6	6.3	6	100	0	76	34	0	50	15	1.45
9292813--9292853	18	2.3	18	86	0	55	34	2	46	17	1.61
9294887--9294972	30	3.0	29	85	12	117	43	6	24	25	1.79
9294885--9294973	25	3.1	30	85	12	125	41	6	25	25	1.80
9299575--9299621	15	3.1	15	73	11	51	40	8	21	29	1.83
9299543--9299630	25	3.1	30	82	12	114	42	6	23	27	1.79
9299776--9299810	2	17.5	2	100	0	70	0	48	0	51	1.00
9304269--9304300	6	5.2	6	96	3	55	81	0	3	15	0.82
9304261--9304300	12	3.2	13	85	7	55	77	0	2	20	0.88
9304796--9304849	27	2.0	27	85	0	72	22	24	29	24	1.99
9309074--9309186	56	2.0	56	96	0	208	19	37	5	38	1.75
9314613--9314711	20	4.9	19	71	7	65	13	27	22	37	1.91
9314615--9314711	40	2.4	40	81	3	115	12	27	21	38	1.89
9318822--9318946	66	1.9	65	81	6	153	12	26	18	43	1.85
9328704--9328818	43	2.7	43	87	2	169	18	17	28	35	1.93
9338655--9338818	43	3.8	43	82	10	210	24	19	26	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9342829--9342891	24	2.5	26	82	7	67	53	0	7	38	1.30
9342932--9342964	15	2.1	16	94	5	59	63	0	0	36	0.95
9343634--9343667	8	4.2	8	89	10	52	88	2	0	8	0.62
9343624--9343667	16	2.8	16	80	13	54	84	4	2	9	0.85
9344414--9345444	128	8.0	128	91	0	1587	25	20	21	32	1.97
9344414--9345444	385	2.7	385	91	1	1629	25	20	21	32	1.97
9344423--9345391	44	22.6	45	64	15	207	25	20	21	32	1.98
9346720--9346753	16	2.1	16	100	0	68	23	23	29	23	1.99
9351613--9351730	56	2.1	57	79	7	125	56	1	6	34	1.36
9351978--9352010	15	2.1	16	94	5	59	63	0	0	36	0.95
9355951--9355997	16	2.9	17	84	9	55	59	2	0	38	1.09
9355944--9355996	16	3.6	16	78	19	53	60	1	0	37	1.08
9355962--9356010	16	2.9	17	82	11	57	57	6	2	34	1.35
9374023--9374074	27	1.9	27	84	7	70	42	9	15	32	1.79
9377875--9377935	31	2.0	31	83	6	79	21	42	16	19	1.89
9382677--9382716	14	3.1	14	82	13	50	75	5	10	10	1.19
9383063--9383268	89	2.3	90	88	4	301	36	21	9	32	1.85
9383267--9383419	10	16.8	10	69	14	75	64	1	1	32	1.13
9383268--9383456	27	7.0	26	73	12	130	62	2	2	32	1.23
9383675--9383710	19	2.0	19	89	10	58	44	2	0	52	1.15
9383757--9383972	87	2.5	87	85	6	285	31	8	20	38	1.83
9387331--9387374	19	2.3	20	84	7	56	27	20	11	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9389304--9389349	21	2.2	21	84	0	56	26	21	2	50	1.60
9390082--9390166	45	1.9	45	85	2	118	43	20	24	11	1.85
9391657--9391739	43	1.9	43	82	4	105	27	19	24	28	1.98
9391468--9392398	132	7.0	132	86	2	1131	27	20	24	27	1.99
9395770--9395981	109	2.0	107	86	5	302	31	18	17	32	1.95
9396191--9396243	18	3.1	16	81	8	52	75	1	1	20	0.99
9396217--9396248	6	5.5	6	92	7	57	84	0	0	15	0.63
9396217--9396249	11	2.9	11	95	4	57	81	0	0	18	0.68
9400313--9400369	29	1.9	30	89	3	89	31	8	12	47	1.72
9402153--9402190	20	1.9	20	84	10	51	60	2	5	31	1.33
9402879--9403026	40	3.7	40	85	0	206	29	20	19	30	1.97
9402919--9403169	137	1.8	137	86	1	369	30	17	20	31	1.96
9403069--9403159	40	2.3	40	86	0	128	28	17	21	31	1.96
9407697--9407735	15	2.6	16	88	12	64	41	5	5	48	1.47
9411397--9411446	18	2.8	18	81	6	57	28	14	10	48	1.75
9411429--9411460	15	2.2	15	94	5	57	37	3	6	53	1.42
9413221--9413252	15	2.1	15	94	0	55	68	9	6	15	1.36
9413273--9413297	4	6.2	4	100	0	50	24	0	0	76	0.80
9415259--9415367	40	2.8	40	85	1	157	33	21	23	21	1.97
9415258--9415395	40	3.5	39	80	2	125	37	19	20	22	1.94
9415429--9415583	41	3.8	41	84	3	195	21	20	29	29	1.98
9415956--9416088	14	9.3	14	69	14	58	22	1	32	43	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9416038--9416089	7	7.3	7	78	10	52	19	0	34	46	1.50
9417524--9417664	43	3.3	43	79	5	160	29	17	24	29	1.97
9419130--9419178	22	2.2	21	89	7	71	61	4	0	34	1.15
9420869--9420903	15	2.4	15	90	4	54	48	0	8	42	1.33
9420907--9420939	18	1.9	17	88	11	50	30	0	12	57	1.35
9423122--9423148	13	2.1	13	100	0	54	22	18	29	29	1.97
9428370--9428420	26	1.9	27	92	4	86	37	5	3	52	1.44
9446736--9446790	21	2.6	22	77	8	60	49	3	0	47	1.19
9451291--9451351	22	2.8	22	92	0	95	8	29	1	60	1.35
9459646--9459681	17	2.1	18	89	5	56	16	33	22	27	1.95

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