genome.fa.s3.2.7.7.80.10.50.1000.21.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  21  of  150  ( 17918 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)
5532329--5532486	82	1.9	82	86	6	223	27	1	27	43	1.63
5532620--5532662	21	2.0	21	90	0	68	27	0	39	32	1.57
5537821--5538080	43	6.1	44	78	11	184	26	19	26	28	1.99
5537859--5538081	85	2.6	84	80	7	252	26	20	26	27	1.99
5537821--5538083	42	6.2	43	80	7	259	25	19	26	27	1.99
5540248--5540287	18	2.2	17	86	8	53	37	0	17	45	1.49
5541141--5541345	114	1.8	113	82	9	265	24	20	25	29	1.99
5541967--5542006	14	2.9	14	80	0	53	15	0	45	40	1.46
5542362--5542396	7	5.0	7	85	0	52	5	0	51	42	1.25
5543318--5543787	147	3.2	143	77	5	372	25	15	23	35	1.94
5545712--5546061	13	26.5	13	72	8	233	40	10	4	45	1.57
5545815--5546070	53	4.8	53	94	0	449	39	10	3	45	1.57
5546338--5546482	28	5.0	28	75	15	123	45	15	1	37	1.55
5546285--5546471	90	2.1	89	82	9	220	45	14	1	37	1.54
5546433--5546482	16	3.4	16	73	21	63	46	18	2	34	1.60
5546237--5546543	157	1.9	158	96	1	562	46	14	1	37	1.55
5546237--5546580	159	2.2	160	92	5	565	45	15	2	36	1.57
5546561--5546854	9	33.8	9	72	16	228	46	20	1	31	1.61
5546237--5546606	157	2.3	158	89	6	529	46	15	1	36	1.57
5546567--5546880	25	12.8	25	75	15	161	47	19	1	31	1.58
5546567--5546870	34	9.3	34	70	20	186	47	20	1	31	1.58
5546640--5546867	123	1.9	120	82	12	284	46	19	1	32	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5546843--5546883	16	2.6	16	96	0	73	48	12	0	39	1.41
5552377--5552445	21	3.3	21	91	0	84	33	20	43	2	1.67
5552891--5553044	42	3.6	42	88	0	218	27	21	17	33	1.96
5552894--5553057	85	1.9	84	86	1	229	26	20	17	35	1.94
5553118--5553157	21	1.9	21	94	0	71	47	27	15	10	1.77
5557962--5558002	19	2.2	18	91	4	64	12	0	7	80	0.90
5558337--5558365	2	14.5	2	100	0	58	48	0	0	51	1.00
5558740--5558777	19	2.0	20	84	5	51	26	2	13	57	1.49
5579349--5579523	96	1.8	97	83	3	237	45	19	20	14	1.85
5580560--5580584	11	2.3	11	100	0	50	16	0	32	52	1.44
5580652--5580684	15	2.2	15	100	0	66	33	0	21	45	1.52
5597607--5597667	28	2.2	29	80	14	74	34	9	9	45	1.70
5602835--5603007	50	3.4	51	80	8	185	40	12	15	32	1.84
5606841--5606925	34	2.5	34	84	3	100	38	23	5	31	1.79
5609010--5609197	102	1.9	102	85	3	263	37	17	11	33	1.86
5609345--5609550	9	22.0	9	69	18	84	61	1	5	31	1.28
5609407--5609459	19	2.7	20	91	5	81	67	0	5	26	1.12
5609409--5609546	29	4.8	28	68	16	77	61	1	7	29	1.31
5609427--5609528	48	2.1	48	82	7	118	61	0	7	29	1.30
5609774--5609843	28	2.5	28	81	6	79	28	2	2	65	1.21
5609957--5610183	89	2.5	90	86	0	303	34	9	18	37	1.83
5618205--5618265	31	2.0	31	86	0	86	39	11	18	31	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5620140--5620187	23	2.1	23	81	11	55	68	6	6	18	1.32
5634506--5634600	9	9.8	10	76	21	80	31	3	0	65	1.08
5634506--5634575	3	23.3	3	83	11	90	32	2	0	64	1.08
5638038--5638081	19	2.2	20	84	4	54	31	22	4	40	1.74
5638182--5638222	20	2.0	21	85	4	57	48	4	19	26	1.69
5644470--5644568	37	2.7	37	88	0	144	41	12	19	27	1.86
5646175--5646458	44	6.3	44	77	7	248	34	19	17	29	1.94
5646269--5646463	88	2.2	88	87	2	284	33	20	15	30	1.94
5648036--5648120	6	14.2	6	92	0	107	25	2	5	65	1.27
5652278--5652330	20	2.7	20	75	0	52	32	5	18	43	1.74
5664425--5664773	152	2.3	153	82	7	413	35	8	18	37	1.80
5664425--5664772	78	4.6	76	78	9	316	35	8	18	37	1.81
5668829--5669307	240	2.0	240	98	0	931	39	22	12	24	1.90
5670410--5670571	43	3.8	43	77	4	132	30	26	13	29	1.94
5681791--5681856	30	2.2	30	94	0	114	19	9	19	51	1.73
5685941--5686027	29	3.0	29	91	0	147	29	14	18	36	1.91
5688943--5688991	15	3.3	15	77	11	55	48	0	14	36	1.44
5689091--5689115	5	5.0	5	100	0	50	80	0	0	20	0.72
5690520--5690569	21	2.4	21	100	0	100	16	24	30	30	1.96
5690508--5690559	21	2.3	23	83	12	81	11	28	28	30	1.92
5692031--5692090	17	3.5	17	84	11	79	63	1	0	35	1.05
5692043--5692089	16	2.8	17	87	9	69	68	2	0	29	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5692033--5692090	25	2.3	26	88	8	84	65	1	0	32	1.03
5692031--5692090	9	7.1	8	83	12	68	63	1	0	35	1.05
5694158--5694185	2	14.0	2	100	0	56	50	0	0	50	1.00
5697299--5697337	3	13.0	3	100	0	78	33	0	0	66	0.92
5699121--5699149	2	14.5	2	100	0	58	48	0	0	51	1.00
5699232--5699256	8	3.1	8	100	0	50	12	0	0	88	0.53
5701443--5701506	29	2.2	29	88	0	92	20	21	35	21	1.96
5701995--5702043	18	2.6	19	78	18	57	22	2	2	73	1.04
5701994--5702043	22	2.3	22	83	10	66	22	2	2	74	1.03
5703187--5703289	5	20.4	5	82	5	91	35	1	23	38	1.66
5703189--5703245	30	1.9	30	100	0	114	33	1	19	45	1.61
5705499--5705549	25	2.0	25	85	7	68	58	9	3	27	1.47
5709431--5709473	21	2.0	21	81	0	50	58	6	0	34	1.25
5719907--5720094	94	2.0	94	97	0	358	30	9	32	27	1.88
5722009--5722153	72	2.0	72	98	0	281	27	20	24	28	1.99
5722478--5722585	54	2.0	54	85	3	146	16	22	27	33	1.95
5734653--5734685	9	3.7	9	100	0	66	36	30	9	24	1.86
5739834--5739866	2	16.5	2	93	0	57	48	3	0	48	1.17
5739833--5739884	12	4.1	13	82	9	54	50	3	7	38	1.50
5740361--5740411	15	3.4	14	81	10	57	56	5	3	33	1.42
5740383--5740427	18	2.5	18	82	10	56	55	2	4	37	1.32
5741652--5741693	17	2.5	17	88	0	57	14	0	9	76	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5748047--5748083	14	2.4	16	86	8	51	54	2	2	40	1.29
5758394--5758462	32	2.1	33	81	2	77	2	17	4	75	1.09
5758995--5759154	63	2.5	63	81	3	187	26	20	25	28	1.99
5759773--5759833	18	3.5	18	75	8	63	24	8	18	49	1.74
5759772--5759847	34	2.2	34	88	0	107	22	9	18	50	1.75
5770125--5770218	4	23.5	4	100	0	188	25	0	24	50	1.50
5770248--5770310	23	2.7	23	82	4	65	28	11	19	41	1.85
5770321--5770352	14	2.3	14	100	0	64	59	15	12	12	1.61
5771972--5772224	125	2.0	125	96	0	461	28	21	12	37	1.89
5774123--5774155	16	2.0	17	94	5	59	84	0	15	0	0.61
5777306--5777333	7	4.0	7	100	0	56	28	0	0	71	0.86
5777411--5777444	14	2.4	14	85	0	50	47	0	0	52	1.00
5777524--5777551	14	2.0	14	100	0	56	64	7	0	28	1.20
5789630--5789675	9	5.1	9	89	0	74	47	13	8	30	1.72
5789775--5789799	5	5.0	5	100	0	50	0	80	0	20	0.72
5790665--5790690	5	5.2	5	100	0	52	19	19	19	42	1.90
5790795--5790845	2	27.0	2	80	11	63	47	0	3	49	1.20
5791669--5791694	5	5.2	5	100	0	52	80	0	0	19	0.71
5791989--5792019	9	3.4	9	90	0	53	25	12	22	38	1.90
5797069--5797118	18	2.8	18	81	0	64	42	2	16	40	1.59
5797445--5797493	25	2.0	25	83	0	62	36	12	18	32	1.88
5803612--5803655	22	2.0	22	95	0	79	29	18	22	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5809115--5809154	21	1.9	21	84	0	53	67	2	2	27	1.16
5814859--5814956	49	2.0	49	92	4	162	39	15	21	23	1.91
5816079--5816104	13	2.0	13	100	0	52	53	15	0	30	1.42
5817340--5817378	17	2.3	17	86	0	51	20	30	35	12	1.90
5823593--5823660	31	2.2	31	86	0	91	32	13	13	41	1.83
5839639--5839707	30	2.3	29	82	2	84	23	26	11	39	1.88
5839725--5839807	30	2.8	30	88	0	130	27	27	9	34	1.88
5839637--5839856	89	2.5	89	84	1	271	24	27	11	36	1.90
5840650--5840679	16	1.9	15	93	6	51	40	13	0	46	1.43
5843389--5843443	25	2.2	24	87	3	74	30	16	29	23	1.96

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