genome.fa.s1.2.7.7.80.10.50.1000.146.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  146  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)
43625263--43625301	13	2.9	14	88	7	62	0	28	0	71	0.86
43625413--43625453	8	5.1	8	85	8	57	0	21	0	78	0.76
43626036--43626165	59	2.2	60	83	9	169	38	1	23	36	1.65
43626029--43626165	30	4.6	30	75	13	131	38	1	23	36	1.64
43626430--43627431	78	13.0	78	88	5	1122	36	19	15	28	1.92
43626430--43627431	157	6.5	156	86	5	1122	36	19	15	28	1.92
43626452--43627431	235	4.2	234	84	7	1096	36	19	15	28	1.92
43628318--43628356	9	4.4	9	87	6	62	0	0	10	89	0.48
43628318--43628346	15	1.9	15	100	0	58	0	0	10	89	0.48
43639358--43639435	19	4.1	19	77	6	59	42	10	10	37	1.73
43639374--43639417	19	2.3	19	88	4	61	45	6	4	43	1.51
43639396--43639597	35	5.6	34	70	13	118	45	10	11	33	1.74
43639470--43639526	21	2.7	21	78	10	71	43	10	7	38	1.66
43639464--43639526	22	3.0	22	82	13	78	39	9	7	42	1.67
43639340--43639632	18	16.2	18	73	13	201	45	9	11	33	1.72
43640459--43640526	28	2.5	28	83	7	77	0	29	0	70	0.87
43640490--43640528	13	2.9	14	88	7	62	0	28	0	71	0.86
43640652--43640685	12	2.7	13	86	9	52	0	17	0	82	0.67
43640652--43640695	18	2.4	19	85	11	65	2	18	0	79	0.83
43641264--43641410	30	5.0	30	74	16	119	38	4	23	33	1.76
43641863--43641900	16	2.3	17	86	4	51	39	13	0	47	1.42
43650621--43650661	20	2.0	20	86	9	57	14	14	4	65	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43651602--43651643	7	6.0	7	81	18	52	66	0	16	16	1.25
43651603--43651643	14	3.0	13	92	7	64	65	0	17	17	1.27
43651602--43651643	21	2.0	21	86	9	59	66	0	16	16	1.25
43652907--43653500	132	4.5	132	87	1	791	27	19	24	27	1.99
43653426--43653929	174	2.9	174	93	1	850	28	19	24	26	1.99
43655497--43655572	24	3.0	24	75	14	64	23	3	5	67	1.29
43660401--43660452	25	2.0	25	85	11	68	65	15	1	17	1.36
43660799--43660832	17	2.0	17	88	11	52	47	8	14	29	1.75
43662119--43662163	23	2.0	23	87	8	67	37	0	0	62	0.96
43662119--43662158	10	3.9	10	80	6	53	32	0	0	67	0.91
43662116--43662161	12	4.2	12	76	18	55	36	0	0	63	0.95
43669489--43669716	42	5.4	42	88	6	286	30	21	24	24	1.99
43669508--43669716	85	2.5	83	87	7	298	31	20	23	23	1.98
43670163--43670231	21	3.3	21	87	0	93	1	43	18	36	1.60
43675771--43676191	9	48.2	9	68	20	150	39	0	14	45	1.51
43675776--43675895	16	7.9	16	69	19	96	35	1	17	45	1.58
43675790--43675944	25	6.2	25	77	11	129	38	1	15	45	1.55
43675816--43675967	34	4.3	35	73	16	118	38	1	16	43	1.56
43675951--43675983	16	2.1	16	100	0	66	30	0	24	45	1.53
43675847--43675988	25	5.6	25	71	17	89	39	0	16	42	1.54
43675847--43676077	34	6.6	34	70	17	129	39	0	14	45	1.51
43676040--43676117	22	3.4	22	82	10	77	41	0	10	48	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43675969--43676208	34	7.1	34	68	24	159	40	0	11	47	1.43
43676121--43676172	21	2.5	21	90	0	86	38	0	11	50	1.39
43676751--43676788	2	19.5	2	94	5	69	52	0	0	47	1.00
43676820--43676861	17	2.5	17	80	3	50	42	0	11	45	1.41
43680804--43680843	15	2.7	14	85	11	53	42	40	0	17	1.49
43681344--43681662	41	7.8	41	82	2	365	36	23	24	15	1.94
43681761--43681836	40	1.9	40	83	0	98	15	25	22	36	1.93
43692443--43692493	20	2.6	20	81	3	68	54	1	0	43	1.11
43693637--43693706	34	2.0	35	91	2	115	45	14	4	35	1.64
43699609--43699665	3	19.3	3	87	3	80	33	1	0	64	1.04
43699664--43699738	3	25.0	3	100	0	150	33	33	0	33	1.58
43703626--43703674	15	3.3	14	80	8	53	81	4	12	2	0.91
43704579--43705445	89	9.8	89	82	1	925	28	23	22	24	1.99
43705494--43711595	50	122.4	50	66	4	1613	31	20	20	25	1.97
43705500--43708360	100	28.8	100	83	2	3201	32	20	20	25	1.97
43705500--43708360	299	9.6	299	83	2	3217	32	20	20	25	1.97
43708463--43722788	100	143.9	100	77	2	6748	30	19	19	24	1.94
43711702--43712855	50	23.0	49	64	8	178	32	21	20	25	1.97
43712019--43713001	50	19.5	51	66	7	264	31	20	21	25	1.98
43713524--43715280	50	35.3	50	62	12	391	32	21	21	25	1.98
43713446--43716065	397	6.6	397	86	2	3032	32	21	20	25	1.98
43716503--43717315	50	16.3	50	67	2	403	32	21	21	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43716657--43716978	149	2.2	150	84	1	423	33	20	21	24	1.97
43716596--43717080	249	2.0	248	89	2	742	32	20	21	25	1.97
43717450--43723918	50	129.9	50	67	8	2408	32	20	20	26	1.98
43717450--43717971	99	5.3	99	82	4	541	33	21	19	25	1.97
43738463--43739462	100	10.0	100	83	3	1101	32	21	21	25	1.98
43738463--43739444	50	19.7	50	67	6	481	32	21	21	25	1.98
43739633--43739899	50	5.3	50	70	12	197	34	22	20	23	1.97
43739570--43742685	100	31.3	100	82	3	3203	32	21	20	25	1.97
43740033--43740219	50	3.7	50	69	9	121	31	22	20	25	1.98
43740086--43742652	50	51.7	51	64	12	371	32	21	20	26	1.97
43742803--43743087	100	2.9	100	80	3	281	32	20	22	24	1.97
43743212--43744020	199	4.1	199	81	3	919	32	22	20	25	1.98
43743258--43749049	50	116.1	50	68	4	2580	32	21	20	25	1.98
43744003--43749049	100	50.6	99	80	3	3450	32	20	21	25	1.97
43749149--43749263	45	2.6	44	84	4	142	25	21	26	26	2.00
43750839--43751059	3	75.3	3	70	9	107	30	6	3	59	1.39
43757681--43757740	12	5.5	11	75	16	54	25	5	0	70	1.08
43757685--43757740	21	2.7	20	78	15	60	23	5	0	71	1.06
43757682--43757744	17	3.7	17	74	18	60	23	4	0	71	1.05
43778597--43778665	26	2.6	26	88	6	95	26	23	18	31	1.97
43778785--43778848	31	2.1	31	100	0	128	37	18	9	34	1.83
43779971--43780015	14	3.1	14	84	6	54	4	20	0	75	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43780031--43780075	23	2.0	23	81	0	54	4	4	8	82	0.94
43786598--43786628	2	15.5	2	93	0	53	48	0	3	48	1.17
43794021--43794069	20	2.7	18	77	22	57	51	4	2	42	1.32
43796509--43796625	61	1.9	61	84	5	155	41	8	14	35	1.77
43802207--43802246	20	2.0	20	90	0	62	27	10	12	50	1.72
43802192--43802258	34	1.9	35	90	3	109	31	8	13	46	1.74
43802186--43802262	14	5.0	15	71	20	52	33	9	14	42	1.77
43803756--43803943	96	2.0	96	84	0	250	32	17	14	35	1.90
43823872--43823922	25	2.0	25	85	7	68	45	3	0	50	1.20
43824014--43824050	16	2.3	17	81	13	51	54	2	2	40	1.29
43828707--43828748	22	1.9	22	90	0	66	69	0	9	21	1.17
43828729--43828810	38	2.2	37	80	2	92	68	1	7	23	1.22
43830144--43830173	15	2.0	15	93	0	51	0	3	20	76	0.92
43830143--43830173	16	2.0	15	93	6	53	0	3	19	77	0.90
43830329--43831088	44	16.7	44	73	9	452	29	18	18	33	1.95
43830361--43830774	89	4.7	89	83	2	442	28	19	18	34	1.95
43830313--43830806	133	3.7	133	78	4	453	28	19	18	33	1.95
43830967--43831099	46	2.7	51	71	18	136	30	16	18	33	1.94
43830963--43831135	51	3.5	50	72	15	144	31	17	17	32	1.94
43837132--43837586	44	10.3	44	80	1	433	28	19	18	34	1.95
43837132--43837579	89	5.1	88	82	1	475	28	19	18	34	1.95
43837141--43837586	133	3.4	133	81	2	473	28	19	17	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43838834--43838872	20	2.0	20	85	5	53	56	5	7	30	1.49
43842532--43842579	6	8.0	6	100	0	96	33	0	16	50	1.46
43845479--43845511	17	2.0	17	88	5	50	57	0	0	42	0.98
43849165--43849381	76	2.9	75	81	5	240	40	18	14	26	1.89
43849692--43849725	2	16.5	2	93	6	59	50	2	0	47	1.16
43850544--43850601	28	2.1	28	100	0	116	27	10	6	55	1.59
43850829--43851031	76	2.7	75	76	6	205	36	19	17	26	1.94
43853887--43854001	43	2.7	43	82	6	144	26	14	28	30	1.95
43854327--43854362	15	2.3	16	90	4	56	36	5	2	55	1.38
43854327--43854378	16	3.3	15	84	7	59	36	7	1	53	1.41

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