genome.fa.s1.2.7.7.80.10.50.1000.142.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  142  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)
42490922--42490983	31	2.0	30	87	9	90	58	22	3	16	1.52
42491216--42491280	34	1.9	34	87	0	94	43	16	10	29	1.82
42491831--42491905	31	2.4	31	95	0	141	18	40	26	14	1.90
42492281--42492343	26	2.5	26	82	7	76	71	4	20	3	1.18
42492301--42492347	13	3.6	13	75	11	51	72	2	23	2	1.06
42501393--42501516	61	2.0	61	100	0	248	33	11	24	31	1.90
42502510--42502632	58	2.1	58	87	3	176	13	8	17	60	1.58
42502616--42502659	19	2.3	19	88	0	61	13	9	25	52	1.70
42505592--42505655	31	2.1	31	83	13	80	40	1	1	56	1.18
42506002--42506028	9	3.0	9	100	0	54	66	0	0	33	0.92
42506674--42506793	59	2.0	59	98	0	231	23	14	16	45	1.84
42513847--42513891	23	1.9	24	82	13	58	0	24	2	73	0.95
42516855--42516943	30	3.0	30	81	0	106	40	21	16	21	1.91
42517483--42517519	16	2.3	16	95	0	65	37	16	16	29	1.90
42521676--42521711	17	2.1	17	90	10	56	61	5	5	27	1.41
42521793--42521835	18	2.3	19	88	4	61	72	2	0	25	0.97
42521600--42521872	9	28.7	9	63	20	51	60	4	3	32	1.33
42522287--42522510	9	24.6	9	65	18	81	33	2	3	60	1.27
42522685--42522724	3	13.3	3	94	0	71	62	0	0	37	0.95
42522961--42523014	27	2.0	27	82	10	65	44	12	1	40	1.54
42524701--42524748	24	2.0	24	95	0	87	43	8	14	33	1.75
42526890--42526967	39	2.0	39	92	0	129	28	30	3	37	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42533300--42533345	20	2.3	20	79	17	60	13	23	6	56	1.60
42533594--42533739	50	2.9	50	78	0	157	23	28	20	28	1.99
42535525--42535675	79	1.9	78	81	6	180	37	0	33	28	1.62
42536182--42536242	26	2.3	26	83	5	79	36	13	9	40	1.77
42539009--42539424	94	4.4	94	79	4	399	33	17	26	23	1.96
42539065--42539405	188	1.8	188	83	1	459	34	16	25	23	1.95
42546211--42546249	19	2.1	18	85	4	51	35	10	2	51	1.50
42548646--42548720	36	2.1	36	85	5	98	38	14	17	29	1.89
42555252--42555277	9	2.9	9	100	0	52	80	7	0	11	0.89
42562724--42562780	21	2.7	21	81	8	71	36	8	33	21	1.84
42568015--42568090	3	25.3	3	94	5	136	32	32	0	34	1.58
42573529--42573638	32	3.7	28	73	14	69	31	9	11	47	1.72
42576842--42576876	18	1.9	18	88	0	52	14	0	25	60	1.35
42580968--42581277	35	8.8	35	74	9	186	21	23	21	32	1.98
42580967--42581277	69	4.4	69	78	9	315	22	23	21	32	1.98
42587995--42588037	16	2.6	17	88	3	61	6	13	2	76	1.08
42590017--42590060	22	2.0	22	100	0	88	22	22	18	36	1.95
42601063--42601167	31	3.4	31	77	7	115	41	2	3	51	1.35
42601041--42601173	61	2.2	61	93	0	221	43	2	4	49	1.35
42602082--42602111	9	3.3	9	95	0	51	33	6	10	50	1.62
42608423--42608515	44	2.1	44	89	4	141	36	30	4	29	1.77
42611383--42611437	3	18.3	3	96	0	101	34	32	0	32	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42612182--42612225	20	2.1	21	84	12	56	70	2	22	4	1.17
42612180--42612233	21	2.5	21	80	14	65	70	1	24	3	1.13
42612205--42612246	15	2.9	14	89	10	66	76	0	21	2	0.90
42612564--42612617	19	2.9	18	81	8	72	20	1	3	74	1.07
42623082--42623120	20	2.0	20	100	0	78	35	15	5	43	1.69
42624036--42624089	3	19.0	3	78	17	62	66	0	31	1	1.02
42624038--42624094	14	4.1	14	76	17	55	68	0	28	3	1.06
42624036--42624086	11	4.8	11	77	22	56	66	0	31	1	1.03
42624036--42624094	20	3.1	18	78	21	66	67	0	28	3	1.06
42625638--42625683	18	2.6	18	89	0	65	15	41	30	13	1.85
42630477--42630673	105	1.9	105	81	2	243	32	17	24	24	1.97
42633135--42633180	16	3.0	16	84	6	60	47	0	4	47	1.21
42634177--42634201	13	1.9	13	100	0	50	40	0	0	60	0.97
42640645--42640669	13	1.9	13	100	0	50	52	0	0	48	1.00
42640906--42640961	24	2.3	23	82	8	76	39	0	1	58	1.08
42645115--42645165	26	2.0	26	92	0	84	41	5	1	50	1.37
42646098--42646141	21	2.0	22	86	4	63	15	18	9	56	1.65
42652991--42653028	14	2.8	13	92	7	67	47	5	10	36	1.61
42653266--42653458	34	5.6	34	78	2	152	19	21	18	40	1.91
42653266--42653452	103	1.8	103	86	0	275	19	20	18	40	1.91
42656136--42656178	21	2.0	23	86	9	63	32	13	9	44	1.76
42660755--42660788	15	2.3	15	100	0	68	29	17	14	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42663727--42663784	30	1.9	30	89	0	89	41	3	24	31	1.71
42663997--42664027	13	2.4	13	94	0	53	32	0	12	54	1.38
42664122--42664363	50	4.7	50	86	3	286	27	23	28	19	1.99
42664122--42664371	100	2.4	103	87	5	353	26	23	28	20	1.99
42665740--42665891	21	7.3	21	75	7	114	18	19	15	46	1.84
42665743--42665893	42	3.6	42	85	3	173	19	19	15	45	1.86
42665750--42665872	63	2.0	63	83	3	158	20	21	13	44	1.85
42677317--42677367	2	25.5	2	100	0	102	49	0	0	50	1.00
42678917--42678947	2	16.0	2	93	6	55	51	0	0	48	1.00
42698026--42698052	2	13.5	2	100	0	54	48	0	0	51	1.00
42699433--42699803	47	7.9	47	89	1	521	43	14	12	28	1.82
42700746--42700844	28	3.6	27	81	11	112	28	28	12	31	1.92
42706435--42706564	64	2.0	62	81	7	145	26	20	5	47	1.71
42713258--42713306	14	3.4	15	76	23	52	71	16	4	8	1.26
42716546--42716576	3	10.3	3	92	0	53	3	0	64	32	1.09
42722675--42722723	15	3.5	15	72	16	59	16	48	0	34	1.46
42724311--42724356	21	2.2	21	88	3	67	36	6	4	52	1.47
42727100--42727154	21	2.6	21	94	0	92	29	25	29	16	1.97
42736451--42736481	15	2.1	15	93	0	53	35	3	19	41	1.67
42736436--42736484	18	2.7	18	77	0	62	40	2	22	34	1.66
42736526--42736560	18	1.9	18	94	0	61	68	0	22	8	1.16
42737583--42737624	15	2.7	16	78	14	52	45	2	0	52	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42739415--42739454	21	1.9	21	85	10	55	22	2	7	67	1.28
42739526--42739564	11	3.4	11	86	10	51	51	0	2	46	1.14
42744958--42745294	72	4.7	71	85	2	381	54	15	5	25	1.63
42746586--42746624	20	2.0	20	90	10	62	15	23	5	56	1.59
42751521--42751601	40	2.0	40	92	0	135	38	16	18	27	1.92
42752306--42752361	21	2.6	21	85	2	76	16	19	25	39	1.91
42755181--42755239	28	2.1	28	100	0	118	23	30	15	30	1.95
42755924--42756010	37	2.4	37	94	0	147	25	1	29	43	1.62
42757343--42757379	2	19.0	2	88	5	58	48	0	2	48	1.15
42759347--42759395	14	3.5	14	79	20	66	30	0	18	51	1.47
42759335--42759394	28	2.1	28	100	0	120	30	0	18	51	1.46
42762902--42762926	5	5.0	5	100	0	50	20	0	20	60	1.37
42779584--42779622	20	2.0	20	84	0	51	43	7	23	25	1.80
42779927--42779951	6	4.2	6	100	0	50	64	16	20	0	1.30
42781144--42781184	15	2.7	15	85	7	57	65	2	4	26	1.25
42781144--42781188	18	2.5	17	83	16	56	64	2	4	28	1.25
42787141--42787294	56	2.7	55	87	5	209	29	7	16	45	1.76
42787309--42787364	2	28.0	2	100	0	112	50	0	0	50	1.00
42793402--42793478	40	1.9	41	81	2	93	31	19	25	23	1.98
42793574--42793878	41	7.4	41	92	1	504	17	22	29	30	1.97
42794050--42794136	21	4.1	21	73	10	61	25	0	39	35	1.56
42794399--42794500	46	2.2	46	84	8	125	38	0	12	49	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42794553--42794580	14	2.0	14	100	0	56	50	0	0	50	1.00
42794720--42794952	83	2.8	82	83	4	299	41	15	14	29	1.86
42797713--42797739	13	2.1	13	100	0	54	22	37	22	18	1.95
42799771--42800038	43	6.3	43	81	4	292	27	17	29	25	1.98
42799769--42800038	129	2.1	127	83	6	339	27	17	29	26	1.97
42800419--42800496	24	3.4	22	75	19	70	70	6	3	19	1.25
42800636--42800812	90	2.0	90	89	0	273	27	24	23	24	2.00
42800723--42800936	114	1.9	114	90	0	338	25	21	26	26	2.00
42800937--42801083	73	2.0	73	90	0	231	25	22	25	26	2.00
42801329--42801366	15	2.6	15	87	4	51	26	0	36	36	1.57

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