genome.fa.s6.2.7.7.80.10.50.1000.131.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  131  of  168  ( 20060 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)
38217891--38217956	19	3.3	19	75	16	53	57	4	0	37	1.19
38217948--38217984	19	1.9	19	88	0	56	54	5	0	40	1.24
38217954--38218028	38	1.9	40	86	10	111	58	5	1	34	1.29
38228632--38228998	114	3.2	112	89	2	545	23	22	26	27	1.99
38228931--38229040	41	2.7	41	91	0	166	18	20	30	30	1.96
38228817--38229154	155	2.2	155	88	3	493	22	21	28	27	1.99
38228973--38229244	114	2.4	113	89	4	397	23	22	27	26	1.99
38228699--38229244	269	2.0	269	86	3	760	23	21	27	27	1.99
38229456--38229566	15	7.5	15	72	12	77	21	0	40	36	1.60
38229523--38229575	15	3.5	15	89	2	52	18	1	45	33	1.61
38229848--38229949	17	5.6	17	71	21	82	17	2	45	34	1.64
38229839--38229949	37	3.0	37	94	2	188	17	3	45	34	1.66
38229868--38229935	20	3.5	20	80	11	88	16	4	47	32	1.66
38231399--38231449	26	1.9	27	96	4	95	43	19	25	11	1.85
38232246--38232401	43	3.6	43	84	0	204	21	19	26	33	1.97
38234186--38234212	7	3.9	7	100	0	54	40	0	29	29	1.57
38234766--38234795	15	2.0	15	100	0	60	26	13	13	46	1.80
38240202--38240337	51	2.7	52	76	8	129	44	2	11	41	1.53
38252696--38252731	2	18.0	2	100	0	72	50	0	0	50	1.00
38254022--38254129	57	1.9	57	94	0	189	31	20	13	34	1.92
38268528--38268557	2	15.0	2	100	0	60	50	0	0	50	1.00
38274507--38274557	25	2.0	25	100	0	102	27	21	15	35	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38275801--38275844	17	2.6	16	82	13	52	52	2	0	45	1.13
38282675--38282702	2	14.0	2	100	0	56	50	0	0	50	1.00
38292623--38292652	2	15.0	2	92	0	51	50	3	0	46	1.18
38302468--38302493	2	13.0	2	100	0	52	50	0	0	50	1.00
38303234--38303261	2	14.0	2	100	0	56	0	50	0	50	1.00
38303261--38303288	2	14.0	2	100	0	56	50	0	0	50	1.00
38307046--38307298	84	3.0	83	91	2	398	18	19	26	35	1.95
38307328--38307495	84	2.0	84	91	0	273	16	19	27	35	1.94
38307130--38307598	198	2.4	196	89	4	713	21	18	26	33	1.97
38307412--38307888	113	4.3	113	79	10	481	23	17	26	32	1.96
38308470--38309142	340	2.0	332	92	4	1109	29	5	22	42	1.77
38309329--38309383	28	2.0	28	88	0	83	49	7	5	38	1.54
38310015--38310071	28	2.1	28	83	3	71	61	7	5	26	1.43
38310028--38310082	28	2.0	28	92	0	92	54	7	5	32	1.51
38310749--38310778	14	2.1	14	100	0	60	26	13	6	53	1.64
38311466--38311581	55	2.1	55	96	0	214	36	6	10	46	1.65
38311653--38311715	32	2.0	32	81	6	74	47	17	3	31	1.63
38311791--38311849	22	2.7	22	100	0	118	45	15	0	38	1.46
38311744--38312107	9	42.0	9	65	22	140	45	18	1	33	1.60
38311826--38311947	34	3.6	34	70	16	117	45	16	2	35	1.61
38311835--38311991	68	2.3	68	97	0	296	45	19	3	32	1.66
38311953--38312016	25	2.6	25	97	0	119	46	21	0	31	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38311835--38312030	68	2.9	68	88	4	218	46	18	2	31	1.63
38312031--38312107	23	3.5	23	85	5	106	41	19	0	38	1.52
38317994--38318064	21	3.4	21	84	0	88	33	18	43	4	1.69
38318400--38318493	42	2.3	42	85	7	122	35	19	24	21	1.96
38323682--38323737	2	28.0	2	100	0	112	50	0	0	50	1.00
38325859--38325905	24	2.0	22	84	8	58	74	0	8	17	1.05
38328913--38328947	6	5.8	6	100	0	70	0	68	0	31	0.90
38335143--38335178	14	2.4	15	86	13	56	44	0	2	52	1.15
38335369--38335406	18	2.2	18	85	4	51	47	0	2	50	1.15
38340050--38340087	17	2.2	18	85	4	51	31	26	5	36	1.79
38340304--38340382	40	2.0	40	92	0	131	29	6	5	59	1.43
38341660--38341844	92	2.0	93	95	1	336	16	11	15	56	1.66
38346002--38346026	5	5.0	5	100	0	50	20	20	20	40	1.92
38346944--38347000	21	2.7	21	78	8	62	70	5	3	21	1.22
38353453--38353497	6	7.5	6	97	0	63	0	60	0	40	0.97
38356051--38356137	33	2.7	33	78	8	97	47	17	9	26	1.77
38356113--38356189	14	5.0	15	71	20	52	42	15	9	32	1.78
38356129--38356168	20	2.0	20	90	0	62	50	12	10	27	1.72
38356117--38356183	34	1.9	35	90	3	109	46	13	8	31	1.74
38356152--38356191	14	2.9	14	84	0	53	42	17	7	32	1.77
38358471--38358528	30	1.9	30	85	0	80	41	1	24	32	1.65
38359094--38359151	30	1.9	30	85	0	80	32	24	1	41	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38366127--38366159	17	1.9	17	100	0	66	42	9	0	48	1.35
38366155--38366387	127	1.8	127	95	1	423	24	12	26	35	1.92
38368872--38368902	2	15.5	2	100	0	62	0	48	0	51	1.00
38375822--38375877	24	2.4	23	82	8	60	41	23	16	19	1.90
38379942--38379970	2	14.5	2	100	0	58	48	0	0	51	1.00
38380142--38380185	2	22.0	2	100	0	88	50	0	0	50	1.00
38381773--38381967	97	2.0	97	95	0	354	29	12	21	36	1.90
38403808--38403832	6	4.2	6	100	0	50	52	0	0	48	1.00
38404249--38404302	28	1.9	28	81	7	65	38	11	12	37	1.79
38404341--38404378	20	1.9	19	89	5	58	23	0	21	55	1.44
38406542--38406600	9	6.4	9	81	11	66	40	25	10	23	1.86
38406662--38406751	40	2.2	40	98	0	171	14	2	30	53	1.53
38406730--38406759	13	2.3	13	100	0	60	16	0	43	40	1.48
38407875--38407907	2	16.0	2	93	6	57	48	3	0	48	1.17
38408812--38408840	14	2.0	15	93	6	51	37	0	0	62	0.96
38409161--38409205	16	2.7	17	82	6	56	40	0	0	60	0.97
38409189--38409256	11	6.4	11	74	17	54	35	2	0	61	1.11
38409172--38409265	41	2.3	40	91	5	163	32	2	0	64	1.05
38409198--38409271	30	2.4	31	82	11	89	36	2	0	60	1.11
38409239--38409278	21	1.9	21	89	0	62	37	2	0	60	1.11
38409238--38409292	21	2.5	20	80	13	56	38	1	3	56	1.28
38409341--38409365	13	1.9	13	100	0	50	32	20	16	32	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38409639--38409698	30	2.0	31	86	3	86	20	40	0	40	1.52
38415138--38415177	13	3.1	13	81	0	53	35	5	15	45	1.68
38416719--38416768	21	2.4	21	86	6	66	52	0	0	48	1.00
38416733--38416772	19	2.0	21	85	9	57	57	0	0	42	0.98
38424924--38424961	19	2.1	18	85	9	51	50	0	7	42	1.31
38426717--38426977	133	2.0	133	81	7	316	36	18	11	34	1.87
38427046--38427096	26	2.0	24	85	7	66	43	5	7	43	1.57
38427765--38427841	14	5.0	15	71	20	52	42	14	9	33	1.77
38427781--38427820	20	2.0	20	90	0	62	50	12	10	27	1.72
38427769--38427835	34	1.9	35	90	3	109	46	13	8	31	1.74
38440959--38440994	18	2.0	18	100	0	72	33	11	33	22	1.89
38443872--38443906	17	2.1	17	89	5	54	34	20	0	45	1.51
38444597--38444635	19	2.1	19	85	0	51	61	0	0	38	0.96
38452674--38452707	17	1.9	17	88	5	50	55	0	8	35	1.31
38457672--38457722	24	2.0	25	82	17	61	33	9	3	52	1.53
38457844--38457877	15	2.3	15	90	10	52	35	0	0	64	0.94
38469772--38469934	80	2.0	80	90	2	256	23	15	22	38	1.92
38470098--38470154	30	1.9	30	89	7	89	63	0	0	36	0.95
38490136--38490165	6	5.0	6	100	0	60	50	16	33	0	1.46
38497471--38497679	101	2.1	101	84	0	265	34	15	21	28	1.93
38505395--38505547	49	3.1	48	79	12	161	18	28	9	43	1.80
38507470--38507619	43	3.5	43	76	1	140	24	16	29	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38509677--38509721	20	2.4	18	85	10	63	15	26	11	46	1.79
38511717--38511865	21	7.1	21	70	7	97	44	16	20	18	1.86
38511717--38511870	42	3.7	42	79	6	152	45	16	20	17	1.85
38511717--38511870	84	1.8	83	86	4	220	45	16	20	17	1.85
38513416--38513675	46	5.8	46	75	18	217	26	21	15	35	1.94
38513525--38513701	36	4.7	36	80	14	205	27	20	14	38	1.91
38517767--38517798	8	3.9	8	92	8	55	50	0	0	50	1.00
38524974--38525003	15	1.9	16	93	6	53	26	0	3	70	1.03
38524944--38525048	53	1.9	55	81	7	126	39	0	4	55	1.28
38525064--38525107	17	2.4	19	88	7	65	59	0	0	40	0.98

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