genome.fa.s6.2.7.7.80.10.50.1000.134.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  134  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)
39134115--39134172	23	2.6	23	86	5	66	25	6	10	56	1.57
39137917--39138014	17	5.4	17	65	13	61	32	3	14	50	1.58
39137933--39137997	20	3.4	19	69	14	62	35	4	15	44	1.67
39137908--39138020	37	3.1	37	94	1	201	32	4	15	47	1.65
39138021--39138074	9	5.7	9	79	12	63	24	5	27	42	1.76
39138021--39138075	20	2.8	20	91	2	85	23	5	27	43	1.75
39138138--39138215	29	2.8	27	76	16	86	29	10	25	34	1.89
39149541--39149587	23	2.0	23	100	0	94	42	4	12	40	1.63
39153886--39153921	2	18.5	2	94	5	65	50	0	0	50	1.00
39157128--39157221	44	2.1	44	86	3	127	34	24	2	39	1.67
39158163--39158187	12	2.1	12	100	0	50	24	36	24	16	1.94
39158348--39158405	9	6.4	9	89	0	71	44	22	6	25	1.77
39158504--39158547	18	2.4	18	88	0	61	13	2	43	40	1.57
39163960--39163999	20	2.0	20	90	5	62	55	0	0	45	0.99
39164195--39164220	12	2.2	12	100	0	52	38	0	15	46	1.46
39165264--39165359	46	2.1	46	98	0	183	35	10	7	46	1.66
39165270--39165342	23	3.2	23	62	14	60	34	12	6	46	1.68
39166946--39167248	89	3.4	88	88	1	419	39	19	7	32	1.81
39167341--39167429	28	3.2	27	78	9	90	66	1	4	28	1.18
39167341--39167437	19	5.2	19	72	15	69	64	1	4	29	1.18
39167331--39167437	56	1.9	56	86	3	153	63	0	5	29	1.23
39167805--39168057	88	2.9	85	85	4	337	34	9	18	37	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39168335--39168401	24	2.9	23	73	6	64	26	8	1	62	1.33
39187739--39187782	22	2.0	21	83	12	54	68	0	22	9	1.18
39189926--39190041	43	2.7	43	90	2	171	17	31	28	22	1.96
39192544--39192573	4	7.5	4	92	0	51	23	3	0	73	0.98
39194153--39194205	24	2.2	24	89	0	79	49	9	3	37	1.53
39214491--39214564	31	2.5	29	84	4	85	40	14	2	41	1.60
39216559--39216601	18	2.4	19	84	7	63	23	4	2	69	1.18
39218000--39218028	13	2.3	13	94	5	51	55	0	0	44	0.99
39219329--39219363	17	1.9	19	88	11	56	20	2	11	65	1.37
39226944--39226975	2	16.0	2	100	0	64	50	0	0	50	1.00
39232118--39232152	17	2.1	17	89	10	54	65	2	0	31	1.07
39234329--39234628	100	3.0	99	90	4	464	36	22	11	29	1.89
39235331--39235380	26	2.0	25	88	4	73	60	4	2	34	1.27
39235570--39235627	3	19.7	3	89	3	91	67	0	0	32	0.91
39237834--39237864	15	2.1	15	100	0	62	45	25	9	19	1.81
39239914--39239954	21	2.0	21	85	0	55	48	14	14	21	1.80
39240981--39241021	3	14.3	3	85	10	59	68	0	31	0	0.90
39241178--39241205	2	14.0	2	100	0	56	50	0	0	50	1.00
39242843--39242882	20	2.0	20	85	0	53	62	5	7	25	1.42
39246284--39246308	2	12.5	2	100	0	50	48	0	0	52	1.00
39245986--39246633	327	2.0	327	100	0	1296	31	16	19	33	1.94
39269881--39269905	8	3.1	8	100	0	50	24	0	0	76	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39276587--39277037	102	4.4	102	89	1	613	30	14	25	29	1.95
39276582--39277031	51	8.9	51	79	6	457	30	14	25	29	1.95
39277936--39277998	5	12.6	5	82	0	81	39	0	34	25	1.56
39277936--39277998	15	4.2	15	89	0	99	39	0	34	25	1.56
39280572--39280611	20	2.0	20	90	0	62	50	12	10	27	1.72
39282505--39282546	21	2.0	21	85	0	57	50	11	0	38	1.40
39283971--39284007	17	2.1	18	90	5	58	40	10	2	45	1.53
39284075--39284123	19	2.5	19	80	6	53	46	8	8	36	1.63
39289786--39289818	2	16.5	2	100	0	66	48	0	0	51	1.00
39293441--39293714	91	3.0	91	96	0	512	39	10	16	33	1.84
39300204--39300234	9	3.4	9	90	0	53	25	12	22	38	1.90
39300287--39300323	9	4.1	9	92	0	65	45	13	10	29	1.77
39301351--39301376	5	5.2	5	100	0	52	19	19	19	42	1.90
39303544--39303605	14	4.3	13	75	16	52	50	0	4	45	1.23
39305585--39305617	13	2.7	13	90	9	52	42	12	9	36	1.74
39306680--39306895	33	6.6	33	70	21	150	19	19	26	33	1.96
39306754--39306863	27	3.9	27	79	13	130	18	22	28	30	1.97
39306756--39306895	60	2.3	60	91	0	226	18	20	27	32	1.96
39313261--39313335	23	3.3	23	90	3	125	32	25	21	21	1.98
39314327--39314440	41	2.8	41	97	0	219	21	29	20	28	1.98
39314332--39314455	41	3.0	41	90	4	196	22	28	20	29	1.98
39316233--39316257	13	1.9	13	100	0	50	40	24	4	32	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39317984--39318017	11	2.8	13	91	8	54	44	11	8	35	1.72
39319199--39319539	33	9.8	33	68	24	166	21	19	26	31	1.98
39319195--39319502	103	3.0	102	91	1	490	21	19	26	32	1.97
39320527--39320554	2	14.0	2	100	0	56	50	0	0	50	1.00
39325713--39325743	15	2.1	15	93	0	53	67	3	3	25	1.20
39326956--39326987	11	2.8	12	86	13	50	65	0	0	34	0.93
39340429--39340719	44	6.6	44	70	12	159	26	20	22	29	1.99
39340794--39340912	45	2.6	45	78	12	136	25	27	19	27	1.99
39340653--39341123	196	2.4	196	95	1	838	26	24	19	29	1.99
39340991--39341112	45	2.7	46	81	12	146	25	27	20	26	1.99
39345889--39345937	6	7.8	6	84	6	62	48	14	18	18	1.80
39345917--39346023	46	2.3	46	85	4	146	42	16	18	22	1.89
39348321--39348370	16	3.0	17	77	8	50	60	4	0	36	1.16
39351782--39351810	12	2.3	13	94	5	51	17	0	0	82	0.66
39357183--39357379	98	2.0	98	92	0	331	38	23	9	28	1.86
39359555--39359594	21	1.9	21	84	0	53	62	2	30	5	1.29
39360405--39360446	5	8.4	5	97	0	57	11	0	59	28	1.33
39361638--39361668	2	15.5	2	100	0	62	48	0	0	51	1.00
39377233--39377285	19	2.8	19	76	0	61	11	11	13	64	1.51
39378443--39378532	46	2.0	46	97	0	171	16	31	6	45	1.73
39383554--39383614	24	2.6	24	76	2	61	63	13	9	13	1.51
39383573--39383617	24	2.0	24	86	8	67	60	8	15	15	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39389036--39389100	29	2.2	30	80	2	69	33	6	24	35	1.80
39393419--39393474	28	2.0	29	86	10	80	60	0	1	37	1.07
39393423--39393481	28	2.1	28	84	6	75	62	0	1	35	1.05
39405879--39405941	29	2.1	30	82	5	74	53	1	11	33	1.46
39409581--39409625	22	2.0	22	82	0	54	60	4	2	33	1.29
39416734--39416772	6	6.2	6	82	11	51	46	15	17	20	1.84
39416734--39416772	13	3.1	12	85	7	51	46	15	17	20	1.84
39416751--39416852	45	2.2	45	86	5	143	41	18	17	22	1.90
39417066--39417142	40	1.9	40	89	0	118	41	22	7	28	1.81
39418242--39418323	35	2.4	35	86	8	107	51	3	0	45	1.19
39422904--39422971	34	2.1	33	89	8	104	52	4	2	39	1.36
39428389--39428796	108	3.8	108	87	5	540	39	13	15	31	1.86
39428426--39428795	105	3.4	106	88	5	505	37	14	16	31	1.88
39431215--39431703	108	4.6	107	87	6	693	32	16	14	36	1.88
39431215--39431703	212	2.3	214	87	4	718	32	16	14	36	1.88
39434449--39434524	23	3.3	23	90	0	125	22	19	26	31	1.98
39441900--39442059	77	2.0	79	88	5	236	47	6	12	33	1.66
39446453--39446493	19	2.2	19	95	0	73	21	34	9	34	1.87
39448648--39448697	20	2.5	19	80	6	55	38	20	6	36	1.77
39452177--39452213	4	10.0	4	83	16	53	72	0	27	0	0.84
39452177--39452213	11	3.4	11	92	7	58	72	0	27	0	0.84
39452175--39452213	18	2.2	18	100	0	78	71	0	28	0	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39452746--39452806	30	2.0	32	87	6	90	63	1	6	27	1.28
39452751--39452815	30	2.2	30	83	8	80	64	3	3	29	1.23
39458608--39458675	28	2.3	30	80	5	77	26	17	16	39	1.90
39478299--39478329	2	15.5	2	100	0	62	48	0	0	51	1.00
39479478--39479542	34	1.9	34	90	0	103	24	23	27	24	2.00
39488233--39488261	13	2.1	14	93	6	51	27	0	0	72	0.85
39492254--39492293	13	3.1	13	92	0	71	30	5	22	42	1.75
39498961--39498990	15	2.0	15	100	0	60	6	26	20	46	1.75
39500020--39500056	19	1.9	19	94	0	65	32	18	18	29	1.96
39502244--39502304	19	2.9	21	69	14	54	50	0	3	45	1.17

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