genome.fa.s4.2.7.7.80.10.50.1000.93.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  93  of  198  ( 23681 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)
29639415--29639439	13	1.9	13	100	0	50	36	40	0	24	1.55
29645411--29645463	27	2.0	27	100	0	106	18	13	26	41	1.87
29647143--29647167	13	1.9	13	100	0	50	36	40	0	24	1.55
29662958--29663022	27	2.4	27	87	7	89	35	21	23	20	1.96
29663155--29663287	27	4.9	26	82	5	106	17	17	23	42	1.89
29663166--29663405	54	4.5	53	77	7	162	19	17	20	42	1.89
29663183--29663648	26	17.7	26	83	3	447	23	17	20	38	1.93
29665455--29665647	50	3.8	50	85	0	269	25	22	30	21	1.99
29666187--29666269	32	2.6	32	92	1	132	26	3	27	42	1.72
29673011--29673141	50	2.6	50	83	1	163	25	25	26	22	2.00
29678876--29678944	21	3.3	21	76	8	68	40	34	13	11	1.80
29698473--29698522	21	2.4	21	82	0	64	40	6	4	50	1.46
29699002--29699030	3	9.7	3	100	0	58	0	0	31	68	0.89
29699153--29699196	3	14.7	3	95	0	79	34	2	31	31	1.70
29699641--29699777	42	3.3	42	92	2	222	36	24	18	20	1.95
29700196--29700231	14	2.5	15	95	4	65	0	5	13	80	0.88
29703780--29703820	15	2.7	15	85	10	57	41	7	0	51	1.30
29710311--29710371	23	2.7	23	79	5	70	42	18	19	19	1.89
29717253--29717337	23	3.7	23	77	10	77	35	17	23	23	1.95
29723450--29723535	42	2.0	43	93	2	147	24	17	25	32	1.97
29723460--29723553	42	2.2	42	82	1	116	30	18	21	29	1.97
29723460--29723569	42	2.6	41	81	2	112	30	16	22	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29725121--29725244	59	2.1	59	95	0	221	30	5	17	45	1.72
29725177--29725319	49	3.0	48	81	13	193	32	4	18	44	1.71
29728954--29729002	23	2.1	23	92	7	82	34	0	6	59	1.22
29728999--29729024	13	2.0	13	100	0	52	15	0	0	84	0.62
29729010--29729179	9	19.1	9	70	16	81	31	3	2	62	1.27
29728977--29729174	36	5.7	36	70	21	111	30	3	3	63	1.24
29729817--29729863	24	2.0	23	91	4	76	59	4	0	36	1.17
29731996--29732080	42	2.0	42	86	4	118	37	17	18	25	1.93
29734921--29734953	2	16.5	2	93	0	57	54	0	45	0	0.99
29737189--29737337	80	1.9	80	91	0	244	41	10	8	38	1.71
29737801--29737846	24	2.0	24	83	8	60	52	8	2	36	1.45
29742807--29742867	29	2.1	29	96	0	113	52	6	14	26	1.66
29756327--29756463	50	2.7	50	86	0	184	24	24	29	21	1.99
29760088--29760138	25	2.0	25	92	0	84	41	17	5	35	1.74
29762387--29762449	6	10.5	6	81	6	65	68	3	3	25	1.19
29762393--29762449	19	3.1	19	78	16	75	66	3	3	26	1.24
29762394--29762498	36	2.9	37	83	8	110	68	3	7	20	1.30
29767667--29767739	37	2.0	37	88	0	110	34	17	13	34	1.90
29770181--29770208	6	4.7	6	100	0	56	67	0	32	0	0.91
29776625--29776659	17	2.1	17	89	10	54	22	31	28	17	1.96
29788068--29788103	19	1.9	19	88	5	56	66	0	2	30	1.06
29796961--29797006	24	1.9	24	95	0	83	36	13	21	28	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29801178--29801229	17	3.0	17	82	17	63	21	1	1	75	1.00
29808058--29808108	22	2.3	22	96	0	93	15	11	37	35	1.84
29808106--29808144	20	2.0	20	90	10	62	10	30	23	35	1.88
29816451--29816510	26	2.2	28	82	5	70	73	5	13	8	1.23
29827245--29827279	10	3.5	10	88	0	52	22	8	22	45	1.79
29833720--29833891	50	3.4	50	90	0	272	19	30	23	26	1.98
29836509--29836598	36	2.5	36	100	0	180	20	16	23	40	1.91
29840102--29840157	21	2.5	22	72	16	53	21	17	8	51	1.72
29854756--29854794	12	3.2	12	85	0	51	20	23	5	51	1.67
29855045--29855239	50	3.8	50	78	6	185	22	28	21	28	1.99
29862321--29862359	12	3.2	12	85	0	51	20	23	5	51	1.67
29878880--29878948	34	2.0	34	100	0	138	52	17	2	27	1.59
29879952--29879979	14	2.0	14	100	0	56	57	0	7	35	1.26
29880761--29880846	29	3.0	29	92	0	136	24	25	12	37	1.91
29883595--29883729	50	2.7	51	87	2	175	33	20	16	29	1.95
29888739--29888781	20	2.1	21	86	4	61	51	0	4	44	1.22
29888876--29888913	20	1.9	20	94	0	67	44	13	7	34	1.72
29893028--29893067	18	2.2	18	86	0	53	42	2	2	52	1.28
29904219--29904286	34	2.0	34	100	0	136	26	20	23	29	1.99
29904688--29904797	45	2.5	44	77	4	114	32	22	19	25	1.97
29906394--29906433	18	2.2	18	86	0	53	42	2	2	52	1.28
29906710--29906738	2	14.5	2	100	0	58	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29917943--29918012	26	2.7	25	76	6	77	32	18	2	45	1.64
29927992--29928103	40	2.7	41	77	5	109	26	16	25	30	1.97
29944970--29945036	35	1.9	35	85	11	93	34	7	1	56	1.36
29945310--29945345	5	7.4	5	87	6	56	0	16	0	83	0.65
29945314--29945344	14	2.2	14	94	0	53	0	16	0	83	0.64
29953546--29953596	22	2.4	22	83	3	59	72	0	27	0	0.85
29956468--29956560	44	2.1	44	86	8	125	36	25	5	32	1.79
29956542--29956612	16	4.4	16	81	10	74	29	22	8	39	1.83
29964545--29964576	15	2.1	16	94	5	57	25	18	6	50	1.70
29975370--29975405	2	18.0	2	94	0	63	47	0	0	52	1.00
29975635--29975746	43	2.6	43	95	0	197	27	32	19	20	1.97
29980409--29980474	21	3.1	21	78	8	62	39	34	0	25	1.56
29980475--29980501	14	1.9	14	100	0	54	37	29	0	33	1.58
29980549--29980599	18	2.6	21	81	9	63	56	13	13	15	1.67
29980755--29980908	7	21.9	7	72	9	80	47	33	0	18	1.53
29980756--29980908	21	7.6	20	72	15	93	47	33	0	18	1.53
29980756--29980908	14	10.9	14	76	9	96	47	33	0	18	1.53
29981181--29981313	41	3.2	41	84	4	169	28	30	20	20	1.97
29990648--29990824	50	3.6	49	83	8	227	20	29	22	27	1.98
29994313--29994345	15	2.3	15	89	5	50	39	18	18	24	1.92
29997750--29997986	50	4.7	49	82	4	267	22	30	21	26	1.99
29998762--29998830	22	3.0	24	73	14	65	30	17	20	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29998999--29999029	14	2.2	14	94	0	53	35	16	19	29	1.93
29999050--29999101	15	3.5	15	76	10	52	23	23	26	26	2.00
30000134--30000173	20	2.0	20	85	9	55	45	5	12	37	1.64
30000761--30002320	778	2.0	778	100	0	3120	31	16	25	26	1.96
30007665--30007708	21	2.2	20	84	8	54	50	20	9	20	1.75
30009141--30009220	35	2.3	35	86	0	115	22	25	23	28	1.99
30010738--30010783	21	2.2	21	84	0	56	32	26	13	28	1.93
30010907--30010946	17	2.4	17	87	4	55	40	2	15	42	1.60
30010972--30011041	34	2.1	34	100	0	140	44	17	8	30	1.78
30017740--30018122	27	14.2	27	85	3	443	37	20	18	23	1.94
30018161--30018230	23	3.0	23	80	2	77	18	5	25	50	1.69
30018162--30018243	24	3.5	24	78	8	87	19	6	25	48	1.71
30018306--30018371	27	2.5	27	83	13	84	21	24	22	31	1.98
30018325--30018377	27	2.0	27	81	7	63	22	26	20	30	1.98
30018418--30018666	32	7.8	32	81	6	227	22	20	20	37	1.94
30018445--30018666	95	2.3	96	82	3	259	22	19	19	38	1.94
30018672--30018718	22	2.1	22	84	0	58	19	17	17	46	1.84
30026416--30026503	20	4.3	20	73	2	77	12	30	20	36	1.90
30038714--30038748	14	2.5	14	86	13	54	60	11	0	28	1.32
30053713--30053755	13	3.1	14	84	12	54	60	0	0	39	0.97
30056462--30056491	3	10.0	3	100	0	60	0	33	0	66	0.92
30056515--30056611	30	3.4	29	68	22	80	25	11	15	47	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30056511--30056624	54	2.1	55	96	1	212	24	12	13	50	1.75
30056757--30056830	24	3.1	23	78	5	85	41	9	6	41	1.64
30068362--30068395	16	2.2	15	89	5	50	41	0	2	55	1.15
30069095--30069132	17	2.2	18	85	4	51	31	0	5	63	1.17
30071726--30071805	37	2.2	37	93	4	135	38	12	10	38	1.77
30071735--30071807	37	2.0	37	100	0	146	38	12	8	41	1.73
30074956--30074987	17	1.9	16	93	6	55	28	28	18	25	1.98
30098840--30098900	28	2.2	27	83	11	88	27	22	26	22	1.99
30099376--30099463	27	3.3	26	78	12	88	19	14	18	47	1.82
30099802--30099846	24	1.9	23	90	4	72	8	17	17	55	1.67

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   188   189   190   191   192   
          193   194   195   196   197   198