genome.fa.s4.2.7.7.80.10.50.1000.170.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  170  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)
53440811--53440925	44	2.6	44	80	0	131	34	18	18	28	1.94
53441002--53441205	44	4.5	44	72	15	153	31	20	17	30	1.95
53440860--53441207	140	2.5	140	89	0	527	30	19	17	31	1.95
53452926--53452990	3	21.0	3	72	12	51	61	1	7	29	1.33
53453603--53453651	24	2.0	24	96	0	89	14	46	4	34	1.63
53458253--53458294	20	2.1	20	100	0	84	28	9	11	50	1.70
53458621--53458660	14	2.9	14	84	0	53	42	17	7	32	1.77
53458586--53458652	34	1.9	35	87	3	100	44	13	10	31	1.77
53460720--53460754	16	2.1	17	89	5	54	28	0	40	31	1.57
53463078--53463113	15	2.4	15	95	0	63	55	0	13	30	1.39
53464586--53464626	20	2.1	19	86	4	55	48	2	2	46	1.28
53464650--53464714	21	3.1	20	80	8	67	61	1	0	36	1.05
53464653--53464714	10	6.1	10	72	10	54	62	1	0	35	1.05
53465015--53465054	21	1.9	21	94	0	71	55	12	12	20	1.69
53469463--53469560	33	2.9	33	70	16	94	25	28	16	29	1.97
53482468--53482515	13	3.7	12	76	17	51	81	2	2	14	0.88
53482975--53483043	27	2.6	27	82	8	79	68	0	10	21	1.19
53486994--53487076	37	2.2	39	80	10	100	37	6	4	51	1.48
53486991--53487075	39	2.3	37	82	9	102	36	7	4	51	1.50
53487058--53487091	16	2.0	17	88	11	52	47	11	0	41	1.40
53490218--53490258	6	6.8	6	100	0	82	34	0	34	31	1.58
53490429--53490458	14	2.2	14	94	5	53	30	0	0	70	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53496283--53496327	3	15.0	3	100	0	90	66	0	0	33	0.92
53500043--53500080	18	2.1	19	90	5	60	28	7	5	57	1.49
53500039--53500122	41	2.1	40	82	10	102	27	9	2	60	1.40
53500438--53500481	20	2.3	19	81	18	56	34	13	2	50	1.55
53500444--53500479	18	1.9	20	88	11	58	33	16	2	47	1.61
53502225--53502289	18	3.4	18	66	25	53	66	23	4	6	1.33
53502405--53502453	19	2.6	19	86	0	71	57	24	6	12	1.58
53503049--53503076	13	2.2	13	100	0	56	60	0	32	7	1.24
53504800--53504950	33	4.5	33	75	18	134	20	19	28	31	1.97
53504727--53504923	102	1.9	102	89	0	304	21	18	26	33	1.96
53509070--53509098	9	3.2	9	100	0	58	44	34	0	20	1.52
53510579--53510623	23	2.0	24	86	8	67	24	0	11	64	1.26
53510749--53510791	14	3.1	14	83	9	54	18	11	0	69	1.17
53511626--53511665	21	1.9	21	94	0	71	52	2	17	27	1.57
53518102--53518128	2	13.5	2	100	0	54	51	0	0	48	1.00
53523813--53523880	34	2.0	34	82	5	84	29	22	25	23	1.99
53524898--53525140	28	8.7	28	88	2	337	30	22	22	24	1.99
53525254--53525303	26	1.9	26	87	0	73	36	22	22	20	1.96
53525420--53525458	15	2.6	14	84	11	51	35	23	7	33	1.83
53531139--53531163	13	1.9	13	100	0	50	32	4	24	40	1.73
53532108--53532141	2	17.0	2	100	0	68	50	0	0	50	1.00
53532736--53532827	41	2.2	41	88	0	130	26	18	25	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53533277--53533310	2	17.0	2	100	0	68	50	0	0	50	1.00
53534019--53534048	13	2.2	14	94	5	53	46	0	0	53	1.00
53539043--53539067	13	1.9	13	100	0	50	32	4	24	40	1.73
53540019--53540054	2	18.0	2	100	0	72	50	0	0	50	1.00
53540645--53540747	41	2.5	41	85	3	127	26	20	27	26	1.99
53541386--53541415	13	2.2	14	94	5	53	46	0	0	53	1.00
53545854--53545922	15	4.7	15	76	16	63	31	2	2	62	1.25
53545873--53545922	5	10.2	5	81	12	59	32	2	2	64	1.16
53555518--53555570	26	2.0	28	88	7	83	64	3	0	32	1.12
53555740--53555775	18	2.1	17	89	5	54	0	41	52	5	1.24
53556243--53556367	41	3.0	42	85	3	180	31	24	18	25	1.98
53556368--53556491	44	2.9	43	79	2	131	32	25	13	28	1.94
53571249--53571557	164	1.9	164	98	0	600	27	16	16	38	1.91
53574619--53574650	3	10.7	3	93	0	55	68	0	31	0	0.90
53576044--53576084	20	2.1	19	86	4	55	31	4	0	63	1.15
53586152--53586183	3	10.7	3	100	0	64	68	0	31	0	0.90
53589915--53589954	20	2.0	20	95	0	71	27	17	25	30	1.97
53590197--53590235	18	2.2	17	95	4	69	64	0	0	35	0.94
53590161--53590296	40	3.3	39	73	19	114	61	0	1	36	1.05
53590281--53590307	11	2.5	11	100	0	54	51	0	7	40	1.30
53590214--53590327	40	2.9	39	81	11	153	63	0	2	34	1.09
53590980--53591127	39	3.7	39	81	11	167	61	0	2	35	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53591086--53591112	11	2.5	11	100	0	54	51	0	7	40	1.30
53591147--53591177	5	6.0	5	92	7	53	0	41	58	0	0.98
53591988--53592056	3	24.0	3	78	14	74	1	33	0	65	1.02
53591981--53592054	8	9.2	8	75	15	64	1	31	0	67	0.99
53598443--53598530	41	2.1	41	82	0	104	31	19	21	27	1.97
53603337--53603384	17	2.8	16	78	12	51	37	0	16	45	1.48
53603888--53603949	21	3.0	21	88	4	92	14	25	19	40	1.90
53609477--53609531	29	1.9	28	82	10	67	36	12	1	49	1.52
53610025--53610159	71	1.9	71	90	0	216	30	18	17	33	1.94
53621822--53622229	45	9.1	45	83	4	466	31	15	22	30	1.95
53622245--53622543	44	6.8	44	77	4	246	31	17	21	29	1.96
53622288--53622535	89	2.8	87	83	8	256	29	18	22	29	1.97
53622245--53622535	133	2.2	133	80	7	308	30	18	21	29	1.97
53622288--53622574	88	3.2	89	80	9	245	30	16	21	31	1.96
53624187--53624246	29	2.1	29	81	12	70	33	11	0	55	1.36
53624832--53624974	70	2.0	72	91	4	236	28	18	17	35	1.93
53626293--53626338	24	2.0	24	86	4	67	58	15	0	26	1.37
53626939--53627012	27	2.8	26	82	10	96	56	0	2	40	1.13
53627031--53627077	10	4.7	10	74	10	51	65	2	0	31	1.04
53626994--53627077	40	2.1	41	86	2	116	63	3	3	29	1.28
53627012--53627077	20	3.3	20	72	8	62	65	4	3	27	1.27
53626994--53627088	40	2.3	39	79	15	102	62	4	3	30	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53627263--53627314	18	2.7	19	82	14	63	25	5	1	67	1.23
53627357--53627423	19	3.5	19	81	4	71	38	2	2	55	1.31
53627319--53627411	19	4.7	21	69	16	72	36	5	2	55	1.35
53627387--53627511	29	4.5	29	71	18	95	30	4	0	64	1.17
53627397--53627458	18	3.4	19	76	10	67	29	1	1	67	1.09
53628075--53628104	13	2.3	13	94	0	51	53	6	0	40	1.27
53637634--53637675	3	14.0	3	94	0	75	0	35	0	64	0.94
53644607--53644633	6	4.5	6	100	0	54	37	14	33	14	1.88
53651836--53651897	29	2.2	29	97	2	117	41	0	37	20	1.53
53651979--53652026	22	2.2	22	84	0	60	31	14	18	35	1.91
53658951--53659005	2	27.5	2	96	0	101	47	0	1	50	1.11
53667508--53667552	3	15.0	3	100	0	90	33	0	0	66	0.92
53668259--53668294	16	2.2	16	100	0	72	25	0	36	38	1.56
53668275--53668365	45	2.0	45	85	2	121	27	6	28	37	1.82
53668530--53668564	18	2.0	17	88	5	52	54	0	0	45	0.99
53668417--53668732	156	2.0	157	96	0	589	42	3	5	48	1.42
53668666--53668707	15	2.7	16	82	14	52	47	2	0	50	1.14
53668669--53668893	120	1.9	119	94	0	396	47	6	1	45	1.36
53668806--53668840	18	2.0	17	88	5	52	54	0	0	45	0.99
53668894--53668975	26	3.0	27	75	12	87	52	2	1	43	1.22
53676558--53676610	26	2.0	26	88	0	79	45	18	3	32	1.68
53680483--53680567	42	2.0	42	100	0	170	32	29	21	16	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53692296--53692407	25	4.5	25	71	14	81	19	25	19	34	1.96
53692280--53692375	50	1.9	50	85	4	131	21	27	17	33	1.96
53692410--53692498	25	3.5	25	76	13	76	23	24	17	33	1.96
53692837--53692889	25	2.1	25	100	0	106	35	22	13	28	1.92
53706360--53706399	20	2.0	20	90	0	62	27	10	12	50	1.72
53706346--53706411	35	1.9	34	87	6	98	30	7	13	48	1.70
53715446--53715694	50	4.8	50	86	5	329	21	30	22	25	1.99
53716032--53716089	30	1.9	31	82	6	75	29	22	5	43	1.75
53718250--53718293	24	1.9	23	90	9	72	29	11	18	40	1.85
53729159--53729197	18	2.2	17	86	13	53	33	0	20	46	1.51

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