genome.fa.s4.2.7.7.80.10.50.1000.92.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  92  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)
29365984--29366083	28	3.6	28	80	2	112	27	27	14	32	1.94
29371321--29371353	17	1.9	17	93	0	57	51	6	0	42	1.26
29377514--29377559	17	2.4	20	75	24	62	43	0	13	43	1.43
29377523--29377563	17	2.4	17	100	0	82	39	0	14	46	1.45
29377941--29378034	25	3.8	25	78	2	91	32	23	18	25	1.97
29378467--29378499	17	2.0	16	94	5	57	24	18	27	30	1.98
29382978--29383019	9	4.7	9	90	0	66	30	11	21	35	1.90
29386527--29386576	20	2.5	20	83	9	66	24	8	18	50	1.73
29396190--29396244	27	2.0	27	100	0	110	34	18	7	40	1.78
29402350--29403230	443	2.0	443	96	0	1627	23	19	19	36	1.95
29407081--29407108	13	2.2	13	100	0	56	53	7	7	32	1.55
29412356--29412395	21	1.9	21	89	0	62	60	12	0	27	1.33
29414132--29414160	12	2.3	13	94	5	51	3	20	27	48	1.66
29414231--29414493	43	6.1	43	85	3	334	29	30	18	21	1.97
29418959--29419008	21	2.4	21	100	0	100	40	24	8	28	1.83
29419503--29419544	16	2.5	17	92	7	68	45	0	0	54	0.99
29419518--29419591	27	2.5	28	77	18	71	47	4	0	48	1.20
29419651--29419854	7	29.0	7	71	6	81	39	37	0	22	1.61
29419738--29419867	21	6.1	21	71	8	93	45	33	1	20	1.60
29420187--29420374	41	4.6	41	95	1	331	28	32	22	17	1.96
29420187--29420374	83	2.3	82	93	3	333	28	32	22	17	1.96
29420424--29420558	40	3.3	40	87	1	180	25	20	20	34	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29422444--29422493	17	3.3	15	79	17	50	16	2	4	78	1.00
29431135--29431199	20	3.3	20	64	23	57	47	16	1	33	1.56
29431136--29431216	38	2.1	38	100	0	162	48	18	2	30	1.61
29441439--29441476	17	2.2	17	100	0	76	36	5	39	18	1.73
29442545--29442614	6	11.3	6	74	17	63	77	2	17	2	1.02
29442569--29442662	18	5.4	18	69	14	63	68	3	21	7	1.29
29442536--29442614	13	5.5	14	71	20	56	77	2	16	3	1.03
29450829--29450881	21	2.5	21	87	9	72	67	0	1	30	1.01
29451350--29451377	8	3.5	8	100	0	56	53	0	0	46	1.00
29451343--29451402	29	2.1	29	81	12	70	50	0	0	50	1.00
29455790--29455851	30	2.1	30	100	0	124	19	6	32	41	1.77
29455942--29456008	33	2.0	33	100	0	134	70	8	5	14	1.32
29472355--29472454	50	2.0	49	88	1	146	28	17	24	31	1.97
29472565--29472604	19	2.1	19	86	9	55	37	0	30	32	1.58
29476084--29476125	17	2.5	17	81	18	52	42	2	0	54	1.13
29482964--29482988	11	2.3	11	100	0	50	76	0	0	24	0.80
29495015--29495219	97	2.1	95	80	5	216	23	25	13	37	1.91
29496773--29497039	43	6.2	43	81	4	290	31	27	16	23	1.96
29496773--29497047	129	2.1	128	78	7	324	31	27	17	24	1.97
29497886--29498297	23	18.0	23	73	11	321	39	23	6	30	1.79
29497886--29498294	114	3.6	112	85	5	359	39	23	6	30	1.80
29497886--29498192	137	2.2	137	91	4	494	39	23	6	30	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29497886--29498294	137	3.0	135	83	9	474	39	23	6	30	1.80
29501605--29501934	41	8.0	41	87	0	419	28	29	20	21	1.98
29502011--29502119	40	2.7	40	80	4	121	23	19	21	35	1.96
29511090--29511119	2	15.0	2	100	0	60	50	0	0	50	1.00
29511692--29511878	41	4.6	42	85	2	231	25	20	21	31	1.98
29516162--29516359	41	4.8	41	93	1	335	24	23	23	29	1.99
29517007--29517044	2	19.5	2	83	5	51	50	5	0	44	1.24
29525726--29525761	3	12.0	3	93	0	63	0	30	0	69	0.89
29528101--29528167	33	2.0	33	97	0	125	35	13	26	23	1.92
29528555--29528722	40	4.2	39	81	8	139	37	19	20	22	1.94
29528572--29528722	40	3.8	40	82	8	191	39	19	19	21	1.92
29529149--29529346	14	13.9	14	73	12	134	18	1	32	47	1.56
29529212--29529346	7	18.9	7	74	11	78	17	0	34	48	1.48
29529215--29529256	22	2.0	21	90	4	66	16	0	33	50	1.46
29529149--29529347	7	27.9	7	69	12	75	18	1	33	47	1.56
29529392--29529431	14	2.9	14	88	0	62	22	0	30	47	1.52
29529446--29529500	22	2.5	20	83	13	65	21	0	32	45	1.52
29534393--29534541	43	3.5	43	81	0	147	25	16	25	32	1.96
29534486--29534581	42	2.3	42	94	0	165	30	18	28	22	1.98
29536225--29536287	21	2.8	22	71	17	58	42	3	1	52	1.27
29539413--29539488	13	5.7	13	73	10	64	19	0	9	71	1.13
29539414--29539477	16	4.4	16	70	22	68	20	0	7	71	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29539420--29539478	26	2.2	26	82	14	75	20	0	10	69	1.17
29539390--29539477	42	2.1	42	100	0	176	20	0	9	70	1.14
29539430--29539481	28	1.9	26	92	7	86	21	0	11	67	1.22
29539413--29539498	28	3.2	25	77	11	73	19	0	8	72	1.10
29544695--29544742	20	2.4	20	85	0	60	31	6	18	43	1.75
29551070--29551112	21	2.0	21	95	0	77	34	34	9	20	1.85
29551086--29551116	15	2.1	15	93	0	53	35	32	9	22	1.87
29552112--29552184	3	25.3	3	75	8	55	27	4	4	64	1.30
29557249--29557297	25	1.9	26	84	12	66	75	8	8	8	1.19
29558087--29558116	13	2.3	13	94	0	51	70	0	20	10	1.16
29559385--29559506	43	2.8	44	72	7	122	28	22	26	22	1.99
29559366--29560153	88	9.0	88	91	1	1163	25	25	26	23	2.00
29560518--29560560	21	2.0	21	95	0	77	34	34	9	20	1.85
29560534--29560564	15	2.1	15	93	0	53	35	32	9	22	1.87
29561534--29561610	3	25.3	3	71	7	57	25	5	6	62	1.41
29561534--29561610	18	4.4	18	73	17	72	25	5	6	62	1.41
29562556--29562605	19	2.6	19	93	3	82	58	2	10	30	1.42
29567908--29568284	207	1.8	207	87	1	558	33	19	12	33	1.89
29575919--29576010	46	2.0	46	100	0	184	34	8	23	32	1.86
29577315--29577359	23	2.0	23	81	0	54	40	0	2	57	1.11
29577492--29577675	59	3.1	59	66	20	155	41	2	7	48	1.42
29577539--29577573	18	2.0	17	88	5	52	42	2	0	54	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29577444--29577713	120	2.2	120	94	1	461	42	2	6	48	1.40
29577491--29577678	61	3.1	60	68	19	174	42	2	6	48	1.41
29577663--29577704	15	2.9	15	82	10	52	47	0	0	52	1.00
29577927--29577991	16	4.1	16	87	0	103	20	35	4	40	1.73
29578861--29578912	24	2.2	24	83	13	63	65	5	0	28	1.16
29579464--29579556	40	2.3	40	83	3	116	38	21	22	17	1.93
29579781--29579874	45	2.1	46	89	2	145	39	13	18	28	1.89
29580423--29580477	20	2.6	21	85	5	67	18	1	34	45	1.60
29580423--29580477	7	7.9	7	77	6	58	18	1	34	45	1.60
29581783--29581826	21	2.1	21	100	0	88	13	43	15	27	1.85
29582074--29582100	14	1.9	14	100	0	54	14	7	18	59	1.58
29583178--29583319	69	2.1	69	90	2	223	46	5	3	44	1.44
29583614--29583654	21	2.0	21	90	0	64	31	14	48	4	1.65
29583573--29583745	87	2.0	87	89	0	265	40	17	28	12	1.87
29584070--29584449	43	8.8	43	85	0	454	25	18	31	24	1.98
29587668--29587700	16	2.0	17	88	5	50	6	21	0	72	1.05
29590341--29590544	33	5.6	33	70	20	138	20	18	26	34	1.96
29590337--29590579	76	3.2	75	87	1	360	21	16	27	34	1.95
29592683--29592781	43	2.3	43	83	0	135	28	17	26	28	1.97
29592685--29592808	43	2.9	42	83	2	133	29	13	26	30	1.94
29597668--29597722	29	1.9	28	88	3	83	16	1	18	63	1.39
29607057--29607097	17	2.4	17	83	0	55	17	21	31	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29609590--29609628	3	13.0	3	100	0	78	0	33	0	66	0.92
29621102--29621150	8	5.9	8	84	15	64	51	0	0	48	1.00
29621092--29621150	19	3.3	18	77	22	63	50	0	0	49	1.00
29621170--29621225	6	9.0	6	80	3	58	41	42	0	16	1.48
29621218--29621263	21	2.2	21	96	0	83	45	26	0	28	1.54
29621274--29621314	22	1.9	22	85	5	57	51	31	0	17	1.46
29629033--29629276	101	2.4	104	82	6	291	27	21	29	21	1.98
29629033--29629324	50	5.7	50	81	4	271	27	21	29	21	1.99
29629148--29629373	50	4.5	50	79	6	167	28	22	26	21	1.99
29636645--29636939	50	5.8	50	81	5	283	26	20	28	23	1.99

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