genome.fa.s4.2.7.7.80.10.50.1000.189.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  189  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)
58631117--58631169	18	2.9	18	86	13	65	0	5	11	83	0.81
58631514--58631590	29	2.7	29	77	0	91	37	3	23	35	1.73
58631796--58631881	27	3.2	25	73	22	77	25	2	1	70	1.06
58631859--58631913	10	5.5	10	73	16	51	34	0	1	63	1.05
58631798--58631921	18	6.7	19	70	22	70	27	1	2	68	1.11
58631811--58631901	46	2.0	43	81	6	101	28	2	2	67	1.15
58631796--58631920	9	13.7	9	70	20	57	28	1	2	68	1.12
58632979--58633182	46	4.5	46	95	1	351	27	23	15	34	1.94
58633163--58633201	19	2.1	19	95	0	69	20	23	7	48	1.75
58639990--58640700	381	1.9	378	82	5	907	38	8	17	35	1.80
58641730--58641868	46	3.0	46	92	0	224	35	10	25	28	1.89
58642181--58642236	2	28.0	2	100	0	112	50	0	0	50	1.00
58644416--58644493	21	3.7	21	75	0	66	12	20	20	46	1.83
58644355--58644499	42	3.5	42	81	1	148	15	20	19	44	1.86
58646162--58646223	18	3.5	17	79	12	54	70	9	6	12	1.31
58647151--58647179	7	4.1	7	100	0	58	72	0	0	27	0.85
58649484--58649512	2	15.0	2	92	7	51	48	0	0	51	1.00
58649694--58649745	26	2.0	26	88	7	79	53	7	0	38	1.30
58649747--58649780	2	17.5	2	87	6	52	50	0	2	47	1.16
58660511--58660545	17	2.1	17	94	0	61	51	8	17	22	1.72
58668965--58669002	19	2.0	20	94	5	69	23	2	5	68	1.23
58686826--58686869	20	2.2	20	84	11	56	65	2	6	25	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58695893--58695941	21	2.4	21	90	10	75	38	8	32	20	1.82
58701736--58701902	41	4.1	40	88	3	199	29	16	19	34	1.94
58703631--58703823	42	4.6	42	81	3	201	44	17	22	16	1.86
58703631--58703819	21	9.0	21	67	4	103	43	17	22	16	1.87
58705328--58705365	10	3.8	10	82	10	51	65	2	0	31	1.06
58713017--58713045	15	2.0	15	93	6	51	24	0	6	68	1.13
58713975--58714027	9	6.2	8	77	18	54	67	1	3	26	1.17
58713975--58714023	25	2.0	25	84	8	64	69	2	4	24	1.17
58714174--58714243	23	2.8	24	81	14	72	65	2	4	27	1.25
58714174--58714230	27	2.2	25	82	17	73	68	3	3	24	1.21
58715010--58715044	3	11.7	3	100	0	70	68	0	0	31	0.90
58719516--58719569	11	4.8	12	76	19	62	27	29	1	40	1.67
58719515--58719569	22	2.5	22	80	19	69	27	29	1	41	1.66
58719531--58719628	51	1.9	51	83	4	126	26	24	3	45	1.67
58721218--58721779	124	4.5	124	88	1	791	30	22	16	30	1.96
58721218--58721783	251	2.3	248	89	0	844	30	22	16	30	1.96
58730363--58731066	112	6.3	112	94	2	1173	26	28	17	28	1.97
58731013--58731146	40	3.3	40	92	1	214	20	30	16	32	1.95
58732405--58732441	11	3.4	11	88	0	56	54	0	0	45	1.00
58732410--58732477	24	2.9	23	78	8	91	55	0	1	42	1.08
58734314--58734364	23	2.2	24	82	6	61	49	0	7	43	1.32
58735681--58735734	25	2.2	25	93	3	92	59	1	3	35	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58737110--58737151	17	2.3	19	88	12	61	61	0	0	38	0.96
58740233--58740261	10	2.9	10	100	0	58	6	31	62	0	1.22
58744226--58744311	26	3.1	26	76	12	82	51	8	17	23	1.72
58749636--58749682	5	9.2	5	90	4	76	40	17	2	40	1.61
58753128--58753180	19	2.7	19	88	2	70	60	0	0	39	0.97
58756328--58756358	2	15.5	2	100	0	62	0	48	0	51	1.00
58759776--58759865	45	2.0	45	100	0	180	42	15	13	28	1.85
58761366--58761417	13	4.0	13	76	13	54	50	0	1	48	1.12
58762626--58762666	21	2.0	20	85	4	55	4	14	7	73	1.22
58763595--58763626	2	16.0	2	100	0	64	50	0	0	50	1.00
58774349--58774379	2	15.5	2	100	0	62	51	0	0	48	1.00
58778993--58779058	30	2.2	30	86	0	96	24	16	7	51	1.70
58781476--58781969	84	5.9	83	82	3	487	35	31	14	18	1.91
58783766--58783830	28	2.2	30	86	5	89	33	9	10	46	1.71
58790598--58790633	11	3.2	11	96	4	63	19	36	0	44	1.51
58793272--58793646	124	3.0	124	95	0	653	32	23	15	28	1.95
58794212--58794248	18	2.1	18	90	5	58	40	0	0	59	0.97
58796222--58796342	40	3.0	41	85	2	163	23	16	28	31	1.96
58796225--58796355	41	3.2	41	79	10	153	22	16	27	33	1.95
58796632--58796850	47	4.5	48	88	8	302	25	20	31	22	1.98
58799593--58799658	9	7.4	9	82	3	89	37	25	12	24	1.90
58799593--58799658	18	3.7	18	93	2	116	37	25	12	24	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58802508--58802574	31	2.2	31	81	10	75	47	10	2	38	1.53
58804496--58804558	30	2.1	31	82	8	76	47	11	4	36	1.60
58804839--58804907	31	2.2	31	81	0	84	49	11	7	31	1.66
58816762--58816803	20	2.0	21	86	13	61	38	0	0	61	0.96
58817315--58817355	20	2.0	20	100	0	82	24	41	14	19	1.89
58821979--58822087	30	3.3	30	68	20	83	56	3	32	7	1.44
58822110--58822140	3	10.3	3	92	0	53	64	0	35	0	0.94
58822125--58822275	81	1.9	81	94	2	268	57	1	33	7	1.36
58822043--58822555	183	2.7	187	84	12	667	55	2	33	7	1.42
58822117--58822284	81	2.1	81	88	4	252	57	1	33	8	1.36
58822293--58822335	6	7.2	6	97	0	68	55	0	44	0	0.99
58822203--58822425	114	2.0	114	92	1	376	54	3	34	7	1.45
58822317--58822555	90	2.6	90	88	4	338	57	2	32	7	1.41
58822509--58822563	27	2.0	27	89	0	83	61	3	32	1	1.24
58822119--58822563	204	2.2	202	84	8	505	56	2	33	7	1.42
58823041--58823065	2	12.5	2	100	0	50	52	48	0	0	1.00
58824307--58824347	2	20.5	2	89	0	64	46	0	4	48	1.23
58825994--58826068	39	2.0	38	87	10	109	54	10	2	32	1.49
58826892--58826917	2	13.0	2	100	0	52	50	0	0	50	1.00
58831495--58831524	11	2.6	11	94	5	51	20	3	0	76	0.92
58832240--58832327	45	2.0	45	86	0	122	39	20	18	21	1.92
58842899--58842931	3	11.0	3	100	0	66	0	33	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58847007--58847035	4	7.2	4	100	0	58	75	0	0	24	0.80
58847052--58847087	9	3.9	9	92	3	54	69	2	5	22	1.22
58847166--58847212	3	15.7	3	100	0	94	68	31	0	0	0.90
58853223--58853264	21	2.0	21	81	9	50	40	28	0	30	1.57
58853635--58854064	43	10.1	43	77	6	351	28	23	23	24	2.00
58853824--58853979	84	1.8	86	81	2	199	29	23	21	25	1.99
58854439--58854484	21	2.2	21	88	0	65	2	39	19	39	1.64
58854370--58854550	87	2.1	87	88	4	267	11	29	18	40	1.85
58862516--58862545	11	2.6	11	94	5	51	20	3	0	76	0.92
58864517--58864664	9	17.3	9	66	22	61	33	3	16	46	1.64
58864517--58864575	27	2.3	25	85	5	73	33	1	16	47	1.57
58864517--58864586	16	4.7	16	70	20	53	32	1	18	47	1.58
58864738--58864778	13	2.8	15	85	14	59	34	0	19	46	1.50
58864737--58864815	16	5.0	16	75	13	74	34	1	17	46	1.56
58866596--58866629	12	2.9	12	86	4	52	29	0	41	29	1.57
58868398--58869106	341	2.1	340	93	0	1202	22	21	19	36	1.95
58869649--58869750	45	2.3	46	81	5	127	41	20	17	20	1.91
58869834--58869878	18	2.5	18	96	0	81	48	13	0	37	1.42
58870360--58870476	46	2.6	46	93	4	195	27	23	15	33	1.95
58870774--58870861	45	2.0	45	86	0	122	39	20	18	21	1.92
58871467--58871765	46	6.6	46	95	1	525	28	23	16	32	1.95
58871467--58871765	91	3.3	91	96	1	539	28	23	16	32	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58871467--58871765	137	2.2	137	94	2	523	28	23	16	32	1.95
58872162--58872201	17	2.4	17	91	0	62	10	50	22	17	1.76
58872656--58872882	44	5.2	44	68	16	182	25	22	25	25	2.00
58872586--58873110	88	6.0	88	91	1	713	27	22	24	25	2.00
58873177--58873907	44	16.8	44	68	11	321	31	19	20	28	1.97
58873111--58873723	175	3.5	175	93	0	1001	31	19	20	28	1.97
58873111--58873723	87	7.0	84	69	11	302	31	19	20	28	1.97
58873568--58874014	129	3.5	129	91	0	687	30	19	21	29	1.97
58874551--58874588	17	2.2	17	90	0	58	10	50	21	18	1.76
58875879--58875937	3	19.7	3	76	13	59	33	5	1	59	1.29

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