genome.fa.s4.2.7.7.80.10.50.1000.44.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  44  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)
13239139--13239165	2	13.5	2	100	0	54	51	0	0	48	1.00
13254358--13254418	25	2.4	25	97	0	113	24	16	26	32	1.96
13254563--13254592	13	2.3	13	100	0	60	40	10	13	36	1.78
13255260--13255289	10	3.0	10	95	0	51	23	0	26	50	1.50
13265377--13265414	15	2.4	17	86	8	53	28	0	2	68	1.03
13266780--13267104	43	7.8	44	80	10	346	25	17	30	26	1.97
13266804--13267104	85	3.6	86	80	12	326	25	17	31	25	1.97
13266821--13267047	128	1.8	122	88	7	348	26	18	30	24	1.98
13266979--13267087	37	2.9	37	84	9	141	27	18	33	21	1.96
13267717--13267760	21	2.1	21	91	0	70	40	15	6	36	1.74
13268104--13268595	44	11.2	44	79	3	461	28	25	15	30	1.96
13268104--13268595	89	5.6	88	78	4	445	28	25	15	30	1.96
13268106--13268519	133	3.1	133	90	0	652	29	25	14	31	1.94
13268457--13269245	88	9.0	88	89	0	1044	24	26	22	26	2.00
13268063--13269245	264	4.5	265	82	3	897	26	25	20	27	1.99
13276116--13276187	19	3.7	19	89	7	108	36	16	12	34	1.87
13276697--13276875	49	3.5	50	79	7	155	22	28	21	27	1.99
13281260--13281292	18	1.9	17	88	11	50	27	15	12	45	1.81
13282184--13282339	32	5.0	32	81	4	192	37	18	20	23	1.94
13282185--13282339	61	2.5	61	91	3	238	36	18	20	23	1.95
13282505--13282586	24	3.4	24	82	0	92	43	23	9	23	1.83
13282517--13282638	24	5.1	24	82	0	118	42	22	9	26	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13282690--13282768	27	2.9	27	81	3	97	20	24	18	36	1.95
13303165--13303299	41	3.1	44	74	14	111	30	24	16	28	1.96
13309205--13309586	54	7.1	54	81	3	414	43	21	18	16	1.88
13309205--13309597	27	14.7	27	77	8	324	42	21	18	17	1.89
13309739--13309801	26	2.4	26	86	0	90	15	22	25	36	1.94
13309908--13310001	28	3.4	28	83	1	109	22	21	25	30	1.98
13314354--13314420	19	3.4	19	72	11	71	46	14	7	31	1.73
13314346--13314426	41	2.0	41	100	0	162	44	14	9	30	1.78
13322783--13322816	4	8.8	4	87	6	52	76	0	20	2	0.92
13323972--13324183	68	3.1	67	83	6	275	37	18	19	24	1.94
13326049--13326073	12	2.1	12	100	0	50	60	0	8	32	1.26
13326755--13326799	22	2.0	22	87	8	65	51	20	2	26	1.59
13341648--13341825	39	4.6	39	80	2	187	17	32	17	32	1.94
13341656--13341803	78	1.9	78	87	2	217	18	32	17	31	1.94
13345645--13345698	25	2.2	25	86	0	72	22	7	50	20	1.73
13350380--13350435	25	2.4	22	78	16	67	21	14	48	16	1.81
13350386--13350436	25	2.0	25	92	0	84	23	13	47	15	1.82
13351714--13351748	17	2.0	18	88	5	54	14	28	42	14	1.84
13356927--13356987	32	1.9	32	86	6	88	47	11	6	34	1.66
13359703--13359984	43	6.6	43	83	0	357	32	26	16	24	1.96
13359703--13359984	129	2.2	129	86	0	411	32	26	16	24	1.96
13373747--13374015	43	6.3	43	83	0	250	30	18	23	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13374646--13374683	12	3.5	11	86	10	51	63	2	0	34	1.09
13378137--13378899	27	28.4	27	81	7	768	40	20	18	20	1.92
13379348--13379393	22	2.1	22	100	0	92	26	15	13	45	1.82
13396881--13396915	17	2.0	18	88	5	54	11	34	28	25	1.91
13403613--13403658	22	2.1	22	84	8	58	71	17	0	10	1.13
13407992--13408134	20	7.3	20	70	10	89	18	35	16	29	1.93
13408001--13408103	19	5.3	19	70	9	82	16	33	18	32	1.93
13407990--13408136	39	3.8	39	86	3	197	19	34	15	30	1.93
13407989--13408162	39	4.5	39	83	3	154	21	32	14	31	1.93
13407989--13408155	78	2.1	78	83	0	208	20	32	14	31	1.93
13409727--13409770	22	2.0	22	86	0	61	47	20	4	27	1.69
13417377--13417418	22	1.9	22	85	0	57	14	21	21	42	1.88
13417527--13417785	43	6.0	43	72	5	173	33	21	17	27	1.96
13417549--13417785	86	2.8	85	76	5	201	32	21	17	28	1.96
13420839--13420897	30	2.0	30	83	6	75	28	3	3	64	1.26
13421117--13421272	7	22.1	7	70	8	84	42	36	0	19	1.56
13421118--13421199	43	1.9	43	85	5	112	35	42	1	20	1.60
13421146--13421212	29	2.3	29	86	0	98	34	44	1	19	1.60
13421160--13421220	29	2.1	29	84	6	79	36	44	0	19	1.51
13421438--13421478	14	2.9	14	88	0	64	51	34	0	14	1.43
13421439--13421483	21	2.2	20	84	4	54	51	31	0	17	1.46
13421671--13421761	40	2.3	40	84	3	112	18	20	26	34	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13422015--13422048	14	2.5	13	90	4	50	2	8	5	82	0.93
13423100--13423162	32	2.0	32	84	12	85	41	11	9	38	1.73
13423312--13423344	17	1.9	17	88	11	50	45	3	3	48	1.33
13425025--13425071	20	2.2	22	85	11	62	53	0	2	44	1.12
13425971--13426016	20	2.3	20	88	3	67	30	8	21	39	1.84
13425982--13426021	20	2.0	20	95	0	71	27	10	27	35	1.89
13428769--13428799	16	1.9	16	100	0	62	54	6	6	32	1.51
13438486--13438813	113	2.9	113	80	7	378	25	23	23	26	2.00
13439360--13439403	14	3.1	14	83	3	52	29	2	31	36	1.70
13439570--13439622	22	2.4	22	96	0	97	22	0	41	35	1.54
13440004--13440084	24	3.2	23	77	19	90	44	0	11	44	1.39
13446512--13446561	21	2.4	21	96	0	91	32	20	48	0	1.50
13446881--13447044	42	3.9	42	90	0	274	24	20	22	32	1.98
13449733--13449812	29	2.8	28	75	14	83	23	2	2	71	1.11
13449740--13449812	14	5.4	12	73	20	56	24	2	1	71	1.07
13449744--13449817	17	4.6	17	71	21	54	24	2	1	71	1.07
13449753--13449835	34	2.3	37	83	10	100	22	4	3	68	1.24
13449766--13449829	23	2.8	23	81	11	71	23	4	3	68	1.23
13453295--13453435	1	141.0	1	65	0	57	82	1	16	0	0.75
13453309--13453429	9	12.6	10	75	19	100	81	0	18	0	0.68
13453297--13453435	10	14.4	9	75	20	113	82	1	16	0	0.75
13453295--13453435	16	8.8	16	76	14	130	82	1	16	0	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13453309--13453435	29	4.4	27	81	9	137	81	0	18	0	0.68
13454657--13455124	88	5.3	88	92	0	738	27	24	24	23	2.00
13454657--13455362	176	3.9	176	83	8	944	26	25	24	22	2.00
13455017--13455235	111	2.0	111	92	0	366	23	24	26	26	2.00
13454925--13455323	199	2.0	199	93	0	672	25	24	25	24	2.00
13454837--13455362	287	1.8	287	93	0	910	26	25	24	23	2.00
13455132--13455358	44	5.2	44	68	14	162	25	26	25	22	2.00
13455124--13455362	88	2.7	88	96	0	424	25	26	25	22	2.00
13455244--13455382	43	3.2	41	69	15	100	30	25	24	19	1.98
13457613--13457642	2	15.0	2	100	0	60	50	0	0	50	1.00
13457742--13457820	17	4.9	16	73	16	74	25	3	1	69	1.12
13457753--13457820	3	22.7	3	74	14	52	26	2	1	69	1.12
13457760--13457823	23	2.8	23	81	11	71	25	3	3	68	1.18
13457727--13457813	25	3.3	25	75	22	81	24	2	2	71	1.09
13458730--13458796	2	33.5	2	100	0	134	50	0	0	49	1.00
13460079--13460105	11	2.5	11	100	0	54	11	14	0	74	1.08
13460185--13460549	195	1.9	195	90	0	586	34	20	16	28	1.94
13460599--13460647	14	3.8	14	71	20	52	32	4	0	63	1.13
13460598--13460662	24	2.8	24	97	2	123	32	3	0	64	1.09
13465058--13465116	22	2.7	21	75	10	55	44	15	5	35	1.68
13465548--13465962	132	3.1	131	85	2	492	26	25	18	29	1.98
13465587--13465964	131	2.9	132	85	1	499	26	25	17	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13465964--13466221	89	2.9	89	84	3	306	25	22	24	28	1.99
13466041--13466186	44	3.3	44	69	11	127	20	24	25	29	1.99
13466542--13466656	44	2.7	41	81	6	124	31	20	19	29	1.97
13466805--13467076	44	6.1	45	76	5	241	28	22	19	30	1.98
13468347--13468384	20	1.9	20	84	10	51	7	5	2	84	0.86
13471682--13471725	19	2.3	19	84	7	54	38	13	25	22	1.91
13474356--13474413	22	2.6	22	81	7	64	41	17	5	36	1.72
13478044--13478077	15	2.3	15	89	0	50	14	23	14	47	1.82
13483929--13483978	21	2.4	21	89	0	73	18	8	22	52	1.71
13494543--13494602	26	2.3	26	85	0	84	35	13	13	38	1.84

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