genome.fa.s4.2.7.7.80.10.50.1000.182.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  182  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)
56743979--56744411	108	4.0	108	91	4	674	30	16	18	34	1.93
56748998--56749408	108	3.8	108	93	2	662	31	16	18	33	1.93
56752298--56752345	19	2.3	21	86	10	64	39	4	2	54	1.32
56754011--56754237	33	6.8	33	67	6	89	28	24	17	29	1.97
56754011--56754244	101	2.3	100	93	1	387	28	25	16	29	1.97
56760153--56760210	31	1.9	29	89	6	89	60	3	5	31	1.35
56760196--56760251	20	2.8	20	88	0	76	66	5	0	28	1.14
56762058--56762113	28	2.0	28	82	6	69	53	0	3	42	1.18
56762161--56762239	6	12.7	6	70	11	52	72	6	20	1	1.14
56762209--56762242	17	2.0	17	100	0	68	76	0	23	0	0.79
56766926--56767024	3	33.0	3	100	0	198	33	0	0	66	0.92
56767054--56767100	24	2.0	24	100	0	94	44	12	0	42	1.42
56767496--56767533	20	1.9	20	84	10	51	31	15	2	50	1.58
56768312--56768360	26	1.9	25	84	12	64	18	10	0	71	1.13
56771303--56771346	24	1.9	23	90	9	72	36	0	0	63	0.95
56771446--56771473	9	3.1	9	100	0	56	57	10	0	32	1.33
56771416--56771616	59	3.1	68	84	13	307	45	8	4	40	1.57
56771605--56771646	16	2.6	16	92	0	66	42	7	2	47	1.43
56771620--56771675	23	2.5	23	82	2	69	44	1	1	51	1.22
56783765--56783860	24	3.9	26	80	14	107	70	0	29	0	0.87
56783766--56783878	30	3.4	34	80	14	137	71	0	28	0	0.86
56783937--56783990	28	2.0	28	88	3	83	42	5	9	42	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56784232--56784839	287	2.1	286	94	1	1049	51	6	11	30	1.63
56784834--56785424	278	2.1	279	93	3	1015	49	6	12	31	1.66
56784301--56785354	523	2.0	525	94	2	1830	51	6	10	31	1.63
56786624--56786679	3	18.7	3	83	7	69	32	1	1	64	1.14
56786815--56786871	28	2.0	28	86	6	80	36	10	0	52	1.36
56786829--56786883	26	2.0	28	82	10	69	36	10	1	50	1.48
56787014--56787053	12	3.2	12	82	6	53	30	2	0	67	1.04
56788857--56789022	88	1.9	88	89	0	260	35	13	13	37	1.84
56790426--56790461	16	2.2	17	90	5	56	72	0	2	25	0.98
56793355--56793396	2	21.0	2	95	0	75	52	0	0	47	1.00
56795127--56795457	44	7.6	43	76	9	264	25	19	23	30	1.98
56795168--56795499	41	7.8	41	76	8	268	26	19	22	31	1.98
56795037--56795502	130	3.6	130	88	0	628	26	19	21	31	1.98
56795513--56796230	100	7.2	99	85	2	814	24	22	22	31	1.99
56795739--56796219	51	9.6	51	71	4	332	23	21	23	31	1.98
56797641--56797680	12	3.5	11	83	12	53	0	10	2	87	0.63
56797640--56797669	15	2.0	15	93	0	51	0	16	0	83	0.65
56797635--56797677	22	1.9	23	85	4	61	0	16	2	81	0.79
56807326--56807766	44	10.0	44	80	2	389	28	24	16	30	1.97
56807328--56807766	89	5.0	89	85	1	587	28	24	16	30	1.97
56809027--56809124	48	2.0	48	88	7	146	12	25	16	45	1.82
56809035--56809136	48	2.1	48	82	7	118	11	26	15	46	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56809905--56809950	24	1.9	24	86	8	67	63	8	15	13	1.52
56814125--56814181	3	19.0	3	100	0	114	66	0	0	33	0.92
56817253--56817303	24	2.1	25	85	10	70	54	9	5	29	1.56
56817401--56817448	4	11.8	4	95	4	87	75	0	0	25	0.81
56824035--56824088	15	3.3	15	74	18	54	44	0	1	53	1.11
56826803--56826850	23	2.1	23	100	0	96	25	25	12	37	1.91
56830039--56830072	12	2.8	12	90	0	50	17	47	8	26	1.77
56839825--56839849	2	12.5	2	100	0	50	52	0	0	48	1.00
56842138--56842211	29	2.6	29	77	12	89	52	1	1	44	1.17
56844358--56844403	20	2.2	21	84	3	58	69	2	2	26	1.11
56844357--56844419	29	2.2	28	81	13	74	65	1	3	30	1.18
56847318--56847353	5	7.6	5	87	12	58	61	0	0	38	0.96
56847318--56847353	13	2.6	13	91	8	54	61	0	0	38	0.96
56851544--56851770	106	2.2	106	87	4	316	30	14	14	40	1.86
56851548--56851770	105	2.1	106	87	1	322	30	13	15	40	1.86
56851763--56851794	16	2.0	16	93	0	55	0	12	3	84	0.74
56854363--56854416	22	2.3	24	84	12	76	29	5	5	59	1.43
56854364--56854408	22	2.0	22	95	0	81	31	4	6	57	1.44
56854421--56854455	2	17.5	2	100	0	70	51	0	0	48	1.00
56863888--56863980	11	8.9	11	72	19	74	37	4	0	58	1.18
56863888--56863980	41	2.2	42	96	1	170	37	4	0	58	1.18
56864456--56864536	32	2.5	31	79	18	76	62	4	2	29	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56865186--56865250	32	2.1	32	97	2	123	30	9	12	47	1.72
56865549--56865586	3	12.7	3	100	0	76	31	0	0	68	0.90
56867739--56867803	3	21.7	3	96	0	121	33	1	0	64	1.03
56868306--56868618	112	2.8	111	91	1	495	29	16	21	32	1.96
56872468--56872583	6	19.8	6	76	11	53	69	6	8	14	1.34
56872467--56872553	34	2.5	35	81	7	90	72	6	6	13	1.26
56872566--56872616	18	2.6	21	76	20	56	68	0	21	9	1.18
56874335--56874931	81	7.0	83	87	5	593	28	21	24	25	1.99
56874513--56874635	40	3.0	40	66	15	99	28	19	26	26	1.99
56874335--56874931	164	3.5	164	82	10	582	28	21	24	25	1.99
56874338--56874982	88	7.6	87	85	7	504	27	21	25	25	1.99
56874803--56874941	45	3.1	44	69	15	124	29	21	25	23	1.99
56874760--56874897	43	3.2	43	71	15	147	26	21	26	25	2.00
56874772--56874910	44	3.2	44	71	15	151	23	21	26	28	1.99
56874335--56874982	174	3.8	172	80	9	511	28	21	25	25	1.99
56881955--56882019	32	2.1	32	94	2	114	29	9	13	47	1.74
56882316--56882355	3	13.3	3	100	0	80	32	0	0	67	0.91
56882527--56882607	16	4.8	17	79	14	73	48	3	0	48	1.19
56882546--56882611	18	4.0	15	73	22	53	51	1	0	46	1.10
56882837--56882887	23	2.2	23	92	0	84	25	11	17	45	1.83
56906097--56906149	26	2.0	26	100	0	106	26	26	20	26	1.99
56907941--56908040	29	3.6	29	71	18	77	54	0	2	44	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56910561--56910616	28	2.0	28	82	6	69	23	14	7	55	1.63
56912036--56912103	31	2.2	31	89	0	100	42	10	11	35	1.76
56925849--56926154	149	2.1	149	98	0	594	31	14	16	37	1.88
56926633--56926660	3	9.3	3	100	0	56	35	0	0	64	0.94
56934648--56934708	31	2.0	31	83	0	77	47	9	11	31	1.72
56937335--56937372	19	2.1	19	90	5	60	23	10	10	55	1.65
56938667--56938699	11	3.0	11	91	8	50	30	0	0	69	0.88
56938772--56938830	30	2.0	30	89	0	91	59	15	1	23	1.45
56946761--56946793	17	1.9	17	88	11	50	57	3	0	39	1.14
56951116--56951141	2	13.0	2	100	0	52	50	0	0	50	1.00
56952729--56952768	16	2.5	16	91	0	62	47	2	7	42	1.45
56952701--56952753	22	2.4	22	87	0	70	52	1	1	43	1.23
56952774--56952937	77	2.2	76	94	3	294	38	4	7	50	1.50
56952841--56952877	9	4.1	9	96	0	65	32	0	8	59	1.27
56953033--56953076	23	1.9	22	90	9	70	63	0	0	36	0.95
56956160--56956302	57	2.4	59	82	9	166	31	22	25	20	1.98
56957762--56957842	26	3.3	23	81	11	83	20	24	19	34	1.96
56957798--56957843	25	1.9	25	86	8	69	19	26	21	32	1.97
56957762--56957855	49	1.9	49	80	8	111	23	23	19	34	1.97
56962823--56962849	2	13.5	2	100	0	54	51	0	0	48	1.00
56976276--56976692	151	2.8	150	86	6	548	42	9	19	27	1.82
56979473--56979539	34	2.0	34	96	0	125	29	14	25	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56983920--56983959	21	1.9	21	85	10	55	62	7	0	30	1.23
56988301--56988480	51	3.5	51	77	6	152	24	16	27	31	1.96
56988402--56988482	26	3.2	26	62	28	64	23	14	28	33	1.94
56988300--56988489	102	1.9	101	85	3	265	25	16	27	30	1.97
56991686--56991747	3	20.3	3	86	3	70	32	6	0	61	1.21
56991877--56991920	8	5.5	8	84	10	54	38	2	0	59	1.10
56998851--56998875	13	1.9	13	100	0	50	44	0	8	48	1.32
56999884--56999948	33	2.0	33	90	6	105	63	18	1	16	1.40
57007100--57007142	15	3.2	15	69	30	51	46	0	0	53	1.00
57007098--57007146	25	2.0	24	96	4	89	48	0	0	51	1.00

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