genome.fa.s4.2.7.7.80.10.50.1000.4.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  4  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)
1251076--1251244	24	7.4	23	67	10	78	42	20	12	24	1.87
1251044--1251162	24	5.0	24	71	6	73	46	19	8	26	1.78
1251051--1251248	69	2.9	69	91	0	315	42	20	11	25	1.86
1252745--1252777	15	2.2	15	100	0	66	42	30	9	18	1.81
1254000--1254056	25	2.3	25	100	0	114	36	15	22	24	1.94
1256619--1256667	3	16.3	3	87	8	73	63	0	2	34	1.06
1256712--1256762	3	17.0	3	76	8	50	60	5	3	29	1.38
1258417--1258522	44	2.4	44	81	6	108	23	19	22	33	1.97
1258850--1258957	44	2.5	44	83	6	130	25	25	23	26	2.00
1258809--1259220	228	1.8	227	82	3	533	27	24	18	29	1.98
1259079--1259230	44	3.5	44	76	8	112	27	23	19	29	1.98
1259206--1259287	41	2.0	41	87	0	119	30	19	19	30	1.96
1260910--1261162	69	3.7	69	91	0	398	25	10	19	44	1.83
1261023--1261117	23	4.1	23	72	5	75	23	12	22	42	1.87
1260913--1261156	24	10.5	22	64	16	57	25	9	19	44	1.81
1260923--1261202	138	2.0	137	84	2	355	27	9	18	44	1.81
1265335--1265372	18	2.1	18	100	0	76	28	10	15	44	1.80
1267644--1267687	22	2.0	21	87	12	63	63	0	0	36	0.95
1270760--1270798	2	19.5	2	100	0	78	51	0	0	48	1.00
1273249--1273286	2	19.0	2	100	0	76	50	0	0	50	1.00
1273781--1273836	25	2.2	26	87	9	89	64	0	1	33	1.04
1273762--1273836	30	2.7	27	86	12	91	61	0	2	36	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1280536--1280566	2	15.5	2	100	0	62	51	0	0	48	1.00
1282751--1282790	21	1.9	21	94	0	71	42	15	25	17	1.88
1284341--1284386	4	11.5	4	95	0	83	47	23	0	28	1.52
1291284--1291325	22	1.9	22	85	0	57	64	11	2	21	1.38
1291308--1291373	31	2.1	32	83	8	82	60	15	0	24	1.35
1294612--1294644	15	2.2	15	94	0	57	60	12	9	18	1.57
1297612--1297637	3	8.7	3	100	0	52	69	0	0	30	0.89
1298592--1298625	16	2.1	17	94	5	61	67	0	5	26	1.13
1302030--1302067	17	2.3	17	90	4	60	39	7	10	42	1.69
1313143--1313173	16	2.0	15	93	6	53	35	6	12	45	1.68
1327164--1327210	19	2.5	19	96	0	85	53	10	10	25	1.68
1330872--1330897	13	2.0	13	100	0	52	38	23	23	15	1.92
1337420--1337459	19	2.2	19	86	13	57	65	17	10	7	1.46
1340238--1340917	351	1.9	350	94	0	1191	26	10	18	44	1.83
1352725--1352866	71	2.0	71	100	0	284	43	12	9	33	1.76
1354068--1354143	38	2.0	38	100	0	152	15	18	26	39	1.91
1360088--1360174	43	2.0	43	89	8	133	22	2	11	63	1.39
1365057--1365236	20	8.9	20	65	11	55	54	2	5	38	1.35
1365124--1365236	40	2.8	39	82	10	120	48	1	5	44	1.35
1365441--1365511	10	6.9	10	72	10	54	45	1	2	50	1.25
1365491--1365620	9	13.1	10	69	17	51	35	4	2	57	1.32
1384581--1384635	27	2.0	27	86	6	76	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1384726--1384834	5	21.8	5	98	0	209	59	0	0	39	1.04
1401719--1401780	32	1.9	32	96	0	115	37	14	9	38	1.79
1407536--1407585	25	2.0	25	100	0	100	36	12	12	40	1.79
1409082--1409157	29	2.5	29	76	6	80	51	13	11	23	1.74
1409482--1409519	6	6.3	6	93	0	58	36	0	0	63	0.95
1410405--1410454	24	2.1	24	96	0	91	42	14	30	14	1.84
1412520--1412595	33	2.3	32	80	10	82	34	15	23	26	1.95
1416129--1416157	2	14.5	2	100	0	58	51	0	0	48	1.00
1421364--1421404	3	13.7	3	100	0	82	68	0	0	31	0.90
1424589--1424627	18	2.2	18	90	0	60	56	0	2	41	1.13
1432319--1432361	3	14.3	3	100	0	86	34	0	0	65	0.93
1433931--1433957	4	6.8	4	100	0	54	77	0	0	22	0.76
1436692--1436726	18	1.9	18	88	0	52	37	5	0	57	1.23
1437726--1437756	15	2.0	16	93	6	55	70	6	0	22	1.09
1439861--1439924	3	21.7	3	93	3	112	31	0	1	67	1.00
1442396--1442462	34	1.9	35	87	3	100	31	8	14	44	1.76
1442552--1442599	19	2.5	19	83	10	62	39	2	0	58	1.10
1442554--1442589	18	2.1	19	85	15	51	38	0	0	61	0.96
1443265--1443307	19	2.3	19	83	0	59	27	0	6	65	1.18
1458082--1458197	58	2.0	58	100	0	232	31	18	24	25	1.98
1465676--1465712	19	2.0	18	89	5	56	62	2	2	32	1.23
1474215--1474268	23	2.3	23	87	0	72	25	18	11	44	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1474395--1474425	2	15.5	2	100	0	62	51	0	48	0	1.00
1476207--1476265	28	2.1	29	84	6	77	59	0	5	35	1.20
1476208--1476255	23	2.0	25	84	8	64	58	0	2	39	1.10
1482750--1482806	23	2.7	21	74	12	62	38	0	3	57	1.16
1487865--1487921	26	2.2	26	81	6	62	42	1	8	47	1.45
1494168--1494229	27	2.2	28	82	2	72	20	8	25	45	1.79
1497220--1497246	6	4.5	6	100	0	54	29	0	70	0	0.88
1498211--1498260	11	4.7	11	82	7	59	0	34	0	66	0.92
1503895--1503979	43	2.0	43	100	0	170	42	3	18	35	1.68
1511552--1511591	2	21.0	2	90	10	66	47	0	0	52	1.00
1513750--1513812	30	2.1	30	93	0	108	60	0	1	38	1.07
1513724--1513816	30	2.9	33	78	12	104	58	1	2	38	1.17
1514136--1514196	11	5.7	11	74	18	58	65	1	0	32	1.02
1514126--1514188	30	2.1	30	96	0	117	60	1	0	38	1.07
1514101--1514192	30	2.9	33	79	15	104	59	3	1	35	1.21
1515133--1515165	9	3.7	9	100	0	66	63	0	0	36	0.95
1518325--1518416	44	2.0	45	83	8	116	34	21	5	38	1.77
1523660--1523701	15	2.7	15	88	3	57	61	0	0	38	0.96
1523858--1523903	9	5.3	9	76	10	51	50	0	4	45	1.21
1528651--1528684	11	3.2	11	87	8	52	70	8	0	20	1.13
1528784--1529132	149	2.3	153	85	9	516	32	9	5	52	1.57
1530905--1530929	3	8.3	3	100	0	50	68	0	0	32	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1537453--1537669	108	2.0	108	98	0	416	40	15	11	32	1.83
1538752--1538807	27	2.1	27	100	0	112	39	16	10	33	1.83
1544428--1544603	86	2.1	85	86	3	246	35	9	13	42	1.77
1545547--1545601	21	2.7	19	78	15	56	36	1	0	61	1.06
1545547--1545601	15	3.9	14	77	15	60	36	1	0	61	1.06
1546098--1546435	167	2.0	167	87	2	491	32	16	27	23	1.96
1546640--1546669	13	2.3	13	94	0	51	40	40	0	20	1.52
1546808--1546864	9	6.2	9	78	11	62	19	12	28	40	1.87
1547234--1547278	20	2.2	21	88	4	65	15	8	4	71	1.28
1547236--1547284	20	2.5	20	83	3	55	14	10	6	69	1.35
1550183--1550217	16	2.2	16	94	0	61	42	37	0	20	1.52
1551101--1551215	61	1.9	61	83	3	151	44	20	6	28	1.75
1552781--1552809	2	14.5	2	100	0	58	48	0	0	51	1.00
1561536--1561566	5	6.0	5	92	7	53	58	0	0	41	0.98
1561990--1562034	18	2.6	18	82	3	56	42	8	15	33	1.78
1567578--1567645	17	3.8	17	71	16	57	48	1	5	44	1.36
1567464--1567702	116	2.1	116	94	1	417	44	7	9	38	1.65
1569292--1569332	2	20.5	2	94	0	73	53	0	0	46	1.00
1570590--1570629	18	2.2	18	86	0	53	40	7	30	22	1.81
1571447--1571494	19	2.5	19	83	10	53	18	10	6	64	1.45
1571480--1571515	14	2.6	14	90	0	54	25	5	5	63	1.38
1573702--1573732	2	15.5	2	100	0	62	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1580184--1580316	40	3.3	40	88	2	176	22	28	29	19	1.98
1582952--1582993	18	2.3	19	83	4	50	16	4	4	73	1.17
1582990--1583032	23	1.9	22	81	13	52	16	2	2	79	0.95
1582995--1583048	10	5.9	9	79	18	58	22	0	3	74	0.98
1583089--1583133	11	4.1	11	82	5	56	40	0	0	60	0.97
1583088--1583157	32	2.2	33	82	7	90	40	0	1	58	1.07
1583111--1583152	21	2.0	20	90	4	66	35	0	2	61	1.09
1583119--1583162	21	2.0	21	86	4	61	40	0	2	56	1.11
1583646--1583769	62	2.0	63	88	1	187	51	3	4	40	1.39
1583839--1583872	17	2.0	17	88	11	52	47	0	2	50	1.16

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