genome.fa.s8.2.7.7.80.10.50.1000.44.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  44  of  190  ( 22705 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)
12249299--12249366	18	3.8	18	86	0	100	27	13	20	38	1.90
12249291--12249366	36	2.1	36	85	4	100	27	13	21	38	1.90
12260839--12260886	22	2.2	22	85	3	62	22	18	12	45	1.83
12264019--12264173	80	1.9	80	98	0	301	41	22	16	20	1.90
12266619--12266686	18	3.9	17	73	21	61	10	14	1	73	1.16
12266776--12266844	8	8.2	8	78	15	52	5	8	2	82	0.92
12266776--12266811	17	2.1	17	89	0	54	5	0	5	88	0.61
12266807--12266847	17	2.5	16	84	7	55	4	17	0	78	0.93
12267819--12267866	23	2.0	23	88	4	69	72	0	8	18	1.08
12272066--12272114	5	9.6	5	95	4	89	40	0	0	59	0.98
12272235--12272274	19	2.0	22	85	14	59	42	0	2	55	1.13
12272300--12272338	17	2.2	18	90	4	62	76	5	12	5	1.11
12273228--12273334	21	5.0	22	85	10	159	16	19	24	39	1.92
12273228--12273334	44	2.5	42	90	4	162	16	19	24	39	1.92
12277701--12277766	30	2.2	30	88	2	96	39	9	31	19	1.83
12277710--12277769	30	2.0	30	100	0	120	33	10	30	26	1.89
12279427--12279458	5	6.6	5	92	7	57	40	0	0	59	0.97
12279580--12279622	22	2.0	22	86	9	61	41	0	2	55	1.12
12279648--12279683	17	2.1	18	89	5	56	75	5	13	5	1.17
12280576--12280661	21	4.0	22	85	8	124	16	20	24	38	1.93
12280575--12280661	44	2.0	41	89	6	129	17	20	24	37	1.93
12281867--12281932	25	2.6	25	77	18	64	30	21	25	22	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12289109--12289165	25	2.3	25	78	6	71	33	22	22	21	1.97
12301089--12301124	17	2.1	18	89	5	56	50	25	0	25	1.50
12301315--12301508	42	4.6	42	81	8	207	29	25	15	28	1.96
12303736--12303795	24	2.5	24	78	10	61	55	5	5	35	1.44
12303889--12303930	9	4.8	9	82	14	52	59	2	7	30	1.37
12305557--12306284	44	15.5	44	63	20	165	27	20	18	33	1.96
12305498--12306303	98	8.4	98	68	17	411	26	20	18	33	1.96
12305401--12305863	238	1.9	238	93	0	800	27	20	17	33	1.95
12305596--12306332	142	5.2	142	94	1	1248	27	20	18	33	1.96
12307612--12307647	13	2.6	14	91	8	56	13	16	0	69	1.19
12307612--12307644	7	4.9	7	92	7	59	15	15	0	69	1.19
12307989--12308036	21	2.2	22	82	10	55	0	27	6	66	1.15
12308017--12308100	27	3.2	26	74	12	82	4	20	1	73	1.08
12308005--12308036	7	4.7	7	96	3	57	0	25	0	75	0.81
12308017--12308100	26	3.1	27	72	6	73	4	20	1	73	1.08
12308067--12308113	24	2.0	23	83	8	58	4	10	4	80	0.98
12312505--12312573	24	2.9	24	80	8	70	50	5	5	37	1.50
12312668--12312740	3	24.3	3	97	0	137	65	0	1	32	1.01
12317829--12317856	2	14.0	2	100	0	56	50	0	0	50	1.00
12326122--12326171	24	2.1	24	100	0	100	22	34	24	20	1.97
12326202--12326244	22	2.0	22	100	0	86	25	37	13	23	1.92
12326325--12326382	29	2.0	29	89	3	89	18	24	37	18	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12328199--12328228	14	2.1	15	93	6	53	66	0	6	26	1.16
12328259--12328290	15	2.3	15	89	10	50	75	0	0	25	0.81
12328299--12328447	4	36.5	4	66	14	63	67	2	9	20	1.29
12331408--12331482	27	2.8	27	88	6	100	28	18	9	44	1.81
12343860--12343897	16	2.4	16	87	12	60	84	2	13	0	0.73
12344779--12344841	27	2.3	27	75	0	63	38	7	3	50	1.47
12344819--12344868	19	2.6	19	80	0	64	38	8	0	54	1.30
12346946--12346994	24	2.0	25	84	4	64	28	22	8	40	1.82
12350074--12350133	5	11.8	5	84	10	77	83	0	16	0	0.65
12350062--12350134	27	2.6	27	85	8	85	83	2	13	0	0.75
12351321--12351580	137	1.9	137	85	0	358	33	18	18	29	1.95
12351454--12351665	44	4.6	45	78	8	176	32	19	20	27	1.97
12353473--12353522	19	2.6	19	80	0	64	38	8	0	54	1.30
12354165--12354304	72	1.9	72	94	2	246	34	15	8	41	1.78
12363742--12363780	20	2.0	20	94	0	69	53	12	20	12	1.71
12371306--12371405	30	3.2	31	74	8	105	49	5	3	43	1.40
12373181--12373211	5	6.2	5	100	0	62	19	0	0	80	0.71
12373986--12374077	24	3.6	27	73	17	72	67	1	30	1	1.05
12374242--12374273	7	4.4	7	92	7	55	84	0	15	0	0.63
12374610--12374649	7	5.4	7	82	11	53	80	0	20	0	0.72
12374591--12374651	23	2.7	23	83	11	74	77	0	22	0	0.78
12375052--12375107	17	3.2	18	87	9	80	33	10	10	44	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12375052--12375107	19	3.1	19	90	7	82	33	10	10	44	1.74
12381256--12381297	11	4.0	11	82	17	54	90	7	0	2	0.53
12381263--12381304	9	4.4	10	85	11	52	88	7	2	2	0.69
12381256--12381304	10	5.0	10	80	14	57	87	8	2	2	0.69
12381256--12381297	17	2.5	17	88	7	59	90	7	0	2	0.53
12382179--12383480	75	17.0	77	83	5	1403	27	17	21	33	1.96
12382179--12383480	153	8.5	152	84	3	1483	27	17	21	33	1.96
12384374--12384416	12	3.5	12	81	12	52	79	0	20	0	0.74
12384372--12384421	8	6.1	8	80	13	57	80	0	20	0	0.72
12384385--12384451	20	3.4	19	73	6	62	77	1	19	1	0.92
12384590--12384656	6	11.3	6	70	13	50	77	0	19	2	0.89
12384585--12384624	12	3.2	12	86	10	53	77	0	22	0	0.77
12384585--12384659	26	3.0	24	79	13	71	78	0	18	2	0.86
12384585--12384658	15	4.9	15	73	17	64	78	0	18	2	0.87
12384772--12384805	17	2.0	17	88	0	50	76	0	23	0	0.79
12384991--12385050	11	5.5	11	82	11	70	81	0	18	0	0.69
12385425--12385463	19	2.1	18	86	13	53	35	7	10	46	1.67
12386068--12386334	43	6.2	43	85	0	345	29	33	16	19	1.95
12386708--12386740	17	1.9	17	100	0	66	48	18	9	24	1.76
12390953--12391126	81	2.1	83	82	5	203	45	26	1	26	1.60
12391125--12391162	14	2.7	14	91	0	67	31	34	0	34	1.58
12391118--12391196	28	2.8	29	78	3	72	36	37	1	24	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12391269--12391306	14	2.7	14	87	0	58	44	26	0	28	1.54
12391634--12391711	41	1.9	41	92	5	131	30	30	23	15	1.95
12391709--12391853	22	6.6	22	90	0	209	26	26	14	33	1.94
12399773--12399820	19	2.6	18	80	9	60	29	2	4	64	1.23
12399807--12399888	18	4.6	18	75	18	66	32	2	1	63	1.15
12399861--12399914	3	18.0	3	88	0	81	27	0	5	66	1.13
12405224--12405265	20	2.1	20	86	0	57	57	2	2	38	1.25
12408383--12408415	18	1.9	17	88	11	50	30	6	3	60	1.36
12408387--12408449	20	3.4	19	71	10	58	30	7	1	60	1.35
12408713--12408751	15	2.6	15	80	15	53	25	7	7	58	1.52
12412471--12412516	24	1.9	24	86	0	65	45	15	26	13	1.82
12420795--12421043	44	5.8	42	74	17	172	28	20	22	27	1.99
12420797--12420995	44	4.5	45	78	12	189	28	21	22	27	1.99
12420797--12420995	89	2.3	87	81	9	217	28	21	22	27	1.99
12421187--12421419	44	5.4	44	70	11	160	28	20	23	27	1.99
12430838--12430870	18	1.9	17	88	11	50	21	3	9	66	1.33
12431622--12431747	60	2.1	61	81	7	143	38	3	15	42	1.65
12431981--12432093	41	2.8	41	81	8	124	20	19	26	33	1.96
12432462--12432491	2	15.0	2	92	0	51	53	0	0	46	1.00
12438879--12438907	14	2.1	14	100	0	58	20	27	20	31	1.98
12438893--12439161	50	5.4	50	87	0	358	22	29	20	27	1.98
12438965--12439207	50	4.9	48	90	3	202	22	31	19	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12446692--12446731	4	10.0	4	100	0	80	25	0	0	75	0.81
12446832--12447490	326	2.0	326	91	0	1057	41	21	5	31	1.76
12448280--12448388	31	3.5	31	88	0	164	43	15	10	31	1.80
12468661--12468783	25	5.0	25	76	6	126	35	21	23	18	1.95
12468644--12468754	50	2.2	49	80	3	123	35	20	23	20	1.96
12473175--12473219	20	2.2	20	84	7	56	62	4	0	33	1.15
12473186--12473223	20	2.0	20	90	10	62	65	0	0	34	0.93
12473414--12473468	19	2.9	19	79	12	60	34	0	38	27	1.57
12473418--12473470	9	5.7	9	78	8	61	39	0	37	22	1.54
12483738--12483791	27	2.0	27	96	0	99	20	7	16	55	1.65

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