genome.fa.s4.2.7.7.80.10.50.1000.53.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  53  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)
15935369--15935406	18	2.1	18	95	0	67	2	15	28	52	1.56
15938666--15938755	46	2.0	47	85	10	125	40	2	3	54	1.29
15944551--15944585	15	2.5	13	90	9	52	17	0	8	74	1.06
15944569--15944654	22	3.6	22	79	16	84	18	5	8	67	1.37
15945925--15945953	13	2.2	13	100	0	58	17	6	37	37	1.76
15946902--15946942	19	2.2	19	86	4	57	9	0	12	78	0.98
15947116--15947162	20	2.3	20	82	7	51	38	6	6	48	1.54
15948214--15948280	34	1.9	35	87	3	100	31	8	14	44	1.76
15948518--15948576	23	2.6	23	100	0	118	62	5	8	23	1.43
15949677--15949713	2	19.0	2	94	5	67	48	0	0	51	1.00
15949998--15950042	22	2.1	21	87	4	63	66	4	0	28	1.11
15950461--15950507	20	2.3	20	85	0	58	51	10	6	31	1.62
15955978--15956152	66	2.5	66	84	10	208	47	13	25	13	1.79
15956814--15956849	14	2.6	14	95	0	63	44	30	11	13	1.79
15957389--15958245	45	19.0	45	85	0	1129	29	16	24	30	1.96
15958772--15959805	45	23.4	45	84	4	1302	28	16	25	30	1.96
15959400--15959474	35	2.1	35	92	0	123	25	20	25	29	1.99
15959661--15959734	35	2.1	35	87	5	105	25	20	25	28	1.99
15959919--15960093	44	4.0	44	65	11	106	30	19	24	26	1.98
15959795--15960113	132	2.4	132	87	2	444	29	19	25	26	1.98
15960863--15960907	23	2.0	23	81	0	54	22	0	15	62	1.33
15961194--15961269	36	2.1	36	80	11	84	38	9	1	51	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15961606--15961655	3	16.7	3	95	0	91	34	0	0	66	0.92
15963010--15963202	30	6.4	30	79	4	174	37	11	24	26	1.89
15963100--15963276	60	2.9	61	88	4	243	36	14	26	22	1.93
15963127--15963232	30	3.5	30	77	7	126	37	12	28	21	1.90
15963034--15963248	90	2.4	90	77	7	231	37	13	23	25	1.91
15964928--15964973	23	2.0	23	95	4	85	39	13	17	30	1.87
15965638--15965784	21	7.3	19	69	18	84	19	31	14	33	1.93
15965638--15965786	40	3.7	40	90	1	235	19	31	14	34	1.92
15967273--15967362	35	2.6	35	92	0	153	32	25	24	17	1.97
15968970--15968999	15	2.1	14	93	6	51	83	10	0	6	0.81
15969057--15969148	46	2.0	46	82	4	114	43	14	10	31	1.79
15969629--15969687	30	2.0	30	93	0	100	30	11	10	47	1.73
15970159--15970198	21	1.9	21	100	0	80	47	22	0	30	1.52
15974134--15974196	28	2.2	29	83	11	76	36	9	17	36	1.82
15979477--15979512	18	2.0	18	88	0	54	55	2	5	36	1.38
15980448--15980477	13	2.3	13	94	0	51	83	6	0	10	0.81
15980636--15980757	10	12.3	10	71	20	87	68	0	31	0	0.89
15980636--15980745	4	27.8	4	72	20	56	69	0	30	0	0.89
15980639--15980759	43	2.9	42	76	9	122	68	0	31	0	0.90
15980690--15980759	32	2.3	31	82	5	88	71	0	28	0	0.86
15981124--15981909	159	5.0	152	76	11	785	50	8	10	30	1.66
15981124--15981931	317	2.5	317	94	0	1386	50	8	10	30	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15981907--15981952	21	2.1	22	96	4	85	52	6	4	36	1.47
15981820--15982032	119	1.8	117	86	6	313	46	7	13	32	1.71
15987312--15987418	54	1.9	56	87	7	157	53	12	1	32	1.49
16008877--16008959	40	2.0	43	86	9	120	32	1	0	66	1.00
16020040--16020081	21	2.0	21	85	0	57	30	16	23	28	1.96
16025624--16025656	15	2.2	15	100	0	66	33	6	6	54	1.50
16026861--16026924	6	10.7	6	84	0	83	59	0	23	17	1.37
16026869--16026924	12	4.7	12	100	0	112	58	0	23	17	1.38
16026861--16026924	24	2.7	24	95	4	112	59	0	23	17	1.37
16027067--16027128	26	2.4	26	89	5	90	45	12	9	32	1.75
16027067--16027140	26	2.8	26	78	11	80	45	10	12	31	1.76
16035951--16035988	17	2.2	18	90	4	60	39	0	10	50	1.37
16042307--16042455	75	2.0	75	90	5	239	31	16	8	43	1.78
16067915--16068014	30	3.4	29	87	2	119	31	19	4	46	1.68
16068467--16068535	24	2.8	24	78	12	61	66	0	31	1	1.00
16068608--16068644	17	2.2	17	95	4	67	78	0	21	0	0.75
16068608--16068651	17	2.6	17	89	7	54	79	0	18	2	0.83
16074279--16074316	18	2.1	18	95	0	67	31	7	15	44	1.75
16075590--16075658	18	3.8	17	75	12	57	40	7	18	33	1.78
16081021--16082481	74	19.6	74	85	3	1693	28	18	20	33	1.96
16083059--16083158	29	3.4	29	90	2	137	28	21	7	44	1.78
16083559--16083613	15	3.4	15	77	18	65	69	0	30	0	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16083693--16083737	9	4.9	9	83	5	63	82	0	17	0	0.68
16083685--16083734	22	2.2	24	89	7	77	76	0	24	0	0.80
16083814--16083859	14	3.3	14	90	0	65	45	39	13	2	1.55
16083814--16083911	14	7.0	14	72	17	60	36	40	15	7	1.74
16085252--16085323	25	2.9	25	93	0	117	30	19	15	34	1.93
16109467--16109507	20	2.0	20	85	0	55	29	12	26	31	1.92
16111024--16111059	10	3.4	10	85	14	54	33	8	8	50	1.63
16111934--16111993	26	2.3	26	82	5	68	36	3	3	56	1.32
16111950--16112025	26	3.0	26	85	12	97	39	0	2	57	1.12
16121115--16121233	57	2.1	58	88	6	179	46	6	20	26	1.75
16125423--16125476	23	2.3	23	90	0	90	24	14	24	37	1.93
16131180--16131222	17	2.6	16	85	3	50	34	9	13	41	1.77
16141781--16141810	15	2.0	15	93	0	51	36	6	10	46	1.64
16142796--16142840	20	2.2	21	84	7	58	60	6	13	20	1.55
16143112--16143156	17	2.8	17	90	10	76	55	0	0	44	0.99
16143113--16143156	8	5.5	8	89	10	72	54	0	0	45	0.99
16143242--16143296	20	2.7	21	88	2	69	54	1	0	43	1.10
16143253--16143296	20	2.2	20	95	0	79	61	2	0	36	1.09
16144414--16144459	20	2.4	19	85	3	56	65	2	0	32	1.05
16144418--16144459	18	2.3	19	87	4	59	66	2	0	30	1.04
16144418--16144464	18	2.5	18	86	6	58	63	2	2	31	1.18
16144463--16144539	31	2.5	32	85	8	106	28	15	22	33	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16148682--16148706	12	2.1	12	100	0	50	32	24	36	8	1.84
16149991--16150107	59	2.0	59	91	0	189	18	24	15	41	1.89
16154061--16154211	74	2.0	74	84	0	194	26	11	16	45	1.81
16157890--16157965	38	2.0	38	94	0	134	44	10	13	31	1.77
16158280--16158308	5	5.8	5	100	0	58	82	0	0	17	0.66
16161564--16161625	30	2.1	30	84	6	81	3	8	50	38	1.48
16166670--16166756	25	3.5	25	78	9	88	32	21	21	24	1.98
16166654--16166769	50	2.4	49	76	9	112	36	20	19	23	1.95
16171698--16171772	29	2.6	29	71	12	73	16	14	42	26	1.86
16176993--16177096	42	2.4	43	77	1	111	29	15	22	32	1.94
16181755--16181878	54	2.3	54	84	2	169	34	17	25	22	1.96
16181994--16182032	19	2.0	20	85	9	55	56	2	35	5	1.35
16194448--16194505	30	1.9	30	96	0	107	46	17	17	18	1.84
16196327--16196421	46	2.1	46	93	0	163	38	17	8	34	1.80
16196532--16196571	20	2.0	20	90	0	62	40	20	30	10	1.85
16198572--16198929	43	8.3	42	78	9	332	28	27	20	24	1.99
16198572--16198929	85	4.1	86	80	8	379	28	27	20	24	1.99
16199982--16200044	23	2.7	23	95	0	108	33	12	7	46	1.71
16204622--16204779	41	3.9	41	90	2	203	29	27	20	22	1.98
16205074--16205193	30	4.0	30	67	4	89	24	22	24	29	1.99
16209308--16209648	51	6.7	51	74	6	257	31	26	16	25	1.96
16209308--16209540	101	2.3	101	80	3	245	31	26	16	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16209308--16209648	152	2.2	152	89	2	506	31	26	16	25	1.96
16212358--16212439	42	2.0	42	83	9	105	29	21	13	35	1.92
16215148--16215438	51	5.7	51	77	5	275	30	26	17	25	1.97
16215151--16215334	101	1.8	101	88	3	280	31	25	16	26	1.97
16215148--16215380	101	2.3	101	82	3	272	31	27	16	24	1.96
16215148--16215440	152	1.9	152	92	0	487	30	26	17	25	1.97
16230398--16230437	21	1.9	21	84	0	53	22	32	20	25	1.98
16246849--16247714	443	2.0	443	98	0	1669	40	10	15	33	1.81
16260078--16260105	6	4.7	6	100	0	56	71	0	14	14	1.15
16261342--16261870	87	6.1	87	89	0	781	28	22	24	24	1.99

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