genome.fa.s4.2.7.7.80.10.50.1000.190.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  190  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)
58875880--58875939	21	2.9	20	87	7	84	33	5	1	60	1.29
58875320--58875899	294	2.0	294	99	0	1151	17	15	13	53	1.73
58876010--58876083	14	5.5	14	73	14	66	39	4	0	56	1.18
58876388--58876791	110	3.7	109	89	2	600	30	14	19	35	1.92
58876388--58876791	219	1.9	217	89	3	632	30	14	19	35	1.92
58878683--58878947	46	6.0	46	91	6	431	29	22	15	31	1.95
58878683--58878947	86	3.0	92	89	8	431	29	22	15	31	1.95
58884414--58884439	11	2.4	11	100	0	52	0	42	7	50	1.31
58884443--58884492	10	4.5	11	83	14	59	0	18	8	74	1.06
58884443--58884491	22	2.2	23	79	17	59	0	18	8	73	1.07
58884636--58884671	18	1.9	19	94	5	65	55	5	0	38	1.23
58884640--58884681	18	2.3	18	84	12	50	57	7	0	35	1.26
58888212--58888248	4	9.2	4	93	0	65	72	2	0	24	0.97
58888307--58888334	8	3.5	8	100	0	56	35	0	14	50	1.43
58888374--58888409	3	12.0	3	100	0	72	66	33	0	0	0.92
58889637--58889663	14	1.9	14	100	0	54	3	0	37	59	1.15
58897413--58897456	18	2.4	18	88	0	61	40	43	4	11	1.61
58897599--58897632	9	3.8	9	96	0	59	23	11	29	35	1.90
58902663--58902739	37	2.1	35	83	4	91	33	11	10	44	1.75
58905410--58905437	2	14.0	2	100	0	56	50	0	0	50	1.00
58907311--58907336	2	13.0	2	100	0	52	50	0	0	50	1.00
58907361--58907399	16	2.4	16	91	0	60	48	2	12	35	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58907337--58907401	34	1.9	34	83	0	85	46	4	15	33	1.66
58907861--58907920	29	2.1	28	87	6	86	46	16	13	23	1.82
58910362--58910973	45	13.6	44	76	9	461	31	19	16	32	1.94
58910435--58910973	45	11.9	45	78	6	466	30	19	16	33	1.94
58910362--58910973	134	4.5	134	78	5	507	31	19	16	32	1.94
58910362--58910973	89	6.8	90	76	7	374	31	19	16	32	1.94
58910435--58910973	222	2.4	228	84	5	668	30	19	16	33	1.94
58911594--58911628	15	2.4	15	90	4	54	48	0	8	42	1.33
58920250--58920555	152	2.0	152	99	0	603	29	18	22	29	1.97
58922211--58922278	26	2.6	26	73	13	68	54	8	4	32	1.51
58929667--58929715	20	2.5	20	93	0	89	32	36	10	20	1.86
58930085--58930127	20	2.2	20	91	0	68	30	18	13	37	1.90
58933226--58933268	20	2.2	20	91	0	68	30	18	13	37	1.90
58938840--58938906	25	2.7	25	90	0	98	23	22	22	31	1.98
58949197--58949286	44	2.0	44	97	0	171	21	16	6	55	1.64
58953479--58953557	39	2.0	39	97	0	149	39	16	11	32	1.84
58960392--58960459	18	3.9	17	74	14	59	61	5	0	32	1.20
58964359--58964384	13	2.0	13	100	0	52	15	38	7	38	1.76
58964535--58964580	23	2.0	24	82	4	58	2	6	19	71	1.18
58965338--58965367	6	5.0	6	91	0	51	30	0	16	53	1.44
58970457--58970537	41	2.0	41	85	4	110	49	20	13	16	1.79
58984346--58984378	14	2.4	14	85	5	50	24	0	3	72	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58985159--58985233	29	2.6	29	82	6	89	48	4	17	30	1.66
58985748--58985905	40	4.2	39	81	14	195	36	2	0	61	1.10
58985781--58985886	17	6.0	17	64	16	54	35	1	0	62	1.06
58985798--58985911	11	10.9	11	71	17	91	39	1	0	58	1.08
58985829--58985911	32	2.6	31	92	3	130	39	1	0	59	1.05
58985758--58985911	21	7.5	22	68	20	91	37	2	0	59	1.11
58995387--58995411	7	3.6	7	100	0	50	32	28	12	28	1.92
58997119--58997164	15	3.1	15	76	17	51	34	0	2	63	1.07
58997856--58997885	5	6.0	5	100	0	60	60	0	0	40	0.97
58999193--58999328	40	3.5	39	73	11	125	30	25	18	25	1.98
59005308--59005444	40	3.5	39	73	7	125	30	24	18	27	1.98
59005583--59005629	15	2.9	16	74	22	53	51	10	0	38	1.37
59006489--59006539	25	1.9	28	84	11	72	3	27	1	66	1.20
59009458--59009528	17	4.1	16	73	18	61	64	5	0	29	1.16
59010651--59010879	84	2.7	81	81	8	246	28	17	14	39	1.89
59012178--59012222	13	3.2	13	84	9	54	66	0	0	33	0.92
59037375--59037416	21	2.0	21	100	0	84	52	4	23	19	1.65
59040198--59040240	22	2.0	22	90	0	68	55	11	2	30	1.48
59040400--59040438	13	2.9	13	85	14	53	51	0	0	48	1.00
59041498--59041545	26	1.9	26	83	8	64	31	4	14	50	1.62
59044449--59044658	101	2.1	101	99	0	411	36	5	20	37	1.75
59050895--59051025	40	3.3	40	70	11	117	25	16	24	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59052993--59053050	26	2.2	26	84	0	71	39	17	17	25	1.91
59054980--59055032	16	3.3	15	74	10	52	52	0	28	18	1.46
59057336--59057425	44	2.0	44	84	0	117	45	3	12	38	1.58
59058069--59058093	6	4.2	6	100	0	50	32	36	0	32	1.58
59065215--59065305	44	2.1	44	87	4	130	46	6	10	36	1.65
59075775--59075802	5	5.6	5	100	0	56	21	0	0	78	0.75
59075935--59075961	8	3.4	8	100	0	54	0	11	0	88	0.50
59076685--59076719	2	17.5	2	93	0	61	45	2	0	51	1.16
59076743--59076790	20	2.3	22	82	13	57	43	16	0	39	1.48
59093132--59093174	19	2.1	22	83	12	56	55	4	4	34	1.41
59094047--59094099	18	2.9	18	85	0	79	9	24	47	18	1.78
59094112--59094137	6	4.3	6	100	0	52	15	0	53	30	1.42
59094983--59095020	17	2.3	17	90	4	60	34	0	0	65	0.93
59095372--59095417	20	2.3	20	85	10	60	56	0	2	41	1.11
59095372--59095414	21	2.0	21	86	8	61	53	0	2	44	1.13
59095377--59095430	20	2.7	21	82	5	58	62	0	1	35	1.06
59095617--59095682	10	6.6	10	72	11	55	36	0	4	59	1.18
59095645--59095682	11	3.5	11	89	10	60	42	0	2	55	1.14
59097248--59097288	18	2.3	18	87	4	57	31	7	0	60	1.24
59097764--59097828	27	2.4	27	77	7	71	64	9	9	16	1.48
59100151--59100259	36	3.0	36	97	0	200	37	12	20	29	1.90
59100179--59100244	21	3.5	20	63	25	52	34	12	19	33	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59100115--59100348	82	2.8	84	75	20	244	35	14	22	28	1.93
59100223--59100348	46	2.8	46	93	3	213	32	16	23	27	1.96
59103323--59103365	13	3.2	13	90	6	68	55	9	11	23	1.64
59106497--59106845	171	2.0	171	100	0	698	30	5	22	40	1.77
59108659--59108685	2	13.5	2	100	0	54	48	0	0	51	1.00
59109106--59109164	16	3.8	16	70	17	52	66	1	0	32	1.02
59119301--59119467	83	2.0	83	91	0	271	22	12	17	47	1.81
59119717--59119746	14	2.1	14	93	0	51	83	0	0	16	0.65
59120145--59120185	15	2.7	16	77	11	50	48	2	0	48	1.14
59120371--59120415	17	2.6	19	73	20	53	44	4	6	44	1.50
59120470--59120531	28	2.3	27	83	8	72	25	22	3	48	1.66
59126755--59126782	2	14.0	2	100	0	56	50	0	0	50	1.00
59128197--59128238	10	3.9	11	76	17	52	54	0	0	45	0.99
59128194--59128238	16	2.8	17	83	6	58	53	0	0	46	1.00
59128254--59128300	13	3.4	14	82	14	53	46	4	2	46	1.34
59130638--59130675	21	1.9	21	89	10	62	50	0	0	50	1.00
59133479--59133539	23	2.8	22	76	9	63	40	22	19	16	1.90
59134498--59134543	24	1.9	24	86	8	67	52	0	2	45	1.13
59134678--59134707	6	5.0	6	100	0	60	50	0	0	50	1.00
59135312--59135346	2	18.0	2	94	5	63	51	0	0	48	1.00
59135706--59135732	6	4.5	6	100	0	54	66	0	14	18	1.25
59136370--59136410	21	2.0	21	85	9	57	36	17	19	26	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59138448--59138502	24	2.3	24	87	0	74	34	20	27	18	1.95
59138550--59138603	26	2.1	26	86	6	74	37	22	25	14	1.93
59141099--59141125	2	13.5	2	100	0	54	51	0	0	48	1.00
59142482--59142529	8	5.9	8	78	4	51	6	6	4	83	0.91
59143862--59143894	16	2.1	16	88	5	50	63	12	0	24	1.28
59146914--59146986	10	7.2	10	80	13	69	78	8	8	5	1.10
59146943--59146986	19	2.3	19	84	4	52	79	11	4	4	1.02
59148696--59148893	46	4.3	46	65	16	124	25	17	23	33	1.96
59148587--59148999	136	3.1	135	92	1	675	27	18	23	30	1.98
59149004--59149574	82	7.0	82	95	0	971	32	25	20	21	1.98

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