genome.fa.s1.2.7.7.80.10.50.1000.141.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  141  of  187  ( 22383 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)
42181820--42181871	21	2.5	20	84	9	68	34	13	44	7	1.72
42182248--42182314	34	1.9	35	87	3	100	31	8	14	44	1.76
42182874--42183114	41	5.8	41	79	4	205	25	20	25	28	1.99
42182880--42183114	85	2.8	81	82	5	245	25	20	25	28	1.99
42182879--42183114	42	5.7	41	81	2	238	25	20	25	28	1.99
42183304--42183354	2	26.0	2	96	4	95	50	0	0	49	1.00
42183794--42183851	28	2.1	28	100	0	116	20	15	10	53	1.71
42187747--42187805	30	2.0	30	86	6	84	44	0	37	18	1.50
42187941--42187981	21	2.0	21	85	9	57	43	0	34	21	1.53
42188397--42188427	2	15.5	2	93	0	53	48	0	0	51	1.00
42190537--42190588	23	2.3	22	80	9	59	51	5	23	19	1.67
42190535--42190687	79	1.9	80	81	5	186	57	7	16	18	1.62
42190615--42190666	22	2.3	23	76	3	61	59	7	11	21	1.56
42198835--42198879	5	8.8	5	90	4	72	40	0	0	60	0.97
42198838--42198884	8	6.0	8	80	14	62	40	0	0	59	0.97
42199968--42200038	25	2.8	25	89	4	99	16	22	22	38	1.93
42202134--42202180	24	2.0	24	100	0	94	34	17	12	36	1.87
42202875--42203041	35	4.7	35	65	11	88	28	15	26	29	1.96
42202908--42203072	33	4.8	32	68	15	105	29	15	26	29	1.96
42202857--42203072	107	2.0	107	95	0	387	29	15	25	29	1.96
42211404--42211449	8	5.8	8	100	0	92	50	13	0	36	1.41
42214058--42214103	16	2.9	16	84	9	58	26	13	0	60	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42214071--42214106	17	2.1	18	94	5	65	30	13	0	55	1.39
42214198--42214239	2	21.0	2	100	0	84	50	0	0	50	1.00
42225970--42226481	100	5.1	100	91	1	771	31	19	22	25	1.98
42225972--42226433	50	9.3	50	70	7	294	32	19	22	25	1.98
42228454--42228499	16	2.9	16	84	9	58	26	13	0	60	1.32
42228467--42228502	17	2.1	18	94	5	65	30	13	0	55	1.39
42232848--42232872	2	12.5	2	100	0	50	48	0	0	52	1.00
42233753--42233795	21	2.0	21	86	4	59	20	2	25	51	1.60
42234052--42234107	17	3.3	17	76	0	67	19	10	28	41	1.85
42248440--42248594	79	2.0	79	87	2	222	29	10	14	45	1.79
42250292--42250359	24	3.0	24	67	20	65	52	2	1	42	1.25
42250291--42250340	19	2.7	19	84	9	59	52	0	2	46	1.12
42256058--42256113	28	2.0	29	85	3	78	32	7	12	48	1.68
42256074--42256113	14	2.7	15	80	7	55	32	2	10	55	1.47
42260926--42260962	3	12.3	3	100	0	74	0	35	0	64	0.94
42266753--42266877	62	2.0	62	98	0	241	28	15	27	28	1.96
42271521--42271609	19	4.7	20	70	21	59	57	1	10	31	1.39
42271521--42271616	29	3.4	28	78	10	99	58	1	9	31	1.37
42271649--42271683	4	8.8	4	100	0	70	25	0	22	51	1.48
42271926--42271961	12	3.1	12	92	4	56	66	0	0	33	0.92
42271930--42271967	12	3.2	12	85	7	51	71	0	0	28	0.87
42272367--42272394	14	2.0	14	100	0	56	50	28	7	14	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42274275--42274329	21	2.6	21	85	0	83	21	9	38	30	1.85
42281367--42281404	15	2.5	15	95	0	67	0	26	0	73	0.83
42282704--42282892	91	2.1	91	82	5	231	28	6	20	44	1.76
42283870--42284038	43	4.0	43	77	6	164	23	17	26	31	1.97
42287137--42287187	27	1.9	27	84	11	70	60	15	15	7	1.56
42291234--42291284	27	1.9	27	84	11	70	60	15	15	7	1.56
42295219--42295266	14	3.2	14	78	16	60	41	2	0	56	1.11
42295214--42295301	31	2.9	31	91	1	133	40	2	0	56	1.11
42304496--42304539	23	2.0	22	86	4	61	31	13	22	31	1.93
42304601--42304651	17	3.1	16	78	10	57	37	3	13	45	1.63
42304601--42304669	34	2.0	34	86	5	95	34	4	13	47	1.62
42304648--42304681	17	2.0	17	88	0	50	26	2	14	55	1.53
42323925--42323969	22	2.0	22	95	0	81	20	17	24	37	1.93
42336006--42336041	18	2.0	18	94	0	63	27	19	22	30	1.98
42338838--42338868	15	2.1	15	93	0	53	54	16	9	19	1.68
42338971--42339005	19	1.9	17	88	11	52	62	0	17	20	1.32
42340470--42340522	5	10.8	5	76	11	56	0	18	0	81	0.70
42340464--42340522	10	5.4	11	77	20	61	1	16	0	81	0.78
42340480--42340520	16	2.7	15	85	7	55	0	19	0	80	0.71
42342291--42342321	16	1.9	16	93	0	53	22	3	0	74	0.96
42348698--42348759	31	2.0	31	93	0	106	35	6	11	46	1.65
42351484--42351514	14	2.2	14	100	0	62	58	12	0	29	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42355385--42355459	37	2.0	37	94	0	132	32	21	10	36	1.88
42366428--42367091	220	3.0	220	93	0	1114	39	19	12	28	1.88
42375987--42376020	18	1.9	17	88	5	50	32	8	5	52	1.56
42379116--42379165	19	2.6	19	80	3	55	50	0	2	48	1.12
42379174--42379264	33	2.7	34	81	6	96	53	2	2	41	1.25
42379181--42379264	35	2.5	34	81	7	91	53	2	2	41	1.27
42380038--42380079	3	14.0	3	100	0	84	33	0	0	66	0.92
42384025--42384133	41	2.7	41	94	1	184	21	22	30	26	1.98
42387669--42388224	114	4.9	114	82	3	638	24	23	25	27	2.00
42388143--42388297	73	2.1	73	90	2	240	26	23	23	27	2.00
42388017--42388533	187	2.8	186	84	2	660	23	20	26	29	1.99
42389987--42390969	337	2.9	331	82	4	1098	30	18	17	33	1.94
42391094--42391145	15	3.8	13	76	16	52	65	5	25	3	1.32
42392354--42392386	15	2.1	16	88	11	50	36	3	0	60	1.12
42392374--42392407	17	1.9	18	88	5	52	38	5	0	55	1.24
42392511--42392895	9	44.4	9	81	10	421	46	19	0	33	1.56
42392797--42392854	26	2.3	26	96	3	109	39	18	3	37	1.68
42392857--42392902	7	6.0	7	90	9	56	52	17	0	30	1.45
42398392--42398465	21	3.5	21	83	0	85	35	14	41	8	1.76
42398849--42398965	43	2.7	44	79	6	107	32	20	22	24	1.98
42398902--42399017	42	2.8	40	84	8	142	29	21	17	31	1.96
42405854--42405888	18	1.9	18	88	0	52	51	5	34	8	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42410931--42410959	10	3.0	10	95	5	51	51	0	10	37	1.36
42411202--42411273	37	1.9	37	91	0	117	20	15	30	33	1.94
42413411--42413708	45	6.6	45	84	3	361	28	16	13	41	1.86
42413674--42413778	42	2.4	44	79	7	108	34	19	15	31	1.92
42415656--42415722	29	2.3	29	81	2	80	28	16	16	38	1.90
42416101--42416355	125	2.1	123	87	3	368	30	16	22	30	1.95
42419607--42419640	15	2.3	15	90	5	52	67	5	0	26	1.13
42419877--42419946	22	3.2	22	91	0	113	40	0	28	31	1.57
42420063--42420093	11	2.8	11	95	0	53	22	48	19	9	1.78
42423391--42423431	3	13.7	3	100	0	82	31	0	0	68	0.90
42438119--42438232	54	2.1	54	88	0	165	35	10	20	34	1.87
42438235--42438656	54	7.8	54	76	1	342	40	15	17	27	1.89
42438428--42438656	109	2.1	108	82	2	271	40	14	16	28	1.88
42438264--42438653	163	2.4	161	83	2	460	40	14	17	27	1.88
42438884--42438946	21	3.2	21	69	17	71	39	6	15	38	1.73
42438878--42438950	38	1.9	38	100	0	146	39	8	15	36	1.77
42452637--42452687	20	2.6	19	82	14	52	60	1	0	37	1.08
42457638--42457798	85	1.9	85	83	2	207	29	19	19	31	1.96
42457684--42458727	521	2.0	518	89	1	1579	36	18	13	32	1.89
42462174--42462207	18	1.9	17	88	5	50	47	11	14	26	1.79
42474699--42474751	19	2.7	20	88	2	72	50	5	24	18	1.68
42474690--42474760	20	3.7	20	81	5	92	50	4	30	14	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42475559--42475808	24	10.7	24	71	13	155	34	6	4	55	1.46
42475525--42475798	69	4.0	69	74	13	199	34	6	4	54	1.47
42475906--42475956	23	2.1	25	85	7	70	35	5	3	54	1.43
42475937--42475972	12	3.3	11	85	14	56	25	0	2	72	0.98
42475940--42475973	10	3.2	10	91	8	50	23	0	2	73	0.97
42486939--42486964	5	5.2	5	100	0	52	42	19	19	19	1.90
42487745--42487781	9	4.1	9	92	0	65	29	10	13	45	1.77
42487834--42487864	9	3.4	9	90	0	53	38	22	12	25	1.90
42488704--42488761	24	2.4	23	78	16	55	55	0	27	17	1.42
42489948--42490038	30	2.9	31	69	18	80	30	2	16	50	1.57

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