genome.fa.s13.2.7.7.80.10.50.1000.130.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   199   

This is table  130  of  199  ( 23770 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)
39367959--39368035	20	3.9	19	80	10	75	37	28	11	22	1.89
39367973--39368035	19	3.3	19	80	10	65	39	28	11	20	1.87
39379970--39380009	20	2.0	20	90	0	62	27	10	12	50	1.72
39379955--39380021	34	1.9	35	90	3	109	31	8	13	46	1.74
39379949--39380025	14	5.0	15	71	20	52	33	9	14	42	1.77
39383661--39383738	31	2.6	29	72	18	72	39	3	6	50	1.46
39384403--39384435	17	1.9	17	88	11	50	27	0	3	69	1.03
39384412--39384474	30	2.1	30	90	0	99	26	3	12	57	1.51
39384598--39384631	11	3.0	12	87	12	54	67	0	0	32	0.91
39385711--39385853	66	2.1	67	90	1	234	36	13	9	39	1.78
39387970--39388095	27	4.7	27	84	2	137	28	16	24	30	1.97
39387965--39388094	54	2.4	54	84	0	170	30	16	23	30	1.96
39391849--39391914	23	2.9	23	93	0	114	46	36	7	9	1.64
39392026--39392068	17	2.5	17	82	14	61	34	23	0	41	1.55
39392849--39392881	16	2.1	16	94	0	57	3	12	6	78	1.04
39400820--39401023	44	4.7	45	80	17	225	27	29	17	25	1.97
39403853--39403957	43	2.4	43	88	1	156	31	24	17	26	1.97
39404075--39404281	31	6.7	31	82	3	249	42	15	9	32	1.79
39404075--39404281	61	3.4	62	85	2	267	42	15	9	32	1.79
39404075--39404292	92	2.4	92	84	3	251	43	16	8	31	1.78
39406361--39406534	43	4.1	42	75	9	147	27	13	26	32	1.94
39406354--39406481	43	3.0	41	80	10	159	25	15	27	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39407938--39407978	16	2.6	16	88	7	57	29	14	0	56	1.39
39408003--39408050	3	15.7	3	78	4	51	33	6	0	60	1.22
39411464--39411502	18	2.1	19	85	4	53	30	23	0	46	1.53
39411621--39411685	23	2.8	23	92	0	112	47	32	9	10	1.70
39412644--39412708	3	21.7	3	90	6	105	63	1	0	35	1.04
39413080--39413108	15	1.9	15	100	0	58	55	13	0	31	1.39
39416467--39416510	17	2.4	18	88	7	63	13	9	4	72	1.24
39416480--39416523	23	1.9	23	81	9	54	20	6	4	68	1.31
39425926--39426003	32	2.3	32	82	12	86	48	0	2	48	1.15
39426094--39426138	22	2.0	22	83	8	56	42	0	0	57	0.98
39426114--39426168	8	7.4	8	83	8	55	41	1	0	56	1.10
39426096--39426187	28	3.3	28	79	7	98	41	1	0	57	1.06
39426114--39426186	36	2.0	36	92	5	121	39	1	0	58	1.06
39426185--39426252	31	2.3	30	82	7	93	64	1	0	33	1.02
39430117--39430177	29	2.1	29	84	3	77	45	0	34	19	1.51
39435678--39435709	7	4.6	7	96	0	55	40	9	31	18	1.83
39435638--39435805	58	3.0	58	85	11	260	32	14	25	28	1.94
39435685--39435808	51	2.4	51	95	0	221	33	12	25	28	1.93
39442423--39442450	14	2.0	14	100	0	56	28	7	28	35	1.84
39447038--39447136	42	2.3	43	87	1	137	32	24	17	26	1.97
39447015--39447176	43	3.8	42	76	11	150	32	27	15	24	1.95
39451810--39451874	32	2.0	32	100	0	130	24	21	12	41	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39455984--39456025	20	2.2	20	87	8	61	38	0	9	52	1.34
39458372--39458412	20	2.0	20	90	9	66	31	19	0	48	1.49
39460618--39460647	15	2.1	15	93	6	53	16	6	0	76	0.99
39461597--39461754	84	1.9	84	87	0	235	34	5	16	43	1.70
39476554--39476677	12	9.9	12	70	14	72	50	8	15	25	1.73
39476554--39476677	25	5.0	25	72	14	103	50	8	15	25	1.73
39479249--39479281	7	5.0	7	92	7	52	15	0	0	84	0.61
39479251--39479280	6	4.8	6	92	8	51	13	0	0	86	0.57
39479251--39479280	13	2.4	12	94	5	51	13	0	0	86	0.57
39479288--39479331	3	14.0	3	85	4	52	0	27	0	72	0.85
39479287--39479331	12	3.8	12	85	14	67	0	26	0	73	0.84
39479679--39479854	30	6.0	29	74	5	147	43	5	19	32	1.73
39480040--39481448	78	18.2	77	80	9	1421	35	19	16	27	1.94
39480028--39481448	154	9.2	151	82	7	1475	36	19	16	27	1.94
39480058--39482028	384	5.2	377	79	9	1956	35	19	16	27	1.94
39480061--39482029	231	8.6	226	83	8	2049	35	19	16	27	1.94
39481450--39482031	78	7.6	77	80	7	548	35	18	17	28	1.94
39481450--39482029	155	3.8	154	80	7	646	35	18	17	28	1.94
39482882--39482925	8	5.6	8	89	5	72	0	0	11	88	0.51
39482862--39482925	17	3.8	17	82	14	71	0	6	7	85	0.73
39482862--39482924	9	6.9	9	82	12	58	0	6	7	85	0.73
39488975--39489074	20	5.2	20	70	19	88	45	11	8	36	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39488972--39489074	38	2.8	37	85	8	138	43	10	8	36	1.70
39488975--39489066	19	5.0	18	73	12	71	43	10	8	36	1.71
39488972--39489074	36	2.8	36	85	8	136	43	10	8	36	1.70
39488975--39489084	19	5.9	20	73	15	69	42	10	7	40	1.66
39489754--39489831	7	10.3	7	77	15	50	2	19	0	78	0.87
39489752--39489799	16	2.9	17	85	11	57	6	10	0	83	0.81
39489763--39489831	6	11.3	6	81	10	52	1	21	0	76	0.86
39489792--39489835	3	14.0	3	95	4	70	0	31	0	68	0.90
39490182--39490317	30	4.7	29	78	7	125	41	5	19	33	1.76
39490204--39490310	28	3.7	28	78	12	85	42	4	19	32	1.72
39496321--39496402	37	2.2	37	93	0	137	40	14	8	36	1.77
39496445--39496519	32	2.3	33	95	2	134	44	16	4	36	1.66
39499883--39499918	16	2.2	16	95	0	63	38	33	0	27	1.57
39500435--39500470	5	7.2	5	100	0	72	80	0	0	19	0.71
39500703--39500769	29	2.3	28	80	12	73	47	1	11	38	1.50
39502563--39502693	49	2.7	49	92	0	217	29	20	19	30	1.97
39513052--39513095	22	2.0	22	100	0	88	22	18	18	40	1.91
39516082--39516158	35	2.2	33	84	13	102	51	1	7	38	1.39
39516341--39516414	32	2.2	34	81	9	82	45	2	10	40	1.53
39517371--39517410	6	6.7	6	86	11	55	82	0	5	12	0.82
39517371--39517410	11	3.3	12	89	6	55	82	0	5	12	0.82
39518303--39518327	13	1.9	13	100	0	50	24	0	0	76	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39519036--39519116	37	2.2	37	90	0	126	34	8	14	41	1.77
39521604--39521639	16	2.2	16	100	0	72	25	0	36	38	1.56
39521855--39521896	15	2.7	16	82	14	52	52	2	0	45	1.13
39521864--39521905	15	2.9	15	82	10	52	52	0	0	47	1.00
39521974--39522025	15	3.6	15	80	12	56	53	1	0	44	1.11
39521853--39522150	120	2.5	121	92	4	487	50	4	2	42	1.36
39527760--39527835	33	2.3	33	97	0	143	35	5	15	43	1.70
39527878--39527959	37	2.2	37	93	0	137	36	8	14	40	1.77
39531109--39531134	5	5.2	5	100	0	52	80	0	19	0	0.71
39533840--39533994	82	1.9	82	89	0	238	36	5	14	44	1.67
39536271--39536321	26	2.0	26	84	7	68	19	5	0	74	1.02
39536409--39536449	18	2.3	19	83	12	59	24	9	0	65	1.22
39536980--39537024	22	2.0	22	100	0	90	37	4	0	57	1.19
39538768--39539020	46	5.6	46	95	1	433	28	22	15	33	1.94
39544575--39544634	3	20.0	3	96	0	111	65	0	1	33	1.03
39549536--39549624	44	2.0	44	100	0	178	31	11	13	43	1.79
39550988--39551059	30	2.3	33	79	11	89	33	1	4	61	1.24
39551013--39551059	8	5.9	8	76	18	53	36	0	2	61	1.08
39551009--39551056	15	3.3	14	83	16	62	35	0	2	62	1.07
39555029--39555086	24	2.4	24	94	0	98	39	18	22	18	1.92
39558511--39558543	14	2.4	14	100	0	66	21	12	21	45	1.84
39558563--39558616	24	2.3	24	78	12	58	22	16	0	61	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39563621--39563913	50	5.9	50	70	0	208	26	21	26	25	1.99
39563631--39563937	100	3.1	99	87	2	418	27	20	25	26	1.99
39563979--39564144	82	2.0	82	87	2	235	36	15	17	31	1.91
39563979--39564173	82	2.4	82	83	3	214	35	16	16	31	1.92
39564616--39564675	32	1.9	32	86	6	88	35	1	3	60	1.23
39564626--39564678	15	3.7	14	81	18	65	35	0	1	62	1.06
39578439--39578498	32	1.9	32	86	6	88	35	1	3	60	1.23
39578449--39578501	15	3.7	14	81	18	65	35	0	1	62	1.06
39582812--39583002	44	4.4	44	75	12	198	29	21	20	28	1.98
39582762--39583029	128	2.1	129	92	0	439	28	22	19	29	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   199