genome.fa.s9.2.7.7.80.10.50.1000.99.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  99  of  226  ( 27023 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)
34009689--34009750	31	2.0	31	87	6	90	40	11	4	43	1.62
34011280--34011346	33	2.0	33	85	5	91	34	31	11	22	1.90
34020001--34020075	11	6.8	11	71	24	52	53	2	1	42	1.23
34019985--34020075	36	2.4	37	83	8	105	51	4	2	41	1.34
34028334--34028358	12	2.1	12	100	0	50	20	8	24	48	1.76
34060620--34060913	43	6.8	43	79	4	272	22	15	24	38	1.93
34060620--34060982	86	4.2	86	77	6	324	22	16	22	38	1.93
34060632--34060980	129	2.7	129	78	3	346	22	16	22	37	1.93
34060624--34061050	43	10.0	42	76	5	255	23	16	22	37	1.93
34063609--34063664	29	1.9	29	85	7	78	17	17	41	23	1.90
34065172--34065215	15	3.0	15	90	3	63	25	11	6	56	1.58
34067323--34067549	41	5.5	41	80	4	260	33	22	18	25	1.96
34067320--34067546	123	1.8	123	84	5	307	33	22	18	25	1.97
34073194--34073220	12	2.2	12	100	0	54	55	7	7	29	1.55
34073273--34073340	33	2.1	31	86	10	100	45	1	1	51	1.19
34073308--34073461	51	3.0	51	93	0	254	45	6	0	47	1.33
34073356--34073445	23	3.7	22	71	18	63	45	5	1	47	1.33
34091789--34091911	43	2.9	43	86	0	165	30	21	17	31	1.96
34093643--34093978	43	7.9	43	78	3	293	23	16	22	37	1.93
34093663--34093982	129	2.5	129	81	6	380	24	16	22	37	1.93
34093999--34094082	43	2.0	43	81	9	100	25	21	15	38	1.92
34096677--34096784	38	2.8	38	85	0	153	35	29	18	16	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34111024--34111096	36	2.0	36	100	0	146	35	19	2	42	1.65
34115249--34115301	11	4.6	11	82	17	72	30	13	1	54	1.49
34115260--34115308	24	2.0	24	100	0	98	28	16	4	51	1.63
34115414--34115457	21	2.0	21	86	4	61	29	13	4	52	1.60
34116036--34116090	28	2.0	28	85	3	76	50	16	21	10	1.75
34116097--34116191	43	2.4	37	76	21	111	49	21	20	9	1.76
34122637--34122770	51	2.6	50	79	9	146	25	17	25	32	1.97
34126355--34126392	20	1.9	20	94	0	67	47	2	0	50	1.15
34128774--34128799	13	2.0	13	100	0	52	15	0	0	84	0.62
34129216--34129268	19	2.8	19	81	16	65	64	5	1	28	1.27
34132072--34132214	47	3.1	47	92	3	236	41	19	11	27	1.86
34132079--34132217	45	3.0	46	93	2	226	40	20	12	26	1.88
34132676--34132922	50	4.8	50	81	6	239	23	27	20	28	1.99
34134618--34134685	27	2.5	27	85	0	82	26	23	16	33	1.95
34140582--34140618	19	1.9	18	89	10	56	37	2	8	51	1.46
34142503--34142547	22	2.0	22	82	0	54	31	15	2	51	1.56
34148541--34148581	3	13.7	3	100	0	82	68	0	0	31	0.90
34153441--34153485	23	1.9	24	81	4	56	15	15	2	66	1.35
34169831--34169855	13	1.9	13	100	0	50	44	0	8	48	1.32
34174402--34174440	20	1.9	20	89	5	60	23	2	7	66	1.30
34178077--34178138	32	1.9	33	96	3	117	45	11	8	35	1.70
34179693--34179851	33	4.8	33	68	11	90	30	15	25	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34179625--34179863	101	2.4	101	91	0	379	31	15	25	28	1.96
34180031--34180496	154	3.0	154	97	0	878	37	4	20	37	1.73
34182250--34182287	19	2.0	19	89	0	58	60	5	13	21	1.52
34182647--34182686	20	2.0	20	85	9	55	25	10	7	57	1.57
34182702--34182748	18	2.7	18	73	3	51	48	0	4	46	1.21
34185851--34185903	23	2.3	23	81	15	65	45	0	3	50	1.19
34188052--34188124	29	2.5	30	77	8	78	30	24	16	28	1.96
34193515--34193573	17	3.0	21	76	21	72	42	15	5	37	1.69
34201480--34201536	21	2.7	21	86	0	78	42	21	5	31	1.75
34201482--34201545	21	3.0	21	83	0	74	39	20	6	34	1.78
34201725--34201801	31	2.4	31	81	10	84	20	37	24	16	1.93
34211270--34211360	38	2.4	38	83	3	103	20	24	27	27	1.99
34211937--34212190	27	9.5	27	77	5	230	20	16	18	44	1.87
34211935--34212190	54	4.8	54	79	4	277	21	16	18	44	1.87
34213619--34213886	27	10.0	27	80	3	272	20	16	19	43	1.88
34213630--34213887	82	3.2	80	80	7	292	19	17	18	44	1.87
34216949--34217018	27	2.6	27	86	4	97	18	14	21	45	1.84
34216950--34217027	27	2.9	27	82	3	95	19	12	20	47	1.82
34220491--34220543	20	2.6	20	77	16	56	26	24	33	15	1.95
34230115--34230158	3	14.7	3	100	0	88	65	0	0	34	0.93
34231952--34231985	3	11.3	3	100	0	68	0	32	0	67	0.91
34236418--34236457	18	2.2	18	86	8	55	67	12	0	20	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34240611--34240708	27	3.6	27	83	8	128	28	26	13	31	1.94
34246184--34246313	59	2.1	63	81	9	162	27	3	17	50	1.63
34246219--34246311	32	2.9	32	96	0	168	26	4	18	50	1.65
34247662--34247699	19	2.0	19	100	0	76	47	15	10	26	1.78
34247691--34247726	14	2.5	15	91	8	58	44	19	2	33	1.65
34255040--34255095	3	18.7	3	100	0	112	67	0	0	32	0.91
34255634--34255688	23	2.5	21	80	13	65	54	7	0	38	1.28
34259718--34259758	19	2.2	19	86	0	55	70	2	0	26	0.99
34259898--34259977	30	2.6	29	75	13	81	37	3	1	57	1.25
34259936--34259989	21	2.7	20	74	5	54	42	1	0	55	1.10
34260072--34260130	10	6.0	10	72	18	52	32	1	1	64	1.13
34264486--34264532	18	2.6	17	81	12	51	42	4	17	36	1.68
34264966--34264995	15	1.9	16	93	6	53	56	0	0	43	0.99
34266018--34266072	28	1.9	29	96	3	103	41	14	1	41	1.56
34275092--34275121	2	15.0	2	100	0	60	50	0	0	50	1.00
34275403--34275450	25	1.9	25	83	8	62	41	6	4	47	1.48
34277136--34277199	28	2.2	28	80	2	74	37	0	1	60	1.06
34277167--34277242	22	3.8	21	83	11	97	35	2	0	61	1.10
34277133--34277241	22	5.1	20	71	22	87	35	2	0	60	1.17
34278184--34278223	14	2.9	14	85	3	55	67	0	0	32	0.91
34278191--34278228	20	1.9	20	94	0	67	60	2	0	36	1.11
34278657--34278698	21	1.9	21	85	9	57	61	14	0	23	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34279114--34279164	25	2.0	25	81	7	59	45	7	5	41	1.57
34280924--34281116	50	3.7	50	81	4	197	24	29	20	25	1.99
34283018--34283070	19	2.7	20	76	5	63	52	1	0	45	1.11
34289028--34289334	30	10.2	30	85	0	380	29	10	18	41	1.84
34295922--34296232	30	10.4	30	84	1	399	28	10	19	41	1.84
34300428--34300464	17	2.2	17	90	0	56	5	21	0	72	1.04
34302749--34302817	35	2.0	35	86	11	97	5	20	0	73	1.03
34302873--34303070	105	1.9	107	87	7	296	24	27	2	45	1.64
34313203--34313236	2	17.0	2	100	0	68	50	0	0	50	1.00
34318451--34318501	22	2.3	23	78	21	63	35	19	1	43	1.63
34318752--34318914	33	5.0	32	70	9	105	31	24	15	28	1.95
34325400--34325488	45	2.0	45	95	0	160	34	14	7	42	1.75
34331005--34331149	41	3.5	41	89	2	211	29	20	28	22	1.98
34330960--34331150	82	2.3	82	81	7	210	31	19	26	22	1.98
34331594--34331623	2	15.0	2	100	0	60	50	0	0	50	1.00
34338535--34338720	41	4.6	41	92	2	304	27	19	28	24	1.98
34338481--34338720	82	2.9	81	85	6	308	28	18	27	25	1.98
34359441--34359487	2	23.5	2	100	0	94	0	0	48	51	1.00
34359666--34359826	33	4.8	32	70	8	115	29	15	26	28	1.96
34359600--34359838	101	2.4	101	94	0	415	30	15	25	28	1.96
34381915--34381960	22	2.1	22	100	0	92	26	13	17	43	1.85
34386071--34386130	30	2.0	30	86	0	84	21	33	13	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34391237--34391294	9	6.4	9	76	7	64	39	22	6	31	1.80
34391237--34391294	18	3.2	18	87	0	80	39	22	6	31	1.80
34391334--34391362	6	4.8	6	100	0	58	17	0	17	65	1.27
34391318--34391375	18	3.0	20	82	12	66	22	3	12	62	1.45
34391830--34391890	32	1.9	32	96	0	113	22	19	13	44	1.85
34402169--34402215	5	9.2	5	81	4	58	38	0	21	40	1.53
34402653--34402736	24	3.5	24	67	15	66	16	22	20	40	1.91
34402725--34402795	25	2.8	25	84	0	88	22	26	18	32	1.97
34407423--34407539	43	2.7	43	82	11	132	24	17	26	30	1.97
34416516--34416572	30	1.9	30	85	3	80	42	1	24	31	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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226