genome.fa.s16.2.7.7.80.10.50.1000.129.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: D03
Parameters: 2 7 7 80 10 50 1000
Length:  53248092

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   

This is table  129  of  175  ( 20966 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)
40221755--40221793	3	13.0	3	88	0	60	30	2	2	64	1.21
40222165--40222200	18	2.1	17	89	5	54	13	5	8	72	1.27
40222307--40222854	110	5.0	110	94	1	945	30	16	20	32	1.94
40222307--40222854	222	2.5	220	93	1	938	30	16	20	32	1.94
40224322--40224444	63	2.0	63	86	0	174	34	32	8	23	1.86
40226082--40226231	38	4.0	37	89	5	203	10	21	30	37	1.87
40226143--40226215	22	3.6	21	70	21	66	10	21	28	38	1.88
40226081--40226233	76	2.0	75	88	1	225	11	20	30	37	1.89
40228075--40228267	50	3.8	50	88	0	260	25	22	31	21	1.98
40232953--40233069	38	3.1	38	85	1	146	13	21	27	37	1.91
40233779--40233819	17	2.4	17	100	0	82	14	26	36	21	1.93
40234150--40234190	19	2.0	20	90	9	66	36	0	14	48	1.44
40234491--40234597	55	1.9	55	92	0	178	40	13	8	38	1.74
40237836--40237945	55	2.0	55	92	0	184	39	12	9	39	1.75
40243063--40243139	31	2.5	31	93	2	127	38	2	6	51	1.41
40248098--40248459	190	1.9	187	85	2	501	31	10	14	43	1.79
40256542--40256594	26	2.0	27	89	10	83	30	24	20	24	1.99
40263035--40263106	22	3.3	22	75	11	67	23	27	15	33	1.95
40272064--40272211	43	3.4	44	81	8	178	27	17	25	29	1.97
40275250--40275307	27	2.2	26	81	3	62	22	5	3	68	1.24
40275400--40275435	16	2.1	18	90	10	58	19	5	0	75	1.00
40276429--40276470	21	2.0	21	81	9	50	76	2	9	11	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40277325--40277382	30	1.9	30	85	0	80	18	39	29	12	1.87
40280769--40280856	45	2.0	45	90	0	140	60	11	11	17	1.59
40282300--40282333	17	1.9	17	88	5	50	73	11	8	5	1.24
40292122--40292170	22	2.2	22	82	7	55	42	0	4	53	1.20
40294892--40294928	9	4.1	9	89	0	56	45	10	10	32	1.74
40297577--40297619	19	2.3	18	84	15	52	62	0	0	37	0.95
40298880--40299091	88	2.4	88	90	0	334	32	21	16	29	1.96
40298669--40298971	132	2.3	132	92	0	498	30	23	16	29	1.96
40298746--40299200	220	2.1	219	92	0	757	30	22	18	28	1.97
40298898--40299047	43	3.5	42	65	20	101	31	21	15	32	1.94
40298966--40299744	132	5.9	132	94	0	1326	29	23	18	28	1.98
40298669--40299354	351	2.0	352	91	0	1124	29	23	17	29	1.97
40299229--40299541	44	7.1	44	64	13	133	29	23	19	26	1.99
40299467--40299661	44	4.4	44	65	12	112	28	24	16	30	1.96
40306219--40306333	19	5.7	21	79	12	71	40	14	6	38	1.73
40306219--40306276	22	2.6	22	81	7	64	41	17	5	36	1.72
40306255--40306346	19	4.8	19	91	0	157	36	14	9	39	1.79
40307403--40307446	23	1.9	23	100	0	88	29	6	22	40	1.80
40308777--40308822	4	10.8	4	82	13	56	47	4	0	47	1.21
40309671--40309705	17	2.1	17	89	5	54	57	0	28	14	1.38
40318628--40318668	19	2.0	21	86	9	59	31	9	0	58	1.31
40318628--40318667	21	2.0	21	85	5	55	32	10	0	57	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40337891--40337927	9	4.1	9	89	0	56	45	10	10	32	1.74
40340575--40340617	19	2.3	18	84	15	52	62	0	0	37	0.95
40341670--40341972	132	2.3	132	92	0	498	30	23	16	29	1.96
40341747--40342200	219	2.1	219	92	0	757	30	22	18	28	1.97
40341881--40342091	87	2.4	88	89	0	325	31	21	17	29	1.96
40341967--40342744	132	5.9	131	94	0	1281	29	23	18	28	1.98
40341670--40342354	350	2.0	351	91	0	1122	29	23	17	29	1.97
40342229--40342541	44	7.1	44	64	13	133	29	23	19	26	1.99
40342467--40342661	44	4.4	44	65	12	112	28	24	16	30	1.96
40344146--40344178	14	2.3	15	89	5	50	27	30	15	27	1.96
40349230--40349344	19	5.7	21	79	12	71	40	14	6	38	1.73
40349230--40349287	22	2.6	22	81	7	64	41	17	5	36	1.72
40349266--40349357	19	4.8	19	91	0	157	36	14	9	39	1.79
40351782--40351827	4	10.8	4	82	13	56	47	4	0	47	1.21
40352675--40352709	17	2.1	17	89	5	54	57	0	28	14	1.38
40361610--40361650	20	2.0	20	86	9	57	31	9	0	58	1.31
40372885--40372918	17	2.0	17	94	0	59	38	23	8	29	1.85
40373199--40373888	104	6.7	104	83	3	721	32	14	20	32	1.93
40380181--40380228	16	2.9	16	84	12	62	8	20	0	70	1.12
40380193--40380275	20	4.1	20	71	14	62	6	18	2	73	1.15
40382351--40382388	15	2.4	16	91	4	60	26	7	5	60	1.46
40383972--40384033	20	3.0	20	72	9	52	51	14	4	29	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40392073--40392099	12	2.2	12	100	0	54	37	7	7	48	1.59
40398591--40398617	13	2.1	13	100	0	54	48	14	0	37	1.45
40399463--40399519	21	2.7	21	75	5	62	31	1	5	61	1.28
40401240--40401287	11	4.4	11	75	0	51	47	0	0	52	1.00
40401239--40401290	14	3.0	19	71	26	60	48	0	0	51	1.00
40414771--40414800	15	2.0	15	93	0	51	36	46	0	16	1.47
40415741--40415837	46	2.1	46	88	0	140	29	14	15	40	1.87
40415989--40416110	49	2.5	49	84	0	154	21	20	18	39	1.93
40419852--40419911	30	2.0	31	86	3	86	20	40	0	40	1.52
40425888--40425913	8	3.2	8	100	0	52	11	0	0	88	0.52
40432562--40432586	10	2.5	10	100	0	50	36	0	20	44	1.52
40433197--40433296	21	4.8	21	72	2	76	17	23	18	42	1.89
40433256--40433304	21	2.3	22	82	10	75	14	24	18	42	1.87
40437319--40437365	23	2.1	23	84	7	62	51	12	4	31	1.59
40442687--40442730	17	2.6	17	96	3	81	18	11	4	65	1.40
40442769--40442801	12	2.9	11	91	8	57	18	3	9	69	1.28
40443793--40443839	23	2.1	23	84	7	62	51	12	4	31	1.59
40446254--40446292	14	2.8	14	92	0	60	20	2	10	66	1.33
40455496--40455552	29	2.0	29	89	0	87	26	7	14	52	1.66
40455499--40455562	29	2.2	29	82	0	74	26	9	14	50	1.73
40465075--40465125	24	2.1	24	82	7	59	50	0	0	49	1.00
40465972--40466003	14	2.3	14	100	0	64	15	0	12	71	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40465972--40466010	14	2.9	14	92	3	53	15	2	10	71	1.23
40466075--40466103	4	7.2	4	100	0	58	27	0	0	72	0.85
40466516--40466690	88	2.0	89	88	1	262	44	29	1	24	1.63
40466764--40466796	14	2.3	15	94	5	59	36	33	0	30	1.58
40467453--40467515	30	2.1	30	90	0	99	57	15	1	25	1.48
40467545--40467587	22	2.0	22	85	0	59	58	6	13	20	1.59
40467881--40467997	61	2.0	60	88	5	175	27	9	17	46	1.78
40468641--40468691	23	2.2	24	82	3	59	33	1	23	41	1.66
40470426--40470463	19	2.0	19	89	0	58	10	0	44	44	1.38
40494029--40494167	60	2.3	60	85	2	190	46	2	12	38	1.55
40494060--40494153	30	3.2	30	70	18	88	45	3	10	40	1.55
40504383--40504429	16	2.9	16	84	9	51	48	6	27	17	1.71
40504404--40504434	16	1.9	16	93	0	53	48	3	29	19	1.64
40518574--40518745	25	6.9	25	80	5	177	19	26	17	37	1.93
40518593--40518745	50	3.1	50	86	0	207	19	25	17	37	1.94
40518576--40518740	75	2.2	75	82	7	201	18	26	17	37	1.93
40518626--40518829	25	8.2	25	73	10	85	20	25	18	36	1.95
40518632--40518778	75	2.0	75	82	5	181	19	23	19	37	1.94
40524763--40524899	50	2.7	50	84	4	177	19	26	18	35	1.95
40524763--40524907	25	5.8	25	77	8	143	19	26	17	36	1.94
40524794--40524933	75	1.9	75	81	3	174	20	25	17	35	1.95
40524939--40525024	25	3.4	25	74	15	79	22	23	20	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40530001--40530033	9	3.7	9	91	0	57	51	18	6	24	1.68
40534035--40534080	20	2.3	20	92	0	74	19	2	13	65	1.37
40536741--40536770	6	5.0	6	100	0	60	83	0	0	16	0.65
40539733--40539765	17	1.9	17	88	11	50	45	33	0	21	1.52
40540170--40540260	40	2.2	42	90	7	152	43	24	10	20	1.84
40541294--40541616	95	3.5	93	87	5	447	40	2	17	40	1.62
40541648--40541939	127	2.3	126	83	7	405	34	18	19	27	1.95
40545974--40546005	7	4.7	7	92	7	57	59	12	0	28	1.34
40545974--40546005	13	2.4	14	89	10	57	59	12	0	28	1.34
40564830--40564868	20	2.0	20	90	10	62	71	0	0	28	0.86

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