genome.fa.s4.2.7.7.80.10.50.1000.123.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: A04
Parameters: 2 7 7 80 10 50 1000
Length:  82679320

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   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   

This is table  123  of  255  ( 30512 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)
39270589--39270772	98	1.9	97	93	4	318	30	26	7	35	1.83
39270744--39270889	47	3.1	47	88	0	184	27	29	10	32	1.90
39274918--39275268	40	8.8	40	93	2	564	25	28	21	24	1.99
39276538--39276609	37	1.9	37	94	0	126	27	30	19	22	1.98
39276755--39276939	48	3.8	49	90	5	295	31	25	7	35	1.83
39276755--39276938	98	1.9	97	92	4	309	30	26	7	35	1.83
39276909--39277102	47	4.1	47	89	0	280	26	29	10	33	1.89
39277002--39277073	22	3.1	22	66	24	58	23	29	12	34	1.92
39276862--39277102	94	2.6	94	84	4	290	27	29	9	33	1.88
39282379--39282497	27	4.4	27	80	4	150	25	21	18	34	1.96
39282337--39282512	54	3.3	53	75	10	151	27	23	19	30	1.98
39282338--39282512	27	6.5	27	76	6	115	27	23	18	30	1.98
39300825--39300902	31	2.5	31	89	0	111	10	29	34	25	1.89
39300877--39300920	20	2.3	18	84	7	52	11	36	27	25	1.90
39312260--39312314	4	13.8	4	100	0	110	25	0	23	50	1.49
39326238--39326540	119	2.6	119	88	4	427	25	20	27	26	1.99
39326238--39326540	40	7.7	40	88	5	404	25	20	27	26	1.99
39326238--39326540	79	3.8	80	89	5	404	25	20	27	26	1.99
39334473--39334775	40	7.7	40	89	5	413	25	21	27	25	1.99
39334473--39334775	119	2.6	119	88	4	436	25	21	27	25	1.99
39334473--39334775	79	3.8	80	89	5	413	25	21	27	25	1.99
39341916--39342018	37	2.8	39	73	16	94	41	2	3	51	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39342597--39342673	31	2.5	32	81	8	97	50	7	14	27	1.70
39342691--39342722	13	2.4	14	90	10	50	40	0	0	59	0.97
39342924--39342980	28	2.0	28	96	0	105	10	19	24	45	1.81
39345124--39345299	53	3.1	53	64	20	131	51	7	1	39	1.40
39345145--39345330	55	3.1	63	68	17	187	53	5	2	37	1.39
39345095--39345330	116	2.0	116	97	0	445	52	5	2	39	1.38
39345235--39345303	31	2.2	32	82	10	79	50	7	1	40	1.39
39350910--39351153	43	5.7	43	90	0	389	24	17	33	24	1.96
39355001--39355186	40	4.6	39	84	7	205	24	20	27	26	1.99
39355001--39355186	80	2.3	82	83	5	229	24	20	27	26	1.99
39355053--39355219	40	4.2	40	82	8	207	26	18	26	28	1.98
39360360--39360509	75	2.0	75	98	0	291	40	8	11	40	1.70
39360513--39360634	9	12.9	9	75	10	109	32	1	19	45	1.60
39360537--39360629	48	1.9	48	84	0	123	34	1	20	44	1.59
39360517--39360634	57	2.1	57	86	0	164	32	1	19	46	1.60
39366989--39367141	28	5.5	28	90	4	231	24	13	29	32	1.93
39366989--39367141	83	1.8	83	90	2	245	24	13	29	32	1.93
39375149--39375296	27	5.5	28	87	5	198	25	14	29	31	1.95
39375149--39375271	55	2.3	54	94	2	212	26	13	29	30	1.94
39375149--39375296	55	2.7	55	89	4	203	25	14	29	31	1.95
39387546--39387725	28	6.5	28	92	2	276	26	13	28	31	1.94
39387546--39387725	55	3.3	55	92	1	281	26	13	28	31	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39387521--39387725	83	2.5	83	89	3	297	25	13	28	32	1.93
39392485--39392714	48	4.9	48	76	8	222	30	24	17	27	1.97
39392540--39392621	42	2.0	42	85	0	110	31	24	14	29	1.95
39394142--39394473	48	6.9	48	74	8	246	29	16	27	26	1.97
39394152--39394420	96	2.8	96	85	4	346	30	16	27	24	1.97
39395388--39395451	31	2.1	31	90	0	101	25	23	14	37	1.92
39395645--39395812	25	7.0	24	84	6	180	27	23	20	27	1.99
39395644--39395808	49	3.4	48	81	8	183	28	24	21	26	1.99
39395666--39395811	23	6.1	23	87	5	175	28	23	20	27	1.99
39395925--39395972	25	1.9	25	86	0	69	25	16	25	33	1.96
39397131--39397187	27	2.1	27	87	6	80	21	24	22	31	1.98
39397252--39397584	27	12.3	27	75	8	167	33	9	19	38	1.83
39397336--39397530	81	2.4	81	85	5	245	30	8	21	40	1.82
39397508--39397630	53	2.3	54	82	1	149	40	9	19	30	1.84
39397508--39397636	27	4.9	27	84	2	154	39	9	21	29	1.85
39406404--39406445	21	2.0	21	85	0	57	21	16	42	19	1.89
39409937--39410045	37	2.9	37	95	0	191	26	31	19	22	1.98
39410192--39410375	98	1.9	96	91	4	298	30	26	7	35	1.83
39410192--39410376	48	3.8	48	87	4	273	31	26	7	35	1.83
39410349--39410539	47	4.1	47	89	0	265	27	28	10	33	1.90
39410439--39410510	22	3.1	22	64	24	58	23	29	13	33	1.93
39419526--39419802	96	2.9	94	81	5	299	27	19	28	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39419528--39419800	48	5.7	48	75	3	226	27	20	27	24	1.99
39424545--39424716	93	1.8	93	92	0	290	29	30	20	20	1.97
39424537--39424712	46	3.8	46	78	15	200	30	29	19	20	1.97
39427104--39427171	15	4.7	15	84	10	88	60	11	16	11	1.59
39428779--39428982	40	5.1	40	92	1	286	27	25	21	24	1.99
39437134--39437342	40	5.3	39	92	1	292	26	25	22	24	2.00
39437134--39437342	79	2.6	79	88	3	312	26	25	22	24	2.00
39441977--39442148	93	1.8	93	90	4	276	29	29	20	21	1.98
39441969--39442144	46	3.8	46	75	14	182	30	28	19	21	1.98
39444394--39444425	13	2.5	13	94	0	55	3	15	40	40	1.63
39447662--39447688	14	1.9	14	100	0	54	22	29	3	44	1.70
39458974--39459132	44	3.7	42	78	16	175	30	26	18	23	1.98
39462314--39462688	96	3.9	95	85	5	461	29	31	15	24	1.95
39462355--39462689	143	2.3	144	88	2	487	28	30	16	24	1.96
39462319--39462688	48	7.7	48	83	5	419	29	30	15	24	1.96
39485669--39485782	42	2.7	42	83	5	122	23	18	26	31	1.97
39485704--39485815	42	2.6	42	83	4	127	25	16	25	31	1.97
39486530--39486595	33	2.0	32	85	8	89	27	3	21	48	1.64
39495318--39495346	5	5.8	5	100	0	58	20	0	0	79	0.74
39498797--39498938	51	3.0	50	79	11	154	33	26	14	25	1.95
39501812--39501856	15	3.0	15	86	0	63	55	11	17	15	1.68
39504273--39504338	33	2.0	33	93	0	114	40	21	10	27	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39505803--39505890	43	2.1	42	91	2	140	26	32	19	21	1.97
39513555--39513744	38	4.9	38	86	3	229	30	26	22	21	1.98
39523311--39523488	38	4.6	38	82	9	191	28	24	22	24	1.99
39523311--39523479	76	2.2	78	84	7	220	28	24	21	24	1.99
39531912--39532270	47	7.6	47	89	2	513	33	8	29	28	1.86
39531912--39532270	96	3.8	94	87	4	452	33	8	29	28	1.86
39534105--39534282	27	6.5	28	81	5	179	26	15	27	29	1.96
39534106--39534255	82	1.8	81	87	4	221	26	16	27	29	1.97
39534102--39534282	82	2.2	82	81	4	215	27	16	27	29	1.96
39538237--39538462	48	4.6	49	84	4	267	27	19	25	27	1.99
39541412--39541475	15	4.4	15	77	16	64	9	12	14	64	1.50
39541408--39541475	30	2.3	30	80	16	81	8	11	17	61	1.54
39541460--39541500	22	1.9	22	85	5	57	14	9	14	60	1.57
39543918--39544001	28	3.2	28	64	25	74	25	17	28	28	1.98
39543880--39544094	49	4.3	49	87	2	288	25	19	27	27	1.99
39546546--39546618	30	2.4	30	97	0	137	19	26	35	19	1.95
39548021--39548207	49	3.8	49	84	1	257	31	26	16	26	1.96
39548034--39548213	99	1.8	99	93	0	315	31	27	16	25	1.96
39554675--39554703	11	2.5	12	94	5	51	68	6	0	24	1.13
39554696--39554758	24	2.7	24	85	2	65	55	7	15	20	1.65
39554825--39554877	24	2.2	25	86	3	72	64	9	11	15	1.50
39559032--39559104	35	2.1	35	85	10	96	57	9	5	27	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39559104--39559154	21	2.5	20	76	17	59	37	0	3	58	1.16
39563248--39563280	16	2.1	16	100	0	66	30	30	27	12	1.92
39575641--39575858	40	5.5	40	91	2	334	25	28	22	23	1.99
39580435--39580523	30	3.0	30	79	8	92	57	15	15	11	1.65
39580435--39580514	15	5.4	15	77	7	83	58	13	16	11	1.62
39580446--39580523	15	5.2	15	75	9	70	56	15	15	12	1.68
39593779--39593804	3	8.7	3	100	0	52	0	0	30	69	0.89
39598413--39598894	48	10.0	48	91	0	739	31	24	7	37	1.82
39606277--39606391	56	2.1	56	85	3	151	24	16	23	35	1.95
39606287--39606411	56	2.2	55	80	6	135	25	16	27	31	1.96

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   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255