genome.fa.s4.2.7.7.80.10.50.1000.14.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  14  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)
3911527--3911581	26	2.1	25	83	6	65	21	16	21	40	1.91
3911776--3911825	20	2.5	21	83	9	68	46	6	2	46	1.39
3911900--3911932	12	2.8	12	95	0	57	63	0	12	24	1.28
3913315--3913371	30	1.9	30	82	13	73	47	3	0	49	1.18
3913545--3913610	13	5.1	13	75	0	69	37	25	6	30	1.80
3919419--3919450	16	2.1	16	88	11	50	59	18	0	21	1.38
3936654--3936767	43	2.8	40	76	11	122	21	22	21	33	1.97
3940992--3941047	18	3.1	18	87	7	87	48	10	12	28	1.74
3941062--3941111	17	2.8	18	78	3	57	38	12	18	32	1.87
3941157--3941350	37	5.2	38	73	13	136	42	8	17	31	1.79
3941213--3941706	17	27.2	18	68	14	214	46	7	12	32	1.71
3941160--3941327	75	2.2	77	78	10	177	41	9	16	32	1.80
3941212--3941364	75	2.0	74	83	5	191	43	7	15	33	1.75
3941480--3941527	24	2.0	24	83	0	60	43	6	6	43	1.54
3942019--3942048	5	6.0	5	100	0	60	80	0	0	20	0.72
3942224--3942275	8	6.0	8	82	12	59	0	17	0	82	0.66
3942225--3942277	19	3.1	16	82	17	70	0	18	0	81	0.70
3942231--3942273	20	2.2	19	88	12	61	0	16	0	83	0.64
3942701--3942742	18	2.3	19	84	12	61	0	35	0	64	0.94
3943124--3943180	30	1.9	30	85	3	80	49	1	17	31	1.57
3943138--3943209	30	2.4	30	86	4	92	45	5	20	27	1.73
3944089--3944128	16	2.6	16	92	4	64	52	7	5	35	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3946353--3946423	26	2.8	27	81	12	71	69	5	9	15	1.35
3948426--3948489	33	1.9	33	83	3	83	62	4	1	31	1.25
3951077--3951135	32	2.0	29	81	18	68	55	0	6	37	1.26
3952543--3952617	38	2.0	38	100	0	150	42	5	5	46	1.49
3964367--3964391	12	2.1	12	100	0	50	76	0	24	0	0.80
3965786--3965857	27	2.6	28	73	8	67	61	4	6	27	1.41
3965742--3965949	23	8.6	25	70	15	89	57	3	6	32	1.42
3965890--3965949	22	2.7	21	84	7	66	61	3	3	31	1.28
3965923--3965956	15	2.1	17	89	10	54	73	2	0	23	0.97
3965919--3965958	20	2.0	20	85	9	55	72	2	0	25	0.97
3966205--3966243	16	2.4	16	86	0	51	43	28	5	23	1.75
3966402--3966529	30	4.3	30	92	4	204	18	7	48	25	1.75
3966436--3966489	18	3.3	18	66	28	57	20	7	50	22	1.73
3967175--3967738	87	6.3	88	79	10	450	37	18	16	28	1.92
3967562--3967594	14	2.4	14	94	0	57	63	6	12	18	1.48
3967407--3967738	181	1.8	178	85	4	461	34	18	17	28	1.94
3967405--3967759	91	3.9	88	83	5	399	36	18	18	27	1.93
3967665--3968274	75	8.3	75	85	4	767	33	19	16	30	1.94
3967665--3968274	148	4.1	147	88	2	757	33	19	16	30	1.94
3968444--3968488	13	3.4	13	87	6	72	68	6	11	13	1.37
3968272--3968632	100	3.7	98	83	8	408	38	19	17	24	1.93
3968457--3968632	90	2.0	87	86	3	244	36	20	18	24	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3972201--3972393	100	1.9	100	80	6	221	38	19	11	30	1.87
3972553--3972629	41	1.9	41	82	12	97	32	28	18	20	1.96
3973524--3973577	23	2.4	22	78	9	56	42	5	0	51	1.25
3983512--3983716	23	8.6	25	72	12	110	57	3	6	32	1.42
3984187--3984284	30	3.3	30	92	0	160	20	6	48	24	1.72
3984221--3984274	18	3.3	18	66	28	57	20	7	50	22	1.73
3987356--3987433	39	2.0	39	95	2	140	42	3	29	24	1.72
3987916--3987981	24	2.7	24	75	11	62	39	6	4	50	1.48
3996096--3997745	44	38.1	44	88	2	2218	29	16	31	22	1.96
3999123--3999203	39	2.1	39	95	0	144	43	4	27	24	1.75
3999682--3999748	24	2.8	24	75	11	64	38	5	4	50	1.47
4001268--4001309	17	2.5	17	77	11	50	38	9	19	33	1.84
4003203--4003264	34	1.9	31	87	9	88	40	0	0	59	0.97
4021897--4021929	16	2.1	16	100	0	66	39	6	24	30	1.79
4025703--4025844	64	2.2	65	84	3	180	19	13	23	43	1.86
4025703--4025844	32	4.4	31	71	12	99	19	13	23	43	1.86
4025753--4025853	33	3.1	32	74	16	100	17	13	21	46	1.83
4027810--4027869	21	2.9	21	76	0	66	43	21	8	26	1.81
4037525--4037559	16	2.3	15	90	5	52	62	2	2	31	1.24
4037703--4037745	20	2.1	21	82	4	52	62	6	2	27	1.33
4037875--4037917	23	2.0	23	86	9	63	51	6	13	27	1.67
4037881--4037930	23	2.2	23	82	13	59	54	10	12	24	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4038489--4038513	13	1.9	13	100	0	50	88	0	0	12	0.53
4038762--4038834	27	2.8	25	86	10	101	5	5	35	53	1.47
4039689--4040309	146	4.2	145	88	2	911	31	21	16	30	1.96
4039689--4040310	72	8.5	73	88	3	901	31	21	16	30	1.96
4052147--4052181	16	2.3	15	90	5	52	62	2	2	31	1.24
4052322--4052364	20	2.1	21	82	4	52	62	6	2	27	1.33
4052493--4052535	23	2.0	23	86	9	63	51	6	13	27	1.67
4052499--4052548	23	2.2	23	82	13	59	54	10	12	24	1.67
4053361--4053437	26	3.2	25	87	8	115	3	2	29	63	1.25
4053369--4053434	26	2.6	26	95	2	116	4	3	34	57	1.34
4054831--4054963	3	47.0	3	69	20	74	64	0	3	30	1.16
4054829--4054963	29	4.9	27	72	23	104	64	0	3	31	1.16
4054816--4054948	32	4.1	32	71	14	103	64	0	3	30	1.16
4055096--4055134	15	2.7	15	92	7	64	64	0	10	25	1.25
4055083--4055179	14	7.1	13	78	17	74	62	1	9	26	1.32
4055700--4055754	19	2.8	19	86	2	65	74	3	3	18	1.11
4056169--4056629	44	10.4	44	69	14	205	28	21	19	30	1.98
4056680--4057020	89	3.8	89	69	13	233	26	27	15	30	1.96
4056616--4057019	222	1.8	222	81	5	512	26	26	17	30	1.97
4056697--4057028	44	7.5	45	70	9	189	27	26	16	29	1.97
4056616--4057066	222	2.0	222	79	5	484	26	25	18	29	1.98
4070269--4070542	18	15.1	18	67	17	113	45	11	12	30	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4070276--4070363	42	2.0	42	85	8	115	48	13	12	25	1.77
4070320--4070410	37	2.5	36	76	15	98	41	12	10	35	1.77
4070513--4070562	25	2.0	25	88	4	73	54	14	12	20	1.71
4070495--4070585	43	2.1	44	86	10	125	52	12	12	23	1.71
4070538--4070594	18	3.2	17	80	7	69	50	12	14	22	1.75
4070619--4070710	23	4.2	23	81	12	113	39	11	7	41	1.71
4070689--4070723	18	1.9	18	88	0	52	48	14	11	25	1.77
4071996--4072091	30	3.2	30	80	2	95	43	3	26	27	1.69
4072093--4072127	14	2.4	15	90	4	54	25	0	2	71	1.00
4073455--4073532	38	2.1	38	85	4	104	43	1	1	53	1.16
4073496--4073530	17	2.1	16	89	5	52	42	0	0	57	0.99
4073455--4073539	39	2.2	38	83	8	100	43	1	1	54	1.15
4074291--4074372	37	2.2	36	81	10	94	48	12	12	26	1.75
4074319--4074375	20	3.1	18	85	10	80	47	10	12	29	1.74
4074390--4074439	17	2.8	18	78	3	57	38	12	18	32	1.87
4074437--4074478	21	2.0	22	90	4	68	47	9	2	40	1.49
4074398--4074481	18	4.5	18	70	14	53	44	9	9	36	1.70
4074486--4074680	37	5.2	38	72	14	129	42	9	16	31	1.80
4074542--4075033	17	27.2	18	68	13	235	47	8	12	32	1.71
4074541--4074871	35	9.1	37	70	18	133	45	8	12	32	1.73
4074541--4074694	76	2.0	75	85	5	202	43	8	14	33	1.76
4074618--4075022	35	11.3	35	70	15	156	48	7	12	32	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4075138--4075180	22	2.0	22	86	4	61	39	6	13	39	1.72
4075347--4075409	5	12.0	5	90	6	54	71	0	0	28	0.86
4075348--4075398	22	2.4	22	83	3	59	74	0	0	25	0.82
4075560--4075601	17	2.5	16	82	17	50	0	19	2	78	0.86
4075890--4075948	3	18.0	3	86	13	73	0	33	0	66	0.92
4075880--4075947	16	4.1	16	87	7	91	0	29	0	70	0.87
4075880--4075944	34	1.9	33	87	3	94	0	29	0	70	0.87
4076307--4076423	30	3.9	29	79	11	103	45	3	21	29	1.68
4076322--4076423	30	3.4	30	87	2	143	45	3	21	29	1.70
4076288--4076423	60	2.3	59	83	5	159	42	3	22	31	1.71

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