genome.fa.s4.2.7.7.80.10.50.1000.13.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: Gbar_A04
Parameters: 2 7 7 80 10 50 1000
Length:  81554553

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   

This is table  13  of  253  ( 30316 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)
3926727--3926815	42	2.1	42	91	0	142	51	11	5	31	1.60
3926840--3926879	19	2.2	18	95	4	71	42	15	2	40	1.60
3945324--3945361	20	2.0	20	89	5	60	39	2	13	44	1.57
3945531--3945600	16	4.7	16	70	20	53	60	1	4	34	1.25
3949192--3949282	11	8.2	11	70	19	64	36	0	0	63	0.94
3949191--3949279	20	4.6	20	75	13	89	34	0	0	65	0.93
3949194--3949279	19	4.4	20	75	10	81	34	0	0	65	0.93
3949194--3949282	31	3.0	31	79	10	91	35	0	0	64	0.94
3953356--3953411	19	3.1	18	72	23	55	39	1	3	55	1.28
3953525--3953575	21	2.4	21	90	0	75	31	37	7	23	1.83
3954951--3955027	38	2.0	38	82	5	91	61	7	3	27	1.42
3955040--3955109	23	2.9	23	72	25	63	51	1	14	32	1.51
3955754--3955825	22	3.3	23	75	21	59	59	6	1	31	1.32
3955952--3956028	3	25.7	3	97	0	145	64	0	1	33	1.01
3971783--3971832	15	3.3	15	74	0	55	30	18	26	26	1.98
3971856--3971926	6	11.8	6	84	0	79	25	0	46	28	1.53
3971856--3971926	12	5.9	12	86	6	99	25	0	46	28	1.53
3971852--3971927	36	2.1	36	95	0	134	23	0	48	27	1.51
3976759--3976825	29	2.3	28	80	14	73	59	2	1	35	1.22
3983762--3983805	23	1.9	23	81	9	54	22	2	6	68	1.25
3993932--3993990	24	2.5	24	86	5	75	44	5	8	42	1.57
3994356--3994395	19	2.0	20	90	4	64	47	5	0	47	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3999421--3999485	32	2.0	32	100	0	130	30	6	24	38	1.80
4000968--4001020	26	2.0	26	82	7	63	37	20	15	26	1.92
4004755--4004779	13	1.9	13	100	0	50	32	16	16	36	1.90
4006368--4006400	9	3.8	9	88	4	50	54	0	12	33	1.37
4006736--4006910	3	56.3	3	67	23	62	60	2	3	33	1.26
4006759--4006833	33	2.3	33	82	15	102	61	2	1	34	1.18
4006736--4006895	49	3.4	45	76	20	127	60	2	3	33	1.26
4006717--4006835	19	5.9	19	71	18	64	60	3	1	34	1.23
4006786--4006909	31	4.0	29	71	19	83	62	1	4	32	1.24
4008569--4009690	411	2.7	410	89	2	1631	28	22	18	30	1.97
4008569--4009706	205	5.5	206	90	2	1610	28	22	18	30	1.97
4018327--4018434	26	4.2	26	90	0	171	33	7	24	35	1.83
4019973--4020029	25	2.3	24	80	14	62	17	10	21	50	1.75
4024792--4024824	9	3.8	9	88	4	50	54	0	12	33	1.37
4025120--4025174	21	2.7	20	81	16	60	58	3	7	30	1.43
4025130--4025175	19	2.4	19	89	7	67	58	4	6	30	1.43
4025160--4025338	3	57.3	3	67	23	61	60	2	3	33	1.25
4025161--4025315	50	3.3	47	76	16	128	61	2	3	32	1.26
4025237--4025338	20	4.9	20	71	22	61	60	0	4	33	1.24
4025161--4025337	31	5.6	31	69	22	102	61	2	3	32	1.25
4040284--4040541	131	2.0	131	91	1	419	27	17	18	36	1.94
4041997--4042328	130	2.6	129	87	4	451	27	17	19	35	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4043904--4043948	21	2.1	21	83	0	54	57	0	2	40	1.11
4044318--4044408	19	4.9	19	88	8	143	37	10	15	36	1.83
4044339--4044394	18	3.5	15	81	18	60	37	10	16	35	1.83
4044326--4044415	35	2.5	37	87	10	134	37	11	15	35	1.83
4050129--4050181	8	6.6	8	79	16	65	86	0	13	0	0.56
4050129--4050181	24	2.2	24	90	6	81	86	0	13	0	0.56
4050538--4050639	30	3.4	30	84	2	134	30	22	2	44	1.68
4050535--4050673	60	2.4	59	79	4	165	33	22	2	41	1.68
4051144--4051204	17	3.4	18	72	26	58	70	1	27	0	0.97
4051502--4051561	16	3.3	19	81	15	81	83	1	15	0	0.73
4051500--4051561	8	7.0	8	79	16	61	82	1	16	0	0.75
4051504--4051562	17	3.6	16	82	13	66	81	1	16	0	0.78
4051712--4051759	5	9.6	5	100	0	96	37	0	0	62	0.95
4051711--4051785	15	4.9	15	88	4	87	30	0	0	69	0.89
4052111--4052522	17	22.8	18	67	17	149	32	12	7	47	1.70
4052116--4052236	36	3.4	37	78	7	135	33	10	5	50	1.61
4052625--4052666	21	2.0	22	90	4	68	40	2	9	47	1.49
4052664--4052706	17	2.4	18	76	3	52	37	16	9	37	1.81
4052728--4052781	17	2.9	19	86	10	85	29	12	11	46	1.77
4052728--4052783	18	3.1	18	87	7	87	28	12	10	48	1.74
4053271--4053363	45	2.1	45	100	0	186	23	12	10	52	1.71
4057211--4057343	43	3.1	41	69	18	110	33	22	21	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4057463--4058178	207	3.5	207	94	0	1202	29	17	23	29	1.97
4058572--4058662	19	4.9	19	88	8	143	37	10	15	36	1.83
4058593--4058648	18	3.5	15	81	18	60	37	10	16	35	1.83
4058580--4058669	35	2.5	37	87	10	134	37	11	15	35	1.83
4060615--4060707	29	3.1	29	72	13	82	49	0	4	46	1.21
4064882--4064924	20	2.2	20	91	0	68	25	11	11	51	1.72
4066027--4066196	85	2.0	85	92	0	286	28	7	30	34	1.84
4067424--4067473	20	2.5	20	84	9	66	60	2	4	34	1.27
4067715--4067803	27	3.4	26	75	10	83	55	3	5	35	1.40
4069309--4069368	16	3.8	16	86	0	84	40	1	28	30	1.66
4069309--4069378	32	2.2	32	92	0	113	41	2	25	30	1.70
4069325--4069380	16	3.5	16	85	0	67	44	3	23	28	1.70
4069618--4069657	21	2.0	20	90	5	62	55	2	0	42	1.13
4069829--4069863	13	2.8	12	91	8	61	60	0	8	31	1.27
4073390--4073431	15	2.7	16	82	14	52	52	2	0	45	1.13
4073399--4073440	15	2.9	15	82	10	52	52	0	0	47	1.00
4073547--4073714	47	3.7	46	73	12	148	48	3	2	45	1.32
4073605--4073666	28	2.3	28	86	5	83	51	3	0	45	1.17
4073562--4073748	47	4.1	42	71	18	126	48	3	2	45	1.30
4073572--4073788	91	2.4	89	85	6	299	47	4	2	45	1.38
4076878--4076975	36	2.7	36	79	6	101	57	11	25	6	1.56
4076891--4076975	36	2.3	36	84	6	109	57	11	23	7	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4079279--4079352	34	2.1	34	82	9	87	36	8	13	41	1.74
4079329--4079405	32	2.4	33	76	6	86	35	7	14	42	1.74
4081683--4081725	13	3.3	13	75	12	52	65	9	9	16	1.47
4081790--4081920	3	43.7	3	70	17	51	60	0	9	30	1.28
4081785--4081923	37	3.9	36	69	20	105	58	0	10	30	1.31
4081827--4081856	16	1.9	15	93	6	51	76	0	0	23	0.78
4081828--4081880	22	2.7	19	80	11	54	71	0	3	24	1.02
4081823--4081882	19	3.2	20	80	15	67	66	0	6	26	1.16
4082032--4082057	3	8.7	3	100	0	52	34	0	30	34	1.58
4082056--4082095	3	13.3	3	89	0	62	65	0	5	30	1.14
4083235--4083260	2	13.0	2	100	0	52	50	0	0	50	1.00
4083598--4083636	11	3.6	10	83	16	51	61	2	17	17	1.46
4086124--4086166	18	2.5	17	85	7	59	18	25	39	16	1.91
4086474--4086636	30	5.4	30	89	1	238	26	47	3	22	1.66
4087206--4087260	16	3.5	17	79	18	57	40	1	1	56	1.21
4087277--4087335	25	2.5	24	78	10	68	33	8	6	50	1.59
4087454--4087501	16	3.1	15	90	6	69	31	2	2	64	1.16
4087454--4087505	8	6.5	8	82	8	61	30	1	1	65	1.14
4095822--4096582	74	10.0	73	77	13	671	29	16	19	33	1.94
4095822--4096819	159	6.5	147	78	12	867	28	17	20	33	1.95
4096054--4096398	144	2.3	145	88	4	487	32	16	19	30	1.94
4096054--4096578	76	7.0	75	77	12	504	30	17	19	32	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4096256--4096749	160	3.0	162	83	7	560	28	18	19	33	1.96
4096414--4096817	76	5.2	75	80	13	401	26	19	20	33	1.97
4096562--4096596	14	2.5	14	95	0	61	20	20	2	57	1.54
4096485--4096674	89	2.1	92	88	3	287	27	19	18	34	1.95
4096800--4096843	13	3.3	13	81	6	52	18	13	4	63	1.46
4096800--4096862	14	4.5	14	82	7	65	22	12	3	61	1.45
4096827--4096859	15	2.2	15	94	0	57	21	9	0	69	1.15
4097023--4097057	14	2.5	14	90	0	52	14	20	5	60	1.54
4097112--4097174	14	4.5	14	82	7	74	20	14	4	60	1.52
4097024--4097262	117	2.1	115	80	5	266	25	17	15	42	1.88

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