genome.fa.s6.2.7.7.80.10.50.1000.14.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  14  of  168  ( 20060 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)
3873818--3873849	2	16.0	2	100	0	64	50	0	0	50	1.00
3879636--3879901	43	6.0	44	74	7	180	32	15	21	29	1.95
3879682--3879995	89	3.5	90	81	4	343	31	16	23	28	1.96
3879607--3879995	45	8.8	45	75	6	276	32	15	23	28	1.96
3881492--3881544	3	18.3	3	81	14	67	30	0	1	67	1.01
3881827--3881857	15	2.1	15	93	0	53	19	9	0	70	1.14
3883008--3883058	13	4.1	13	80	9	54	74	7	0	17	1.05
3883624--3883667	17	2.6	17	85	3	63	47	0	11	40	1.39
3883620--3883671	27	1.9	27	84	0	68	53	0	9	36	1.34
3883798--3883857	3	20.0	3	96	0	111	65	0	1	33	1.03
3885472--3885576	44	2.4	44	83	3	131	29	20	20	29	1.98
3885587--3885795	100	2.1	100	84	0	265	26	21	20	32	1.98
3886069--3886165	44	2.2	44	90	3	151	30	24	19	24	1.98
3886179--3886917	88	8.4	88	88	0	1068	20	24	27	28	1.99
3888149--3888173	2	12.5	2	100	0	50	0	48	0	52	1.00
3889118--3889158	22	1.9	22	90	5	66	63	2	12	21	1.40
3892675--3892718	17	2.6	17	85	3	63	47	0	11	40	1.39
3892853--3892906	3	18.0	3	100	0	108	66	0	0	33	0.92
3898082--3898116	10	3.3	10	85	14	52	45	0	8	45	1.34
3901039--3901557	88	5.9	88	83	4	586	30	19	23	26	1.98
3901039--3901557	176	2.9	176	85	2	650	30	19	23	26	1.98
3901061--3901558	264	1.9	263	84	4	680	30	19	23	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3901564--3901684	51	2.4	51	77	2	127	26	19	25	28	1.98
3901757--3901943	50	3.7	50	79	4	207	33	23	18	24	1.97
3901761--3901959	100	2.0	100	88	2	292	33	22	18	25	1.97
3901976--3902097	44	2.8	43	83	2	154	31	18	21	28	1.97
3903467--3903507	3	13.7	3	84	0	55	31	0	0	68	0.90
3912754--3912795	11	3.7	11	81	12	50	19	0	9	71	1.13
3923026--3923107	31	2.7	31	86	1	112	47	7	7	37	1.59
3923049--3923119	31	2.3	31	85	4	90	49	4	7	39	1.49
3925435--3925480	22	2.0	23	83	4	58	43	19	15	21	1.87
3935237--3935269	17	1.9	17	93	0	57	24	30	27	18	1.98
3935952--3935991	19	2.0	20	85	4	55	37	12	2	47	1.55
3937421--3937474	25	2.2	25	83	3	65	35	16	16	31	1.92
3937939--3938630	353	2.0	354	98	0	1341	36	24	11	28	1.89
3940179--3940225	18	2.6	18	96	0	85	53	12	4	29	1.58
3951662--3951809	30	5.0	30	95	1	255	31	10	17	40	1.83
3958765--3958891	30	4.2	30	86	0	173	33	9	14	42	1.77
3965816--3965850	18	1.9	18	100	0	70	57	0	25	17	1.40
3966770--3966810	22	1.9	21	85	5	55	34	21	26	17	1.95
3969202--3969336	58	2.3	59	83	2	166	37	9	28	23	1.87
3977010--3977049	21	1.9	21	84	0	53	5	27	5	62	1.37
3980010--3980350	168	2.0	168	98	0	655	26	11	26	35	1.90
3995822--3995891	35	2.0	35	100	0	140	48	14	17	20	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4000589--4000628	20	1.9	22	85	10	57	65	5	0	30	1.14
4006021--4006084	24	2.7	24	87	4	85	18	3	1	76	1.00
4006022--4006084	6	10.5	6	76	19	60	17	3	1	77	0.97
4006025--4006086	19	3.1	19	84	13	63	17	4	1	75	1.05
4006704--4006758	5	11.0	5	100	0	110	80	0	0	20	0.72
4006906--4007097	105	1.8	105	83	6	255	30	16	24	29	1.96
4008673--4008710	19	2.0	19	89	0	58	15	7	21	55	1.66
4009115--4009153	17	2.4	16	86	4	60	79	0	10	10	0.94
4012253--4012611	18	21.0	17	67	15	120	44	11	13	29	1.80
4012395--4012608	35	6.1	34	72	14	134	41	13	14	30	1.84
4012762--4012800	17	2.3	17	86	8	53	43	7	15	33	1.75
4013411--4013480	32	2.3	32	80	9	85	4	21	1	72	1.09
4014052--4014188	29	4.7	30	77	11	124	38	5	21	34	1.76
4014403--4014714	77	4.1	76	82	5	334	34	22	17	25	1.95
4014403--4014714	149	2.1	152	83	6	384	34	22	17	25	1.95
4015680--4015762	1	83.0	1	73	0	58	2	6	6	85	0.81
4015680--4015762	20	4.3	19	82	13	107	2	6	6	85	0.81
4015687--4015760	19	3.8	19	82	8	80	2	5	6	85	0.83
4021902--4022074	90	1.9	89	85	3	240	43	12	15	28	1.83
4021718--4022078	35	10.5	35	67	16	141	45	11	13	29	1.79
4021718--4022078	18	21.0	18	68	16	160	45	11	13	29	1.79
4022151--4022186	18	1.9	19	94	5	65	36	11	13	38	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4022231--4022269	17	2.3	17	86	8	53	43	7	15	33	1.75
4022880--4022949	32	2.3	32	80	9	85	4	21	1	72	1.09
4023582--4023660	30	2.7	30	92	3	126	40	2	20	36	1.66
4023582--4023675	30	3.2	30	87	4	102	40	3	22	34	1.70
4024886--4025044	48	3.2	50	73	17	125	35	20	24	19	1.95
4024886--4025057	26	6.9	25	72	15	126	35	20	24	19	1.96
4031897--4032016	63	1.9	62	83	5	152	29	25	20	25	1.99
4048954--4049076	46	2.7	46	80	1	140	17	18	16	47	1.83
4049054--4049211	45	3.5	45	82	0	172	23	20	17	38	1.93
4049189--4049298	45	2.4	45	89	0	157	20	14	17	48	1.81
4050310--4050341	11	2.9	11	100	0	64	46	0	6	46	1.27
4053934--4053963	16	1.9	15	93	6	51	3	13	0	83	0.77
4055664--4055694	3	10.3	3	92	0	53	67	3	0	29	1.06
4062219--4062444	124	1.8	124	93	1	391	30	16	21	31	1.95
4065553--4065577	10	2.5	10	100	0	50	48	0	8	44	1.32
4065561--4065852	55	5.3	55	95	1	514	43	5	12	39	1.64
4065847--4065941	29	3.3	29	100	0	190	29	0	27	43	1.55
4066042--4066190	71	2.1	70	93	1	253	46	14	3	35	1.62
4066592--4066626	18	1.9	18	88	0	52	31	8	34	25	1.86
4069894--4069962	33	2.1	33	94	2	122	69	0	0	30	0.89
4069964--4070076	51	2.2	51	93	0	190	43	0	28	28	1.55
4070048--4070098	22	2.3	22	90	6	77	45	0	27	27	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4070048--4070113	22	3.0	22	82	6	64	45	0	28	25	1.54
4070480--4070514	15	2.4	15	90	4	54	25	0	8	65	1.21
4071582--4071614	13	2.5	13	95	0	57	15	33	6	45	1.70
4071862--4071933	13	5.5	13	72	6	65	36	4	23	36	1.74
4071858--4071933	26	2.9	26	78	0	80	34	3	25	36	1.74
4071845--4071931	39	2.2	38	84	6	120	37	4	20	36	1.74
4076627--4076661	3	11.7	3	93	0	61	28	0	2	68	1.04
4091052--4091348	69	4.4	68	69	18	217	38	3	15	41	1.65
4091358--4091386	2	14.5	2	100	0	58	0	0	48	51	1.00
4091623--4091649	2	13.5	2	100	0	54	51	0	0	48	1.00
4091873--4092017	41	3.5	41	88	4	204	24	17	26	31	1.97
4091998--4092099	41	2.5	41	96	0	186	27	20	30	21	1.98
4097947--4098333	101	3.8	101	93	1	643	23	18	27	29	1.98
4097941--4098341	51	8.0	49	78	5	392	23	18	28	29	1.98
4098342--4098423	43	1.9	42	90	2	128	24	14	25	35	1.94
4108618--4108669	21	2.4	22	87	3	70	13	11	19	55	1.68
4108615--4108669	22	2.6	21	85	5	76	16	10	18	54	1.70
4109246--4109305	30	2.0	30	86	0	84	35	3	11	50	1.56
4113810--4113884	3	24.7	3	79	2	69	57	1	4	37	1.26
4122656--4122743	25	3.5	24	75	14	81	34	20	21	23	1.97
4122756--4122829	25	3.0	24	82	7	94	33	17	29	18	1.94
4123534--4123589	22	2.5	22	91	2	94	28	28	0	42	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4123542--4123641	52	1.9	52	89	0	155	30	31	0	39	1.57
4123594--4123646	22	2.4	22	84	6	72	33	32	0	33	1.58
4123678--4123736	30	2.0	28	87	12	84	38	0	3	57	1.15
4123681--4123743	29	2.1	30	83	13	78	38	0	3	58	1.14
4125698--4125753	24	2.3	24	93	0	94	26	37	17	17	1.93
4126039--4126490	29	15.4	29	87	2	591	45	23	0	30	1.55
4126039--4126490	59	7.7	58	88	2	627	45	23	0	30	1.55
4126039--4126490	88	5.1	88	93	1	728	45	23	0	30	1.55
4126568--4126612	21	2.1	22	91	4	74	37	11	15	35	1.83
4128075--4128356	125	2.3	125	88	4	408	32	22	16	28	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