genome.fa.s8.2.7.7.80.10.50.1000.22.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  22  of  190  ( 22705 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)
6155033--6155085	27	2.0	26	82	13	65	49	1	5	43	1.37
6155969--6156079	43	2.6	44	83	11	140	21	19	27	30	1.98
6160755--6160817	31	2.0	31	100	0	126	31	22	23	22	1.98
6164961--6165038	13	6.3	13	73	19	60	28	7	1	62	1.30
6164960--6165010	23	2.3	23	82	3	68	29	5	1	62	1.29
6165224--6165253	16	1.9	15	93	6	51	20	6	3	70	1.25
6171218--6171302	29	3.0	29	80	16	115	34	29	15	21	1.94
6171212--6171294	26	3.1	26	80	16	105	34	30	15	19	1.93
6171686--6171739	22	2.5	22	87	3	74	38	24	16	20	1.92
6184320--6184365	18	2.6	18	92	0	74	28	4	2	65	1.23
6184340--6184385	23	2.0	23	82	0	56	23	2	6	67	1.25
6188314--6188380	6	11.3	6	85	6	59	17	1	11	68	1.27
6188308--6188396	6	14.5	6	79	9	54	15	2	10	71	1.22
6189970--6190016	23	2.1	23	84	4	60	17	31	21	29	1.96
6189980--6190035	25	2.3	23	78	6	58	17	28	23	30	1.97
6193292--6193380	30	3.0	30	89	0	142	19	34	31	14	1.92
6204955--6204991	13	2.7	14	87	8	58	13	0	35	51	1.41
6212678--6212702	2	12.5	2	100	0	50	48	0	0	52	1.00
6214800--6214851	23	2.2	25	89	6	81	71	3	13	11	1.28
6215183--6215242	19	3.0	20	76	9	61	28	5	1	65	1.23
6215322--6215554	92	2.5	90	79	10	274	30	9	21	38	1.85
6218564--6218619	27	2.1	26	83	9	69	28	26	10	33	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6220568--6220699	34	3.8	35	71	9	101	25	4	34	36	1.76
6222725--6222965	129	2.0	123	88	11	363	52	1	11	34	1.46
6226191--6226233	12	3.6	12	93	0	77	32	32	25	9	1.88
6226191--6226239	24	2.0	24	96	0	89	30	28	28	12	1.93
6232774--6232812	19	2.1	19	85	9	53	38	7	5	48	1.54
6235369--6235403	13	2.7	13	86	0	52	45	0	2	51	1.16
6237330--6237446	43	2.7	43	84	3	139	32	28	16	23	1.96
6240234--6240292	25	2.4	25	82	5	75	49	15	5	30	1.66
6249555--6249579	9	2.8	9	100	0	50	48	24	0	28	1.52
6253701--6253763	27	2.3	27	86	0	90	39	15	22	22	1.92
6253701--6253778	27	2.9	27	80	3	68	35	17	21	24	1.95
6264540--6264571	15	2.1	15	94	0	55	15	6	9	68	1.36
6268047--6268101	5	11.0	5	92	0	92	40	23	0	36	1.55
6269372--6269715	37	9.2	37	79	8	329	30	14	16	38	1.89
6269358--6269715	75	4.8	75	87	0	484	30	15	16	37	1.89
6273440--6273535	37	2.6	39	76	18	98	41	4	4	50	1.41
6273514--6273630	62	1.9	59	84	5	153	41	4	3	51	1.38
6276974--6277074	45	2.2	45	89	0	148	34	21	16	26	1.95
6277651--6277707	25	2.2	25	81	9	62	63	3	3	29	1.28
6285041--6285110	22	3.2	22	89	0	104	35	25	0	38	1.56
6285082--6285141	30	2.0	30	90	0	93	31	33	0	35	1.58
6285349--6285382	15	2.3	15	90	5	52	26	0	5	67	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6287542--6287682	23	5.7	23	84	14	183	46	21	0	32	1.52
6287521--6287711	28	7.1	28	84	11	249	45	21	0	31	1.56
6287521--6287711	51	3.6	51	84	11	210	45	21	0	31	1.56
6287569--6287698	23	5.2	23	77	17	125	46	20	0	32	1.51
6290655--6290899	125	2.0	124	89	2	375	31	22	15	30	1.95
6299346--6299373	6	4.7	6	100	0	56	14	14	17	53	1.73
6303683--6303737	21	2.6	21	80	11	58	43	0	1	54	1.10
6303898--6303976	29	2.6	30	84	6	97	46	11	6	35	1.65
6304016--6304059	20	2.1	21	83	4	54	40	6	2	50	1.42
6305779--6305803	11	2.3	11	100	0	50	32	0	40	28	1.57
6314065--6314147	33	2.5	33	79	7	98	66	0	1	32	1.00
6316142--6316169	14	2.0	14	100	0	56	35	7	14	42	1.73
6318025--6318056	15	2.1	15	100	0	64	15	12	12	59	1.61
6324426--6324463	10	3.6	11	86	6	53	0	18	0	81	0.69
6324427--6324469	14	3.1	13	83	12	50	0	18	0	81	0.69
6326554--6326583	12	2.5	12	94	0	51	36	10	0	53	1.35
6331637--6331669	12	2.8	12	95	0	57	36	9	0	54	1.32
6332081--6332105	6	4.2	6	100	0	50	48	0	0	52	1.00
6332356--6332433	30	2.6	29	81	4	75	39	10	17	32	1.84
6333845--6333879	18	1.9	18	88	0	52	5	48	0	45	1.26
6339283--6339388	34	3.2	33	82	5	133	33	0	15	50	1.44
6341078--6341157	40	2.0	40	95	0	142	40	8	16	35	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6341319--6341836	126	4.2	125	86	5	665	38	17	16	27	1.91
6342002--6342063	28	2.2	28	97	0	115	35	16	16	32	1.91
6344923--6344979	25	2.3	23	78	18	62	52	5	0	42	1.24
6345360--6345396	18	2.1	18	89	0	56	40	8	24	27	1.83
6347140--6347208	30	2.3	30	87	5	104	39	1	26	33	1.65
6348247--6348322	38	2.0	38	97	0	143	26	7	9	56	1.58
6348259--6348320	20	3.2	20	65	9	56	29	6	11	53	1.61
6371757--6371784	14	2.0	14	100	0	56	64	7	7	21	1.43
6375513--6375558	24	2.0	24	91	4	76	32	0	15	52	1.43
6377401--6377448	17	2.8	17	93	0	78	60	6	14	18	1.55
6383927--6384003	38	2.0	38	89	0	118	25	12	10	50	1.72
6385928--6385964	17	2.1	18	95	5	67	10	13	24	51	1.73
6396770--6396992	77	2.9	76	80	11	247	15	16	16	51	1.77
6409308--6409333	7	3.7	7	100	0	52	15	0	0	84	0.62
6410450--6410509	30	2.0	30	96	0	111	43	5	6	45	1.52
6410551--6410612	28	2.1	27	82	11	70	29	12	8	50	1.69
6415112--6415155	2	22.0	2	100	0	88	50	0	0	50	1.00
6416812--6416854	21	2.1	21	86	4	61	39	20	20	18	1.93
6417288--6417432	71	2.0	71	98	0	281	40	27	7	24	1.82
6417689--6417802	56	2.0	56	98	0	219	57	4	22	14	1.55
6419965--6420027	16	3.9	16	77	4	65	42	4	23	28	1.74
6419968--6420036	16	4.3	16	73	14	52	44	4	20	30	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6420188--6420251	26	2.7	24	81	13	78	54	0	0	45	0.99
6420301--6420353	20	2.5	22	82	14	60	54	0	3	41	1.18
6422490--6422515	3	8.7	3	100	0	52	69	0	0	30	0.89
6422820--6422884	32	2.1	32	97	2	123	46	12	9	32	1.73
6428929--6429025	32	3.1	32	98	1	187	47	12	9	30	1.73
6429580--6429632	25	2.1	25	96	0	97	47	9	3	39	1.54
6432510--6432557	21	2.3	21	92	0	78	14	25	18	41	1.88
6442863--6442967	42	2.5	43	81	4	124	29	25	16	28	1.97
6443950--6443980	15	2.1	15	100	0	62	41	12	12	32	1.81
6455204--6455244	9	4.6	9	93	0	73	14	0	7	78	0.96
6455295--6455346	23	2.3	23	90	6	79	34	13	9	42	1.77
6455295--6455410	59	2.0	59	92	0	196	29	14	11	44	1.80
6455351--6455405	23	2.4	23	87	6	76	29	14	14	41	1.85
6460378--6460402	13	1.9	13	100	0	50	24	16	8	52	1.70
6464858--6464882	13	1.9	13	100	0	50	24	16	8	52	1.70
6470811--6470903	46	2.0	46	100	0	186	54	12	10	21	1.68
6471587--6471640	22	2.5	22	78	6	56	51	1	1	44	1.22
6471700--6471758	29	2.1	28	80	3	64	38	3	1	55	1.26
6476022--6476084	18	3.2	20	80	14	71	20	6	0	73	1.05
6476029--6476085	6	9.2	6	80	14	62	21	3	0	75	0.95
6506005--6506030	4	6.5	4	100	0	52	76	0	0	23	0.78
6507499--6507596	7	14.0	7	76	4	81	28	31	1	38	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6512050--6512190	42	3.4	41	81	3	147	43	15	24	16	1.86
6518700--6518728	11	2.5	12	94	5	51	37	0	3	58	1.15
6520502--6520571	21	3.3	21	70	4	68	21	22	18	37	1.94
6520514--6520582	22	3.2	21	70	4	66	23	20	15	40	1.91
6525521--6525549	14	2.1	14	93	6	51	48	13	6	31	1.69
6537695--6537721	5	5.4	5	100	0	54	81	0	0	18	0.69
6539661--6539705	18	2.5	18	86	13	58	60	8	4	26	1.46
6539755--6539810	20	2.7	21	83	5	69	71	8	8	10	1.31
6540157--6540222	31	2.2	31	78	5	73	40	9	9	40	1.68
6546453--6546860	46	9.6	45	78	16	417	35	13	21	28	1.92

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