genome.fa.s5.2.7.7.80.10.50.1000.62.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  62  of  208  ( 24913 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)
17923760--17923838	26	3.0	26	98	0	149	15	30	22	31	1.95
17932885--17932984	40	2.5	40	75	12	98	38	16	22	24	1.93
17933061--17933281	75	2.9	74	75	12	209	23	34	3	39	1.70
17933206--17933320	61	1.9	61	89	5	180	18	37	4	40	1.70
17933329--17933411	25	3.3	25	84	3	114	12	40	21	25	1.88
17934680--17934708	11	2.7	11	94	5	51	34	0	0	65	0.93
17934780--17934849	20	3.6	19	87	9	88	34	0	2	62	1.10
17934967--17935302	59	5.6	59	89	2	485	43	5	4	47	1.45
17937912--17938124	115	1.8	115	90	3	347	37	18	14	30	1.90
17943945--17944035	43	2.1	43	87	4	130	27	30	16	25	1.97
17951703--17951747	24	2.0	22	86	8	63	60	0	0	40	0.97
17951698--17951741	16	2.9	16	80	6	56	63	0	0	36	0.95
17952391--17952445	10	5.5	10	72	23	53	67	0	5	27	1.12
17952385--17952450	30	2.1	32	86	5	91	60	1	7	30	1.33
17952631--17952698	20	3.2	21	74	18	61	25	7	8	58	1.54
17952639--17952723	40	2.1	40	82	8	102	24	5	5	63	1.40
17952733--17952798	9	7.0	9	77	13	53	30	1	1	66	1.10
17952700--17952818	49	2.4	47	80	6	130	32	3	1	62	1.22
17952736--17952791	19	2.9	19	82	12	69	30	1	1	66	1.12
17952700--17952771	10	7.3	10	75	12	60	31	2	1	63	1.17
17953467--17953503	3	12.7	3	94	5	67	35	0	0	64	0.94
17953938--17953975	18	2.0	20	90	10	62	76	5	0	18	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17959388--17959441	27	2.0	27	92	7	92	22	7	16	53	1.67
17959389--17959454	27	2.4	27	85	12	89	24	9	13	53	1.69
17960129--17960210	20	4.2	20	70	16	73	60	4	2	31	1.30
17960131--17960186	21	2.7	21	81	8	69	62	5	0	32	1.18
17960467--17960595	40	3.2	40	81	3	100	33	21	19	25	1.97
17960479--17960589	40	2.8	40	87	4	154	30	23	20	25	1.99
17960648--17960728	40	2.0	40	83	4	101	28	23	25	22	1.99
17960782--17960807	9	2.9	9	100	0	52	19	11	34	34	1.88
17960946--17961004	31	1.9	31	83	13	77	62	1	3	32	1.21
17961008--17961068	14	4.4	14	76	17	56	19	1	26	52	1.55
17961054--17961111	21	3.0	20	76	16	59	13	0	32	53	1.40
17967115--17967253	71	2.0	71	100	0	278	40	19	16	23	1.91
17967494--17967526	14	2.3	15	89	5	50	27	12	33	27	1.92
17968868--17969175	88	3.5	87	88	0	436	28	27	23	20	1.99
17969176--17969274	44	2.2	44	84	7	121	25	20	24	30	1.99
17969260--17969904	44	14.9	43	69	14	249	30	20	21	27	1.98
17969257--17969686	172	2.5	172	87	3	571	30	20	21	27	1.98
17969434--17969847	217	1.9	218	88	2	627	29	20	21	28	1.98
17970450--17970541	19	4.8	19	93	0	157	35	8	17	38	1.81
17970450--17970564	38	2.9	38	92	5	176	35	7	17	39	1.79
17970635--17970776	27	5.3	27	86	1	169	19	17	21	41	1.90
17973394--17973476	43	1.9	43	83	9	107	33	26	20	19	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17974666--17974726	23	2.6	24	84	5	88	39	32	11	16	1.84
17978382--17978409	13	2.2	13	100	0	56	21	7	0	71	1.09
17978565--17978590	13	2.0	13	100	0	52	23	0	0	76	0.78
17979831--17979861	9	3.4	9	90	0	53	38	22	12	25	1.90
17986119--17986318	45	4.5	45	79	1	179	33	26	16	24	1.96
17986156--17986320	90	1.8	90	85	0	231	33	24	16	25	1.96
17993194--17993283	45	2.0	45	86	4	128	34	25	14	25	1.94
17995957--17996009	25	2.1	25	85	0	70	35	11	24	28	1.90
17997101--17997145	23	2.0	23	95	0	81	24	15	8	51	1.72
17998333--17998392	30	2.0	30	84	12	79	33	23	16	26	1.96
17999602--17999712	6	18.0	6	71	5	69	69	2	22	5	1.22
17999589--17999618	15	1.9	16	93	6	53	80	0	16	3	0.85
17999602--17999661	24	2.5	24	86	5	86	73	1	21	3	1.07
17999590--17999712	18	6.8	18	69	14	76	69	2	21	5	1.21
17999700--17999734	18	1.9	18	88	11	54	57	0	20	22	1.41
18005799--18005980	25	7.3	25	76	2	159	35	17	14	32	1.90
18005799--18005993	50	3.9	51	80	5	220	35	17	14	31	1.90
18005800--18005982	100	1.8	100	84	2	251	35	18	14	32	1.90
18007904--18007968	32	2.0	32	100	0	130	23	18	27	30	1.97
18007911--18007983	32	2.6	27	85	12	85	23	21	27	27	1.99
18013860--18013926	35	1.9	35	84	0	89	26	29	23	19	1.98
18017210--18017275	33	2.0	33	100	0	132	12	24	21	42	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18020157--18020193	11	3.4	11	92	0	56	21	5	43	29	1.75
18025860--18025934	39	1.9	39	86	5	107	16	25	18	40	1.91
18027665--18027699	17	2.1	17	89	5	54	54	14	0	31	1.40
18030982--18031059	41	1.9	41	83	0	102	47	24	10	17	1.79
18037058--18037083	8	3.2	8	100	0	52	11	73	15	0	1.11
18038629--18038699	35	2.0	35	86	0	97	26	21	12	39	1.89
18043714--18043802	25	3.6	25	73	13	85	33	29	14	22	1.94
18043714--18043832	50	2.4	50	88	2	168	35	26	14	23	1.93
18045666--18045733	26	2.7	25	82	6	93	35	25	16	23	1.95
18048009--18048051	20	2.2	20	95	0	77	25	9	13	51	1.71
18050951--18051052	50	2.0	50	96	0	186	15	32	15	36	1.90
18056114--18056181	21	3.3	21	70	12	59	32	16	30	20	1.94
18056115--18056257	41	3.5	41	85	0	196	37	14	26	21	1.92
18058538--18058629	46	2.0	46	80	4	105	50	21	4	23	1.67
18059108--18059180	28	2.6	28	86	2	101	35	4	36	23	1.74
18060138--18060200	28	2.2	28	91	0	99	38	1	36	23	1.65
18061678--18061741	26	2.5	26	89	5	94	34	14	17	34	1.89
18080028--18080145	9	13.6	9	70	13	70	33	1	16	47	1.57
18080016--18080084	36	2.0	34	88	5	102	34	1	17	46	1.57
18080016--18080123	18	6.2	17	68	14	67	35	1	15	47	1.57
18080028--18080146	52	2.3	52	94	2	204	34	1	16	47	1.57
18081821--18081876	29	1.9	29	82	13	71	50	8	1	39	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18082473--18082526	24	2.2	25	86	3	74	24	14	46	14	1.83
18085100--18085127	14	2.0	14	100	0	56	21	35	14	28	1.92
18085264--18085309	6	7.5	6	83	13	58	76	0	2	21	0.90
18091135--18091180	15	3.1	15	87	9	60	52	30	2	15	1.55
18091116--18091208	7	13.0	7	75	4	60	48	30	1	20	1.57
18091150--18091208	21	2.8	21	87	5	75	50	27	0	22	1.49
18091116--18091208	14	6.5	14	76	8	71	48	30	1	20	1.57
18091410--18091638	124	1.8	124	90	0	368	31	21	16	31	1.95
18091541--18091720	86	2.1	86	90	0	279	30	21	17	31	1.96
18091417--18091844	210	2.0	210	87	1	608	31	19	17	31	1.95
18091627--18091938	124	2.5	123	84	1	408	31	18	18	32	1.95
18093388--18093453	3	21.3	3	73	17	55	36	0	0	63	0.95
18093388--18093451	18	3.7	17	77	10	76	35	0	0	64	0.94
18093388--18093450	21	3.0	21	79	6	65	36	0	0	63	0.95
18093388--18093451	34	2.0	32	85	14	87	35	0	0	64	0.94
18093593--18093624	14	2.3	15	89	10	50	6	3	6	84	0.86
18093615--18093661	20	2.5	18	83	16	60	25	6	0	68	1.13
18093628--18093670	18	2.2	20	84	8	54	34	4	2	58	1.32
18093626--18093673	20	2.4	20	86	6	62	35	6	2	56	1.36
18097891--18097931	7	5.9	7	86	11	57	70	0	17	12	1.16
18097891--18097933	21	2.1	20	91	4	68	67	0	18	13	1.23
18099288--18102023	132	20.7	132	89	2	3908	28	18	25	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18100023--18100463	44	10.0	44	65	14	140	27	18	25	28	1.98
18103486--18103547	21	2.9	21	80	7	63	37	1	0	61	1.06
18103683--18103714	14	2.3	15	89	10	50	6	3	6	84	0.86
18103705--18103751	20	2.5	18	83	16	60	25	6	0	68	1.13
18103718--18103760	18	2.2	20	84	8	54	34	4	2	58	1.32
18103716--18103763	20	2.4	20	86	6	62	35	6	2	56	1.36
18104946--18104989	22	2.1	21	83	8	54	40	0	2	56	1.11
18108602--18108651	22	2.3	22	92	0	82	4	12	14	70	1.31
18109163--18109212	22	2.3	20	77	12	55	20	2	12	66	1.34
18109464--18109514	26	2.0	25	88	7	75	60	7	5	25	1.47

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