genome.fa.s5.2.7.7.80.10.50.1000.128.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  128  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)
39210561--39210718	74	2.1	75	79	5	169	20	27	18	33	1.96
39210687--39210742	25	2.2	25	96	0	103	26	28	14	30	1.95
39212725--39213284	274	2.1	273	89	4	848	42	10	26	21	1.84
39213820--39213893	21	3.5	21	77	17	89	58	4	21	16	1.55
39213820--39213909	43	2.1	43	100	0	180	55	4	24	15	1.59
39213837--39213909	22	3.4	22	78	17	98	56	4	26	13	1.55
39227816--39227872	21	2.7	20	71	10	51	33	10	8	47	1.69
39235347--39235399	24	2.2	24	82	0	61	22	30	5	41	1.77
39245270--39245325	25	2.2	26	83	3	69	51	0	19	28	1.47
39256497--39256558	22	2.8	22	77	0	61	19	25	14	40	1.90
39258369--39258401	16	2.1	16	94	0	57	57	15	12	15	1.65
39258417--39258703	78	3.7	78	86	5	366	44	13	11	29	1.79
39258417--39258703	155	1.8	156	83	6	384	44	13	11	29	1.79
39264410--39264447	2	19.0	2	100	0	76	50	0	0	50	1.00
39264552--39264585	2	17.5	2	93	6	61	50	0	0	50	1.00
39268463--39268514	16	3.3	17	75	22	51	17	28	1	51	1.56
39270067--39270099	9	3.8	9	84	8	50	33	0	0	66	0.92
39270091--39270149	30	1.9	31	82	3	75	38	15	6	38	1.74
39270571--39270599	12	2.3	13	94	5	51	24	0	0	75	0.80
39275946--39276534	50	11.8	50	78	1	583	29	22	23	25	1.99
39275956--39276605	100	6.6	100	88	1	902	30	21	22	25	1.99
39278838--39278866	12	2.3	13	94	5	51	24	0	0	75	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39278892--39278949	27	2.1	27	96	0	107	20	5	8	65	1.40
39281112--39281151	21	1.9	21	94	0	71	60	2	17	20	1.48
39299490--39299545	23	2.7	20	75	17	60	41	0	0	58	0.98
39300614--39300692	40	2.0	40	94	0	140	37	5	15	41	1.69
39310967--39311020	6	9.0	6	100	0	108	83	0	0	16	0.65
39318595--39318645	25	2.0	25	100	0	102	41	19	7	31	1.80
39318890--39323073	694	6.0	695	93	1	7119	37	18	15	27	1.92
39321254--39321298	22	2.0	22	83	8	56	77	0	4	17	0.92
39322686--39322734	20	2.5	20	72	0	53	67	4	8	20	1.34
39323581--39323636	13	4.5	13	78	13	73	48	16	0	35	1.46
39326435--39326474	20	2.0	20	95	0	71	42	12	25	20	1.86
39328124--39328295	87	2.0	87	95	0	308	33	21	18	27	1.96
39331211--39332068	298	2.8	297	88	4	1229	47	16	14	21	1.82
39333543--39333743	30	6.7	30	85	0	276	38	17	10	32	1.85
39333543--39333743	60	3.3	60	92	0	339	38	17	10	32	1.85
39334142--39334239	5	19.6	5	97	0	187	60	18	0	21	1.37
39334953--39335015	15	4.2	15	73	4	56	47	7	0	44	1.32
39335312--39335360	19	2.5	20	83	3	64	30	0	18	51	1.47
39339144--39339393	41	6.1	41	81	3	279	34	17	28	19	1.95
39366541--39367354	44	18.4	44	81	4	839	29	24	15	30	1.96
39366513--39367325	133	6.1	134	87	1	969	28	24	15	30	1.96
39366511--39367358	177	4.8	176	84	3	945	29	24	15	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39368645--39368689	20	2.2	20	84	7	56	15	17	0	66	1.25
39368652--39368689	13	2.8	13	92	4	58	13	18	0	68	1.21
39368652--39368690	7	5.7	7	84	6	53	12	17	0	69	1.19
39368653--39368690	20	1.9	20	89	10	60	13	18	0	68	1.21
39372045--39372080	17	2.1	17	89	0	54	44	22	16	16	1.86
39376544--39376595	24	2.3	22	78	15	61	5	21	0	73	1.04
39377062--39377107	19	2.3	20	81	3	58	21	6	2	69	1.22
39377189--39377260	19	3.9	18	74	13	65	40	1	0	58	1.07
39377212--39377250	20	1.9	21	89	5	62	38	0	0	61	0.96
39377130--39377262	28	4.6	28	73	16	94	36	2	1	60	1.19
39378875--39378918	23	1.9	23	81	9	54	25	4	9	61	1.45
39385404--39385466	30	2.1	31	96	3	119	34	19	17	28	1.94
39385745--39385916	34	5.0	34	68	8	98	20	24	22	31	1.98
39385747--39385916	68	2.5	69	84	2	218	20	24	22	31	1.98
39387324--39387486	43	3.8	43	90	0	254	28	32	17	21	1.96
39387685--39387744	18	3.4	18	64	13	52	40	10	6	43	1.64
39390567--39390636	22	3.2	22	83	0	95	31	12	27	28	1.93
39393911--39393948	7	5.4	7	96	0	67	31	50	0	18	1.47
39393903--39393954	21	2.5	21	80	0	68	30	44	0	25	1.54
39393991--39394045	27	2.0	27	82	6	67	38	43	0	18	1.50
39394003--39394041	20	2.0	19	90	5	60	38	46	0	15	1.46
39393889--39394093	95	2.1	97	85	5	281	41	31	0	25	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39394255--39394291	14	2.6	14	91	0	65	45	29	0	24	1.53
39394662--39394948	41	7.0	41	88	1	414	28	27	23	20	1.99
39394982--39395115	40	3.4	38	78	9	144	20	22	20	36	1.95
39394982--39395133	40	3.8	38	78	9	135	22	23	19	34	1.96
39398701--39398732	15	2.2	15	94	5	57	75	6	6	12	1.19
39403115--39403307	50	3.8	50	86	0	260	21	29	21	27	1.99
39403402--39403431	13	2.3	13	94	0	51	50	13	3	33	1.58
39408867--39408896	15	2.1	15	93	6	53	76	6	6	10	1.15
39411115--39411148	14	2.4	14	95	0	59	29	14	26	29	1.95
39411350--39411413	29	2.2	28	86	2	83	46	12	4	35	1.62
39417364--39417639	29	9.6	29	76	4	193	28	12	21	37	1.90
39417395--39417651	58	4.4	58	79	5	223	28	12	21	38	1.89
39417383--39417620	87	2.7	87	77	3	228	30	10	21	37	1.88
39425239--39425587	95	3.7	95	79	4	366	32	15	13	38	1.86
39425745--39425970	95	2.4	95	87	1	310	32	17	13	36	1.89
39442893--39442990	23	4.3	23	77	5	99	42	20	14	22	1.88
39442885--39442990	46	2.3	46	81	0	122	41	19	15	23	1.89
39447949--39448010	22	2.8	22	87	0	88	38	16	30	14	1.88
39451657--39451742	25	3.2	25	68	23	75	52	3	16	27	1.60
39458575--39458612	19	2.0	19	100	0	76	42	10	5	42	1.62
39460381--39460521	22	6.4	22	89	0	201	26	26	14	33	1.94
39467266--39467314	7	7.1	7	81	4	64	36	0	48	14	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39467266--39467314	20	2.4	21	86	3	64	36	0	48	14	1.44
39470495--39470547	25	2.1	25	92	0	88	47	11	3	37	1.58
39471207--39471244	17	2.2	17	95	0	67	42	15	15	26	1.87
39475185--39475386	68	3.2	60	79	15	214	51	4	2	41	1.37
39478861--39478914	18	3.0	18	71	10	56	46	11	0	42	1.39
39480241--39480279	20	2.0	20	90	5	62	35	5	5	53	1.45
39487948--39487981	15	2.3	15	94	0	59	58	0	8	32	1.29
39498290--39498359	31	2.2	32	80	7	81	30	8	17	44	1.78
39499641--39499739	40	2.5	40	81	4	128	43	21	15	20	1.88
39499641--39499751	40	2.8	38	77	8	114	44	19	16	19	1.87
39501210--39501281	36	2.0	35	81	7	83	22	15	34	27	1.94
39501247--39501364	43	2.7	42	85	5	155	23	16	34	25	1.95
39502912--39502952	21	2.0	21	85	9	57	43	2	7	46	1.44
39504341--39504476	42	3.2	42	77	2	130	41	16	20	21	1.90
39504569--39504632	24	2.7	24	85	9	94	21	25	4	48	1.69
39511759--39511797	18	2.2	18	85	0	51	48	10	7	33	1.66
39511892--39511945	18	2.9	19	83	10	67	51	9	0	38	1.34
39511909--39511945	19	2.0	18	89	5	56	54	10	0	35	1.36
39511951--39512014	9	6.6	10	72	13	62	65	6	3	25	1.31
39511951--39512003	18	2.9	18	84	13	72	66	5	3	24	1.31
39512102--39512134	16	2.0	17	88	5	50	33	3	12	51	1.54
39513984--39514052	4	16.0	4	77	16	52	0	21	4	73	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39513985--39514050	24	2.7	25	88	4	91	0	21	4	74	1.00
39515056--39515105	25	2.0	25	88	7	75	44	0	6	50	1.26
39515988--39516115	43	3.0	43	75	13	136	21	17	29	31	1.96
39527560--39527737	87	2.0	87	97	0	338	31	24	23	21	1.98
39539400--39539476	14	5.0	15	71	20	52	44	14	7	33	1.74
39539404--39539470	34	1.9	35	87	3	100	47	13	7	31	1.70
39540465--39540502	17	2.3	17	86	4	51	31	42	0	26	1.56
39543721--39544003	85	3.3	83	85	4	352	32	21	21	24	1.98
39543721--39544003	42	6.6	42	85	8	340	32	21	21	24	1.98
39543721--39544003	127	2.2	127	85	7	369	32	21	21	24	1.98

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