genome.fa.s4.2.7.7.80.10.50.1000.133.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  133  of  198  ( 23681 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)
42413411--42413451	20	2.0	20	100	0	82	46	4	39	9	1.58
42418186--42418255	31	2.3	31	82	0	86	50	10	5	34	1.60
42422287--42422475	42	4.5	41	92	5	299	37	21	20	21	1.95
42422287--42422475	83	2.3	84	92	2	319	37	21	20	21	1.95
42422845--42422891	21	2.2	21	84	0	58	2	40	19	38	1.63
42426384--42426614	9	26.4	9	70	14	162	31	1	20	46	1.61
42426368--42426472	25	4.2	25	77	13	117	32	2	19	45	1.65
42426383--42426565	34	5.6	33	70	17	123	31	1	20	46	1.61
42426447--42426573	62	2.0	63	83	7	161	29	0	21	48	1.56
42426506--42426707	25	7.7	25	68	18	74	31	1	18	48	1.59
42426460--42426602	44	3.2	44	78	8	114	30	1	20	47	1.59
42426588--42426679	39	2.4	39	85	5	116	33	2	15	48	1.57
42427584--42427722	67	2.1	67	98	0	269	45	13	4	36	1.64
42427782--42427817	16	2.2	16	95	0	63	55	5	11	27	1.57
42427858--42427896	10	3.9	10	96	0	60	53	0	0	46	1.00
42430079--42430130	21	2.5	21	87	0	68	50	40	0	9	1.35
42430105--42430159	29	1.9	28	85	3	74	47	38	3	10	1.56
42431254--42431515	113	2.3	112	79	6	269	29	23	15	31	1.95
42431194--42431737	114	4.8	114	73	11	386	27	24	17	30	1.97
42435185--42435234	23	2.2	23	88	0	73	38	2	10	50	1.48
42436088--42436164	22	3.6	21	71	15	68	24	2	2	70	1.13
42441573--42441627	26	2.1	27	86	3	76	60	3	1	34	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42441587--42441621	11	3.0	12	91	8	63	60	0	0	40	0.97
42441574--42441618	15	3.3	14	84	12	58	62	4	0	33	1.15
42441648--42441685	16	2.4	16	86	8	51	63	2	5	28	1.30
42443502--42444097	100	6.0	100	83	3	657	26	17	22	33	1.96
42443502--42444097	200	3.0	198	84	3	759	26	17	22	33	1.96
42443487--42444095	50	12.2	50	76	5	444	25	18	22	33	1.96
42447942--42448011	34	2.1	34	97	0	131	57	2	10	30	1.46
42450008--42450054	19	2.5	19	86	6	60	44	8	21	25	1.80
42450516--42450550	16	2.2	16	89	0	52	42	22	17	17	1.88
42452291--42452325	11	3.0	12	91	8	63	60	0	0	40	0.97
42452277--42452330	26	2.1	25	86	3	72	61	3	1	33	1.25
42452278--42452322	15	3.3	14	84	12	58	62	4	0	33	1.15
42452352--42452389	16	2.4	16	86	8	51	63	2	5	28	1.30
42452577--42452634	25	2.3	26	82	8	75	56	3	6	32	1.42
42457214--42457263	23	2.2	24	85	10	77	40	0	8	52	1.31
42458028--42458069	17	2.4	17	88	8	57	21	4	0	73	1.01
42460486--42460550	32	2.1	32	97	2	123	47	12	9	30	1.72
42483048--42483081	16	2.2	16	90	10	54	0	17	0	82	0.67
42498894--42498935	2	21.5	2	95	4	77	52	0	0	47	1.00
42505333--42505419	40	2.2	39	82	10	115	35	2	1	60	1.17
42512696--42512740	21	2.1	21	91	0	72	17	28	22	31	1.97
42518680--42518723	23	1.9	24	86	9	65	68	2	0	29	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42519914--42519985	3	25.3	3	72	10	62	29	0	2	68	1.04
42521701--42521764	3	21.3	3	100	0	128	67	0	0	32	0.91
42521760--42521790	4	7.8	4	100	0	62	74	0	0	25	0.82
42523525--42523709	44	4.2	45	66	12	114	32	22	17	27	1.96
42523305--42524160	132	6.5	132	89	2	1267	29	24	18	28	1.98
42523624--42524089	44	10.6	44	65	15	169	28	24	18	28	1.98
42523326--42524160	396	2.1	395	92	0	1402	29	24	18	28	1.98
42524160--42524335	87	2.0	88	84	3	230	25	22	22	30	1.99
42525563--42525616	7	7.9	7	80	19	69	14	14	0	70	1.17
42525563--42525617	13	4.1	13	92	4	83	14	16	0	69	1.20
42525563--42525627	13	4.6	14	88	7	80	15	16	0	67	1.23
42525573--42525608	6	5.7	6	90	9	54	13	13	0	72	1.13
42527033--42527125	41	2.2	43	94	5	163	2	18	8	70	1.22
42540363--42540547	44	4.2	44	67	8	124	29	21	24	24	1.99
42542155--42542200	3	15.3	3	100	0	92	67	0	0	32	0.91
42543575--42543619	17	2.8	17	83	12	51	40	8	2	48	1.47
42552608--42552633	12	2.2	12	100	0	52	69	0	0	30	0.89
42555328--42555363	18	2.0	18	100	0	72	33	27	5	33	1.80
42558788--42558828	16	2.6	16	80	0	55	26	24	12	36	1.91
42566557--42566646	43	2.1	43	100	0	180	31	17	10	41	1.83
42569934--42570180	50	4.8	50	84	4	282	22	27	22	27	1.99
42586673--42586728	24	2.3	25	81	9	71	44	14	5	35	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42594577--42595375	44	18.3	44	72	13	271	26	19	26	27	1.99
42594445--42595578	218	5.2	218	92	0	1866	27	18	26	27	1.98
42595601--42595799	44	4.5	44	74	9	131	27	17	26	28	1.98
42620288--42620358	37	1.9	37	94	0	124	38	29	9	22	1.86
42620288--42620366	37	2.1	37	90	0	122	37	32	8	20	1.83
42620612--42620655	21	2.1	21	86	0	61	43	15	6	34	1.74
42627370--42627541	92	1.9	93	84	6	233	34	14	15	36	1.88
42630763--42630824	29	2.1	29	93	0	106	33	20	19	25	1.96
42632218--42632251	13	2.7	13	90	4	52	61	5	0	32	1.20
42632930--42632955	5	5.2	5	100	0	52	19	0	0	80	0.71
42632978--42633005	5	5.6	5	100	0	56	35	0	0	64	0.94
42640101--42640174	36	2.1	35	87	5	105	35	10	16	37	1.83
42644576--42644630	23	2.5	21	77	11	56	23	1	14	60	1.44
42644487--42644724	82	2.9	82	79	7	261	31	5	12	50	1.62
42648131--42648170	18	2.2	18	90	0	62	2	30	42	25	1.68
42650329--42650390	4	13.5	4	78	21	52	1	29	0	69	0.98
42650314--42650387	20	3.5	20	76	15	78	1	28	0	70	0.96
42650329--42650386	24	2.4	24	94	5	100	1	29	0	68	0.99
42650321--42650399	28	3.0	28	80	15	107	1	31	0	67	0.99
42650454--42650512	27	2.2	26	79	8	64	10	33	33	22	1.87
42650866--42650900	10	3.6	10	92	3	54	31	0	0	68	0.90
42650865--42650915	10	4.9	10	83	11	50	31	1	0	66	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42652617--42652664	20	2.5	19	86	3	60	35	6	2	56	1.36
42655947--42655981	10	3.4	10	84	7	52	11	8	2	77	1.10
42658701--42658769	29	2.3	29	85	5	84	47	11	15	24	1.79
42663518--42663546	14	2.1	14	100	0	58	44	13	27	13	1.82
42663995--42664027	2	16.5	2	93	0	57	54	0	45	0	0.99
42666826--42666868	20	2.2	20	83	8	52	44	0	34	20	1.52
42679568--42679641	34	2.2	34	97	2	141	50	9	2	37	1.49
42687466--42687510	17	2.6	17	85	0	54	57	2	0	40	1.11
42687516--42687581	34	1.9	34	82	14	82	59	1	3	36	1.22
42695119--42695164	3	15.3	3	100	0	92	65	0	34	0	0.93
42695900--42695932	18	1.9	17	88	11	50	48	0	21	30	1.50
42696742--42696785	22	1.9	24	86	9	65	40	4	13	40	1.65
42698300--42698331	2	16.0	2	100	0	64	50	0	0	50	1.00
42701990--42702027	9	4.1	9	93	3	58	52	2	23	21	1.59
42701995--42702056	9	6.9	9	77	14	56	46	0	30	22	1.52
42702296--42702321	5	5.2	5	100	0	52	80	0	0	19	0.71
42704398--42704446	24	2.0	24	100	0	98	20	22	16	40	1.91
42706356--42706395	7	5.7	7	90	0	62	27	10	12	50	1.72
42706323--42706396	7	10.6	7	85	0	58	22	5	13	58	1.56
42706400--42706446	22	2.1	22	100	0	94	19	4	17	59	1.53
42707739--42707778	19	2.2	18	90	4	62	57	5	2	35	1.34
42709123--42709204	37	2.2	37	82	8	96	43	7	25	23	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42719207--42719241	17	2.1	17	100	0	70	48	5	22	22	1.72
42719244--42719275	8	4.0	8	91	0	55	25	9	25	40	1.85
42719244--42719278	12	2.9	12	86	0	52	25	11	22	40	1.88
42720539--42720568	7	4.3	7	100	0	60	56	0	0	43	0.99
42723257--42723298	20	2.1	20	95	0	75	38	11	19	30	1.88
42739793--42739838	16	2.8	16	78	21	51	73	2	23	0	0.94
42746511--42746544	17	1.9	18	88	5	52	29	11	11	47	1.76
42749111--42749194	41	2.0	41	90	0	132	42	16	19	21	1.89
42750334--42750371	18	2.1	18	90	0	58	31	18	31	18	1.95
42752299--42752346	25	1.9	25	95	0	87	12	37	29	20	1.90

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