genome.fa.s4.2.7.7.80.10.50.1000.129.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  129  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)
41083822--41083883	27	2.2	27	80	5	70	27	3	1	67	1.15
41084182--41084212	16	1.9	16	93	0	53	48	9	6	35	1.62
41084301--41084367	29	2.3	28	80	12	82	31	2	1	64	1.18
41084372--41084424	20	2.7	20	85	11	65	30	1	7	60	1.35
41084828--41084884	21	2.8	20	89	5	69	22	1	1	73	1.02
41091648--41091700	22	2.4	21	90	6	79	41	28	13	16	1.86
41091670--41091911	38	6.4	38	81	4	283	36	32	19	11	1.88
41091604--41091738	60	2.2	60	83	6	166	40	31	14	13	1.85
41091670--41091911	76	3.2	76	84	4	319	36	32	19	11	1.88
41095273--41095334	23	2.7	22	80	14	63	38	1	6	53	1.37
41095290--41095355	21	3.0	22	81	14	82	40	3	6	50	1.43
41095298--41095366	23	2.8	23	79	18	77	43	1	7	47	1.39
41095298--41095364	27	2.7	24	80	14	82	43	1	7	47	1.40
41101667--41101888	88	2.5	89	79	2	243	27	24	25	23	2.00
41102405--41103008	44	14.0	43	68	13	235	31	19	20	28	1.97
41102399--41102829	217	2.0	218	85	3	582	30	20	21	27	1.98
41102579--41102922	173	2.0	174	82	4	426	31	20	19	27	1.97
41104390--41104448	27	2.1	28	84	9	75	37	1	5	55	1.32
41104406--41104486	23	3.2	24	80	13	92	38	1	6	54	1.33
41125214--41125264	24	2.1	25	82	17	63	41	0	35	23	1.55
41128336--41128369	17	2.0	17	94	0	59	38	5	20	35	1.77
41131855--41131913	20	3.0	20	83	11	77	38	3	1	55	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41131867--41131918	25	2.1	25	82	7	61	40	1	0	57	1.10
41132673--41132841	25	6.8	25	74	2	133	25	14	23	36	1.93
41132668--41132840	50	3.5	50	87	0	229	26	15	23	35	1.94
41134575--41134606	3	10.7	3	100	0	64	65	0	34	0	0.93
41136363--41136408	21	2.2	21	92	0	74	15	32	21	30	1.94
41136379--41136420	21	2.0	21	85	0	57	21	30	23	23	1.99
41142511--41142542	17	1.9	16	93	6	55	28	31	18	21	1.97
41161676--41161732	2	29.0	2	96	3	107	50	0	0	49	1.00
41163750--41163792	22	2.0	22	100	0	86	37	13	25	23	1.92
41164884--41164969	42	2.0	43	95	2	156	46	23	12	17	1.82
41168625--41168664	18	2.2	18	86	0	53	15	40	7	37	1.75
41180745--41180769	13	1.9	13	100	0	50	56	0	8	36	1.29
41184399--41184429	15	2.1	15	93	0	53	80	0	19	0	0.71
41186549--41186601	26	2.0	26	100	0	106	33	20	18	26	1.96
41198462--41198486	13	1.9	13	100	0	50	56	4	8	32	1.47
41208017--41208181	89	1.9	89	90	2	269	50	12	12	23	1.74
41232867--41232920	25	2.2	24	86	3	72	14	27	22	35	1.93
41233214--41234027	404	2.0	405	95	0	1477	29	12	20	38	1.88
41240960--41241024	25	2.7	24	76	4	67	18	27	13	40	1.89
41241742--41241807	33	2.0	33	96	0	123	27	15	28	28	1.96
41244735--41244774	18	2.2	18	90	0	62	17	30	10	42	1.82
41245147--41245263	62	1.9	60	85	3	162	35	4	10	49	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41246782--41246822	16	2.6	16	96	0	73	0	48	34	17	1.47
41247881--41247942	26	2.3	27	76	17	67	24	4	8	62	1.42
41247939--41248008	34	2.0	35	97	2	133	42	0	0	57	0.99
41248570--41248613	17	2.5	18	88	3	63	20	2	15	61	1.45
41251700--41251897	97	2.0	98	87	0	281	28	14	17	39	1.89
41251790--41252319	126	4.2	126	88	2	726	28	17	16	37	1.91
41251790--41252322	251	2.1	251	86	2	739	28	17	16	37	1.91
41252946--41252992	23	2.0	23	92	8	78	48	19	8	23	1.75
41254111--41254138	10	2.8	10	100	0	56	39	17	0	42	1.50
41254623--41254674	27	1.9	27	84	7	70	69	1	0	28	0.99
41256673--41256779	53	2.0	53	90	0	169	23	5	22	48	1.71
41256882--41256908	14	1.9	14	100	0	54	51	3	7	37	1.48
41257348--41257806	159	2.9	156	81	4	510	33	12	17	36	1.88
41261476--41261636	41	3.9	39	73	16	135	24	13	26	35	1.92
41266905--41266938	17	2.0	17	100	0	68	29	11	29	29	1.92
41267013--41267080	34	2.0	34	100	0	136	29	5	23	41	1.78
41268642--41268780	40	3.4	39	77	14	143	25	15	25	34	1.94
41268633--41268823	40	4.6	39	73	12	123	25	14	25	35	1.94
41278153--41278190	19	2.0	19	85	10	51	42	0	15	42	1.47
41282959--41283069	42	2.7	40	79	12	116	24	18	26	30	1.98
41283366--41283410	17	2.6	18	76	16	51	44	0	20	35	1.51
41285682--41285720	20	2.0	20	89	0	60	35	0	2	61	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41287288--41287319	14	2.3	14	100	0	64	50	6	43	0	1.27
41287626--41287668	17	2.5	17	81	7	52	32	0	2	65	1.06
41292649--41292708	30	2.0	30	83	3	75	43	0	36	20	1.52
41292922--41292958	9	4.1	9	89	0	56	32	10	10	45	1.74
41294664--41294700	5	7.4	5	96	0	65	21	40	0	37	1.54
41298408--41298450	22	2.0	22	100	0	86	37	13	25	23	1.92
41302157--41302221	7	9.0	7	73	18	53	81	1	15	1	0.84
41302171--41302218	21	2.3	20	83	13	62	81	0	16	2	0.79
41302159--41302219	12	4.9	12	73	15	52	81	1	14	1	0.84
41303459--41303662	44	4.6	44	83	2	230	28	21	26	23	1.99
41303454--41303662	88	2.4	88	84	3	260	28	21	26	23	1.99
41303614--41304782	132	8.9	132	88	3	1616	28	17	23	29	1.97
41303868--41304049	44	4.1	45	65	12	99	30	17	22	29	1.97
41303609--41304782	395	3.0	393	89	2	1729	28	17	23	29	1.97
41305896--41306013	3	40.0	3	84	1	150	27	0	0	72	0.91
41306403--41306428	2	13.0	2	100	0	52	50	0	0	50	1.00
41306406--41306482	35	2.2	35	81	6	93	44	3	0	51	1.19
41306755--41306785	15	2.1	15	93	0	53	19	9	6	64	1.45
41306846--41307268	108	3.9	109	91	2	658	29	15	18	35	1.92
41307825--41307909	28	3.1	28	89	1	127	25	23	23	27	2.00
41308055--41308128	26	2.8	27	83	4	89	39	22	20	17	1.92
41308277--41308498	27	8.3	27	80	5	209	21	17	18	42	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41308322--41308503	80	2.3	80	86	0	247	21	19	19	39	1.93
41308277--41308498	54	4.1	53	82	5	234	21	17	18	42	1.89
41316758--41316820	27	2.3	28	77	2	65	20	4	1	73	1.11
41323114--41323180	29	2.3	29	84	0	80	22	25	28	23	1.99
41323128--41323199	29	2.5	29	90	0	117	15	22	34	27	1.94
41326073--41326103	16	1.9	16	100	0	62	35	6	25	32	1.82
41326041--41326154	59	1.9	59	96	0	210	27	4	16	51	1.63
41331690--41331722	16	2.0	17	88	5	50	45	9	0	45	1.35
41331968--41332026	19	3.0	19	82	9	57	44	1	5	49	1.34
41337848--41337883	11	3.4	11	88	3	56	30	0	0	69	0.89
41337964--41338023	30	2.0	30	96	0	111	56	15	3	25	1.54
41338631--41338697	21	3.2	21	81	10	75	34	7	1	56	1.36
41338987--41339089	50	2.0	51	98	1	199	33	7	20	37	1.81
41346740--41347341	94	6.4	94	82	1	661	36	18	18	26	1.94
41346740--41347182	44	9.5	47	65	20	157	34	19	19	26	1.96
41354466--41354552	43	2.0	43	100	0	174	39	16	17	27	1.90
41357933--41357975	20	2.2	20	100	0	86	39	20	9	30	1.84
41359902--41359950	22	2.2	23	85	10	66	24	0	8	67	1.18
41361718--41361761	20	2.3	19	84	4	52	40	2	0	56	1.11
41361735--41361770	18	1.9	19	88	5	56	50	0	0	50	1.00
41361735--41361773	19	2.1	19	85	9	53	51	0	0	48	1.00
41361728--41361778	18	2.9	17	75	11	50	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41363863--41363943	32	2.5	32	88	4	119	18	27	40	13	1.88
41363923--41363966	18	2.5	18	88	3	63	11	25	47	15	1.79
41364117--41364147	2	15.0	2	93	6	53	48	0	3	48	1.17
41366327--41366370	21	2.2	20	88	8	63	70	2	2	25	1.10
41366389--41366442	17	3.1	16	75	19	54	62	3	0	33	1.12
41366388--41366502	10	11.9	10	70	18	59	60	2	0	35	1.16
41366388--41366502	21	6.0	18	73	17	81	60	2	0	35	1.16
41367007--41367062	8	6.4	8	77	18	58	37	0	1	60	1.07
41367007--41367079	9	8.0	9	77	18	71	34	1	1	63	1.12
41367002--41367078	19	4.2	18	78	15	68	35	1	1	62	1.12

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