genome.fa.s7.2.7.7.80.10.50.1000.34.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  34  of  204  ( 24458 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)
12315674--12315780	21	5.2	20	75	8	81	42	21	23	12	1.86
12315692--12315906	42	5.1	42	79	3	184	45	17	20	16	1.85
12315717--12315924	83	2.5	84	79	9	203	43	17	21	17	1.88
12315737--12315928	42	4.6	41	75	10	131	45	16	20	17	1.86
12318225--12318353	9	14.1	9	64	17	52	61	2	1	34	1.18
12318282--12318353	17	4.1	18	77	8	69	63	1	1	33	1.11
12318515--12318625	38	2.9	37	85	5	141	31	11	18	37	1.87
12318687--12318850	44	3.8	44	82	5	185	26	21	16	35	1.95
12320079--12320254	9	19.3	9	65	19	64	60	2	2	34	1.24
12320061--12320167	47	2.3	47	80	11	121	61	3	3	30	1.31
12320081--12320169	27	3.2	27	72	12	74	61	3	3	31	1.28
12320632--12320696	30	2.3	29	82	17	75	35	1	1	61	1.15
12320639--12320730	46	2.0	47	83	10	118	31	4	2	61	1.27
12321271--12321346	29	2.8	28	79	18	88	61	1	5	31	1.26
12321341--12321393	19	2.7	19	82	11	54	69	3	0	26	1.05
12321380--12321426	19	2.3	21	89	10	71	61	0	0	38	0.96
12321367--12321424	31	1.9	29	82	6	71	63	0	0	36	0.94
12321396--12321453	19	3.0	19	85	7	64	63	3	0	32	1.11
12321396--12321454	20	3.0	20	85	7	68	64	3	0	32	1.10
12321728--12321812	27	3.1	27	71	18	70	32	2	0	64	1.06
12321751--12321869	9	13.0	9	66	18	50	33	4	1	60	1.26
12325937--12325977	19	2.1	20	90	4	66	53	0	4	41	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12325938--12325976	10	3.9	10	83	10	53	51	0	5	43	1.24
12327242--12327322	23	3.5	23	81	3	92	33	3	6	56	1.42
12329789--12329831	3	14.3	3	80	9	52	65	2	0	32	1.06
12331589--12331779	36	5.0	36	83	12	238	28	20	13	36	1.91
12331661--12331815	46	3.6	46	76	16	195	28	22	12	36	1.91
12331625--12331815	82	2.3	82	94	0	337	28	21	12	36	1.90
12331546--12331779	118	2.0	115	93	2	396	28	21	13	36	1.92
12333119--12333228	21	5.3	21	86	6	163	36	10	10	42	1.74
12333902--12333940	19	2.0	20	90	5	62	56	0	5	38	1.22
12337898--12337930	2	16.0	2	93	6	57	48	0	3	48	1.17
12340289--12340389	41	2.5	41	88	0	148	15	15	29	38	1.89
12340328--12340418	41	2.2	41	84	0	110	16	16	31	35	1.91
12354246--12354303	29	2.0	29	82	3	71	44	3	22	29	1.69
12354535--12354590	22	2.3	26	82	14	68	30	0	5	64	1.16
12356795--12356829	17	2.1	17	88	0	52	34	2	2	60	1.26
12358290--12358370	31	2.6	31	82	5	92	49	9	11	29	1.70
12359189--12359236	19	2.7	18	84	9	62	66	0	2	31	1.03
12359192--12359245	19	3.2	16	78	19	56	61	0	1	37	1.07
12359653--12359691	15	2.6	15	80	15	53	7	10	0	82	0.86
12360373--12360418	24	1.9	24	95	0	83	43	19	4	32	1.71
12360370--12360423	24	2.4	21	80	16	72	40	18	5	35	1.74
12369301--12369354	26	2.0	27	89	3	83	66	1	0	31	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12373148--12373172	4	6.2	4	100	0	50	28	24	24	24	2.00
12373170--12373222	4	13.5	4	92	4	90	24	1	24	49	1.61
12378005--12378047	21	2.0	22	90	4	70	55	9	9	25	1.61
12378791--12378833	21	2.0	22	90	4	70	55	9	9	25	1.61
12377436--12379003	785	2.0	785	98	0	3019	37	13	13	36	1.83
12379310--12379338	5	5.8	5	100	0	58	41	0	0	58	0.98
12382186--12382242	29	1.9	30	86	10	82	59	1	0	38	1.08
12391590--12391646	16	3.6	16	87	0	87	43	3	7	45	1.48
12391566--12391616	22	2.3	23	86	3	68	49	1	3	45	1.32
12391691--12391867	93	2.0	90	87	7	263	39	6	7	46	1.57
12391785--12391834	16	2.8	19	66	27	54	38	0	12	50	1.40
12391916--12391958	22	2.0	22	86	4	61	55	4	2	37	1.33
12399778--12399839	14	4.8	14	69	16	53	41	1	1	54	1.19
12399785--12399844	24	2.6	24	81	5	70	41	1	1	55	1.20
12399787--12399844	22	2.6	23	78	10	66	41	1	1	55	1.20
12400126--12400536	109	3.8	109	88	3	632	30	17	18	33	1.94
12400120--12400536	217	1.9	218	94	0	737	31	17	18	32	1.94
12404193--12404258	8	7.8	8	80	6	60	80	4	0	15	0.87
12404203--12404258	9	6.3	9	83	8	62	82	3	0	14	0.81
12404192--12404251	27	2.2	27	82	11	70	80	5	0	15	0.88
12404194--12404263	17	4.2	16	82	13	79	78	5	0	15	0.93
12404278--12404308	14	2.3	13	94	5	53	83	0	16	0	0.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12406617--12406808	85	2.2	87	77	8	194	30	19	21	28	1.98
12406617--12406819	44	4.7	43	72	7	151	30	19	22	28	1.98
12406612--12406852	44	5.6	43	71	7	148	31	19	21	28	1.97
12406609--12406926	129	2.5	129	88	0	465	29	20	21	28	1.98
12408585--12408628	2	23.0	2	86	9	65	50	0	2	47	1.13
12408742--12408803	14	4.8	14	69	16	53	41	1	1	54	1.19
12408749--12408808	24	2.6	24	81	5	70	41	1	1	55	1.20
12408751--12408808	22	2.6	23	78	10	66	41	1	1	55	1.20
12409090--12409516	109	3.9	109	88	3	628	29	17	18	33	1.94
12409084--12409500	217	1.9	218	94	0	737	31	17	18	32	1.94
12414389--12414426	19	2.0	19	89	0	58	39	15	5	39	1.70
12414731--12414757	14	1.9	14	100	0	54	33	0	0	66	0.92
12416359--12416424	34	1.9	35	85	14	93	48	3	1	46	1.26
12417293--12417326	3	11.3	3	100	0	68	0	32	0	67	0.91
12425082--12425600	109	4.8	109	92	0	797	35	18	15	31	1.92
12425723--12425762	4	9.8	4	97	2	71	75	2	0	22	0.93
12425741--12425823	38	2.2	36	81	12	89	65	6	8	20	1.42
12426084--12426119	2	18.0	2	94	0	63	50	2	0	47	1.15
12426288--12426411	3	41.7	3	80	4	135	61	2	4	32	1.28
12427169--12427207	19	2.1	19	90	0	60	74	5	12	7	1.20
12428293--12428963	44	15.5	44	72	9	434	26	20	21	32	1.98
12428175--12428886	129	5.5	129	89	0	1046	26	19	21	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12428776--12429193	218	1.9	217	84	3	554	27	23	19	29	1.98
12428253--12429241	44	22.9	43	70	11	364	26	21	20	31	1.98
12429274--12429511	125	1.9	125	84	3	318	25	18	21	34	1.96
12429387--12429866	50	9.6	50	73	2	347	25	18	21	34	1.96
12429387--12429887	100	5.0	98	87	3	653	25	19	21	33	1.97
12429387--12429881	199	2.5	199	88	1	688	25	19	21	33	1.97
12430082--12430110	12	2.3	13	94	5	51	13	0	0	86	0.58
12430076--12430111	17	2.1	17	90	10	56	13	0	0	86	0.58
12432092--12432189	47	2.1	48	83	9	121	9	10	6	74	1.22
12432111--12432186	13	5.8	13	72	7	55	10	5	7	76	1.15
12432156--12432200	21	2.2	21	88	4	65	11	4	6	77	1.09
12435590--12436215	109	5.8	109	93	0	959	34	17	15	31	1.92
12435590--12436215	217	2.9	218	91	0	977	34	17	15	31	1.92
12436874--12437009	3	45.7	3	80	4	123	58	1	7	33	1.35
12439410--12439490	25	3.2	25	84	3	101	19	28	19	32	1.97
12439450--12439518	25	2.8	25	82	2	77	21	23	21	33	1.97
12445327--12445374	16	2.9	17	80	17	57	70	8	0	20	1.12
12449799--12449859	16	3.6	16	72	14	52	40	1	3	54	1.27
12478081--12478151	37	1.9	37	91	0	115	53	9	16	19	1.71
12480067--12480121	27	2.1	27	86	6	78	18	27	21	32	1.96
12482237--12482284	24	2.0	24	84	8	62	64	0	2	33	1.05
12482656--12482861	90	2.3	90	80	8	211	31	8	20	39	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12485070--12485110	17	2.5	17	84	11	50	41	7	2	48	1.44
12485203--12485242	2	20.0	2	84	0	53	47	7	0	45	1.31
12488875--12488914	8	4.8	8	90	9	62	77	10	0	12	0.99
12488875--12488914	17	2.4	17	91	8	64	77	10	0	12	0.99
12488874--12488916	9	4.9	9	91	8	63	76	9	0	13	1.01
12489760--12489804	7	6.3	7	85	14	65	73	0	13	13	1.10
12489759--12489804	22	2.1	22	92	8	76	73	0	13	13	1.09
12491057--12492030	100	9.9	100	86	3	1002	32	23	20	23	1.98
12491067--12492244	50	24.0	50	73	7	638	32	23	20	24	1.98
12491761--12492248	95	5.0	95	83	6	230	30	21	21	26	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