genome.fa.s4.2.7.7.80.10.50.1000.105.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  105  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)
33662697--33662840	17	7.7	17	66	27	62	29	2	22	44	1.67
33662668--33662882	39	5.5	39	90	1	333	29	3	22	45	1.68
33672757--33672791	15	2.2	16	90	5	54	65	5	5	22	1.36
33673009--33673057	19	2.6	18	81	9	55	71	0	10	18	1.13
33676361--33676386	11	2.4	11	100	0	52	73	15	0	11	1.11
33682923--33682966	22	2.0	22	82	8	54	52	18	6	22	1.69
33683353--33683441	41	2.2	41	81	0	106	24	23	33	17	1.96
33685493--33685535	19	2.3	18	81	18	52	34	23	20	20	1.96
33686129--33686199	21	3.4	21	82	3	90	33	21	29	15	1.94
33698896--33698924	15	1.9	15	100	0	58	34	6	13	44	1.71
33698829--33699017	104	1.8	104	97	0	360	41	11	18	28	1.85
33707186--33707273	45	1.9	46	81	2	106	39	5	21	32	1.77
33707277--33707318	6	6.8	6	91	2	66	54	0	28	16	1.42
33717250--33717297	15	3.1	15	88	8	62	20	4	12	62	1.46
33717691--33717729	2	19.5	2	100	0	78	0	0	48	51	1.00
33721840--33721902	7	8.9	7	77	16	58	82	11	0	6	0.83
33721864--33721901	13	2.8	13	88	4	58	78	10	0	10	0.95
33721840--33721902	13	4.4	14	76	20	51	82	11	0	6	0.83
33721864--33721901	20	1.9	19	94	5	67	78	10	0	10	0.95
33721897--33721953	26	2.1	27	83	3	71	78	1	15	3	0.96
33721911--33721953	13	3.3	12	81	15	50	83	0	16	0	0.64
33724055--33724844	88	9.0	88	93	0	1323	27	22	25	24	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33724061--33724815	44	17.2	44	67	14	351	27	22	24	24	2.00
33724828--33725939	132	8.4	132	93	2	1772	30	18	23	27	1.98
33724942--33725939	44	22.7	44	64	14	245	30	18	23	26	1.98
33727414--33727461	15	3.1	15	88	8	62	20	4	12	62	1.46
33727848--33727872	2	12.5	2	100	0	50	0	0	48	52	1.00
33729357--33729401	19	2.4	19	88	7	65	35	0	6	57	1.25
33729357--33729402	18	2.4	19	82	10	58	34	0	6	58	1.24
33730446--33730472	9	3.0	9	100	0	54	33	0	0	66	0.92
33733600--33733641	8	5.1	8	78	16	50	2	14	0	83	0.75
33734472--33734536	25	2.5	25	90	5	94	27	4	7	60	1.44
33734473--33734559	25	3.3	26	84	7	79	28	6	5	58	1.47
33746815--33747380	44	13.0	44	92	1	890	28	21	25	24	1.99
33749354--33749387	17	1.9	18	88	5	52	8	11	0	79	0.94
33750222--33750285	24	2.5	24	87	7	83	28	6	6	59	1.46
33750243--33750308	27	2.5	26	81	11	73	30	6	4	59	1.42
33754292--33754324	14	2.4	14	90	5	50	66	3	9	21	1.33
33755977--33756025	21	2.3	22	79	10	57	4	24	2	69	1.17
33768819--33768850	9	3.6	9	100	0	64	31	0	21	46	1.52
33769172--33769244	19	3.9	18	72	11	58	46	2	1	49	1.24
33771501--33771537	18	2.1	18	89	0	56	45	21	10	21	1.82
33771964--33771990	14	1.9	14	100	0	54	22	0	37	40	1.54
33771999--33772028	14	2.1	14	93	0	51	56	0	33	10	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33772100--33772196	41	2.4	41	87	3	133	13	27	19	39	1.89
33778172--33778225	15	3.5	15	80	5	54	59	0	3	37	1.15
33779205--33779234	15	2.1	14	93	6	51	70	0	3	26	1.03
33782304--33782347	19	2.5	16	82	17	52	43	11	0	45	1.40
33790659--33790708	20	2.3	20	80	10	55	26	6	12	56	1.58
33797973--33798017	4	11.2	4	85	0	54	24	28	0	46	1.53
33801234--33801470	42	5.6	42	87	1	332	21	18	25	34	1.96
33801443--33801498	28	2.0	28	89	0	85	23	21	21	33	1.97
33801359--33801561	112	1.8	112	93	0	352	21	19	23	35	1.96
33801403--33801540	70	2.0	70	89	0	213	22	19	23	34	1.97
33801471--33801608	42	3.3	42	91	0	222	21	19	21	37	1.94
33801321--33801606	154	1.9	154	92	0	482	22	19	23	34	1.97
33802431--33802862	153	2.9	148	86	6	579	40	4	10	44	1.60
33802841--33802893	20	2.7	19	71	5	52	41	1	11	45	1.51
33805248--33805320	37	2.0	37	94	0	128	35	10	26	27	1.90
33805992--33806083	41	2.3	40	83	3	121	29	0	27	43	1.55
33806231--33806549	126	2.5	126	87	3	446	37	15	18	28	1.92
33808081--33808153	37	1.9	38	88	2	112	31	21	2	43	1.67
33808344--33808740	51	7.8	51	74	6	342	29	26	14	28	1.95
33808349--33808740	102	3.9	102	91	0	606	29	27	14	28	1.95
33812949--33812996	25	1.9	25	87	8	71	58	4	0	37	1.18
33812946--33813001	25	2.3	24	79	11	69	51	3	0	44	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33813403--33813437	18	1.9	18	94	0	61	34	11	28	25	1.91
33815192--33815260	30	2.3	30	89	0	102	34	1	27	36	1.66
33815702--33815783	41	2.0	41	97	0	155	40	6	4	48	1.49
33815998--33816052	16	3.5	16	80	9	51	21	3	3	70	1.18
33816012--33816055	16	2.8	15	83	10	52	20	4	4	70	1.23
33821846--33822119	146	1.9	145	85	3	381	35	12	6	45	1.67
33827139--33827186	3	16.0	3	86	0	69	60	0	0	39	0.97
33827181--33827209	4	7.2	4	100	0	58	51	0	0	48	1.00
33827593--33827622	5	6.0	5	92	0	51	23	0	56	20	1.42
33828722--33828767	2	23.0	2	100	0	92	50	0	0	50	1.00
33829081--33829135	4	13.8	4	96	0	101	25	1	23	49	1.60
33831798--33831841	18	2.5	17	78	10	52	40	15	2	40	1.60
33833856--33833886	13	2.3	14	94	5	55	67	3	22	6	1.28
33835098--33835144	25	2.0	24	84	12	62	68	2	2	27	1.13
33835755--33835799	21	2.1	21	84	8	56	42	4	0	53	1.21
33842587--33843167	289	2.0	289	92	0	955	26	20	16	35	1.94
33845622--33845667	21	2.3	18	82	17	56	73	0	10	15	1.08
33845694--33845718	11	2.3	11	100	0	50	84	0	0	16	0.63
33850775--33850803	14	2.1	14	100	0	58	20	48	6	24	1.74
33852091--33852135	19	2.3	20	85	7	58	51	4	8	35	1.54
33852101--33852140	20	2.0	20	90	4	64	52	2	5	40	1.37
33853162--33853292	40	3.3	40	75	9	135	25	16	25	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33858722--33858766	24	1.9	24	86	4	65	17	4	0	77	0.92
33860206--33860247	6	6.8	6	86	5	57	26	0	2	71	0.98
33860217--33860277	25	2.5	24	82	12	70	18	3	6	72	1.21
33860200--33860277	6	12.5	6	75	12	50	17	3	5	73	1.18
33870349--33870376	2	14.0	2	100	0	56	50	50	0	0	1.00
33873168--33873203	15	2.3	16	90	4	56	16	2	2	77	1.00
33879835--33879933	45	2.3	44	79	11	107	44	18	22	15	1.86
33882482--33882525	14	2.9	15	83	6	54	40	0	2	56	1.11
33882517--33882561	21	2.1	21	84	8	56	31	4	4	60	1.37
33885750--33885779	14	2.1	14	100	0	60	13	33	13	40	1.83
33889093--33889366	137	2.0	137	98	0	530	32	22	14	30	1.94
33890058--33890106	20	2.5	20	86	0	62	34	8	14	42	1.75
33891764--33891817	21	2.5	23	80	14	62	14	27	27	29	1.95
33893461--33893512	21	2.6	21	77	17	56	73	3	9	13	1.23
33898318--33898360	20	2.2	20	91	0	68	41	9	11	37	1.74
33900253--33900289	18	2.1	19	90	10	60	29	5	5	59	1.42
33905108--33905153	21	2.1	21	84	11	58	45	19	0	34	1.51
33912075--33912160	20	4.3	20	79	5	84	13	25	18	41	1.88
33914510--33914566	27	2.2	26	80	3	60	59	5	0	35	1.20
33915223--33915271	9	5.2	9	76	9	53	48	0	2	48	1.12
33915218--33915274	29	2.0	29	92	0	96	47	0	1	50	1.11
33915681--33915809	67	1.9	67	88	0	195	44	27	3	24	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33918840--33918902	31	2.0	31	100	0	126	33	9	12	44	1.75
33920178--33920228	23	2.2	23	89	0	75	29	5	19	45	1.74
33927745--33927784	2	20.0	2	100	0	80	50	0	0	50	1.00
33936554--33936605	3	16.7	3	76	7	50	28	5	1	63	1.28
33936980--33937019	18	2.1	20	86	9	57	45	2	0	52	1.14
33939682--33939726	23	2.0	23	86	0	63	15	24	24	35	1.94
33941262--33941316	23	2.3	23	84	6	65	49	18	16	16	1.81
33947840--33947908	34	2.0	34	100	0	138	23	5	37	33	1.79
33950294--33950350	28	2.1	27	90	3	87	14	15	19	50	1.77
33953675--33953907	49	4.8	49	73	6	184	30	12	28	29	1.92

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