genome.fa.s7.2.7.7.80.10.50.1000.63.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  63  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)
20118642--20118750	46	2.4	46	95	1	193	30	21	17	31	1.96
20118642--20118860	37	5.2	45	84	11	191	29	21	15	34	1.93
20131646--20131685	20	2.0	21	85	5	55	25	30	15	30	1.95
20132364--20132444	41	1.9	42	85	5	110	35	13	2	48	1.56
20141035--20141094	26	2.3	26	88	0	93	40	11	15	33	1.83
20149406--20149457	1	52.0	1	80	0	59	3	0	5	90	0.55
20149406--20149457	15	3.7	14	85	7	70	3	0	5	90	0.55
20149406--20149460	22	2.6	22	85	5	69	3	0	7	89	0.60
20149890--20149946	6	9.2	6	81	14	53	73	0	3	22	0.98
20152256--20152327	29	2.4	29	81	4	81	25	12	13	48	1.78
20154933--20155021	44	2.0	44	97	0	169	28	14	21	35	1.93
20166122--20166172	11	4.5	11	87	2	75	21	33	1	43	1.64
20167322--20167378	21	2.7	22	86	10	68	28	0	17	54	1.43
20167338--20167381	7	6.3	7	100	0	88	29	0	13	56	1.38
20168023--20168065	18	2.4	18	84	0	50	18	20	9	51	1.74
20168770--20168834	30	2.3	27	84	7	76	52	0	3	44	1.16
20169180--20169217	6	6.2	6	87	6	58	81	0	18	0	0.69
20169172--20169217	13	3.5	13	88	8	67	80	0	19	0	0.71
20169169--20169224	19	2.9	19	81	2	67	75	0	25	0	0.81
20169854--20169906	3	17.7	3	100	0	106	33	0	0	66	0.92
20170912--20170951	20	2.0	20	90	0	62	32	10	12	45	1.75
20170899--20170964	34	1.9	35	90	3	107	33	7	15	43	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20182171--20182196	11	2.4	11	100	0	52	61	0	0	38	0.96
20182146--20182210	30	2.1	32	88	5	98	56	0	0	43	0.99
20183251--20183297	23	2.0	23	95	0	85	51	21	27	0	1.48
20183556--20183610	27	2.0	27	92	0	92	25	30	5	38	1.79
20185980--20186034	21	2.6	22	88	8	87	25	9	38	27	1.86
20190275--20190312	6	6.2	6	87	6	58	39	0	60	0	0.97
20190275--20190310	18	2.0	18	100	0	72	38	0	61	0	0.96
20190280--20190321	18	2.3	18	87	0	57	40	0	59	0	0.97
20191998--20192117	51	2.4	51	90	1	179	31	24	0	44	1.54
20193253--20193277	7	3.6	7	100	0	50	28	0	12	60	1.32
20193930--20193964	18	1.9	18	94	0	61	25	31	8	34	1.86
20194522--20194945	21	16.3	29	63	29	131	45	25	1	26	1.63
20194476--20195001	50	10.9	50	82	6	591	45	25	2	26	1.65
20194530--20195001	235	2.0	235	89	0	721	45	26	2	26	1.65
20194580--20194945	185	2.0	186	91	0	590	45	26	1	26	1.63
20194729--20194807	36	2.2	36	93	0	131	43	30	2	24	1.67
20194629--20195001	136	2.6	139	84	7	466	45	26	1	26	1.62
20194481--20195001	285	1.8	284	88	1	801	45	26	2	26	1.65
20195010--20195227	116	1.9	116	98	0	418	38	9	9	42	1.70
20195203--20195244	17	2.4	18	80	4	50	42	9	2	45	1.49
20196061--20196411	126	2.8	123	84	4	463	34	21	13	30	1.92
20196696--20196769	39	1.9	38	94	2	130	54	1	1	43	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20196835--20196941	51	2.1	51	96	0	196	40	0	14	44	1.46
20201499--20201627	18	6.8	19	71	16	90	41	0	1	55	1.14
20201494--20201581	21	4.2	20	70	25	58	40	0	1	57	1.06
20201548--20201693	58	2.6	54	78	12	134	42	0	2	54	1.20
20201573--20201707	58	2.3	57	85	2	180	43	0	2	52	1.21
20201665--20201705	14	3.1	14	79	10	50	41	0	0	58	0.98
20201874--20201928	16	3.5	15	82	9	65	32	27	5	34	1.80
20203184--20203264	3	27.0	3	97	0	153	65	0	33	1	1.01
20204267--20204337	26	2.8	24	73	21	72	69	1	0	29	0.98
20204533--20204601	30	2.3	29	85	12	86	56	0	0	43	0.99
20204742--20204891	29	5.5	28	64	27	81	33	2	3	60	1.27
20204737--20204891	56	2.9	49	83	15	193	33	2	3	60	1.26
20206011--20206116	53	2.0	54	86	1	151	29	7	13	50	1.69
20207921--20207962	22	1.9	22	85	0	57	45	4	2	47	1.36
20217153--20217191	21	1.9	19	85	10	51	61	10	10	17	1.55
20225509--20225552	23	1.9	23	85	0	61	38	13	15	31	1.87
20226031--20226084	18	3.1	17	80	17	65	33	0	1	64	1.04
20226041--20226091	27	1.9	27	84	11	70	33	0	1	64	1.05
20235569--20235623	21	2.6	22	82	5	69	32	3	32	30	1.75
20240606--20240642	16	2.2	17	90	4	58	40	2	51	5	1.39
20246470--20246518	13	3.8	13	76	12	57	63	8	6	22	1.44
20246472--20246523	26	2.0	25	88	3	77	67	5	5	21	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20253516--20253604	25	3.5	26	78	4	76	23	23	20	32	1.98
20272163--20272207	2	22.5	2	100	0	90	48	0	0	51	1.00
20272533--20272577	2	22.5	2	100	0	90	48	0	0	51	1.00
20274313--20274346	3	11.3	3	100	0	68	32	0	0	67	0.91
20275968--20276091	46	2.8	45	91	3	198	28	22	16	33	1.95
20276053--20276228	37	4.8	37	92	0	264	28	20	12	38	1.89
20283502--20283570	33	2.1	33	100	0	138	33	2	21	42	1.68
20285549--20285593	23	2.0	23	100	0	90	22	20	22	35	1.96
20291267--20291461	98	2.0	98	94	0	345	36	25	10	27	1.88
20292390--20292538	19	7.8	19	86	0	199	39	15	9	35	1.80
20293696--20293740	23	2.0	23	86	8	65	20	15	13	51	1.76
20293707--20293753	23	2.0	23	87	0	67	19	17	17	46	1.84
20299221--20299296	38	2.0	38	97	0	143	26	19	27	26	1.99
20303647--20303760	43	2.7	43	91	0	183	30	15	28	25	1.96
20307944--20308017	34	2.1	35	85	9	98	37	20	9	32	1.85
20308184--20308383	41	4.8	41	81	5	206	24	24	21	31	1.98
20308184--20308352	82	2.0	84	86	4	236	24	24	21	29	1.99
20308701--20308910	78	2.8	78	80	8	202	40	18	4	37	1.71
20309063--20309431	74	4.8	75	90	5	514	43	14	4	37	1.65
20309063--20309431	154	2.4	156	87	7	535	43	14	4	37	1.65
20314695--20314768	38	1.9	38	86	5	105	31	31	1	36	1.66
20316169--20316236	22	3.1	22	93	0	109	30	16	27	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20316331--20316371	19	2.1	20	86	4	57	46	4	0	48	1.23
20316331--20316384	19	2.7	20	82	8	56	46	7	1	44	1.42
20316442--20316480	18	2.2	18	86	4	53	64	0	7	28	1.21
20320697--20320736	18	2.3	18	86	4	55	37	0	0	62	0.95
20330453--20330513	32	1.9	32	96	3	115	32	9	13	44	1.76
20332009--20332074	34	1.9	35	81	9	82	40	24	4	30	1.75
20337940--20337987	25	1.9	25	83	8	62	31	2	0	66	1.03
20338264--20338356	45	2.1	45	97	0	177	33	26	15	24	1.95
20338339--20338370	16	2.0	16	93	0	55	25	28	12	34	1.92
20338590--20338634	23	2.0	23	90	0	72	55	4	11	28	1.54
20338582--20338639	23	2.7	21	79	10	71	53	3	12	31	1.54
20341375--20341437	23	2.7	23	90	0	90	15	49	14	20	1.80
20341286--20341414	56	2.3	56	83	2	179	18	45	12	23	1.83
20341432--20341500	33	2.1	33	88	0	102	14	43	15	26	1.85
20351773--20351862	42	2.1	42	84	8	112	16	23	17	42	1.89
20354128--20354400	61	4.5	61	80	0	287	25	27	16	30	1.97
20354138--20354400	122	2.2	121	83	0	328	25	27	16	30	1.97
20354525--20354625	53	1.9	53	89	4	159	29	27	10	31	1.91
20355937--20356185	50	4.8	50	84	4	300	20	29	23	26	1.99
20355936--20356185	100	2.4	104	88	5	355	20	29	23	26	1.99
20363599--20363837	50	4.6	50	84	3	280	21	29	23	25	1.99
20363598--20363848	100	2.4	104	86	5	330	21	29	22	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20363942--20363973	13	2.5	13	94	0	55	56	12	0	31	1.37
20364185--20364242	30	1.9	30	89	0	89	31	24	3	41	1.71
20371382--20371450	25	2.8	25	82	4	68	42	0	0	57	0.98
20373914--20373989	20	3.8	20	77	3	73	25	10	11	52	1.69
20374057--20374122	21	3.1	21	76	10	71	21	10	12	56	1.65
20374069--20374122	21	2.6	21	85	5	74	25	11	11	51	1.70
20374108--20374161	21	2.5	22	72	3	56	20	11	14	53	1.71
20374154--20374203	20	2.5	20	83	0	64	26	16	12	46	1.81
20374911--20374964	24	2.3	24	83	3	65	59	0	1	38	1.08
20374894--20375009	59	2.1	54	84	12	146	58	0	1	38	1.14

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