genome.fa.s11.2.7.7.80.10.50.1000.40.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   205   206   207   208   
          209   210   

This is table  40  of  210  ( 25152 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)
12688475--12688611	62	2.2	61	96	1	247	22	9	21	45	1.80
12690448--12690527	26	3.1	25	87	3	97	27	8	17	46	1.77
12690541--12690622	26	3.1	25	87	7	110	30	9	15	43	1.79
12690418--12690717	95	3.2	95	92	0	487	27	7	18	46	1.76
12690729--12690816	2	44.0	2	100	0	176	0	0	50	50	1.00
12690999--12691057	18	3.1	18	70	13	55	37	37	13	11	1.82
12691048--12691099	21	2.5	21	87	6	70	32	44	7	15	1.75
12691793--12691871	36	2.2	36	97	0	149	48	22	8	20	1.77
12691809--12691874	20	3.5	20	68	29	63	53	22	6	18	1.66
12691809--12691895	36	2.4	36	88	3	122	54	20	5	19	1.65
12692730--12692754	6	4.2	6	100	0	50	16	68	16	0	1.22
12700463--12700501	21	1.9	19	85	10	51	41	5	2	51	1.38
12703062--12703140	23	3.5	22	77	5	70	22	18	20	37	1.94
12703094--12703159	22	2.9	22	84	8	71	18	19	18	43	1.88
12706002--12706455	218	2.1	217	83	2	550	31	12	14	41	1.83
12706852--12707028	37	4.8	37	74	4	142	20	35	3	40	1.72
12706852--12707013	74	2.2	74	80	2	173	22	35	4	38	1.74
12706974--12707086	37	3.1	37	78	7	104	23	29	5	42	1.76
12706852--12707052	111	1.8	111	81	2	251	21	33	4	39	1.74
12709204--12709347	37	3.9	37	77	5	121	21	34	4	39	1.73
12709101--12709243	74	1.9	74	81	0	169	20	33	4	40	1.74
12709096--12709254	74	2.2	73	77	7	167	21	33	4	40	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12709093--12709299	111	1.9	110	81	6	256	21	34	4	39	1.73
12709092--12709324	111	2.1	110	78	5	238	21	34	3	39	1.72
12712613--12712794	37	4.9	37	76	5	152	21	32	4	40	1.75
12712613--12712831	74	3.0	74	78	2	233	21	33	5	39	1.75
12715437--12715568	37	3.6	37	79	6	124	20	28	6	45	1.74
12715406--12715581	74	2.4	74	81	8	191	20	30	5	44	1.73
12716637--12716909	37	7.4	38	73	8	165	18	37	4	39	1.71
12716645--12716909	74	3.6	73	74	4	190	18	36	4	39	1.72
12716638--12716909	111	2.4	110	79	9	268	18	37	4	40	1.71
12717821--12718127	37	8.3	37	74	6	158	18	36	5	40	1.73
12717747--12718109	74	4.9	73	75	5	214	18	36	5	39	1.74
12719227--12719402	37	4.8	36	70	9	113	20	35	3	40	1.69
12721606--12721796	37	5.2	36	77	11	127	20	35	4	39	1.72
12721862--12721941	37	2.2	37	86	0	106	17	35	5	42	1.71
12723596--12723642	18	2.6	18	76	6	51	27	0	4	68	1.08
12727083--12727331	50	4.8	50	89	3	345	21	30	22	26	1.99
12727669--12727726	30	1.9	30	89	0	89	29	24	5	41	1.76
12728418--12728444	13	2.1	13	100	0	54	29	7	14	48	1.71
12729312--12729362	15	3.4	15	73	10	59	23	35	33	7	1.84
12730262--12730303	17	2.5	17	88	7	59	0	14	7	78	0.95
12730262--12730303	12	3.7	12	81	6	52	0	14	7	78	0.95
12733458--12733687	27	8.6	27	88	0	327	40	21	20	17	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12735559--12735713	30	5.2	30	90	1	242	30	9	17	42	1.80
12737357--12737406	24	2.1	24	84	0	64	24	36	8	32	1.84
12737525--12737647	37	3.3	37	67	13	90	16	35	5	42	1.72
12740435--12740567	72	1.9	71	87	1	194	25	6	20	48	1.72
12740653--12740685	13	2.6	13	90	4	50	30	0	15	54	1.41
12749006--12749034	15	1.9	15	100	0	58	34	0	31	34	1.58
12752984--12753455	103	4.6	103	95	1	804	20	20	28	30	1.98
12758950--12759005	27	2.1	27	90	3	87	41	0	3	55	1.17
12758950--12758999	26	2.0	25	81	11	59	40	0	4	56	1.18
12760286--12760480	106	1.9	105	92	3	331	29	0	15	55	1.41
12760461--12760496	16	2.2	16	90	5	54	30	0	2	66	1.06
12762493--12762610	33	3.6	33	79	2	121	18	42	11	27	1.84
12762836--12763070	75	3.1	74	87	5	321	28	6	10	54	1.59
12766143--12766209	32	2.1	32	88	5	100	38	11	7	41	1.70
12769883--12769969	31	2.9	29	74	17	79	42	12	10	34	1.77
12779494--12779562	28	2.5	28	90	6	106	39	10	1	49	1.46
12783157--12783203	23	2.0	23	87	0	67	0	31	0	68	0.90
12783162--12783287	10	12.7	10	70	18	77	0	31	0	66	1.03
12783162--12783273	38	3.1	37	85	8	124	0	32	0	66	1.04
12783186--12783295	38	2.9	38	89	2	150	0	33	0	64	1.06
12783236--12783307	10	6.6	10	73	17	54	0	30	1	68	0.99
12783225--12783307	28	2.8	29	74	22	82	0	31	1	67	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12783356--12783423	27	2.5	27	95	0	118	19	27	26	26	1.99
12783356--12783434	27	2.9	27	88	7	108	16	27	26	29	1.97
12783464--12783499	17	2.1	17	89	5	54	11	0	11	77	0.99
12783487--12783558	29	2.5	29	90	2	110	48	1	9	40	1.45
12784721--12784750	2	15.0	2	100	0	60	50	0	0	50	1.00
12784880--12784904	9	2.8	9	100	0	50	56	0	8	36	1.29
12786023--12786060	13	2.9	13	96	0	67	42	28	7	21	1.81
12786244--12786273	16	1.9	16	93	6	53	50	20	0	30	1.49
12788323--12788361	14	2.7	14	84	4	51	58	2	2	35	1.25
12789892--12790047	25	6.4	24	78	13	158	30	20	24	25	1.99
12789878--12790001	50	2.5	50	89	7	184	29	20	24	25	1.99
12789908--12790047	73	1.9	74	89	4	221	30	20	25	24	1.99
12789892--12790047	49	3.2	48	84	8	174	30	20	24	25	1.99
12791444--12791468	2	12.5	2	100	0	50	52	0	0	48	1.00
12794014--12794055	21	1.9	23	90	9	70	11	23	0	64	1.27
12800929--12800971	22	2.0	22	100	0	86	37	13	25	23	1.92
12818324--12818442	59	2.0	59	95	0	211	31	23	6	37	1.81
12821125--12821171	7	5.9	8	85	14	62	2	10	2	85	0.78
12822112--12822182	13	5.3	13	76	17	65	80	5	7	7	1.03
12822139--12822192	20	2.7	19	83	16	74	75	7	7	9	1.18
12823648--12823709	3	20.3	3	85	9	81	66	1	0	32	1.02
12823925--12824028	19	5.4	18	71	24	63	71	2	5	20	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12823924--12823969	18	2.5	19	78	3	58	69	6	8	15	1.34
12823973--12824031	6	9.8	6	73	14	50	72	0	3	23	0.99
12823979--12824031	13	4.2	13	88	11	74	71	0	3	24	1.02
12829976--12830019	19	2.3	19	96	0	79	29	11	31	27	1.91
12832097--12832127	16	1.9	16	93	0	53	54	9	22	12	1.67
12832745--12832951	88	2.2	94	79	10	237	36	16	9	37	1.82
12832769--12832951	88	2.0	93	85	5	250	37	16	9	37	1.81
12833057--12833134	20	3.8	20	73	10	77	64	2	5	28	1.28
12833355--12833425	35	2.0	35	83	0	88	39	1	2	56	1.23
12833432--12833511	20	4.0	20	68	9	56	28	2	1	67	1.11
12833517--12833711	92	2.2	89	82	6	250	33	7	21	38	1.80
12835926--12835966	3	13.7	3	100	0	82	31	0	0	68	0.90
12837487--12837591	54	2.0	50	91	8	167	54	7	13	24	1.65
12842290--12842341	18	2.8	18	91	2	77	50	3	0	46	1.20
12849851--12849908	29	1.9	30	82	6	73	13	1	6	77	1.05
12849850--12849897	21	2.3	21	78	7	53	12	2	6	79	1.01
12850093--12850132	19	2.1	19	90	9	64	30	0	0	70	0.88
12851139--12851191	16	3.5	15	80	16	56	43	1	0	54	1.11
12851141--12851250	7	15.9	7	67	15	50	41	1	0	55	1.16
12851161--12851247	24	3.6	24	71	17	72	40	1	1	57	1.14
12868832--12868889	23	2.5	22	76	17	64	44	3	6	44	1.47
12871478--12871566	24	3.7	24	79	5	90	19	34	20	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12875096--12875141	21	2.2	21	84	0	56	56	21	4	17	1.58
12876194--12876487	42	7.0	42	91	3	434	31	20	23	24	1.98
12876931--12876999	21	3.3	21	83	4	86	5	40	15	37	1.72
12881865--12882116	9	30.2	9	69	17	109	37	1	16	44	1.58
12881870--12881989	16	7.9	16	67	19	87	34	2	17	45	1.62
12881884--12882032	25	6.0	25	76	7	133	36	2	16	44	1.59
12881910--12882061	34	4.3	35	75	13	125	37	1	17	43	1.60
12882045--12882075	16	1.9	16	100	0	62	32	0	25	41	1.56
12881941--12882082	25	5.6	25	70	17	71	38	1	18	42	1.59
12882063--12882172	34	3.3	34	84	7	163	40	0	12	46	1.48

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   205   206   207   208   
          209   210