genome.fa.s6.2.7.7.80.10.50.1000.39.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  39  of  168  ( 20060 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)
10696357--10696388	12	2.7	12	90	0	55	40	15	12	31	1.85
10697552--10697585	18	1.9	17	88	5	50	67	2	0	29	1.05
10716516--10716580	32	2.0	32	96	0	121	35	9	18	36	1.83
10717813--10717881	37	1.9	35	82	11	86	62	1	1	34	1.13
10724004--10724043	17	2.4	17	91	0	62	25	12	30	32	1.92
10726156--10726189	17	2.0	17	100	0	68	41	23	0	35	1.55
10734384--10734448	4	16.2	4	96	0	103	50	0	20	29	1.48
10743416--10743477	30	2.2	27	85	8	79	51	4	0	43	1.23
10743696--10743728	16	2.0	17	88	5	50	42	9	3	45	1.51
10743805--10743833	15	1.9	15	100	0	58	48	3	6	41	1.47
10743455--10744083	250	2.6	230	79	9	603	45	6	9	38	1.63
10743894--10743932	20	2.0	20	84	0	51	56	0	0	43	0.99
10745861--10745972	32	3.5	30	74	21	104	39	5	3	51	1.42
10745880--10745925	20	2.3	19	85	11	56	43	2	6	47	1.41
10748615--10748648	17	1.9	18	88	5	52	58	8	26	5	1.51
10752935--10752963	6	5.0	6	95	4	51	48	0	0	51	1.00
10754494--10754519	5	5.2	5	100	0	52	38	0	0	61	0.96
10757656--10757694	18	2.2	18	95	0	69	58	10	2	28	1.44
10757729--10757792	29	2.2	29	94	0	110	34	21	1	42	1.63
10767054--10767098	23	2.0	23	86	0	63	40	11	8	40	1.72
10767869--10768129	134	1.9	138	84	7	352	42	4	13	38	1.66
10767869--10768144	142	2.0	134	83	8	340	43	5	13	37	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10775491--10775689	59	3.3	58	73	12	204	40	1	2	55	1.20
10775611--10775745	18	8.0	18	70	17	94	39	0	1	58	1.12
10775395--10775711	120	2.6	121	94	1	557	41	1	3	52	1.28
10775547--10775730	41	4.6	40	69	21	116	40	1	3	54	1.26
10778235--10778263	13	2.2	13	100	0	58	34	17	13	34	1.89
10787155--10787207	22	2.3	23	81	15	65	45	11	11	32	1.76
10787162--10787207	23	2.0	23	83	8	58	47	10	10	30	1.73
10789348--10789384	3	12.3	3	100	0	74	32	0	0	67	0.91
10798888--10798921	16	2.1	16	100	0	68	17	20	11	50	1.77
10803871--10803902	12	2.7	12	95	0	55	62	0	3	34	1.11
10803942--10804008	29	2.2	30	78	5	73	59	5	16	17	1.56
10806698--10806770	27	2.7	27	78	0	83	17	23	24	34	1.96
10808888--10808983	45	2.2	44	88	5	140	29	5	29	36	1.79
10809124--10809606	120	4.0	120	96	0	851	51	5	1	42	1.34
10809124--10809606	239	2.0	241	94	0	853	51	5	1	42	1.34
10811000--10811102	49	2.1	49	90	3	163	50	9	8	31	1.66
10814775--10814818	22	2.0	22	95	0	79	52	4	29	13	1.60
10815853--10815910	9	6.4	9	78	7	64	44	18	8	27	1.79
10815861--10815904	18	2.4	18	96	0	79	43	18	11	27	1.84
10815852--10815910	27	2.2	27	82	8	75	45	18	8	27	1.78
10815852--10815910	18	3.3	18	85	0	73	45	18	8	27	1.78
10816577--10816640	31	2.2	28	84	13	78	59	3	12	25	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10817794--10817991	97	2.1	96	97	0	369	40	10	14	34	1.80
10820006--10820034	14	2.1	14	93	6	51	0	27	0	72	0.85
10826462--10826496	15	2.4	15	90	4	54	48	0	8	42	1.33
10827944--10828055	55	2.0	55	98	0	215	30	24	17	27	1.97
10830465--10830529	4	15.5	4	74	17	53	23	4	0	72	1.03
10830473--10830537	18	3.6	17	77	20	62	23	6	0	70	1.09
10830683--10830732	22	2.3	22	86	6	66	24	46	10	20	1.81
10835066--10835104	14	2.8	14	84	11	53	74	7	5	12	1.20
10839211--10839240	15	2.0	15	93	0	51	10	6	13	70	1.34
10840177--10840227	23	2.3	23	82	3	68	17	15	19	47	1.83
10840165--10840300	57	2.4	57	82	8	179	18	16	17	47	1.84
10853146--10853194	6	8.0	6	78	13	55	63	0	0	36	0.95
10853140--10853184	20	2.2	20	88	0	63	62	0	2	35	1.08
10856510--10856767	84	3.1	84	85	3	299	44	13	10	31	1.78
10856580--10856767	84	2.2	84	94	0	322	45	12	10	31	1.75
10856811--10857140	78	4.1	81	80	10	306	38	12	16	33	1.85
10856850--10857144	78	3.6	79	84	8	310	38	12	16	32	1.86
10864495--10864549	27	2.0	27	89	0	83	32	16	10	40	1.83
10876221--10876253	6	5.8	6	96	3	52	0	9	0	90	0.44
10876212--10876253	12	3.5	13	84	12	54	0	14	0	85	0.59
10876212--10876253	19	2.3	18	88	8	59	0	14	0	85	0.59
10879112--10879143	3	10.7	3	100	0	64	34	0	31	34	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10888648--10888691	3	14.7	3	100	0	88	34	0	31	34	1.58
10890408--10890481	10	7.9	10	75	14	77	28	16	9	45	1.78
10890408--10890481	20	4.0	20	77	16	86	28	16	9	45	1.78
10890439--10890469	15	2.0	16	93	6	55	29	19	6	45	1.75
10891072--10891141	20	3.5	21	73	9	65	37	10	7	45	1.65
10891089--10891141	19	2.7	19	77	11	63	35	9	7	47	1.64
10893148--10893191	21	2.2	21	84	8	56	47	20	22	9	1.78
10893286--10893524	101	2.4	101	85	3	320	29	24	12	33	1.93
10893636--10893682	2	23.5	2	100	0	94	51	48	0	0	1.00
10898273--10898499	33	6.8	33	67	7	98	29	23	14	31	1.94
10898261--10898500	101	2.4	101	87	0	345	29	23	14	32	1.94
10900214--10900274	24	2.5	24	83	0	77	27	3	19	49	1.64
10901126--10901166	22	2.0	22	85	9	59	48	2	4	43	1.37
10904023--10904472	51	8.9	51	76	5	394	29	14	26	29	1.95
10904022--10904472	102	4.4	102	88	1	613	29	14	25	29	1.95
10914125--10914178	16	3.4	16	89	0	81	33	1	35	29	1.69
10914157--10914266	45	2.6	42	83	8	127	35	6	27	30	1.82
10914427--10914614	61	3.1	61	70	14	199	47	6	2	43	1.42
10914395--10914626	120	1.9	120	97	0	437	49	6	2	41	1.42
10914511--10914562	15	3.6	15	80	12	56	53	1	0	44	1.11
10914395--10914575	59	3.0	59	70	15	181	50	6	1	41	1.34
10914430--10914613	59	3.1	59	68	20	173	47	7	2	42	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10914649--10914856	91	2.3	91	88	4	285	47	3	3	45	1.39
10914716--10914856	44	3.0	47	67	18	123	46	4	4	44	1.44
10914677--10914816	44	3.1	43	66	18	97	49	3	2	44	1.34
10916266--10916292	11	2.5	11	100	0	54	51	18	7	22	1.70
10917867--10917910	6	6.7	6	85	14	52	45	2	0	52	1.13
10919018--10919048	14	2.1	15	94	5	55	19	19	6	54	1.65
10925280--10925322	23	1.9	22	85	4	59	62	6	2	27	1.33
10928196--10928279	42	2.0	42	100	0	168	42	21	7	28	1.79
10928498--10928522	12	2.1	12	100	0	50	36	0	0	64	0.94
10930922--10930960	20	2.0	20	89	0	60	35	15	10	38	1.81
10934970--10935265	18	16.4	18	72	13	198	34	16	17	31	1.92
10935004--10935217	56	3.8	56	83	9	254	34	15	16	32	1.91
10934972--10935217	38	6.5	38	76	5	185	34	16	17	31	1.93
10935059--10935217	20	8.4	20	72	13	95	34	16	16	32	1.92
10946763--10946821	25	2.4	25	85	5	75	52	20	20	6	1.69
10947744--10947802	29	2.0	29	83	0	73	18	42	22	16	1.89
10950304--10950370	34	2.0	34	82	11	84	58	19	14	7	1.60
10950404--10950475	35	2.1	35	82	10	85	52	16	22	8	1.70
10951360--10951424	28	2.2	30	81	10	82	18	38	23	20	1.93
10953950--10954008	25	2.4	25	76	0	64	30	20	18	30	1.96
10957494--10957533	20	2.0	20	90	5	62	35	2	0	62	1.09
10960307--10960337	16	1.9	16	93	0	53	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10960535--10960568	14	2.4	14	90	0	50	41	0	2	55	1.15
10962960--10963018	3	19.7	3	100	0	118	33	0	0	66	0.92
10963220--10963265	22	2.0	24	87	8	69	60	6	0	32	1.22
10964287--10964407	49	2.5	49	84	0	152	23	18	36	22	1.95
10966133--10966339	48	4.3	48	81	3	218	27	21	28	22	1.99
10966155--10966328	96	1.8	96	84	0	240	27	21	30	20	1.98
10971906--10972110	48	4.2	48	84	1	223	26	20	28	24	1.99
10979217--10979303	42	2.0	43	95	2	158	29	9	10	50	1.67
10981219--10981251	16	2.1	16	100	0	66	24	12	45	18	1.83
10989469--10989529	21	2.8	22	80	9	72	50	1	8	39	1.42

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