genome.fa.s3.2.7.7.80.10.50.1000.134.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  134  of  150  ( 17918 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)
40235311--40235542	114	2.0	114	90	2	360	32	0	15	52	1.46
40235618--40235678	27	2.3	27	94	0	104	24	42	18	14	1.88
40235618--40235685	27	2.5	27	90	0	82	25	42	17	14	1.87
40238460--40238489	15	2.0	15	93	0	51	76	0	16	6	0.99
40244780--40244810	9	3.4	9	90	0	53	25	12	22	38	1.90
40252955--40252996	16	2.6	16	82	17	52	40	2	9	47	1.49
40256933--40256987	26	2.1	26	100	0	110	29	14	27	29	1.95
40261635--40261676	2	21.0	2	95	0	75	50	0	2	47	1.14
40266474--40266552	29	2.7	29	69	7	70	22	24	8	44	1.81
40274337--40274384	8	5.3	9	83	11	55	56	0	2	41	1.11
40274343--40274459	27	4.3	26	77	15	96	58	0	1	38	1.14
40274439--40274507	24	3.0	23	80	20	74	60	4	1	33	1.25
40274337--40274568	10	24.0	9	70	20	89	59	1	2	36	1.21
40281214--40281269	23	2.4	24	90	6	96	41	3	0	55	1.17
40281786--40281827	22	1.9	22	90	0	66	50	7	16	26	1.71
40281785--40281833	22	2.2	22	81	0	62	55	6	14	24	1.62
40283316--40283362	16	2.9	16	81	6	60	40	2	25	31	1.68
40283948--40283985	3	12.7	3	94	0	67	31	0	2	65	1.06
40294286--40294312	12	2.2	12	100	0	54	81	0	7	11	0.87
40300144--40300447	37	8.0	37	88	7	405	37	14	20	27	1.92
40300294--40300489	82	2.4	81	93	2	324	34	15	21	27	1.94
40303905--40303961	20	2.9	19	70	12	53	61	7	3	28	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40304619--40304653	18	1.9	18	100	0	70	34	2	5	57	1.37
40304658--40304732	23	3.3	23	88	0	114	34	1	14	49	1.52
40304667--40304732	13	5.5	13	71	20	63	34	1	15	48	1.54
40304975--40305032	28	2.1	28	100	0	116	41	10	3	44	1.55
40307103--40307139	2	18.5	2	100	0	74	51	0	0	48	1.00
40309847--40309880	8	4.0	8	88	11	50	26	0	0	73	0.83
40315872--40315916	23	2.0	23	82	8	56	37	2	4	55	1.32
40317523--40317601	3	26.3	3	74	5	70	34	2	3	59	1.29
40317543--40317595	18	2.9	18	88	0	79	33	3	3	58	1.34
40317817--40317868	18	2.9	18	80	8	61	40	5	0	53	1.25
40317910--40317945	18	2.0	18	88	0	54	41	5	5	47	1.50
40318463--40318534	35	2.1	35	97	0	135	25	19	13	41	1.88
40320392--40320433	16	2.4	17	84	11	50	59	7	2	30	1.37
40326609--40326654	24	1.9	24	86	0	65	71	0	15	13	1.14
40329386--40329428	21	2.0	21	90	0	68	25	23	27	23	2.00
40330601--40330681	27	3.0	26	84	14	85	44	1	0	54	1.08
40331091--40331131	7	5.9	7	100	0	82	87	0	0	12	0.53
40338402--40338457	29	1.9	29	85	0	76	35	14	10	39	1.81
40339868--40339914	25	1.9	25	83	12	62	27	6	10	55	1.58
40342209--40342267	21	2.7	22	72	17	61	66	6	1	25	1.26
40344030--40344125	45	2.1	45	88	0	138	42	18	16	21	1.89
40347291--40347583	109	2.7	109	91	1	457	32	19	17	30	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40347628--40347668	20	2.0	20	86	9	57	53	4	14	26	1.61
40348023--40348071	2	25.5	2	79	8	57	46	2	4	46	1.33
40348179--40348228	3	16.7	3	100	0	100	68	0	0	32	0.90
40352617--40352711	32	2.9	33	77	9	95	41	0	4	54	1.20
40352654--40352710	29	2.0	30	89	6	91	43	0	3	52	1.18
40352629--40352700	37	1.9	37	86	5	101	41	0	1	56	1.07
40354112--40354244	38	3.4	38	78	7	117	24	20	26	29	1.99
40359175--40359208	16	2.1	16	88	0	50	79	0	17	2	0.86
40360358--40360445	41	2.2	41	95	2	160	48	11	6	32	1.65
40364347--40364401	27	2.0	27	82	6	67	49	3	0	47	1.19
40366806--40366897	26	3.6	26	78	10	93	33	19	28	18	1.95
40369968--40370029	31	2.0	31	87	9	90	61	0	1	37	1.06
40369968--40370020	11	4.9	11	77	11	56	58	0	1	39	1.09
40369981--40370113	44	3.2	40	87	9	196	63	0	3	33	1.09
40370038--40370113	39	1.9	39	94	0	134	61	0	3	34	1.14
40370349--40370400	15	3.2	15	73	19	50	44	0	1	53	1.11
40370480--40370523	22	2.0	22	86	0	61	43	0	0	56	0.99
40374338--40374404	31	2.2	31	81	7	75	59	11	5	22	1.54
40377783--40377824	2	21.0	2	95	0	75	50	2	47	0	1.14
40379152--40379180	11	2.5	12	88	11	51	62	0	0	37	0.96
40388991--40389041	16	3.3	16	83	8	70	64	0	0	35	0.94
40390502--40390563	25	2.4	26	82	12	74	61	1	1	35	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40391892--40391916	13	1.9	13	100	0	50	64	4	0	32	1.12
40392232--40392258	14	1.9	14	100	0	54	37	0	0	62	0.95
40392767--40392824	29	2.0	30	82	3	73	50	3	17	29	1.62
40394394--40394420	13	2.1	13	100	0	54	0	0	18	81	0.69
40403207--40403239	14	2.4	14	94	0	57	30	0	0	69	0.88
40406953--40407010	27	2.1	27	87	0	80	31	36	22	10	1.88
40407942--40407976	3	11.7	3	100	0	70	0	65	0	34	0.93
40407975--40408032	30	1.9	30	89	0	89	13	34	1	50	1.52
40411002--40411057	15	3.8	15	76	4	60	48	3	16	32	1.63
40410998--40411056	29	2.0	29	96	0	109	49	1	16	32	1.56
40410998--40411043	14	3.2	14	75	6	56	47	2	17	32	1.60
40424984--40425015	2	16.0	2	100	0	64	50	0	0	50	1.00
40430329--40430405	14	5.0	15	71	20	52	42	14	9	33	1.77
40430345--40430384	20	2.0	20	90	0	62	50	12	10	27	1.72
40430333--40430399	34	1.9	35	90	3	109	46	13	8	31	1.74
40430439--40430504	7	8.4	8	75	18	50	45	3	0	51	1.16
40430522--40430558	13	2.8	13	92	8	58	75	10	13	0	1.04
40430528--40430600	12	6.1	12	74	16	55	71	5	19	4	1.22
40430543--40430607	10	6.2	10	72	22	53	70	3	21	4	1.19
40430572--40430621	21	2.3	21	86	3	64	70	0	30	0	0.88
40431440--40431577	40	3.5	39	73	8	111	28	18	21	30	1.97
40440032--40440082	24	2.1	24	100	0	102	29	19	11	39	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40444207--40444241	18	1.9	18	88	0	52	42	0	5	51	1.25
40445362--40445401	16	2.5	16	84	11	55	20	30	2	47	1.63
40447182--40447424	50	4.9	50	82	4	233	28	20	27	23	1.99
40457552--40457611	29	2.1	29	100	0	120	41	26	6	25	1.80
40460844--40460872	14	2.0	15	93	6	51	48	3	6	41	1.47
40464094--40464139	3	15.3	3	100	0	92	67	0	0	32	0.91
40467615--40467661	18	2.6	19	83	12	55	46	6	4	42	1.48
40467895--40467927	2	17.0	2	93	6	59	51	0	0	48	1.00
40469456--40470059	50	12.1	50	68	5	317	25	24	21	28	1.99
40469442--40470042	100	6.0	100	86	1	780	25	23	21	29	1.99
40470067--40470254	88	2.1	88	86	0	259	25	24	21	28	1.99
40471498--40471535	17	2.2	17	90	0	58	13	13	0	73	1.09
40478939--40478978	5	8.2	5	86	2	55	77	2	2	17	0.99
40479103--40479144	2	21.0	2	100	0	84	50	0	0	50	1.00
40479292--40479389	36	2.9	35	80	7	87	61	1	6	31	1.27
40479341--40479448	24	4.5	24	72	15	89	57	0	5	36	1.28
40484313--40484470	79	2.0	80	80	3	176	46	10	7	34	1.67
40485334--40485376	22	2.0	21	86	13	61	32	25	2	39	1.69
40486784--40486861	31	2.5	31	95	2	138	28	10	8	52	1.65
40487080--40487115	17	2.2	17	90	5	56	47	5	0	47	1.25
40490091--40490131	3	13.7	3	94	0	73	2	31	0	65	1.05
40491301--40491341	7	5.9	7	94	0	73	26	0	26	46	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40491365--40491397	5	6.6	5	100	0	66	36	0	0	63	0.95
40492531--40492580	26	1.9	26	84	8	66	24	12	14	50	1.76
40494509--40494576	33	2.1	33	97	0	127	44	19	16	20	1.87
40502328--40502382	22	2.5	22	76	8	58	47	18	18	16	1.83
40508187--40508245	31	1.9	31	92	0	100	44	13	6	35	1.71
40510371--40510411	21	2.0	21	100	0	82	26	19	29	24	1.98
40512072--40512231	85	1.9	85	86	0	230	24	31	21	22	1.98
40515355--40515555	21	9.5	21	68	1	96	41	18	25	14	1.89
40515357--40515556	42	4.7	42	86	1	229	42	18	25	15	1.88
40515357--40515556	85	2.4	84	82	0	247	42	18	25	15	1.88

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