genome.fa.s12.2.7.7.80.10.50.1000.1.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  1  of  120  ( 14336 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)
5037--5114	30	2.5	31	81	4	95	32	25	23	19	1.98
20598--20632	5	7.4	5	90	9	56	62	0	0	37	0.95
27862--27899	17	2.2	18	86	9	53	31	10	2	55	1.48
54802--54940	30	4.7	29	77	6	136	23	23	12	41	1.88
54766--54932	88	1.9	89	86	1	237	22	26	12	38	1.90
54831--54958	60	2.2	59	88	1	184	22	25	11	39	1.88
54860--55047	30	6.3	30	77	4	173	25	23	12	38	1.90
56616--56967	178	2.0	178	94	0	614	30	16	15	36	1.90
60815--60844	15	2.0	15	100	0	60	40	20	0	40	1.52
66985--67024	19	2.1	19	85	0	53	37	20	0	42	1.52
67298--67335	19	2.0	20	89	5	60	5	26	0	68	1.11
67456--67496	2	21.0	2	85	5	57	48	2	0	48	1.14
75026--75138	25	4.6	25	74	11	99	39	19	23	16	1.91
75073--75165	25	3.7	25	75	5	80	35	19	26	18	1.95
77002--77300	50	5.9	50	80	5	282	27	21	27	23	1.99
88169--88383	51	4.6	44	82	14	259	30	15	24	28	1.96
88220--88387	51	3.3	50	90	4	273	32	14	25	27	1.95
88179--88387	95	2.1	98	89	6	325	32	15	24	28	1.95
100260--100481	111	2.0	111	99	0	435	37	22	15	24	1.93
105112--105380	135	2.0	135	91	2	434	33	8	16	42	1.78
106037--106120	32	2.6	31	79	5	87	30	19	9	40	1.83
112830--112891	32	2.0	32	96	3	117	32	8	12	46	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
113427--113515	13	6.5	13	75	18	67	75	12	12	0	1.05
117044--117196	22	7.0	22	90	0	225	32	14	26	26	1.94
119057--119121	32	2.1	32	97	2	123	30	9	12	47	1.72
123735--123762	3	9.3	3	100	0	56	64	0	35	0	0.94
127947--128005	30	2.0	30	83	3	75	44	3	15	37	1.63
128881--128905	13	1.9	13	100	0	50	8	8	20	64	1.46
134602--134655	27	2.0	28	85	3	74	40	3	0	55	1.17
134624--134662	16	2.5	16	87	4	53	46	2	0	51	1.14
144176--144294	58	2.1	58	100	0	238	42	18	3	35	1.67
144998--145044	17	2.8	17	75	15	53	38	27	19	14	1.91
145839--145870	12	2.5	13	90	10	57	21	0	78	0	0.76
145841--145870	6	4.8	6	95	4	51	20	0	80	0	0.72
146627--146683	27	2.1	27	100	0	114	31	21	15	31	1.94
148792--148878	43	2.0	42	95	2	156	43	21	12	21	1.86
150506--150562	29	1.9	30	82	10	73	52	5	15	26	1.64
153259--153298	20	2.0	20	90	0	62	50	0	17	32	1.47
159784--159814	15	2.0	16	93	6	55	3	19	0	77	0.90
161431--161499	31	2.2	31	92	0	111	47	13	7	31	1.69
170712--170844	70	1.9	72	84	7	182	25	4	16	53	1.62
173035--173073	2	19.5	2	100	0	78	48	0	0	51	1.00
177677--177702	2	13.0	2	100	0	52	0	0	50	50	1.00
185707--185739	8	4.1	8	100	0	66	27	0	12	60	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
202189--202229	15	2.8	16	79	20	54	36	0	4	58	1.20
207778--207814	9	4.1	9	92	0	65	29	10	13	45	1.77
216212--216324	22	5.1	22	87	0	154	32	14	25	27	1.94
217562--217603	19	2.3	18	91	4	66	45	0	0	54	0.99
223173--223214	21	2.0	21	95	0	75	30	42	16	9	1.80
225047--225076	2	15.0	2	100	0	60	50	0	0	50	1.00
228545--228592	19	2.5	20	86	6	64	50	4	8	37	1.52
228555--228593	20	2.0	20	95	5	71	51	2	5	41	1.38
229407--229453	24	2.0	24	84	16	62	34	0	14	51	1.43
229456--229496	2	20.5	2	100	0	82	48	0	0	51	1.00
229644--229781	40	3.5	40	76	8	140	28	15	24	31	1.96
235540--235595	19	2.9	19	86	7	69	28	3	7	60	1.40
236210--236258	25	2.0	25	84	8	64	42	2	0	55	1.11
244637--244684	21	2.2	21	92	3	78	43	14	12	29	1.82
245318--245361	21	2.0	21	82	4	52	34	22	13	29	1.93
245790--245824	11	3.2	11	91	0	52	28	2	0	68	1.04
245790--245835	22	2.1	22	84	8	58	28	2	2	67	1.14
279178--279209	2	17.0	2	87	12	50	50	0	0	50	1.00
281393--281423	8	4.0	8	95	4	55	0	9	0	90	0.46
283106--283144	12	3.2	12	85	0	51	43	0	23	33	1.54
284417--284468	25	2.1	25	100	0	104	46	13	7	32	1.72
286177--286234	19	3.0	19	82	7	55	44	12	1	41	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
306649--306957	160	1.9	161	89	1	485	20	16	17	45	1.86
322265--322298	17	2.0	17	88	0	50	41	14	8	35	1.77
333609--333725	8	13.4	9	78	18	92	42	0	2	54	1.14
333613--333725	12	10.8	10	80	16	83	42	0	2	54	1.14
333641--333725	2	46.5	2	82	17	114	45	0	0	54	1.00
333730--333773	16	2.8	16	86	10	56	65	2	27	4	1.23
333746--333802	8	8.0	7	75	16	55	68	1	29	0	1.00
333752--333801	21	2.4	21	96	0	91	68	2	30	0	1.01
333746--333794	21	2.2	23	85	10	75	67	2	30	0	1.02
335254--335295	6	6.8	6	86	2	57	16	21	16	45	1.86
348413--348544	28	4.7	28	70	3	113	30	11	19	38	1.87
351555--351620	3	22.3	3	78	9	73	62	3	1	33	1.20
353366--353864	43	11.5	44	72	11	196	27	21	21	29	1.98
353273--353873	217	2.8	218	86	3	829	27	20	20	30	1.98
353712--353821	44	2.6	41	81	4	121	30	22	17	29	1.97
354014--354051	3	12.7	3	100	0	76	31	0	0	68	0.90
366711--366741	3	10.3	3	92	0	53	64	0	3	32	1.09
368938--368996	28	2.1	28	81	6	66	47	5	1	45	1.34
378551--378587	2	18.5	2	100	0	74	48	0	0	51	1.00
380352--380376	6	4.2	6	100	0	50	0	16	0	84	0.63
385327--385378	24	2.2	24	89	0	77	55	9	1	32	1.43
387293--387344	24	2.2	24	89	0	77	55	9	1	32	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
388230--388281	26	2.0	26	96	0	95	38	11	13	36	1.81
399079--399271	44	4.5	43	81	7	180	30	13	25	30	1.94
399101--399268	85	1.9	87	83	7	216	30	13	25	30	1.94
406433--406509	38	2.0	38	84	0	100	28	20	15	35	1.94
414873--415034	84	1.9	84	94	0	288	30	19	24	24	1.98
415916--415991	33	2.3	33	81	0	89	32	0	40	26	1.56
415969--416014	18	2.6	18	89	0	74	19	0	52	28	1.47
416023--416144	33	3.7	33	74	4	102	29	7	42	20	1.79
416781--416820	11	3.6	11	96	0	71	7	35	17	40	1.78
423532--423563	4	8.0	4	92	0	55	46	25	3	25	1.67
427863--427906	24	1.9	23	82	17	56	43	0	0	56	0.99
433541--433930	196	2.0	196	89	2	595	30	13	21	35	1.91
440904--440952	19	2.7	17	79	14	53	65	2	18	14	1.37
441815--441887	3	25.0	3	75	5	69	34	5	1	58	1.29
443579--443637	20	2.9	19	74	18	57	40	10	10	38	1.73
443662--443705	22	1.9	24	90	9	74	40	11	2	45	1.53
446203--446287	31	2.9	29	80	7	91	52	8	3	35	1.48
449693--449743	16	3.1	17	80	11	52	70	1	0	27	0.98
449690--449731	13	3.1	14	78	21	54	71	0	0	28	0.86
455359--455435	38	2.0	38	100	0	154	31	7	15	45	1.75
472903--472932	14	2.1	14	100	0	60	13	33	33	20	1.91
486731--486767	2	19.0	2	94	5	67	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
487548--487620	13	6.1	12	72	15	62	46	1	0	52	1.09
487548--487611	11	5.6	11	70	7	56	46	1	0	51	1.10
491761--491836	37	2.1	36	97	2	143	46	14	15	23	1.83
492493--493110	290	2.1	288	79	6	628	38	12	15	32	1.85
495583--495626	21	2.2	20	87	4	61	34	36	4	25	1.76
496054--496123	21	3.4	21	78	4	79	24	8	24	42	1.82
496048--496132	41	2.1	41	86	4	118	25	10	24	38	1.88
497826--497887	29	2.1	30	82	17	76	37	20	9	32	1.86
500161--500204	6	7.2	6	79	5	52	61	0	0	38	0.96
507117--507147	2	15.5	2	93	0	53	51	0	0	48	1.00

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