genome.fa.s12.2.7.7.80.10.50.1000.34.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  34  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)
9172796--9172850	20	2.8	20	82	0	65	12	21	40	25	1.89
9172852--9172898	22	2.1	22	84	0	58	17	10	44	27	1.81
9173251--9173418	89	1.9	89	88	4	259	42	2	4	50	1.36
9173488--9173538	24	2.2	23	79	6	59	39	1	1	56	1.22
9183145--9183188	22	2.0	22	82	8	54	54	2	0	43	1.12
9184156--9184203	20	2.5	20	74	16	55	50	0	0	50	1.00
9192854--9192895	2	21.0	2	100	0	84	50	0	0	50	1.00
9203300--9203386	42	2.1	42	85	8	115	28	26	24	20	1.99
9206220--9206267	19	2.5	19	76	6	53	29	16	2	52	1.56
9216836--9216877	20	2.1	20	86	0	57	64	0	2	33	1.07
9217047--9217093	22	2.0	24	84	8	62	31	0	0	68	0.90
9217114--9217152	17	2.3	17	95	0	69	17	12	7	61	1.54
9217926--9218015	31	2.9	31	85	9	114	47	4	4	43	1.43
9221940--9221970	2	15.5	2	100	0	62	51	0	0	48	1.00
9226556--9226594	17	2.3	17	90	0	60	10	10	51	28	1.68
9227593--9227619	14	1.9	14	100	0	54	37	3	7	51	1.48
9235911--9235959	3	16.3	3	100	0	98	0	32	0	67	0.91
9243215--9243275	31	2.1	31	81	9	74	26	13	13	47	1.79
9246884--9246919	2	18.0	2	100	0	72	50	0	0	50	1.00
9249550--9249611	24	2.5	25	73	7	63	17	3	4	74	1.13
9249543--9249609	24	3.0	22	77	12	55	16	5	2	74	1.14
9249679--9249755	21	3.9	19	80	13	86	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9249816--9249861	22	2.0	23	87	4	67	43	0	2	54	1.12
9250020--9250071	19	2.7	19	76	11	61	65	0	3	30	1.10
9251712--9251758	22	2.3	20	82	13	60	65	0	2	31	1.04
9251714--9251760	21	2.2	22	88	3	69	70	0	2	27	0.99
9257356--9257384	14	2.1	14	93	6	51	68	0	0	31	0.89
9257356--9257415	30	1.9	30	86	6	84	65	1	0	33	1.03
9257312--9257424	32	3.5	32	77	10	97	57	0	1	39	1.15
9257369--9257402	17	1.9	18	94	5	61	64	0	0	35	0.94
9257380--9257424	22	2.0	23	83	12	58	64	2	0	33	1.06
9257486--9257567	21	3.8	22	85	9	116	59	0	0	40	0.97
9257487--9257566	22	3.8	21	82	12	92	58	0	0	41	0.98
9257594--9257641	24	2.0	24	88	8	71	72	6	2	18	1.15
9259662--9259697	18	1.9	19	88	5	56	19	11	19	50	1.77
9262307--9262339	10	3.2	11	87	12	52	78	0	0	21	0.75
9262861--9262951	17	5.4	17	67	23	50	37	2	0	60	1.09
9268580--9268606	13	2.1	13	100	0	54	55	0	0	44	0.99
9268609--9268633	6	4.2	6	100	0	50	80	0	0	20	0.72
9275434--9275540	41	2.6	41	86	5	153	30	24	20	24	1.98
9275479--9275629	41	3.6	41	77	8	144	33	25	15	24	1.95
9277000--9277077	24	3.2	23	80	10	84	32	23	28	16	1.96
9277007--9277054	25	2.0	24	91	4	78	35	18	27	18	1.95
9279991--9280109	59	2.0	59	100	0	238	53	18	10	17	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9282180--9282212	14	2.3	15	89	5	50	0	24	0	75	0.80
9285091--9285466	187	2.0	187	97	0	707	40	18	11	29	1.86
9285869--9285952	24	3.5	24	75	13	82	32	21	28	17	1.96
9286255--9286296	21	2.0	21	85	0	57	35	23	0	40	1.55
9294761--9294826	34	1.9	34	93	0	114	46	15	6	31	1.70
9301818--9302338	261	2.0	261	95	0	934	32	18	15	34	1.92
9304706--9304782	15	4.9	15	71	18	50	44	14	9	32	1.76
9304722--9304761	20	2.0	20	90	0	62	50	12	10	27	1.72
9304710--9304776	34	1.9	35	90	3	109	46	13	8	31	1.74
9305154--9305178	7	3.6	7	100	0	50	60	0	0	40	0.97
9311450--9311483	17	2.0	18	88	11	54	50	0	8	41	1.34
9311838--9311924	36	2.4	37	90	1	131	25	26	21	26	2.00
9311979--9312027	22	2.2	22	89	7	73	30	24	12	32	1.92
9321381--9321451	29	2.4	29	95	0	124	43	12	25	18	1.85
9321352--9321596	29	8.4	29	72	6	118	37	12	26	22	1.90
9321548--9321609	29	2.1	30	81	3	72	38	16	22	22	1.92
9323342--9323371	12	2.5	12	88	0	51	23	40	30	6	1.80
9324528--9324801	68	4.0	67	76	10	234	27	23	10	37	1.88
9324739--9324867	68	1.9	68	83	0	168	30	24	10	35	1.88
9333028--9333080	28	1.9	28	84	3	72	35	15	13	35	1.86
9336819--9336858	9	4.4	9	84	12	55	40	17	10	32	1.83
9336819--9336863	18	2.4	18	88	3	72	40	17	11	31	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9336979--9337022	18	2.4	18	88	0	61	13	2	43	40	1.57
9341474--9341579	54	2.0	54	94	0	185	25	31	23	19	1.98
9344720--9344768	23	2.1	23	85	7	64	44	2	8	44	1.45
9346166--9346199	16	2.2	15	89	5	50	50	5	5	38	1.51
9352259--9352313	23	2.4	23	81	0	74	54	9	1	34	1.43
9355350--9355399	25	2.0	25	84	11	66	36	22	0	42	1.54
9356292--9356336	23	2.0	22	91	4	72	66	2	0	31	1.04
9356278--9356331	12	4.4	12	83	9	65	61	1	0	37	1.07
9356294--9356336	10	4.0	10	80	16	50	67	2	0	30	1.03
9356275--9356373	8	10.9	9	74	13	62	55	2	0	42	1.11
9363263--9363290	2	14.0	2	100	0	56	50	0	0	50	1.00
9364101--9364174	36	2.1	36	89	0	112	52	0	4	43	1.20
9365633--9365671	6	6.5	6	100	0	78	15	0	15	69	1.20
9365714--9365757	18	2.4	18	88	0	61	13	2	43	40	1.57
9367761--9368071	33	8.8	33	69	22	177	21	20	26	31	1.98
9367794--9367930	42	3.5	41	77	17	173	21	18	27	32	1.97
9367756--9367932	75	2.4	75	95	1	311	22	19	26	32	1.97
9367907--9367959	27	1.9	28	96	3	99	16	24	32	26	1.97
9367833--9368034	102	2.0	102	95	1	361	20	20	28	30	1.98
9367728--9368067	177	1.9	178	93	0	592	21	20	27	31	1.98
9371095--9371322	123	1.9	123	83	7	302	42	14	13	28	1.84
9376500--9376557	7	7.7	7	79	12	62	67	1	3	27	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9376486--9376540	23	2.6	21	86	11	69	65	1	1	30	1.13
9380455--9380492	13	2.8	14	84	8	51	31	0	0	68	0.90
9388366--9388395	16	1.9	16	93	6	53	50	20	0	30	1.49
9389473--9389600	25	5.2	25	70	14	95	32	15	23	28	1.95
9389528--9389590	24	2.6	24	82	14	76	34	12	25	26	1.92
9389473--9389620	49	3.0	49	84	4	156	33	15	22	27	1.95
9389514--9389616	25	4.2	25	78	8	95	34	15	24	25	1.94
9391396--9391427	16	2.0	16	100	0	64	62	6	12	18	1.50
9394221--9394311	46	2.0	46	95	0	164	29	5	12	52	1.61
9399141--9399246	41	2.6	41	83	4	135	28	16	23	31	1.97
9399393--9399520	44	2.9	44	80	1	148	28	22	19	29	1.98
9412428--9412457	15	2.0	15	100	0	60	53	0	13	33	1.40
9413163--9413262	48	2.1	48	100	0	200	40	4	21	35	1.72
9432242--9432388	63	2.4	62	80	2	161	27	28	18	25	1.98
9433429--9433478	16	3.2	16	85	2	66	48	4	20	28	1.67
9439221--9439252	15	2.2	15	94	5	57	81	0	6	12	0.87
9441850--9441905	28	2.0	28	89	0	85	28	26	17	26	1.98
9441859--9441913	28	2.0	28	88	0	83	32	29	14	23	1.94
9447899--9447969	30	2.4	30	97	0	133	36	25	0	38	1.56
9449512--9449631	41	2.9	41	86	4	170	20	22	29	27	1.99
9450487--9450561	30	2.5	30	95	0	132	24	32	26	17	1.97
9456751--9456786	11	3.2	12	84	15	58	38	8	8	44	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9457592--9457721	30	4.3	30	81	5	156	25	26	23	23	2.00
9457573--9457721	60	2.5	60	91	0	235	26	28	22	22	1.99
9464186--9464220	15	2.3	15	90	0	52	31	11	0	57	1.34
9480831--9480864	10	3.4	10	87	0	50	14	0	2	82	0.79
9489937--9489970	2	16.5	2	93	6	59	50	2	0	47	1.16
9490677--9490708	16	1.9	17	93	6	57	37	21	0	40	1.54
9490869--9491039	43	4.0	43	80	10	174	33	27	16	22	1.96
9490869--9491023	84	1.8	84	84	5	215	31	28	17	22	1.96
9493994--9494018	13	1.9	13	100	0	50	40	8	0	52	1.31
9494366--9494402	19	1.9	19	88	0	56	64	2	2	29	1.21

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