genome.fa.s12.2.7.7.80.10.50.1000.11.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  11  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)
3235227--3235271	18	2.5	18	88	0	72	15	48	6	28	1.70
3235908--3236030	63	2.0	63	87	3	178	49	9	4	36	1.55
3236080--3236123	3	14.7	3	100	0	88	65	0	0	34	0.93
3236200--3236224	9	2.8	9	100	0	50	68	20	0	12	1.21
3236249--3236288	11	3.7	11	86	6	64	0	30	0	70	0.88
3236251--3236289	21	1.9	20	94	5	69	0	30	0	69	0.89
3236426--3236463	10	3.8	10	89	0	58	10	18	18	52	1.73
3236426--3236463	20	1.9	20	94	0	67	10	18	18	52	1.73
3236474--3236543	30	2.5	27	86	13	106	47	0	7	45	1.30
3236474--3236543	27	2.5	29	84	15	94	47	0	7	45	1.30
3237001--3237066	30	2.2	32	82	15	88	27	27	4	40	1.75
3244116--3244154	20	2.0	20	94	0	69	71	5	0	23	1.05
3245640--3245679	21	2.0	21	85	9	57	37	0	12	50	1.41
3253612--3253672	2	30.5	2	83	0	68	44	4	1	49	1.33
3253782--3253814	2	16.5	2	100	0	66	48	0	0	51	1.00
3256434--3256699	86	3.1	86	92	1	462	32	17	21	28	1.96
3256696--3256772	37	2.1	37	92	0	127	42	15	12	28	1.84
3257438--3257490	27	2.0	28	85	7	74	50	5	5	37	1.50
3263045--3263106	20	3.1	20	85	0	79	37	8	9	45	1.67
3263057--3263113	20	2.8	20	86	0	60	35	12	8	43	1.73
3266737--3266768	15	2.3	15	89	10	50	53	0	6	40	1.26
3266811--3266844	14	2.4	14	90	5	50	44	2	11	41	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3267049--3267088	20	2.0	20	100	0	80	35	30	10	25	1.88
3267188--3267221	2	17.0	2	100	0	68	50	0	0	50	1.00
3268674--3268717	14	3.3	12	80	20	52	79	2	6	11	1.01
3270220--3270256	3	12.3	3	88	0	56	72	0	27	0	0.84
3287982--3288048	25	2.7	23	80	13	64	23	23	22	29	1.99
3291646--3291699	19	2.8	20	77	11	58	25	5	12	55	1.59
3294793--3294817	4	6.2	4	100	0	50	0	28	0	72	0.86
3303981--3304080	42	2.4	42	88	3	148	38	12	29	21	1.89
3304850--3304874	2	12.5	2	100	0	50	52	0	0	48	1.00
3307016--3307077	31	2.0	30	84	3	79	40	3	9	46	1.53
3308206--3308266	25	2.5	24	75	15	63	29	3	4	62	1.32
3310551--3310586	3	12.0	3	100	0	72	0	33	0	66	0.92
3323033--3323109	17	4.5	17	69	15	59	36	9	15	38	1.79
3323033--3323123	35	2.6	34	77	3	92	36	9	14	39	1.79
3325337--3325387	26	2.0	26	84	7	68	29	5	0	64	1.17
3328105--3328197	48	1.9	48	82	0	114	21	20	3	54	1.58
3328348--3328408	28	2.1	31	85	14	85	27	14	6	50	1.68
3337287--3337327	9	4.6	9	81	0	55	53	2	0	43	1.13
3342541--3342574	15	2.3	15	89	0	50	55	14	0	29	1.40
3348279--3348312	13	2.5	13	85	4	50	88	0	5	5	0.64
3349707--3349743	19	1.9	19	89	10	58	62	5	2	29	1.31
3353410--3353445	2	18.0	2	100	0	72	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3353734--3353789	27	2.1	27	100	0	112	30	16	17	35	1.92
3355505--3355551	23	2.0	23	100	0	94	44	8	17	29	1.78
3357808--3357966	25	6.4	25	77	2	113	26	27	15	30	1.96
3357911--3357984	25	3.0	24	76	9	78	24	29	16	29	1.96
3365278--3365359	42	2.0	42	100	0	164	32	26	24	15	1.95
3365276--3365382	21	5.0	22	80	6	121	34	25	23	16	1.95
3366571--3366602	16	2.1	16	94	5	57	40	0	0	59	0.97
3371073--3371108	17	2.1	17	90	10	56	50	0	2	47	1.15
3389232--3389279	2	24.0	2	100	0	96	50	0	0	50	1.00
3389414--3389440	1	27.0	1	100	0	54	0	0	0	100	0.00
3398749--3398944	97	2.0	97	96	0	365	32	11	15	40	1.83
3399324--3399367	23	1.9	23	85	0	61	50	0	0	50	1.00
3401544--3401715	74	2.4	72	88	2	245	29	24	24	22	1.99
3401617--3401920	114	2.7	114	91	3	470	25	21	26	26	2.00
3402242--3402273	14	2.3	14	100	0	64	28	0	34	37	1.57
3402291--3402339	7	6.4	7	78	17	53	18	2	46	32	1.60
3402291--3402339	15	3.2	15	85	8	55	18	2	46	32	1.60
3402288--3402338	23	2.2	24	92	3	86	15	1	49	33	1.56
3402566--3402606	21	1.9	22	85	5	57	21	0	36	41	1.54
3402589--3402637	14	3.5	13	86	13	62	22	0	44	32	1.53
3402625--3402655	15	2.1	15	93	0	53	32	0	29	38	1.57
3402120--3402751	303	2.1	299	89	5	959	29	1	27	41	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3402764--3402961	106	1.9	106	89	2	308	50	11	10	28	1.70
3402858--3403146	154	1.9	148	87	6	422	45	13	14	27	1.81
3403014--3403223	104	2.0	104	89	3	321	48	11	12	28	1.75
3403272--3403381	58	1.9	59	92	3	188	58	10	3	27	1.49
3404577--3404641	30	2.1	31	83	8	80	32	4	12	50	1.60
3404778--3404838	31	2.0	31	83	6	79	42	6	9	40	1.64
3418278--3418335	23	2.6	23	83	8	66	62	3	18	15	1.47
3423632--3423675	20	2.2	21	84	12	65	61	4	0	34	1.16
3423633--3423703	19	3.7	19	83	9	83	57	4	1	36	1.27
3423754--3423783	9	3.4	9	90	9	53	53	0	10	36	1.35
3427199--3427266	20	3.5	19	82	8	75	54	4	2	38	1.36
3427199--3427276	19	4.1	19	79	9	79	55	5	2	37	1.36
3430691--3430771	40	2.0	40	100	0	162	39	2	22	35	1.67
3430688--3430782	40	2.4	40	91	5	140	44	3	21	31	1.68
3444415--3444505	6	16.0	6	82	11	102	29	0	0	70	0.88
3444427--3444505	21	3.5	22	84	6	97	29	0	0	70	0.87
3450002--3450094	46	2.0	46	100	0	186	31	15	19	34	1.92
3453891--3454290	47	8.6	47	94	1	635	38	14	19	28	1.90
3453891--3454290	93	4.3	94	93	1	635	38	14	19	28	1.90
3455131--3455246	43	2.7	43	80	12	148	28	29	20	21	1.98
3455475--3455507	17	2.1	16	88	11	50	24	0	18	57	1.40
3460279--3460311	17	2.1	16	88	11	50	24	0	18	57	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3467655--3467732	6	12.5	6	72	20	54	5	15	1	78	0.99
3480675--3480727	17	3.2	17	86	5	72	50	3	1	43	1.30
3480686--3480726	16	2.5	16	84	4	55	51	4	2	41	1.36
3480773--3480798	3	8.7	3	100	0	52	69	0	30	0	0.89
3483276--3483313	18	2.2	17	90	4	58	34	0	0	65	0.93
3483568--3483605	9	4.3	9	80	6	51	26	0	2	71	1.00
3485829--3485858	11	2.7	11	89	0	51	26	0	0	73	0.84
3485897--3485984	30	2.8	32	75	14	87	52	12	11	23	1.71
3487185--3487248	23	2.8	22	80	4	74	17	15	26	40	1.89
3489664--3489841	89	2.0	89	100	0	356	39	26	4	29	1.76
3495377--3495514	74	1.9	74	84	6	190	31	10	21	35	1.88
3495633--3495675	7	5.7	7	86	10	50	41	0	0	58	0.98
3495633--3495673	8	5.1	8	88	8	57	39	0	0	60	0.96
3495639--3495673	17	2.1	17	94	0	61	37	0	0	62	0.95
3498238--3498379	62	2.2	65	85	6	184	33	9	15	41	1.79
3498527--3498640	41	2.8	40	92	5	183	26	20	21	31	1.98
3503690--3503716	2	13.5	2	100	0	54	51	0	0	48	1.00
3504051--3504170	41	2.9	41	92	0	186	31	22	19	26	1.97
3520542--3520584	3	14.3	3	100	0	86	67	0	0	32	0.91
3521307--3521333	13	2.1	13	100	0	54	77	7	0	14	0.97
3522084--3522551	132	3.5	132	89	1	697	27	22	18	32	1.97
3522652--3523215	100	5.7	100	94	0	925	20	21	26	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3522656--3523200	50	10.9	50	64	11	231	19	21	26	32	1.97
3523143--3523692	95	5.8	95	88	0	744	26	21	20	31	1.98
3525830--3525868	12	3.2	12	89	7	53	2	15	0	82	0.79
3525907--3525941	7	4.7	7	86	13	52	0	17	0	82	0.66
3528545--3528743	108	1.9	106	88	5	303	35	19	16	29	1.93
3529540--3529582	3	14.3	3	100	0	86	67	0	0	32	0.91
3530248--3530274	13	2.1	13	100	0	54	77	7	0	14	0.97
3540726--3540758	13	2.5	13	95	0	57	57	6	9	27	1.53
3548206--3548262	27	2.2	26	81	9	62	26	8	1	63	1.34
3548376--3548420	22	2.0	24	86	8	67	55	4	0	40	1.20

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