genome.fa.s6.2.7.7.80.10.50.1000.9.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: Chr1
Parameters: 2 7 7 80 10 50 1000
Length:  35726063

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   

This is table  9  of  109  ( 13028 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)
2854142--2854242	27	3.7	26	81	9	114	65	2	11	19	1.38
2854537--2854575	16	2.5	16	87	4	53	64	0	12	23	1.28
2854647--2854753	28	3.8	28	79	7	119	49	0	18	31	1.48
2854699--2854742	5	8.2	5	80	14	52	54	0	20	25	1.45
2854699--2854891	23	8.7	22	72	21	86	58	0	16	24	1.42
2854764--2854807	18	2.6	17	89	7	63	65	2	11	20	1.35
2854782--2854842	24	2.6	24	82	10	74	62	0	13	24	1.31
2854765--2854833	19	3.5	19	81	16	70	62	1	11	24	1.37
2854829--2854891	5	11.6	5	86	9	81	58	0	22	19	1.39
2854829--2854888	28	2.2	28	90	3	95	56	0	23	20	1.42
2859819--2859843	2	12.5	2	100	0	50	48	0	0	52	1.00
2877838--2877881	23	1.9	23	86	9	63	61	0	2	36	1.09
2885981--2886008	2	14.0	2	100	0	56	50	0	0	50	1.00
2903301--2903394	47	2.0	47	93	0	161	38	9	7	44	1.65
2905479--2905516	19	2.0	19	100	0	76	42	15	15	26	1.87
2915198--2915321	55	2.3	55	91	1	196	33	33	9	22	1.87
2928321--2928366	8	5.4	9	87	7	53	58	26	0	15	1.37
2928321--2928368	17	2.8	18	78	9	55	58	27	0	14	1.37
2929940--2929969	15	2.0	15	100	0	60	26	20	13	40	1.89
2930896--2930947	21	2.5	21	80	0	59	34	32	7	25	1.84
2931286--2931314	15	1.9	15	100	0	58	51	6	6	34	1.55
2931930--2932425	174	2.8	179	89	3	725	31	13	20	35	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2932700--2932777	39	2.0	39	100	0	156	20	10	33	35	1.86
2936290--2936334	21	2.1	21	100	0	90	64	17	8	8	1.47
2939313--2939611	146	2.0	146	96	0	553	26	6	24	42	1.79
2945621--2945675	21	2.6	21	82	5	67	65	0	3	30	1.10
2945638--2945674	10	3.7	10	89	10	58	62	0	2	35	1.10
2945638--2945676	11	3.7	11	90	6	55	61	0	2	35	1.10
2945621--2945685	21	3.1	21	76	12	62	64	1	3	30	1.18
2949497--2949559	30	2.1	30	90	0	99	26	28	12	31	1.93
2951731--2951783	26	2.1	25	85	3	70	24	5	7	62	1.44
2954459--2954518	31	1.9	32	83	10	79	36	0	1	61	1.06
2960352--2960388	12	3.1	12	96	0	65	40	16	2	40	1.62
2961197--2961234	17	2.2	17	95	0	67	63	13	5	18	1.48
2967085--2967324	100	2.4	100	79	6	238	32	11	20	35	1.88
2972235--2972285	22	2.3	22	80	6	59	56	0	0	43	0.99
2973889--2973955	31	2.2	30	84	10	82	55	7	8	28	1.58
2984220--2984302	25	3.3	25	75	0	85	31	20	28	19	1.97
2984294--2984409	49	2.4	49	81	8	130	38	20	21	18	1.93
2984333--2984410	25	3.2	26	69	10	74	37	20	24	17	1.94
2984392--2984473	26	3.2	26	77	8	87	35	20	23	20	1.96
2984557--2984618	24	2.6	24	84	5	81	32	17	30	19	1.95
2985614--2985694	39	2.1	39	100	0	162	53	12	14	19	1.73
2994396--2994420	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3012088--3012144	28	2.0	28	100	0	114	40	14	3	42	1.62
3013438--3013470	16	1.9	18	88	11	52	33	15	18	33	1.92
3016798--3016839	21	2.1	21	86	8	61	38	4	4	52	1.44
3018372--3018427	26	2.2	26	90	0	85	17	23	19	39	1.92
3018380--3018436	26	2.2	26	84	3	71	21	21	21	36	1.95
3029772--3029817	3	15.3	3	100	0	92	32	0	0	67	0.91
3038894--3038940	17	2.7	18	76	3	51	17	4	23	55	1.59
3051421--3051450	15	2.0	15	93	0	51	70	0	0	30	0.88
3051484--3051520	15	2.4	16	95	4	67	67	2	0	29	1.04
3051466--3051548	9	9.7	9	70	18	61	67	2	2	27	1.16
3051464--3051548	42	2.0	40	86	6	116	65	2	2	29	1.17
3051464--3051563	42	2.4	41	78	9	94	69	3	3	25	1.17
3051644--3051725	18	4.4	18	73	13	69	35	3	1	59	1.23
3054140--3054211	35	2.0	36	83	2	92	29	5	8	56	1.51
3065667--3066014	112	3.1	111	78	8	332	24	22	23	29	1.99
3066351--3066399	18	2.5	21	80	9	59	61	10	2	26	1.39
3066657--3066687	15	2.0	16	93	6	55	16	0	45	38	1.47
3067597--3068195	231	2.6	230	92	1	968	28	18	20	33	1.96
3068530--3068566	19	1.9	19	88	0	56	29	40	2	27	1.70
3073343--3073504	9	18.8	9	68	13	99	42	20	3	33	1.70
3073400--3073476	33	2.3	34	93	4	138	38	20	5	35	1.75
3074005--3074134	66	2.0	66	89	3	199	41	17	25	15	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3074520--3074853	42	8.0	41	81	5	346	24	21	22	31	1.98
3074570--3074853	42	6.7	42	85	3	392	22	21	22	33	1.97
3074570--3074853	85	3.4	83	86	5	390	22	21	22	33	1.97
3078071--3078109	19	2.0	21	85	10	55	46	28	7	17	1.76
3078756--3078886	42	3.1	42	82	4	149	42	17	22	16	1.88
3078819--3078892	21	3.5	21	73	0	76	43	18	21	16	1.88
3078783--3078907	42	3.0	42	79	11	139	43	17	22	16	1.88
3083658--3083710	8	7.0	8	74	20	51	56	0	16	26	1.41
3087313--3087406	3	30.7	3	79	12	102	64	2	3	29	1.20
3088998--3089057	28	2.1	28	81	6	68	48	8	10	33	1.67
3092275--3092571	67	4.4	67	92	0	504	38	3	16	41	1.64
3092531--3092607	23	3.2	23	62	16	57	35	3	22	38	1.72
3092816--3092933	23	5.1	23	77	5	96	19	22	20	38	1.94
3092793--3092933	23	6.0	23	73	13	92	20	21	20	36	1.95
3092843--3092931	45	2.0	45	86	4	126	20	24	21	33	1.97
3097524--3097553	15	2.1	14	93	6	51	43	13	23	20	1.86
3098182--3098286	42	2.5	42	81	4	115	21	23	16	38	1.93
3098208--3098308	42	2.4	42	79	0	112	18	28	16	35	1.93
3098260--3098308	21	2.3	21	75	0	53	12	30	20	36	1.89
3112487--3112519	13	2.4	14	85	10	50	75	0	24	0	0.80
3113222--3113276	2	27.5	2	100	0	110	0	0	49	50	1.00
3114267--3114295	14	2.1	14	100	0	58	20	6	41	31	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3118917--3118946	2	15.0	2	100	0	60	0	50	0	50	1.00
3126621--3126824	100	2.0	100	100	0	408	40	21	17	20	1.92
3129813--3130340	176	2.9	176	87	7	661	36	21	14	26	1.93
3142859--3142897	9	4.3	9	86	0	60	48	12	7	30	1.69
3143603--3143676	34	2.2	34	100	0	148	29	22	12	35	1.91
3158551--3158719	82	2.1	82	97	2	322	51	8	13	27	1.68
3161765--3161955	89	2.1	89	96	3	357	24	26	30	18	1.98
3161956--3162012	25	2.3	25	75	9	71	38	1	0	59	1.08
3161973--3162016	19	2.3	19	80	7	54	34	2	0	63	1.07
3161974--3162016	20	2.2	19	87	4	59	32	2	0	65	1.06
3166492--3166526	15	2.4	15	90	4	54	34	8	0	57	1.29
3167192--3167397	107	1.9	107	89	0	322	28	18	20	31	1.97
3174544--3174575	12	2.6	13	85	14	50	56	6	0	37	1.25
3179128--3179255	42	2.9	43	79	12	145	32	25	17	24	1.97
3180342--3180368	13	2.1	13	100	0	54	48	22	0	29	1.51
3181239--3182218	489	2.0	487	97	0	1834	28	21	20	29	1.98
3182485--3182551	9	7.4	9	89	0	107	40	23	11	23	1.88
3182485--3182551	27	2.5	27	95	0	125	40	23	11	23	1.88
3182651--3182697	18	2.6	18	93	0	76	19	2	38	40	1.63
3184899--3184941	22	1.9	23	90	4	70	34	4	0	60	1.17
3185035--3185081	23	2.0	23	87	0	67	63	0	2	34	1.06
3186726--3186874	72	2.1	73	98	1	291	67	6	14	11	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3188498--3188535	14	2.8	13	88	11	58	31	0	0	68	0.90
3190582--3191061	239	2.0	239	92	1	793	31	19	23	25	1.98
3198497--3198536	3	13.3	3	100	0	80	67	0	32	0	0.91
3199023--3199140	44	2.6	45	77	9	134	33	16	22	27	1.95
3198884--3199147	139	1.9	139	82	3	334	32	17	23	27	1.96
3199109--3199277	44	3.8	44	78	7	139	33	16	20	29	1.94
3204697--3204753	25	2.3	25	79	8	64	36	22	24	15	1.94
3206389--3206588	107	1.9	107	91	0	328	24	26	17	32	1.97
3221899--3221950	24	2.1	25	82	3	61	40	19	23	17	1.91
3222691--3222739	18	2.8	17	82	11	55	38	16	4	40	1.67

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