genome.fa.s7.2.7.7.80.10.50.1000.9.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: Chr3
Parameters: 2 7 7 80 10 50 1000
Length:  26558743

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   

This is table  9  of  79  ( 9388 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)
3076063--3076461	160	2.5	160	90	5	619	25	7	10	57	1.58
3076063--3076461	81	5.0	80	90	5	594	25	7	10	57	1.58
3079247--3079613	46	7.9	46	73	5	272	40	18	14	26	1.89
3079358--3079610	23	11.0	22	71	14	172	39	19	15	26	1.91
3079173--3079613	93	4.7	94	89	2	600	39	17	14	28	1.89
3080141--3080266	28	4.5	28	89	2	164	30	26	11	30	1.92
3080587--3082864	190	12.0	190	99	0	4529	34	12	10	42	1.78
3083802--3083890	27	3.3	27	82	6	99	26	38	17	16	1.92
3083980--3084017	20	1.9	20	88	0	58	68	0	0	31	0.90
3084585--3084637	17	3.1	16	76	17	54	81	3	1	13	0.92
3090948--3090984	10	3.6	10	88	3	56	70	0	29	0	0.88
3096279--3096713	155	2.8	155	81	12	568	30	10	6	51	1.62
3096476--3096505	15	1.9	16	93	6	53	26	0	0	73	0.84
3097043--3097118	31	2.5	31	78	22	88	0	31	0	68	0.90
3097051--3097146	38	2.5	38	80	9	108	0	33	0	66	0.92
3097047--3097143	40	2.6	39	83	9	121	0	31	0	68	0.90
3097067--3097142	10	7.9	10	74	20	56	0	28	0	71	0.87
3097072--3097141	20	3.6	20	72	11	65	0	27	0	72	0.84
3101988--3102122	66	2.1	65	91	1	216	31	14	11	41	1.83
3106304--3106438	66	2.0	66	98	0	261	28	21	14	34	1.93
3107131--3107185	10	5.3	10	79	18	51	3	21	0	74	0.97
3107141--3107185	20	2.2	21	84	11	58	2	24	0	73	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3109075--3109139	29	2.2	31	83	10	82	47	4	3	44	1.39
3117298--3117327	5	6.0	5	96	0	51	63	0	0	36	0.95
3126988--3127140	46	3.6	44	74	21	155	35	14	22	28	1.93
3127024--3127096	36	2.0	36	94	0	128	38	15	19	27	1.91
3135130--3135195	13	5.1	13	80	7	80	39	22	6	31	1.79
3140450--3140531	25	3.3	25	81	3	76	35	20	23	20	1.96
3140486--3140538	25	2.1	25	85	0	70	35	20	28	15	1.93
3144547--3144612	26	2.5	26	78	7	71	34	22	25	16	1.95
3149650--3149693	4	11.0	4	100	0	88	25	0	25	50	1.50
3153889--3153984	48	2.0	49	81	6	115	46	17	4	31	1.67
3165754--3165812	31	1.9	31	89	0	91	40	6	6	45	1.57
3170482--3170553	21	3.3	21	69	7	63	50	5	4	40	1.45
3170466--3170556	44	2.1	44	89	2	139	45	6	4	43	1.50
3170649--3170678	3	10.0	3	100	0	60	33	0	0	66	0.92
3181000--3181039	9	4.4	9	87	0	62	42	20	10	27	1.83
3182164--3182214	25	2.0	25	96	0	93	39	19	19	21	1.93
3182798--3182827	15	2.0	15	93	0	51	33	16	3	46	1.64
3188887--3188912	13	2.0	13	100	0	52	84	0	0	15	0.62
3192557--3192658	46	2.2	47	98	1	197	29	16	17	36	1.92
3192851--3193008	74	2.1	74	92	1	264	53	10	12	23	1.68
3197024--3197069	3	15.3	3	100	0	92	34	0	32	32	1.58
3201198--3201244	21	2.2	21	88	7	69	23	2	42	31	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3205510--3205570	30	2.0	30	100	0	122	42	16	24	16	1.88
3206341--3206366	12	2.2	12	100	0	52	42	19	7	30	1.79
3208740--3208797	21	2.8	21	78	19	59	46	1	0	51	1.11
3215853--3215883	14	2.2	14	100	0	62	38	0	0	61	0.96
3219718--3219748	16	1.9	16	93	0	53	41	3	0	54	1.16
3222841--3222892	22	2.4	21	81	12	61	63	5	0	30	1.18
3223710--3223747	11	3.5	11	85	3	51	2	13	15	68	1.32
3223708--3223756	22	2.3	21	85	3	62	8	14	12	65	1.47
3223747--3223784	19	2.0	19	89	0	58	23	18	5	52	1.65
3235849--3235873	13	1.9	13	100	0	50	80	0	16	4	0.87
3238659--3238723	20	3.3	19	78	8	67	32	13	13	40	1.85
3238804--3238870	20	3.4	19	74	12	64	44	13	5	35	1.68
3238804--3238870	19	3.4	18	76	13	62	44	13	5	35	1.68
3238863--3238901	20	2.0	20	89	0	60	38	12	2	46	1.56
3239134--3239225	20	4.6	20	71	15	57	42	6	7	43	1.59
3239974--3240047	29	2.5	30	86	4	96	52	13	10	22	1.71
3255421--3255479	21	2.7	22	76	15	59	59	5	0	35	1.20
3261787--3261820	2	17.0	2	100	0	68	0	50	0	50	1.00
3263763--3263789	3	9.0	3	100	0	54	33	0	0	66	0.92
3270894--3270920	4	6.8	4	100	0	54	22	0	0	77	0.76
3271637--3271666	15	2.0	15	93	0	51	43	13	3	40	1.60
3275687--3275716	2	15.0	2	100	0	60	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)
3285006--3285038	16	2.1	16	100	0	66	60	12	27	0	1.32
3299495--3299527	17	2.0	16	94	5	57	48	0	0	51	1.00
3302028--3302074	2	23.5	2	100	0	94	51	0	0	48	1.00
3343472--3343549	35	2.2	34	80	11	86	35	1	0	62	1.03
3355962--3356202	124	1.9	124	97	1	457	38	8	10	41	1.71
3359231--3359274	16	2.7	16	78	3	52	40	0	0	59	0.98
3359242--3359328	39	2.2	40	84	10	126	36	4	0	58	1.19
3369850--3369874	12	2.1	12	100	0	50	8	0	40	52	1.31
3379161--3379198	20	1.9	20	100	0	76	34	0	0	65	0.93
3379405--3379440	15	2.4	15	95	0	63	16	22	5	55	1.62
3380584--3380621	14	2.7	14	91	0	58	18	63	5	13	1.48
3382264--3382305	20	2.2	20	95	4	77	35	0	0	64	0.94
3384995--3385054	22	3.1	21	64	35	53	36	3	15	45	1.62
3390814--3391121	170	1.8	170	96	0	571	37	13	21	27	1.90
3393455--3393504	22	2.1	22	85	10	64	56	4	2	38	1.30
3394227--3395865	853	1.9	851	98	0	3152	33	12	11	42	1.79
3395958--3396007	22	2.1	22	85	10	64	56	4	2	38	1.30
3407868--3407932	30	2.2	30	83	5	78	24	7	4	63	1.41
3407896--3407944	21	2.3	20	76	10	53	26	12	0	61	1.31
3408050--3408085	17	2.1	17	94	0	63	44	0	5	50	1.25
3408664--3408728	30	2.2	30	83	5	78	24	7	4	63	1.41
3408692--3408740	21	2.3	20	76	10	53	26	12	0	61	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3408859--3408910	12	4.7	12	79	13	58	44	3	0	51	1.19
3412931--3412971	6	6.8	6	100	0	82	68	14	0	17	1.22
3413872--3413932	7	9.0	7	80	12	74	70	0	14	14	1.17
3413873--3413932	20	3.0	20	80	4	77	70	0	15	15	1.18
3413872--3413932	13	4.5	14	87	8	74	70	0	14	14	1.17
3415339--3415437	44	2.2	44	79	10	105	34	22	25	18	1.96
3415423--3416055	141	4.5	141	86	3	864	33	19	19	27	1.96
3415830--3416250	44	9.4	43	69	13	149	29	20	22	27	1.98
3415927--3416431	217	2.3	217	85	5	664	29	20	24	25	1.99
3416278--3416385	44	2.5	44	75	3	110	32	22	22	23	1.98
3420276--3420340	30	2.2	30	83	5	78	24	7	4	63	1.41
3420304--3420352	21	2.3	20	76	10	53	26	10	0	63	1.26
3421561--3421600	16	2.5	16	91	0	62	47	2	7	42	1.45
3421582--3421664	33	2.5	33	84	4	103	42	6	8	43	1.59
3427223--3427278	22	2.5	23	82	2	69	51	1	1	44	1.22
3427254--3427293	16	2.5	16	91	0	62	47	2	7	42	1.45
3427366--3427393	9	3.1	9	100	0	56	32	0	10	57	1.33
3427282--3427623	68	5.1	68	98	0	661	39	4	9	46	1.55
3427434--3427461	9	3.1	9	100	0	56	32	0	10	57	1.33
3427502--3427529	9	3.1	9	100	0	56	32	0	10	57	1.33
3427570--3427597	9	3.1	9	100	0	56	32	0	10	57	1.33
3435293--3435349	25	2.2	26	84	3	71	43	3	1	50	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3435613--3435654	21	2.0	21	90	4	68	66	0	0	33	0.92
3436273--3436314	20	2.1	20	86	0	57	47	0	7	45	1.30
3438939--3439345	154	2.7	151	88	4	591	29	10	7	53	1.61
3439445--3439477	15	2.1	16	88	5	50	81	0	12	6	0.85
3439638--3439716	34	2.3	35	82	6	90	64	2	6	26	1.30
3439730--3440195	153	3.1	149	87	6	624	52	8	9	29	1.62
3443056--3443117	19	3.1	19	82	13	63	58	9	1	30	1.40
3444838--3444872	18	1.9	18	88	0	52	85	11	0	2	0.69
3445048--3445094	15	3.1	14	85	14	58	78	2	2	17	0.94
3445053--3445098	17	2.7	18	80	10	60	76	2	2	19	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