genome.fa.s1.2.7.7.80.10.50.1000.20.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  20  of  52  ( 6211 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)
3109887--3110356	30	15.8	30	75	3	281	32	12	30	25	1.92
3109888--3110241	59	6.0	60	76	6	229	33	13	26	25	1.93
3110068--3110241	89	2.0	89	79	6	192	33	14	25	25	1.95
3110175--3110296	61	2.0	61	87	4	176	30	15	31	22	1.95
3110264--3110356	29	3.1	29	83	9	116	22	9	45	22	1.81
3111113--3111138	13	2.0	13	100	0	52	30	15	15	38	1.88
3111093--3111156	33	2.0	32	90	3	101	26	14	20	39	1.90
3111238--3111262	13	1.9	13	100	0	50	36	16	16	32	1.90
3120295--3120364	28	2.5	28	90	0	104	35	14	27	22	1.93
3120291--3120389	28	3.8	25	78	15	94	34	14	27	24	1.94
3120291--3120444	80	1.9	80	81	5	186	33	12	27	25	1.93
3120324--3120592	29	9.5	28	74	11	142	31	11	30	27	1.92
3120511--3120591	30	2.6	31	88	3	119	32	8	32	27	1.87
3124703--3124807	30	3.2	32	81	9	115	25	27	13	33	1.93
3124703--3124773	33	2.2	32	87	7	101	26	25	15	32	1.95
3124760--3124838	34	2.4	34	85	8	101	22	29	8	39	1.84
3124826--3124965	27	5.0	27	80	10	147	25	28	10	36	1.88
3124817--3124944	59	2.2	59	88	4	186	23	28	8	39	1.84
3124766--3124989	86	2.5	86	82	6	252	24	29	9	37	1.86
3124766--3125010	32	8.1	31	79	11	156	23	28	9	38	1.87
3125008--3125466	129	3.6	128	80	7	482	29	32	16	21	1.95
3125009--3125466	32	14.2	32	78	6	401	29	32	16	21	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3125009--3125450	193	2.3	192	82	6	525	30	31	16	20	1.95
3125518--3126428	52	16.9	52	73	9	594	25	23	14	36	1.93
3125664--3126428	164	4.7	164	84	1	951	25	23	14	36	1.92
3125567--3126268	216	3.3	214	74	10	563	25	22	14	37	1.93
3125825--3126489	112	6.1	111	73	10	435	25	23	13	37	1.92
3125664--3126409	328	2.3	328	87	1	1048	25	23	14	36	1.93
3126230--3126435	113	1.8	113	80	0	250	26	24	12	36	1.91
3127130--3127199	21	3.4	20	82	7	70	42	10	14	32	1.78
3132926--3132984	20	3.0	19	80	7	73	35	10	22	32	1.87
3134365--3134428	27	2.4	27	94	0	110	20	20	35	23	1.96
3143076--3143123	21	2.3	20	79	10	53	39	20	0	39	1.53
3145603--3145655	13	4.5	13	73	22	55	33	13	15	37	1.86
3145589--3145653	33	2.0	33	87	6	96	33	13	16	35	1.89
3145684--3145732	20	2.5	20	96	0	89	46	10	12	30	1.74
3146411--3146596	95	2.0	94	86	1	264	37	10	22	29	1.88
3149207--3149259	20	2.6	21	90	3	81	26	16	15	41	1.88
3151198--3151241	12	3.7	12	84	9	63	15	2	2	79	0.93
3151196--3151236	19	2.2	18	86	4	55	14	2	0	82	0.76
3151198--3151249	23	2.3	21	78	18	59	17	1	3	76	1.02
3155316--3156071	166	4.5	167	80	8	683	32	11	7	48	1.67
3155465--3156071	333	1.8	333	82	7	784	32	11	7	48	1.67
3156374--3156412	20	2.0	20	89	0	60	76	0	23	0	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3157112--3157136	13	1.9	13	100	0	50	32	20	16	32	1.94
3159492--3159563	28	2.6	27	80	8	83	23	26	18	31	1.97
3161894--3161919	13	2.0	13	100	0	52	38	15	15	30	1.88
3165981--3166011	15	2.1	15	93	0	53	48	16	22	12	1.80
3168026--3168103	20	3.6	21	73	15	70	25	12	16	44	1.83
3168090--3168128	13	3.0	13	96	0	69	30	17	15	35	1.91
3168249--3168295	21	2.3	21	79	20	55	34	23	4	38	1.74
3168251--3168293	20	2.2	19	84	16	52	32	23	4	39	1.75
3169922--3169985	32	2.0	32	96	0	119	26	3	23	46	1.67
3170694--3170719	13	2.0	13	100	0	52	38	15	15	30	1.88
3177146--3177171	13	2.0	13	100	0	52	30	15	15	38	1.88
3179236--3179278	20	2.1	20	82	4	50	9	27	44	18	1.80
3181825--3181855	15	2.1	15	93	0	53	12	22	16	48	1.80
3185919--3185944	13	2.0	13	100	0	52	30	15	15	38	1.88
3191658--3191692	12	2.8	12	86	4	52	88	8	2	0	0.61
3192709--3192946	94	2.5	94	87	1	325	26	28	17	27	1.97
3192898--3193446	62	9.0	62	87	4	764	25	26	18	29	1.98
3192898--3193495	123	4.9	123	88	3	779	25	27	19	27	1.99
3192898--3193495	185	3.3	184	87	3	811	25	27	19	27	1.99
3195304--3195329	13	2.0	13	100	0	52	38	15	15	30	1.88
3195282--3195349	33	2.1	33	88	2	102	33	11	19	35	1.88
3195371--3195423	20	2.5	22	82	11	67	30	15	15	39	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3195410--3195435	13	2.0	13	100	0	52	38	15	15	30	1.88
3197188--3197259	28	2.6	28	76	10	76	27	22	16	33	1.95
3198987--3199020	5	6.4	5	90	10	50	79	0	0	20	0.73
3198987--3199028	22	1.9	22	85	9	59	78	2	0	19	0.86
3198987--3199020	16	2.1	16	89	10	52	79	0	0	20	0.73
3205759--3206257	256	1.9	259	81	6	598	40	13	11	34	1.81
3208135--3208160	13	2.0	13	100	0	52	30	15	15	38	1.88
3210295--3210320	13	2.0	13	100	0	52	38	15	15	30	1.88
3214227--3214271	21	2.1	21	84	8	56	22	20	4	53	1.63
3216489--3216514	13	2.0	13	100	0	52	30	15	15	38	1.88
3217659--3218205	87	6.3	87	76	9	404	35	11	23	28	1.90
3221251--3221308	16	3.5	16	92	4	89	29	12	32	25	1.92
3221515--3221614	20	5.7	20	69	29	93	40	12	11	37	1.78
3221534--3221594	13	5.2	13	70	22	62	36	13	13	37	1.83
3221515--3221629	33	3.5	33	98	0	221	40	12	11	36	1.78
3221721--3221849	52	2.5	52	92	0	222	35	17	17	30	1.92
3226424--3226448	11	2.3	11	100	0	50	60	16	8	16	1.58
3228280--3228329	19	2.6	19	93	0	82	36	18	14	32	1.90
3228318--3228342	13	1.9	13	100	0	50	32	16	16	36	1.90
3230383--3230818	164	2.7	165	85	2	583	40	13	10	34	1.79
3232332--3232711	165	2.3	164	79	8	355	52	7	10	28	1.63
3233612--3233941	42	7.9	41	73	7	204	38	13	26	21	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3233612--3234234	84	7.4	84	72	9	345	38	14	26	20	1.91
3233589--3233877	126	2.3	126	79	5	282	37	15	26	19	1.92
3233912--3234046	42	3.2	42	71	13	114	41	17	22	18	1.90
3234087--3234189	43	2.4	42	87	3	143	41	15	24	18	1.89
3234118--3234231	42	2.7	42	83	6	124	40	14	27	17	1.89
3234545--3234614	20	3.6	19	77	9	70	38	17	14	30	1.89
3234585--3234721	53	2.6	53	94	0	238	35	17	16	29	1.92
3234744--3234805	10	6.1	10	76	10	54	29	24	4	41	1.75
3234862--3234886	13	1.9	13	100	0	50	32	16	20	32	1.94
3235274--3235340	37	1.9	35	88	11	102	32	11	25	29	1.92
3235634--3235731	42	2.3	42	80	3	108	40	20	25	13	1.88
3236961--3237076	53	2.2	53	90	3	180	18	13	18	49	1.80
3239078--3239102	13	1.9	13	100	0	50	36	16	16	32	1.90
3239058--3239123	32	2.0	33	94	2	116	34	12	16	36	1.86
3239089--3239209	52	2.3	52	98	0	233	38	14	13	33	1.85
3239216--3239240	13	1.9	13	100	0	50	32	16	16	36	1.90
3239249--3239379	52	2.5	52	96	0	235	34	18	16	30	1.93
3253052--3253116	23	2.7	23	86	9	78	83	9	4	3	0.90
3254562--3254624	30	2.1	31	82	11	78	28	30	11	30	1.91
3254600--3254778	34	5.5	34	77	10	203	18	35	13	31	1.90
3254599--3254780	67	2.9	61	84	8	256	18	36	13	31	1.89
3254599--3254864	128	2.1	131	83	7	339	20	34	13	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3254810--3254877	36	2.0	35	88	8	104	27	23	17	30	1.97
3254851--3254982	32	4.2	31	86	4	183	30	34	18	16	1.93
3254849--3254982	64	2.1	63	89	5	207	29	35	17	17	1.93
3254985--3255391	43	8.9	43	80	10	418	26	24	17	31	1.97
3254985--3255435	92	4.9	92	92	1	724	26	24	17	31	1.97
3255345--3255498	55	2.9	53	79	6	177	24	22	16	36	1.94
3255345--3255482	52	2.6	52	81	3	143	24	23	16	35	1.95
3255540--3255682	52	2.7	53	80	9	139	24	23	13	37	1.92
3255590--3255709	55	2.2	52	79	7	125	24	24	16	35	1.95
3256390--3256414	13	1.9	13	100	0	50	36	16	16	32	1.90

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