genome.fa.s1.2.7.7.80.10.50.1000.19.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  19  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)
2937118--2937550	129	3.3	129	85	4	525	29	23	11	35	1.90
2937402--2937521	51	2.3	52	82	1	161	30	21	10	36	1.88
2937502--2937556	28	2.0	28	92	0	92	25	30	14	29	1.95
2937632--2937830	79	2.5	79	77	6	215	29	22	13	34	1.92
2939476--2939540	22	2.9	22	74	2	67	16	18	29	35	1.93
2940084--2940130	15	3.0	15	72	22	51	25	14	19	40	1.90
2940417--2940462	21	2.1	22	84	8	58	34	6	8	50	1.59
2940746--2940837	39	2.3	39	81	10	107	35	21	4	38	1.74
2948860--2948885	13	2.0	13	100	0	52	30	15	15	38	1.88
2948840--2948903	32	2.0	33	93	3	112	28	12	15	43	1.83
2948840--2948903	19	3.6	19	72	25	68	28	12	15	43	1.83
2951734--2951775	13	3.2	13	82	0	57	40	11	11	35	1.79
2951802--2951836	17	2.1	17	94	0	61	48	5	20	25	1.71
2951874--2951907	10	3.4	10	87	0	50	38	5	29	26	1.80
2951935--2951959	13	1.9	13	100	0	50	36	16	16	32	1.90
2954123--2954160	16	2.4	16	86	4	51	71	5	2	21	1.19
2955228--2955257	3	10.0	3	100	0	60	33	0	0	66	0.92
2956138--2956177	18	2.2	18	86	0	53	30	2	0	67	1.04
2957435--2957489	22	2.6	22	80	5	60	54	0	1	43	1.10
2957477--2957553	11	7.1	11	71	16	54	55	1	0	42	1.07
2957498--2957553	21	2.7	20	77	20	60	55	1	0	42	1.10
2957897--2957925	2	14.5	2	100	0	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2958223--2958256	16	2.1	17	94	5	61	38	0	0	61	0.96
2958492--2958529	20	2.0	20	90	10	62	52	2	0	44	1.14
2958852--2958885	9	3.4	10	88	11	52	52	0	0	47	1.00
2958917--2958957	21	1.9	22	95	5	75	43	0	0	56	0.99
2958911--2958988	22	3.4	23	73	8	70	50	0	0	50	1.00
2959003--2959109	42	2.6	39	78	16	110	54	0	0	45	0.99
2959086--2959186	5	19.8	5	79	11	107	55	2	0	41	1.15
2959733--2959770	2	19.0	2	94	0	67	47	0	52	0	1.00
2960274--2960315	12	3.5	12	90	0	66	42	9	35	11	1.74
2966017--2966051	17	1.9	18	88	11	54	57	5	20	17	1.60
2967897--2967937	20	2.0	20	86	9	57	36	0	0	63	0.95
2967977--2968027	2	25.5	2	100	0	102	49	0	50	0	1.00
2969659--2969700	18	2.3	18	87	0	57	42	7	2	47	1.43
2976375--2976415	21	2.0	20	85	4	55	24	0	4	70	1.06
2978914--2979005	47	2.0	46	91	2	148	38	16	26	19	1.92
2978794--2979245	242	1.9	242	88	0	688	36	13	21	29	1.91
2979156--2979537	46	8.4	46	75	6	271	42	18	20	18	1.89
2979157--2979537	135	2.8	136	77	8	371	42	18	20	18	1.89
2979158--2979514	89	3.9	90	81	4	342	42	17	20	19	1.89
2982665--2982705	16	2.6	16	78	17	50	4	9	2	82	0.89
2987314--2987364	20	2.5	20	87	3	66	35	19	9	35	1.85
2991201--2991412	97	2.2	97	84	4	268	36	12	23	27	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2994002--2994056	20	2.7	21	80	5	67	32	18	10	38	1.85
2994022--2994075	20	2.7	20	88	2	81	37	16	7	38	1.77
2995554--2996024	165	2.8	165	81	7	433	27	11	9	52	1.67
2996871--2996909	22	1.9	20	85	15	53	41	10	5	43	1.61
2996984--2997022	20	1.9	21	89	5	62	38	17	17	25	1.92
2997031--2997055	13	1.9	13	100	0	50	32	20	16	32	1.94
2997012--2997075	32	2.0	33	84	3	85	32	17	12	37	1.87
3002642--3002678	13	2.8	13	91	0	56	32	16	16	35	1.91
3004178--3004220	8	5.1	8	81	10	50	79	0	0	20	0.74
3004172--3004238	3	25.0	3	75	17	51	73	0	1	25	0.92
3004172--3004226	17	3.3	17	85	9	78	76	0	0	23	0.79
3004190--3004238	14	3.4	14	86	13	57	69	0	2	28	1.00
3004172--3004228	15	3.7	15	84	9	78	77	0	0	22	0.77
3004738--3004829	29	3.2	29	87	0	130	52	20	17	9	1.73
3008036--3008164	52	2.5	52	92	0	213	31	17	16	35	1.92
3008036--3008184	52	2.9	51	86	4	201	32	16	16	34	1.92
3008173--3008197	13	1.9	13	100	0	50	36	16	16	32	1.90
3012363--3012415	19	2.7	20	88	2	72	26	16	16	39	1.91
3016525--3016565	20	2.0	22	90	9	68	34	9	14	41	1.79
3021254--3021284	15	2.1	15	93	0	53	12	22	16	48	1.80
3024433--3024491	32	1.9	30	83	13	75	59	10	10	20	1.58
3024772--3024797	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3024751--3024815	32	2.0	34	90	6	107	30	12	13	43	1.81
3024866--3024922	20	2.8	20	86	7	80	26	15	15	42	1.87
3026162--3026236	20	3.8	20	78	0	87	34	13	12	40	1.81
3026162--3026239	40	2.0	39	87	2	111	34	12	12	39	1.82
3027151--3027205	22	2.5	22	100	0	110	18	10	9	61	1.54
3027151--3027212	22	2.9	21	90	4	63	20	11	9	58	1.61
3040271--3040323	11	4.6	11	84	9	70	86	9	3	0	0.68
3040272--3040315	12	3.6	12	88	11	63	90	6	2	0	0.51
3040271--3040323	23	2.3	22	75	18	54	86	9	3	0	0.68
3040272--3040328	10	5.9	10	79	6	55	85	7	5	1	0.78
3040272--3040315	1	44.0	1	81	0	52	90	6	2	0	0.51
3041542--3042457	28	31.9	29	89	3	1292	28	31	17	21	1.96
3041541--3042469	114	8.1	114	89	3	1339	28	32	17	22	1.96
3042983--3043057	20	3.8	20	78	0	87	34	13	12	40	1.81
3042983--3043060	40	2.0	39	87	2	111	34	12	12	39	1.82
3050762--3050823	32	1.9	32	86	3	88	29	16	14	40	1.88
3050788--3050845	19	2.9	19	84	5	71	34	15	15	34	1.89
3050875--3050927	20	2.7	19	88	11	72	37	13	18	30	1.89
3053102--3053183	34	2.5	34	88	4	114	54	1	20	23	1.51
3054124--3054175	20	2.6	20	90	0	86	40	11	15	32	1.83
3060464--3060742	79	3.6	77	77	9	269	32	14	25	28	1.94
3063236--3063335	42	2.4	42	78	8	107	40	11	30	19	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3063473--3063631	61	2.6	61	89	4	232	28	22	23	25	1.99
3063473--3063718	61	4.3	54	73	8	161	26	20	26	26	1.99
3063741--3064246	60	8.4	61	84	5	620	27	20	27	24	1.99
3063741--3064248	122	4.2	123	85	5	614	27	20	27	24	1.99
3063741--3064246	182	2.8	182	85	5	643	27	20	27	24	1.99
3064264--3064585	63	5.3	60	81	8	320	26	20	27	26	1.99
3064044--3064464	219	1.9	213	83	8	537	25	19	28	25	1.99
3064264--3064555	55	5.0	56	77	12	252	25	20	28	26	1.99
3064264--3064551	60	4.9	58	78	13	277	24	20	28	26	1.99
3070949--3071062	51	2.2	51	85	0	147	31	10	26	31	1.90
3070707--3071013	79	3.9	79	75	7	266	31	12	26	29	1.93
3074574--3074636	20	3.2	19	84	8	81	41	12	15	30	1.85
3074678--3074704	14	1.9	14	100	0	54	40	14	14	29	1.86
3082572--3082679	53	2.1	52	89	1	162	47	10	22	20	1.80
3083356--3083546	78	2.4	78	80	5	188	33	24	14	27	1.94
3084135--3084238	53	2.0	53	86	0	145	22	32	14	30	1.93
3084191--3084346	42	3.7	42	76	5	154	17	28	19	34	1.95
3084468--3084637	85	2.0	84	82	3	207	20	30	18	30	1.96
3085012--3085036	13	1.9	13	100	0	50	36	16	16	32	1.90
3084990--3085055	32	2.0	33	85	2	89	34	16	12	36	1.86
3085025--3085075	19	2.6	19	84	3	66	35	19	9	35	1.85
3085107--3085171	33	2.0	33	84	6	87	36	13	15	33	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3095696--3095732	15	2.4	16	86	9	58	43	18	21	16	1.88
3097805--3097840	13	2.8	13	91	0	54	36	19	11	33	1.87
3100413--3100492	34	2.4	34	100	0	160	42	20	12	25	1.86
3102770--3102817	23	2.0	25	88	8	73	31	4	18	45	1.68
3103394--3103420	13	2.1	13	100	0	54	29	14	14	40	1.86
3103402--3103458	19	2.9	19	76	2	69	36	17	10	35	1.84
3103490--3103552	33	1.9	33	87	6	92	34	11	17	36	1.85
3105977--3106020	17	2.4	18	81	7	54	20	11	4	63	1.44
3105951--3106314	164	2.2	166	85	5	479	28	9	9	53	1.64
3107757--3107999	126	1.9	128	80	2	283	34	10	11	42	1.76

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