genome.fa.s4.2.7.7.80.10.50.1000.11.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  11  of  31  ( 3628 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)
2621653--2621715	17	3.8	17	68	18	51	42	0	3	53	1.16
2621637--2621717	32	2.5	33	85	6	110	46	0	2	50	1.14
2628367--2628422	9	5.7	9	78	21	51	30	0	0	69	0.89
2628420--2628487	32	2.2	32	84	10	88	54	0	0	45	0.99
2630286--2630357	31	2.4	31	84	11	96	63	1	0	34	1.03
2633331--2633374	22	2.0	22	91	8	72	47	0	0	52	1.00
2634330--2634374	21	2.0	23	84	16	60	51	6	20	22	1.70
2638811--2638860	13	3.8	14	75	19	54	38	0	0	62	0.96
2638820--2638882	24	2.5	25	80	10	67	41	0	0	58	0.98
2639823--2639885	25	2.4	25	79	12	65	60	1	1	36	1.16
2639843--2639900	28	2.1	27	81	9	64	58	1	1	37	1.18
2639874--2639941	31	2.2	30	85	12	86	52	0	0	47	1.00
2639874--2639921	17	2.9	17	77	17	57	52	0	0	47	1.00
2641946--2641986	17	2.4	18	88	8	59	41	0	0	58	0.98
2643146--2643180	4	8.2	4	87	12	52	74	2	0	22	0.95
2643135--2643186	18	2.8	18	77	13	61	73	3	0	23	1.00
2643130--2643186	22	2.4	26	83	16	70	71	3	0	24	1.01
2648556--2648608	15	3.8	15	76	23	62	39	0	0	60	0.97
2648558--2648620	26	2.4	26	92	5	101	34	0	0	65	0.93
2650520--2650564	19	2.4	19	81	11	65	46	0	0	53	1.00
2650771--2650814	3	14.3	3	95	4	79	65	0	0	34	0.93
2654792--2654826	3	11.7	3	100	0	70	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2655367--2655429	24	2.7	24	72	20	62	63	1	3	31	1.19
2655842--2655892	23	2.3	21	80	6	57	68	5	5	19	1.31
2656073--2656127	21	2.6	21	81	13	60	61	0	0	38	0.96
2656086--2656127	22	2.0	22	90	4	68	59	0	0	40	0.97
2656070--2656127	22	2.5	23	81	16	66	63	0	0	36	0.94
2659617--2659659	15	2.8	16	92	7	79	18	37	4	39	1.72
2662450--2662495	25	1.9	23	82	8	56	54	0	2	43	1.12
2662488--2662546	6	9.3	6	75	17	57	62	0	0	37	0.95
2662480--2662549	14	4.7	14	69	23	54	61	0	0	38	0.96
2662464--2662537	33	2.2	35	88	9	109	59	0	0	40	0.97
2662488--2662594	43	2.6	41	77	13	112	56	0	0	42	1.05
2664850--2664889	15	2.4	18	84	16	59	52	0	0	47	1.00
2664863--2664913	25	2.0	27	92	7	88	56	0	0	43	0.99
2664860--2664933	15	4.9	15	71	12	55	59	0	0	40	0.97
2664876--2664922	13	3.7	13	72	16	53	59	0	0	40	0.97
2664855--2664933	27	3.0	27	78	16	85	58	0	0	41	0.98
2665355--2665499	9	16.4	9	72	20	67	44	0	0	54	1.05
2665398--2665455	23	2.5	23	86	8	82	53	0	0	46	1.00
2665397--2665458	15	4.1	15	81	8	63	51	0	0	48	1.00
2665427--2665513	5	19.2	5	68	23	59	36	0	1	62	1.03
2665429--2665518	27	3.3	27	76	16	87	37	1	1	60	1.12
2665438--2665509	9	8.1	9	77	13	78	34	0	1	63	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2665466--2665510	8	5.1	8	84	15	54	26	0	2	71	0.98
2665438--2665513	18	4.2	18	84	3	91	34	0	1	64	1.02
2667203--2667243	21	2.0	21	85	0	55	36	9	17	36	1.82
2667563--2667604	2	21.0	2	100	0	84	50	0	0	50	1.00
2669429--2669453	2	12.5	2	100	0	50	48	0	52	0	1.00
2677560--2677585	2	13.0	2	100	0	52	50	0	0	50	1.00
2678010--2678061	27	1.9	27	100	0	104	38	15	17	28	1.90
2685069--2685102	2	17.0	2	100	0	68	50	0	0	50	1.00
2685792--2685869	30	2.6	29	77	6	75	53	0	0	46	1.00
2685798--2685843	24	2.0	24	86	4	67	56	0	0	43	0.99
2686502--2686662	5	32.8	5	66	18	63	39	0	0	60	0.97
2686508--2686630	35	3.6	35	69	20	91	42	0	0	57	0.98
2686583--2686655	16	4.9	16	71	18	59	38	0	0	61	0.96
2686960--2686998	2	20.0	2	94	5	71	48	0	0	51	1.00
2687457--2687503	21	2.3	21	82	7	53	51	0	0	48	1.00
2688216--2688249	2	17.0	2	87	0	50	44	0	5	50	1.26
2693319--2693354	18	2.0	18	100	0	72	44	5	22	27	1.75
2694762--2694825	27	2.3	27	76	7	67	59	0	0	40	0.97
2695422--2695466	22	2.1	21	84	12	56	44	0	2	53	1.13
2696572--2696615	18	2.4	18	76	0	52	81	0	18	0	0.68
2696859--2696913	22	2.4	23	74	14	60	61	1	5	30	1.29
2697483--2697547	28	2.2	31	75	8	73	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2697535--2697577	21	2.0	21	82	8	52	55	4	0	39	1.20
2697754--2697796	5	8.0	5	80	14	50	23	0	2	74	0.93
2697733--2697794	18	3.5	17	74	12	54	27	0	1	70	0.96
2698266--2698316	22	2.3	22	84	15	70	35	0	0	64	0.94
2699002--2699049	21	2.2	22	89	10	73	35	0	0	64	0.94
2699003--2699056	23	2.4	22	81	12	65	33	0	0	66	0.92
2699332--2699385	21	2.5	21	85	8	74	24	1	5	68	1.21
2699343--2699377	10	3.4	10	84	7	52	22	0	2	74	0.95
2699332--2699383	11	4.8	11	79	11	54	23	1	5	69	1.20
2699998--2700053	28	2.0	28	86	3	78	35	3	0	60	1.14
2700052--2700104	24	2.1	26	89	6	83	52	1	1	43	1.23
2701630--2701679	2	25.0	2	100	0	100	50	0	0	50	1.00
2702874--2702911	2	19.0	2	100	0	76	50	0	0	50	1.00
2703743--2703799	21	2.6	22	83	10	64	43	0	1	54	1.10
2705136--2705235	37	2.8	36	78	17	91	38	0	1	61	1.03
2705159--2705235	37	2.2	33	86	9	100	35	0	1	63	1.03
2705190--2705238	12	4.5	11	83	16	66	30	0	0	69	0.89
2705190--2705238	22	2.2	22	86	13	66	30	0	0	69	0.89
2705179--2705238	12	5.2	12	75	22	58	33	0	1	65	1.03
2705190--2705247	22	2.5	24	81	15	61	31	0	3	65	1.09
2707474--2707515	2	21.0	2	100	0	84	50	0	0	50	1.00
2707778--2707803	2	13.0	2	100	0	52	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2711460--2711506	18	2.5	20	75	13	53	65	6	2	25	1.27
2712106--2712170	21	3.1	21	80	8	71	55	4	1	38	1.30
2731070--2731109	16	2.5	16	87	0	53	65	7	2	25	1.32
2731084--2731136	16	3.1	16	73	19	52	50	7	5	35	1.54
2741855--2741920	29	2.3	27	77	12	69	45	0	0	54	0.99
2743767--2743791	3	8.3	3	100	0	50	32	32	0	36	1.58
2748099--2748124	2	13.0	2	100	0	52	50	0	0	50	1.00
2751102--2751146	24	1.9	23	86	13	65	53	11	6	28	1.61
2751838--2751879	19	2.2	20	86	4	59	59	9	16	14	1.60
2759437--2759466	2	15.0	2	100	0	60	50	0	50	0	1.00
2768544--2768568	12	2.1	12	100	0	50	0	24	0	76	0.80
2768539--2768572	15	2.4	14	85	5	50	0	29	0	70	0.87
2769657--2769699	20	2.3	19	84	15	54	65	18	13	2	1.38
2770198--2770247	20	2.5	20	84	12	75	48	0	0	52	1.00
2770482--2770540	20	2.8	20	74	25	59	50	0	0	49	1.00
2771978--2772016	5	7.8	5	100	0	78	41	0	0	58	0.98
2772403--2772427	2	12.5	2	100	0	50	48	0	0	52	1.00
2772689--2772732	20	2.2	20	84	8	54	65	2	0	31	1.05
2773780--2773816	16	2.4	15	86	8	56	45	0	0	54	1.00
2774049--2774089	2	20.5	2	100	0	82	51	0	0	48	1.00
2774426--2774455	2	15.0	2	100	0	60	50	0	0	50	1.00
2774711--2774749	16	2.4	16	86	0	60	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2774805--2774843	16	2.4	16	82	0	51	46	17	15	20	1.84
2775851--2775964	32	3.5	33	76	4	117	43	27	13	15	1.84
2776103--2776132	10	3.0	10	95	0	51	36	0	10	53	1.35
2776260--2776304	23	2.0	22	87	12	65	46	0	0	53	1.00
2776680--2776735	14	4.0	14	73	21	55	51	0	0	48	1.00
2777393--2777424	17	1.9	17	93	6	57	43	0	0	56	0.99
2777584--2777646	26	2.5	23	75	14	63	47	0	0	52	1.00
2777665--2777719	28	2.0	27	82	10	67	52	1	0	45	1.11
2778025--2778068	2	22.0	2	100	0	88	50	0	0	50	1.00
2779998--2780337	75	4.5	75	87	3	463	20	25	13	41	1.88

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