genome.fa.s99.2.7.7.80.10.50.1000.5.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: Scaffold99
Parameters: 2 7 7 80 10 50 1000
Length:  1377724

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  5  of  10  ( 1130 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)
536566--536610	21	2.1	21	84	8	56	53	6	17	22	1.67
538415--538445	15	2.1	15	93	0	53	48	16	22	12	1.80
540459--540536	20	3.7	20	71	15	66	30	15	12	41	1.85
540657--540702	21	2.2	20	81	11	58	32	19	4	43	1.71
543090--543115	13	2.0	13	100	0	52	38	15	15	30	1.88
546080--546105	13	2.0	13	100	0	52	30	15	15	38	1.88
546060--546123	32	2.0	33	90	3	103	28	14	15	42	1.86
546059--546288	97	2.4	97	94	2	401	29	18	15	36	1.91
546177--546202	13	2.0	13	100	0	52	30	15	15	38	1.88
554938--554995	13	4.0	13	74	23	53	32	17	15	34	1.91
554939--555016	32	2.4	32	95	0	138	33	16	14	35	1.89
554951--555036	19	4.7	19	71	20	76	32	16	12	38	1.86
558123--558218	50	1.9	51	85	6	133	43	12	15	28	1.83
558172--558228	30	1.9	30	85	7	80	47	12	15	24	1.80
558255--558329	21	3.7	21	92	5	120	38	12	13	36	1.82
561779--561890	51	2.2	51	90	0	170	42	12	16	27	1.85
563082--563107	13	2.0	13	100	0	52	30	15	15	38	1.88
563701--563837	61	2.2	61	85	2	177	40	10	27	21	1.87
563797--563920	52	2.4	52	76	4	142	34	18	25	21	1.96
564035--564438	32	12.7	32	84	7	513	19	18	30	31	1.96
564620--564691	28	2.6	28	80	2	83	25	18	30	26	1.98
565961--566033	1	73.0	1	72	0	56	1	1	10	86	0.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
565942--566033	10	9.0	10	77	9	96	2	1	14	82	0.82
565942--566033	5	16.7	6	68	20	51	2	1	14	82	0.82
565960--566033	17	4.3	17	78	14	71	1	1	12	85	0.74
565961--566033	16	5.0	14	79	12	76	1	1	10	86	0.70
571250--571485	102	2.3	104	85	3	327	30	26	11	31	1.92
571250--571485	51	4.6	50	82	7	269	30	26	11	31	1.92
571494--571779	79	3.6	79	90	0	419	26	27	16	30	1.96
571736--571806	28	2.5	28	86	0	97	22	29	16	30	1.96
571654--571856	107	1.9	107	80	6	241	26	25	15	33	1.95
571793--571908	51	2.3	51	86	3	153	31	25	9	33	1.88
571818--571934	51	2.3	51	76	2	119	32	25	8	33	1.86
579874--579948	23	3.2	24	80	14	86	85	10	2	1	0.76
579874--579948	11	6.9	11	76	13	75	85	10	2	1	0.76
579872--579948	1	77.0	1	72	0	55	85	10	2	1	0.75
580916--581578	55	11.4	61	85	7	736	25	29	20	24	1.99
581033--581122	26	3.3	26	66	19	76	28	32	17	21	1.96
581173--581258	27	3.1	27	62	15	68	25	25	20	27	1.99
581597--581956	55	6.3	57	84	8	441	27	27	20	23	1.99
582777--582848	32	2.2	32	90	0	108	36	9	15	38	1.80
582873--582898	13	2.0	13	100	0	52	30	15	15	38	1.88
584183--584301	21	5.7	21	87	2	168	34	12	18	34	1.89
584183--584301	42	2.8	42	91	2	186	34	12	18	34	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
584358--584382	13	1.9	13	100	0	50	36	16	16	32	1.90
584391--584417	13	2.1	13	100	0	54	29	14	14	40	1.86
594257--594303	23	2.0	23	83	4	58	42	8	8	40	1.66
595078--595103	13	2.0	13	100	0	52	30	15	15	38	1.88
595802--595845	21	2.1	21	83	8	54	25	31	4	38	1.76
597649--597674	13	2.0	13	100	0	52	38	15	15	30	1.88
599754--599784	15	2.1	15	93	0	53	12	22	16	48	1.80
601588--601632	21	2.1	21	84	8	56	22	20	4	53	1.63
603849--603874	13	2.0	13	100	0	52	30	15	15	38	1.88
604564--604618	20	2.8	20	94	0	92	30	10	14	43	1.80
605753--605797	22	2.0	22	100	0	90	22	17	8	51	1.73
605787--605865	26	3.0	26	72	7	79	37	8	10	43	1.70
611168--611227	27	2.3	27	82	2	77	35	15	25	25	1.94
616579--616650	21	3.5	20	83	9	83	36	19	9	34	1.85
623102--623360	130	2.0	130	92	0	430	29	25	12	32	1.93
623517--624012	30	17.1	29	78	8	368	26	31	12	30	1.92
623526--623630	53	2.0	52	83	1	129	24	34	11	29	1.91
623637--624541	58	15.6	60	76	12	554	26	31	12	29	1.93
623581--624558	88	11.2	87	74	13	589	26	31	12	29	1.93
623581--624013	30	14.8	29	79	7	385	26	30	11	31	1.92
623978--624057	41	2.0	41	97	0	151	26	28	12	32	1.93
624017--624118	30	3.5	29	83	5	125	27	28	12	31	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
624069--624216	49	3.0	49	93	3	237	27	30	14	27	1.95
624167--624558	30	13.4	28	78	10	351	27	32	12	27	1.93
624167--624558	59	6.7	58	80	10	388	27	32	12	27	1.93
624548--624757	31	6.7	31	83	9	248	34	25	17	22	1.96
624538--624757	62	3.5	62	88	3	305	33	26	16	23	1.96
624533--624766	31	7.4	31	81	7	238	32	26	17	23	1.97
624538--624759	93	2.3	96	82	7	274	33	26	16	22	1.96
624777--624836	26	2.3	27	85	2	77	36	30	18	15	1.91
624789--624844	27	2.1	26	86	3	76	33	30	21	14	1.93
624853--625364	100	4.9	103	77	7	368	27	26	14	32	1.94
624851--625197	53	6.7	52	75	5	213	27	25	13	33	1.94
624870--625373	52	9.6	52	75	9	321	27	26	13	32	1.94
626809--626833	13	1.9	13	100	0	50	36	16	16	32	1.90
626822--626875	20	2.8	19	80	5	63	38	12	14	33	1.85
628482--628603	19	7.1	18	70	25	95	36	13	16	33	1.87
628528--628584	13	3.9	13	76	24	60	35	14	17	33	1.90
628509--628616	32	3.4	32	96	0	189	35	13	16	34	1.89
629559--629626	33	2.1	32	88	2	100	33	14	16	35	1.89
629581--629606	13	2.0	13	100	0	52	38	15	15	30	1.88
629649--629699	20	2.5	20	87	0	66	31	13	13	41	1.84
629687--629711	13	1.9	13	100	0	50	36	16	16	32	1.90
630267--630310	21	2.0	21	82	4	52	29	31	2	36	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
630331--630401	23	3.0	23	78	9	81	23	29	0	46	1.53
630343--630402	25	2.6	22	76	19	68	28	28	0	43	1.55
632021--632061	22	2.0	21	86	13	59	41	4	21	31	1.74
638390--638415	13	2.0	13	100	0	52	38	15	15	30	1.88
638467--638514	20	2.4	20	82	6	62	29	14	16	39	1.88
648930--649101	79	2.2	78	86	2	227	31	13	26	27	1.94
649050--649264	79	2.7	77	89	7	315	32	17	25	25	1.97
649219--649290	27	2.6	27	86	2	90	23	20	31	23	1.98
649275--649453	51	3.5	51	84	6	236	32	11	25	30	1.90
651810--651835	13	2.0	13	100	0	52	38	15	15	30	1.88
651859--651931	32	2.3	32	90	0	119	36	16	12	34	1.86
652139--652324	62	3.0	62	97	0	347	29	30	12	28	1.93
656977--657024	5	9.4	5	84	10	62	83	16	0	0	0.65
656977--657030	22	2.3	24	87	9	76	83	16	0	0	0.65
658466--658810	29	12.0	29	87	4	475	29	31	17	21	1.96
658864--659166	49	6.2	49	76	10	282	23	26	17	32	1.97
658902--659045	43	3.2	43	79	12	173	24	23	18	34	1.96
658804--659045	92	2.7	90	90	4	373	23	24	18	33	1.97
659850--659908	19	3.4	19	71	26	67	30	11	22	35	1.90
659869--659893	13	1.9	13	100	0	50	36	16	16	32	1.90
659850--659925	32	2.4	32	93	0	125	31	15	19	32	1.94
659942--659996	20	2.8	20	83	5	67	30	14	14	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
664857--664898	21	2.0	21	90	4	68	38	9	19	33	1.84
664959--665010	20	2.6	20	81	0	59	38	13	13	34	1.84
666467--666491	13	1.9	13	100	0	50	36	16	16	32	1.90
666447--666511	33	2.0	33	87	0	94	32	12	15	40	1.84
666480--666535	20	2.8	20	97	2	105	26	10	10	51	1.69
666550--666608	21	2.8	21	100	0	118	38	16	10	33	1.83
676717--676761	18	2.5	18	96	0	81	37	8	20	33	1.83
683876--683946	9	7.4	9	76	17	72	83	11	4	1	0.86
683876--683946	18	3.7	18	81	10	88	83	11	4	1	0.86
683874--683946	30	2.6	27	87	10	101	80	13	4	1	0.92

Tables:   1   2   3   4   5   6   7   8   9   10