genome.fa.s2.2.7.7.80.10.50.1000.3.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  3  of  38  ( 4457 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)
390450--390595	20	6.8	20	73	18	105	41	13	14	30	1.83
390468--390606	71	2.0	71	89	2	217	43	12	15	28	1.82
390400--390595	91	2.2	91	87	0	284	40	12	15	30	1.85
390541--390609	20	3.2	21	86	12	88	43	10	15	30	1.80
391505--392005	28	17.5	28	85	4	572	22	16	30	30	1.96
393253--393300	8	5.8	8	77	18	53	0	0	16	83	0.65
406860--407027	20	7.9	19	72	20	111	41	12	16	29	1.85
406812--406988	51	3.7	49	73	17	167	40	12	16	30	1.85
406812--407038	91	2.5	91	91	1	366	41	12	16	29	1.85
408268--408294	13	2.1	13	100	0	54	29	14	14	40	1.86
408280--408334	20	2.8	19	78	5	65	32	14	12	40	1.84
408363--408414	20	2.6	20	93	0	86	34	13	21	30	1.92
415668--415741	37	2.0	37	94	0	130	39	16	5	39	1.71
418870--418947	34	2.3	34	95	0	138	26	28	6	38	1.81
419389--419444	20	2.7	20	86	10	69	39	10	10	39	1.75
427632--427694	28	2.2	28	77	5	74	55	7	9	26	1.59
428009--428325	51	6.2	50	73	5	206	34	23	18	23	1.96
428269--428445	85	2.1	86	84	3	232	32	21	22	24	1.98
428916--429185	113	2.3	115	82	9	318	37	9	9	43	1.69
432059--432083	13	1.9	13	100	0	50	36	16	16	32	1.90
432039--432105	33	2.0	33	85	0	89	32	10	14	41	1.80
432144--432183	13	3.1	13	100	0	80	40	15	15	30	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
432192--432306	43	2.5	47	86	8	166	33	17	19	29	1.94
436051--436098	13	3.2	16	77	19	59	77	14	8	0	0.99
436051--436114	29	2.3	27	84	12	78	76	14	9	0	1.01
436052--436118	28	2.4	29	80	14	79	77	11	10	0	0.99
436932--436977	8	5.6	8	92	5	65	43	23	6	26	1.78
437138--437463	34	9.9	33	71	18	150	19	36	11	31	1.89
437180--437257	27	2.8	28	90	3	131	23	41	15	20	1.90
437146--437481	68	5.1	67	84	9	408	19	35	12	32	1.89
437150--437477	102	3.3	101	78	12	337	19	35	11	32	1.88
437498--437543	23	2.0	23	86	0	65	30	30	19	19	1.97
437524--437704	36	5.4	33	79	8	195	19	33	14	32	1.92
437521--437712	100	1.9	100	86	0	276	20	32	14	32	1.93
437719--437958	32	7.5	32	87	7	355	27	35	17	18	1.94
437719--437958	64	3.8	64	93	1	403	27	35	17	18	1.94
437997--438362	43	8.1	43	81	11	437	25	24	18	31	1.98
437946--438406	92	5.0	92	92	1	742	26	25	17	31	1.97
438202--438269	21	3.2	20	66	25	50	26	27	17	27	1.98
438316--438655	52	6.1	55	72	14	155	25	24	12	37	1.91
438419--438545	67	1.9	68	85	1	175	24	25	11	38	1.89
438486--438662	52	3.3	52	78	5	158	25	25	12	36	1.91
439297--439321	13	1.9	13	100	0	50	36	16	16	32	1.90
439384--439408	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
439417--439545	52	2.5	52	94	0	222	35	17	17	30	1.92
440391--440431	21	1.9	22	90	5	66	21	17	17	43	1.87
450689--450736	10	4.6	10	80	14	53	22	0	4	72	1.01
450689--450735	22	2.1	22	100	0	94	21	0	4	74	0.99
450689--450749	22	2.8	21	87	9	61	27	0	3	68	1.05
451018--451058	2	20.5	2	100	0	82	51	0	0	48	1.00
451683--451714	2	16.0	2	100	0	64	50	0	0	50	1.00
451958--451997	16	2.5	16	83	0	53	55	0	2	42	1.13
452251--452316	7	9.0	7	74	9	60	46	0	1	51	1.10
452243--452319	24	3.2	25	83	10	90	46	0	2	50	1.15
452214--452347	26	5.1	26	69	15	73	48	0	2	48	1.19
452975--453054	41	2.0	41	92	5	135	40	5	12	42	1.64
453983--454036	21	2.6	21	83	13	67	48	0	1	50	1.11
454721--454786	29	2.3	28	79	7	80	36	4	0	59	1.18
454765--454799	16	2.1	17	89	5	54	42	0	0	57	0.99
454942--454983	21	2.2	20	83	12	52	54	7	7	30	1.54
458397--458546	74	2.0	74	98	0	291	22	16	24	36	1.94
461378--461408	3	10.7	3	93	6	55	32	0	0	67	0.91
462375--462421	20	2.3	20	92	0	76	27	10	17	44	1.81
462383--462425	20	2.2	20	100	0	86	25	13	13	46	1.81
465810--465850	16	2.5	17	80	7	50	26	2	0	70	0.99
466354--466399	16	2.9	16	76	0	56	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
468141--468259	42	2.8	42	92	0	193	42	1	45	10	1.47
473442--473482	19	2.3	19	87	8	59	63	2	2	31	1.20
476597--476675	20	3.9	20	86	1	95	44	12	10	32	1.76
476731--476767	19	2.0	18	89	5	56	37	8	13	40	1.74
483124--483303	78	2.3	78	81	7	206	27	22	14	36	1.93
492950--493360	167	2.4	169	83	5	501	29	9	9	51	1.65
493917--493970	8	7.1	7	78	21	56	79	0	16	3	0.87
493915--493954	11	3.5	11	86	3	53	82	0	17	0	0.67
493917--493974	25	2.6	21	82	17	64	79	0	17	3	0.87
493917--493976	18	3.1	19	83	9	77	80	0	16	3	0.85
494191--494260	30	2.3	30	95	4	124	11	2	44	41	1.55
498808--498932	52	2.4	52	97	0	232	28	17	17	36	1.93
498969--499066	28	3.5	28	87	0	142	39	27	15	17	1.89
498965--499087	28	4.3	29	83	8	121	38	26	14	20	1.91
499112--499389	48	5.8	48	81	8	325	26	24	17	31	1.97
499256--499345	43	2.1	43	91	0	144	27	23	17	31	1.97
499299--499448	52	2.8	55	83	3	198	25	24	16	34	1.95
500237--500264	13	2.2	13	100	0	56	32	14	14	39	1.86
500218--500282	32	2.0	33	93	3	114	36	12	12	38	1.80
500325--500349	13	1.9	13	100	0	50	32	16	16	36	1.90
500358--500487	53	2.5	53	94	1	226	33	17	18	30	1.94
504457--504519	13	4.5	13	80	11	72	84	15	0	0	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
504456--504528	16	4.4	16	78	11	76	83	16	0	0	0.64
504455--504519	14	4.4	14	84	11	78	84	15	0	0	0.62
504768--504820	16	3.2	17	81	13	74	86	5	7	0	0.69
504768--504827	15	4.1	14	82	6	66	85	6	8	0	0.76
505851--505935	30	2.8	31	83	3	109	24	25	17	31	1.97
505915--506299	37	11.3	36	82	11	374	20	35	12	31	1.90
505912--506282	71	5.5	71	80	11	422	20	34	12	32	1.90
506285--506419	33	4.1	33	90	4	211	28	34	17	20	1.95
506288--506419	65	2.0	66	97	1	248	28	34	18	18	1.95
506465--507097	43	14.1	43	79	15	669	25	25	18	30	1.98
506424--507040	92	6.9	90	79	12	639	25	26	18	29	1.98
506702--506760	31	1.9	31	100	0	118	23	27	23	25	2.00
506731--507097	49	7.7	49	85	8	481	24	25	18	31	1.97
506730--507045	140	2.3	136	90	6	490	24	25	18	30	1.98
507101--507227	67	1.9	68	85	1	175	24	25	12	37	1.90
507994--508058	33	2.0	33	87	0	94	35	13	13	36	1.85
508100--508124	13	1.9	13	100	0	50	32	16	16	36	1.90
508133--508256	52	2.4	52	93	4	207	34	18	17	29	1.94
522546--522594	13	3.8	13	83	0	62	83	16	0	0	0.64
522546--522593	5	10.2	5	82	13	50	83	16	0	0	0.65
522546--522593	9	5.1	10	80	14	50	83	16	0	0	0.65
524032--524205	29	6.0	29	79	7	174	26	30	16	26	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
524033--524186	56	2.7	58	81	5	168	28	29	17	24	1.97
524026--524186	86	1.9	86	85	5	227	28	30	16	24	1.97
524181--524255	35	2.2	35	83	7	100	21	32	9	37	1.85
524312--524339	13	2.2	13	100	0	56	39	14	14	32	1.86
524294--524358	33	2.0	33	93	3	114	38	12	12	36	1.80
531217--531710	49	10.4	49	69	17	251	30	18	26	24	1.98
531217--531486	101	2.7	101	80	5	291	32	18	26	22	1.97
531413--531658	88	2.8	86	76	13	286	28	19	26	26	1.99
531970--532094	28	4.3	29	81	7	155	17	18	33	30	1.94
532075--532382	33	9.8	33	75	15	183	32	13	32	21	1.92

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