genome.fa.s2.2.7.7.80.10.50.1000.29.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  29  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)
4418484--4418916	111	3.8	110	79	11	442	26	26	20	26	1.99
4418525--4418895	121	3.2	120	81	11	343	25	26	20	27	1.99
4418481--4418924	55	7.7	60	83	7	423	26	27	19	26	1.99
4419583--4419657	20	3.8	20	84	7	107	25	18	13	42	1.87
4422004--4422144	51	2.8	51	75	4	140	32	24	9	32	1.88
4422131--4422204	28	2.7	27	85	10	105	22	31	20	25	1.98
4422239--4422314	28	2.8	26	84	8	89	18	31	21	28	1.97
4422296--4422467	51	3.4	51	82	4	211	30	29	11	28	1.92
4422084--4422361	110	2.6	107	77	5	326	26	26	13	33	1.93
4429427--4429487	28	2.2	28	78	0	68	36	18	19	26	1.94
4429456--4430357	79	11.4	79	76	11	445	35	13	22	29	1.92
4429481--4430357	158	5.5	158	82	4	844	35	13	22	29	1.92
4429481--4430357	238	3.7	234	81	8	902	35	13	22	29	1.92
4432749--4432841	20	4.7	20	81	7	100	40	11	15	32	1.83
4439665--4439689	13	1.9	13	100	0	50	36	16	16	32	1.90
4440012--4440080	32	2.1	33	94	2	122	34	10	18	36	1.85
4440118--4440142	13	1.9	13	100	0	50	32	16	16	36	1.90
4440151--4440281	52	2.5	52	93	0	226	34	18	17	29	1.94
4442483--4443046	28	19.5	28	82	6	590	27	31	17	22	1.97
4442483--4443046	59	9.7	58	82	5	628	27	31	17	22	1.97
4443653--4443727	20	3.8	20	78	0	87	34	13	12	40	1.81
4443653--4443730	40	2.0	39	87	2	111	34	12	12	39	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4444643--4444696	22	2.5	22	96	3	101	18	11	9	61	1.55
4447600--4447648	19	2.6	19	86	0	71	38	18	12	30	1.87
4448572--4449172	43	13.1	43	77	13	574	30	18	26	24	1.98
4448526--4449172	92	7.0	92	91	1	1010	31	18	25	24	1.98
4449034--4449101	21	3.2	20	66	25	50	29	16	27	26	1.97
4449177--4449428	32	7.9	32	84	8	302	19	19	32	29	1.96
4449177--4449430	65	4.0	64	87	6	331	19	18	32	29	1.96
4449458--4449716	67	3.9	68	79	8	223	32	14	34	18	1.91
4449506--4449871	32	11.4	32	76	11	232	31	15	31	21	1.94
4449463--4449748	100	2.9	96	81	9	285	31	14	34	19	1.92
4449708--4449938	30	7.5	29	85	10	291	30	15	28	25	1.96
4449632--4449933	62	4.9	62	85	6	364	29	16	30	23	1.97
4449663--4449938	30	8.9	29	80	12	266	30	16	28	23	1.96
4451228--4451252	13	1.9	13	100	0	50	8	12	0	80	0.92
4457859--4457987	52	2.5	52	92	0	204	28	17	17	36	1.93
4457859--4458007	52	2.9	52	86	2	174	30	17	17	34	1.93
4458063--4458125	19	3.7	18	72	24	64	36	15	12	34	1.86
4458058--4458158	32	3.1	32	91	1	157	37	16	9	35	1.82
4461769--4462025	44	5.7	43	74	10	176	19	20	15	44	1.86
4461760--4462118	138	2.6	134	80	8	325	20	20	15	43	1.88
4461745--4462024	94	3.1	87	77	7	274	19	21	15	43	1.87
4461853--4462168	44	6.8	46	74	11	216	20	20	16	42	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4462495--4462615	41	2.9	39	72	13	100	18	24	15	41	1.89
4464265--4464376	20	5.7	19	85	4	134	30	17	13	38	1.88
4464265--4464376	39	2.9	40	90	5	160	30	17	13	38	1.88
4464421--4464450	13	2.3	13	94	0	51	36	16	10	36	1.82
4466216--4466291	38	2.0	38	92	0	125	38	15	19	26	1.92
4467143--4467190	19	2.5	20	89	3	71	35	12	16	35	1.87
4478850--4478921	20	3.7	19	87	7	83	29	15	18	37	1.91
4478951--4479015	33	2.0	33	84	6	87	35	13	16	33	1.89
4481782--4481846	20	3.3	20	64	23	57	38	16	10	33	1.84
4485611--4485667	19	2.9	19	81	2	69	33	14	15	36	1.88
4485696--4485733	20	1.9	20	88	0	58	31	15	15	36	1.90
4485787--4485824	20	2.0	20	89	5	60	39	10	13	36	1.79
4491776--4491802	13	2.1	13	100	0	54	29	14	14	40	1.86
4491929--4491968	20	2.0	20	85	14	55	32	22	0	45	1.53
4494378--4494431	20	2.7	20	88	5	74	33	12	18	35	1.89
4494456--4494493	20	2.0	20	94	5	69	36	10	15	36	1.82
4496284--4496394	50	2.2	51	85	4	145	41	13	14	30	1.84
4500323--4500378	20	2.8	21	83	5	80	32	14	12	41	1.83
4500323--4500394	20	3.6	20	76	10	67	33	13	13	38	1.85
4501052--4501095	21	2.0	22	86	4	63	34	25	2	38	1.68
4502941--4502965	13	1.9	13	100	0	50	36	16	16	32	1.90
4509136--4509213	20	3.9	20	82	0	93	32	10	14	43	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4515335--4515376	20	2.2	20	91	4	68	35	9	14	40	1.78
4515346--4515406	28	2.2	27	85	8	86	31	11	16	40	1.84
4516124--4516195	20	3.7	19	78	17	76	27	16	13	41	1.87
4516143--4516195	19	2.7	20	88	2	72	28	16	13	41	1.86
4517022--4517327	155	2.0	154	87	3	436	28	10	10	50	1.69
4517166--4517678	168	3.1	163	75	8	435	28	11	8	50	1.69
4517220--4517537	167	1.9	165	82	5	390	28	11	8	51	1.66
4518004--4518034	11	2.7	11	95	5	53	80	0	19	0	0.71
4526612--4526656	22	2.0	22	86	0	63	31	6	2	60	1.35
4528882--4528915	13	2.7	13	90	4	52	11	20	5	61	1.50
4529547--4529614	20	3.3	20	81	2	73	35	11	11	41	1.78
4531687--4531873	93	2.0	93	96	0	347	33	20	15	29	1.94
4533384--4533447	33	2.0	32	87	3	92	35	14	12	37	1.83
4536679--4537088	79	5.2	78	83	5	457	32	14	24	28	1.94
4536671--4537088	158	2.6	158	86	5	551	32	14	25	27	1.95
4537098--4537330	51	4.5	50	80	5	243	33	11	25	30	1.90
4537098--4537318	102	2.1	103	82	6	270	32	11	25	29	1.92
4539623--4539677	20	2.8	20	97	0	101	40	9	14	36	1.78
4539715--4539740	13	2.0	13	100	0	52	38	15	15	30	1.88
4539778--4539832	13	3.9	13	78	17	65	30	16	14	38	1.89
4539758--4539832	30	2.4	31	88	6	125	32	17	13	37	1.88
4543057--4543122	33	2.0	33	90	0	105	27	18	18	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4543432--4543498	33	2.0	33	85	0	89	34	10	13	41	1.79
4543452--4543476	13	1.9	13	100	0	50	36	16	16	32	1.90
4543539--4543563	13	1.9	13	100	0	50	32	16	16	36	1.90
4543572--4543691	52	2.3	52	94	4	208	33	18	18	30	1.95
4546831--4546855	13	1.9	13	100	0	50	32	16	16	36	1.90
4546811--4546878	33	2.1	33	88	2	102	35	17	14	32	1.91
4548957--4548981	13	1.9	13	100	0	50	36	16	16	32	1.90
4548939--4549003	33	2.0	33	88	11	98	29	16	15	38	1.90
4552757--4552798	3	14.0	3	100	0	84	33	0	0	66	0.92
4553781--4553806	13	2.0	13	100	0	52	30	23	15	30	1.95
4553883--4553941	22	2.7	22	94	0	100	40	11	22	25	1.88
4553874--4553956	10	8.0	10	71	16	62	39	10	25	24	1.87
4553982--4554116	53	2.5	53	93	1	234	27	18	17	37	1.93
4554086--4554156	20	3.5	20	77	11	74	29	12	16	40	1.86
4554196--4554236	21	2.0	21	85	9	57	39	9	12	39	1.76
4558976--4559101	52	2.4	52	88	5	184	41	14	14	30	1.85
4560582--4560625	21	2.1	21	100	0	88	34	34	22	9	1.86
4561058--4561144	45	1.9	45	85	0	120	21	5	51	20	1.68
4563242--4563281	2	20.0	2	100	0	80	50	0	50	0	1.00
4565949--4566062	34	3.3	34	77	10	106	50	0	0	47	1.13
4565986--4566036	25	2.1	24	82	13	61	49	0	1	49	1.12
4565985--4566070	31	2.7	31	72	21	81	48	0	1	50	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4579564--4579618	22	2.5	22	90	0	92	34	27	12	25	1.92
4579824--4581197	27	49.9	27	81	3	1339	24	31	14	29	1.95
4579824--4581197	56	25.0	55	80	3	1295	24	31	14	29	1.95
4579824--4581197	83	16.6	81	80	5	1265	24	31	14	29	1.95
4581189--4581550	28	12.9	28	82	6	251	27	27	17	27	1.97
4581166--4581550	56	6.9	56	82	5	354	27	27	17	27	1.97
4581166--4581550	84	4.6	86	83	5	414	27	27	17	27	1.97
4579856--4581287	247	5.8	251	78	6	835	24	30	15	29	1.95
4587795--4587994	78	2.6	79	83	3	235	30	16	28	25	1.97
4587948--4588020	27	2.7	27	86	0	92	20	20	36	21	1.95

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