genome.fa.s7.2.7.7.80.10.50.1000.30.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: Scaffold7
Parameters: 2 7 7 80 10 50 1000
Length:  6555642

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   

This is table  30  of  37  ( 4421 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)
5242368--5242437	20	3.5	20	76	9	72	40	15	14	30	1.87
5242409--5242545	53	2.6	53	94	1	229	37	17	16	27	1.92
5243659--5243709	22	2.4	22	83	9	61	37	0	0	62	0.95
5243710--5243771	23	2.8	23	78	9	58	64	1	1	32	1.13
5245267--5245313	24	2.0	24	82	0	58	29	31	21	17	1.96
5247749--5247823	20	3.8	20	76	0	78	34	14	10	40	1.81
5247749--5247826	40	2.0	39	84	2	102	34	14	11	39	1.82
5254906--5254984	1	79.0	1	74	0	68	87	12	0	0	0.55
5254912--5254984	15	4.6	16	80	14	89	86	13	0	0	0.58
5254909--5254977	19	3.7	19	80	7	79	85	14	0	0	0.60
5254912--5254984	32	2.3	31	93	4	128	86	13	0	0	0.58
5256190--5256304	31	3.7	31	88	6	178	25	32	18	24	1.97
5256190--5256310	63	1.9	62	94	1	215	23	32	17	26	1.97
5256284--5256413	35	3.8	34	83	6	154	20	30	13	35	1.91
5256284--5256434	36	4.3	35	81	6	162	21	31	12	34	1.91
5256425--5256527	33	3.2	32	89	10	167	29	36	18	15	1.92
5256520--5257403	49	18.7	49	82	7	1074	25	25	17	31	1.97
5256520--5257402	141	6.2	137	82	9	983	25	25	17	31	1.97
5256520--5257403	190	4.7	190	90	3	1290	25	25	17	31	1.97
5257136--5257403	92	2.9	92	97	0	500	24	25	18	31	1.98
5258026--5258098	20	3.7	20	74	7	60	34	15	10	39	1.82
5262884--5262910	13	2.1	13	100	0	54	29	14	14	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5262894--5262950	19	2.9	19	89	2	87	31	15	17	35	1.92
5262995--5263025	13	2.4	13	94	0	53	35	12	12	38	1.82
5264656--5264680	13	1.9	13	100	0	50	20	8	24	48	1.76
5267080--5267116	13	2.7	14	84	15	51	13	5	0	81	0.86
5267077--5267111	7	4.9	7	89	3	52	14	5	0	80	0.89
5269358--5269405	24	2.0	24	100	0	96	37	16	12	33	1.86
5269967--5270044	23	3.3	23	66	16	68	41	12	24	21	1.88
5269956--5270063	49	2.2	49	100	0	216	44	14	21	19	1.86
5270905--5271043	52	2.7	51	81	5	172	41	11	15	31	1.83
5271538--5271605	19	3.9	19	78	21	85	35	11	14	38	1.83
5271559--5271583	13	1.9	13	100	0	50	36	16	16	32	1.90
5271540--5271602	32	2.0	32	96	0	117	34	12	15	36	1.86
5271645--5271670	13	2.0	13	100	0	52	30	15	15	38	1.88
5271625--5271691	33	2.0	33	88	0	98	25	14	16	43	1.86
5274093--5274271	80	2.2	82	88	2	290	29	27	13	29	1.94
5274232--5274303	28	2.6	28	88	0	99	22	34	19	23	1.96
5274257--5274461	79	2.6	79	83	1	241	23	30	17	28	1.97
5280595--5280697	36	3.2	36	60	28	84	26	25	19	29	1.99
5280592--5281863	55	22.5	55	86	7	1573	27	28	19	23	1.98
5280902--5280984	27	3.0	27	60	16	62	28	30	19	21	1.98
5280597--5281863	342	3.7	334	86	6	1741	28	28	19	23	1.98
5282423--5282490	19	3.9	19	78	21	85	35	11	14	38	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5282444--5282468	13	1.9	13	100	0	50	36	16	16	32	1.90
5282425--5282487	32	2.0	32	96	0	117	34	12	15	36	1.86
5282530--5282555	13	2.0	13	100	0	52	30	15	15	38	1.88
5282510--5282576	33	2.0	33	88	0	98	25	14	16	43	1.86
5284975--5285153	80	2.2	82	87	2	281	29	27	13	29	1.95
5285114--5285185	28	2.6	28	88	0	99	22	34	19	23	1.96
5285139--5285343	79	2.6	79	81	1	232	23	29	17	29	1.97
5288992--5289056	32	2.0	33	87	3	96	29	15	12	43	1.83
5293817--5293849	10	3.3	10	95	0	57	36	18	12	33	1.88
5293936--5294000	32	2.0	33	87	3	96	29	15	12	43	1.83
5294903--5294950	21	2.3	21	82	17	64	33	8	16	41	1.78
5296081--5296173	30	3.1	29	67	22	75	53	6	20	19	1.66
5296063--5296184	60	2.0	60	93	0	208	54	5	21	18	1.63
5298242--5298280	20	1.9	21	94	5	71	38	20	20	20	1.94
5298270--5298332	33	1.9	33	87	3	92	30	12	17	39	1.87
5298823--5298867	23	2.0	23	82	8	56	28	13	22	35	1.92
5300004--5300042	9	4.3	9	90	0	51	43	0	30	25	1.55
5300010--5300040	3	10.3	3	92	0	53	38	0	32	29	1.57
5304545--5304587	20	2.0	20	82	8	50	51	16	6	25	1.69
5309604--5309638	15	2.3	16	90	9	56	54	0	2	42	1.15
5312411--5312447	2	18.5	2	100	0	74	51	0	0	48	1.00
5312988--5313053	27	2.4	27	89	0	105	27	7	7	57	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5315665--5315704	3	13.3	3	94	0	71	35	2	0	62	1.09
5318289--5318316	2	14.0	2	100	0	56	50	0	0	50	1.00
5318517--5318543	2	13.5	2	100	0	54	51	0	0	48	1.00
5318727--5318801	6	12.5	6	74	20	68	61	0	0	38	0.96
5318727--5318803	19	3.5	24	76	18	94	61	0	0	38	0.96
5318751--5318821	9	8.2	9	75	15	53	56	1	0	42	1.08
5318725--5318823	42	2.4	42	86	5	137	57	1	0	41	1.05
5321186--5321216	15	2.0	16	93	6	55	48	0	0	51	1.00
5323484--5323599	60	1.9	62	81	8	141	55	0	1	43	1.10
5323973--5324010	18	2.1	18	100	0	76	10	44	0	44	1.38
5327957--5328132	68	2.6	68	79	6	196	23	15	28	32	1.95
5327957--5328143	69	2.7	67	74	7	164	22	15	29	32	1.95
5336300--5336380	39	2.1	39	88	0	117	28	34	12	24	1.92
5336314--5336393	39	2.1	39	87	0	115	30	31	15	23	1.95
5337843--5338139	79	3.8	79	80	7	302	32	16	24	26	1.96
5337845--5338139	157	1.9	158	80	6	357	32	16	24	26	1.96
5340427--5340514	20	4.8	20	76	18	91	44	11	15	28	1.81
5340427--5340496	33	2.1	33	89	0	104	42	10	17	30	1.81
5340447--5340476	13	2.3	13	94	0	51	40	10	20	30	1.85
5341534--5341606	33	2.2	33	83	14	96	52	4	2	41	1.35
5342453--5342491	7	5.6	7	96	0	69	10	58	15	15	1.62
5346278--5346324	18	2.7	18	84	12	62	51	2	0	46	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5346430--5346471	19	2.4	17	78	21	50	50	2	0	47	1.14
5346600--5346637	20	2.0	20	94	5	69	65	0	2	31	1.06
5354161--5354190	11	2.7	11	94	0	51	80	0	20	0	0.72
5355012--5355068	3	18.7	3	85	3	78	70	0	29	0	0.88
5355320--5355396	2	38.5	2	89	0	109	46	3	0	49	1.20
5356633--5356658	13	2.0	13	100	0	52	38	15	15	30	1.88
5359967--5359997	15	2.1	15	93	0	53	48	16	22	12	1.80
5362057--5362123	20	3.7	20	74	25	85	23	14	11	49	1.77
5362076--5362147	13	6.0	13	78	18	93	27	15	13	43	1.85
5362057--5362136	33	2.4	33	100	0	160	25	15	12	47	1.80
5362268--5362313	21	2.2	20	81	11	58	32	19	4	43	1.71
5364693--5364718	13	2.0	13	100	0	52	38	15	15	30	1.88
5365869--5365987	53	2.2	53	79	10	127	30	25	5	38	1.79
5365884--5365986	53	2.0	53	84	5	138	32	21	4	41	1.74
5365922--5366310	81	4.8	81	79	9	384	30	25	8	35	1.86
5365922--5366310	160	2.4	163	84	3	493	30	25	8	35	1.86
5368333--5368366	4	8.5	4	86	0	50	26	0	2	70	1.01
5378697--5378733	16	2.2	17	90	4	58	78	8	13	0	0.96
5379712--5380403	65	11.0	61	76	10	465	26	23	16	34	1.95
5379741--5380348	65	9.7	64	78	9	490	26	23	15	35	1.94
5379712--5380348	251	2.5	248	80	9	668	26	23	15	34	1.95
5379741--5380292	126	4.4	124	77	11	421	26	23	15	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5379741--5380295	186	2.9	188	81	8	499	26	23	15	34	1.95
5380240--5380403	68	2.5	67	81	4	192	25	22	17	35	1.95
5380241--5380452	68	3.2	68	79	7	179	25	22	16	35	1.94
5380854--5380878	11	2.3	11	100	0	50	92	0	8	0	0.40
5383339--5383603	81	3.3	80	81	5	275	31	26	8	33	1.86
5388849--5388965	51	2.3	51	86	2	155	34	12	23	29	1.92
5388900--5389072	79	2.2	79	89	2	267	33	15	23	27	1.94
5389030--5389098	28	2.5	28	97	0	129	26	18	30	24	1.98
5388950--5389161	107	2.0	107	86	3	302	33	14	24	28	1.94
5395041--5395343	164	1.8	165	86	3	441	41	11	10	35	1.77

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