genome.fa.s4.2.7.7.80.10.50.1000.18.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  18  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)
4119991--4120026	2	18.0	2	100	0	72	50	0	0	50	1.00
4122523--4122595	36	2.0	36	100	0	146	45	10	19	24	1.82
4125458--4125488	10	3.1	10	95	0	53	41	22	19	16	1.89
4125987--4126017	2	15.5	2	100	0	62	51	0	48	0	1.00
4127163--4127264	54	1.9	53	82	6	125	37	3	13	45	1.63
4130261--4130407	73	2.0	73	97	0	276	29	8	17	44	1.78
4132307--4132341	18	1.9	18	88	11	54	34	0	0	65	0.93
4133121--4133159	14	2.7	14	88	4	51	30	0	0	69	0.89
4133654--4133706	24	2.2	24	89	0	79	49	0	0	50	1.00
4137085--4137116	2	16.0	2	93	0	55	50	3	0	46	1.17
4137783--4137816	2	17.0	2	100	0	68	50	0	50	0	1.00
4140575--4140599	2	12.5	2	100	0	50	0	52	0	48	1.00
4141153--4141187	14	2.5	14	90	9	54	8	5	0	85	0.73
4141585--4141627	21	2.0	22	86	8	63	4	39	0	55	1.20
4142902--4142937	18	2.0	18	100	0	72	66	5	5	22	1.34
4142903--4142944	18	2.3	18	91	4	66	66	4	7	21	1.35
4142903--4142950	19	2.6	18	86	3	51	62	8	6	22	1.46
4144235--4144333	32	3.1	31	80	10	101	55	0	2	42	1.11
4144285--4144334	18	3.0	18	71	28	56	52	0	0	48	1.00
4144276--4144342	32	2.0	32	85	5	89	55	0	0	44	0.99
4146511--4146569	26	2.3	26	84	0	73	44	5	3	47	1.42
4151018--4151089	24	2.9	25	91	4	110	19	8	25	47	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4151018--4151089	25	3.0	24	87	4	108	19	8	25	47	1.77
4155708--4155776	32	2.2	31	86	2	102	49	2	0	47	1.16
4155773--4155858	20	4.4	18	67	24	50	44	0	3	52	1.18
4155766--4155874	23	4.9	23	67	16	61	45	0	2	51	1.15
4156588--4156612	3	8.3	3	100	0	50	32	36	0	32	1.58
4159200--4159274	10	7.0	11	69	14	50	44	1	2	52	1.23
4159249--4159296	17	2.9	15	84	12	51	58	0	0	41	0.98
4159272--4159327	26	2.1	27	78	15	64	57	0	0	42	0.99
4160123--4160191	23	3.0	23	80	6	68	40	1	0	57	1.07
4160105--4160184	11	7.0	11	76	13	65	35	1	0	63	1.02
4160131--4160192	23	2.6	23	82	5	70	41	0	0	58	0.98
4160509--4160570	13	4.7	14	73	15	60	32	1	0	66	1.02
4160504--4160570	25	2.6	25	84	11	75	29	1	0	68	0.98
4160509--4160578	25	2.8	24	79	14	70	32	2	0	64	1.08
4161297--4161367	29	2.4	30	77	9	76	39	14	0	46	1.44
4161653--4161682	3	10.0	3	100	0	60	33	0	0	66	0.92
4162468--4162539	19	3.8	19	78	10	67	48	0	0	51	1.00
4162475--4162529	29	2.0	27	85	7	74	47	0	0	52	1.00
4162491--4162552	19	3.3	20	75	20	71	46	0	0	53	1.00
4162631--4162667	16	2.3	16	90	0	56	59	0	0	40	0.97
4163841--4163865	3	8.3	3	100	0	50	68	0	0	32	0.90
4164681--4164740	30	1.9	33	83	12	83	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4164715--4164757	16	2.9	15	80	10	52	55	0	0	44	0.99
4164686--4164753	28	2.3	31	77	12	70	57	0	0	42	0.98
4164311--4165347	525	2.0	523	86	5	1452	43	6	5	44	1.54
4166270--4166311	16	2.6	16	78	14	50	47	4	2	45	1.36
4169665--4169697	2	17.0	2	87	6	50	54	0	0	45	0.99
4181508--4181536	2	14.5	2	100	0	58	51	0	0	48	1.00
4186715--4186759	15	2.8	17	74	22	51	44	4	0	51	1.21
4189121--4189149	14	2.1	14	93	6	51	17	6	13	62	1.52
4189356--4189395	19	2.1	19	85	0	53	47	0	2	50	1.14
4190886--4190948	22	2.9	21	77	17	67	57	0	0	42	0.99
4191038--4191096	25	2.4	25	100	0	118	47	10	0	42	1.37
4193538--4193570	17	2.0	17	94	5	59	66	0	0	33	0.92
4194603--4194687	36	2.3	35	81	15	102	38	0	2	58	1.11
4195018--4195117	30	3.3	31	76	16	79	55	1	1	43	1.13
4195068--4195120	15	3.4	15	74	25	56	58	1	0	39	1.09
4196277--4196314	2	19.0	2	100	0	76	50	0	0	50	1.00
4196314--4196351	2	19.0	2	94	0	67	52	0	47	0	1.00
4198459--4198487	2	14.5	2	100	0	58	0	51	0	48	1.00
4201002--4201048	2	23.5	2	95	0	85	46	2	0	51	1.13
4205469--4205508	20	2.0	20	95	0	71	37	0	0	62	0.95
4205561--4205633	33	2.2	34	82	7	87	31	0	2	65	1.06
4205578--4205633	11	5.0	11	77	16	53	28	0	3	67	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4209804--4209860	28	2.0	28	89	0	87	33	17	21	28	1.96
4214578--4214637	20	3.0	20	78	7	61	46	3	1	48	1.28
4216584--4216628	18	2.4	19	85	7	65	53	0	0	46	1.00
4216983--4217057	29	2.4	32	84	13	120	28	9	6	56	1.56
4216993--4217057	29	2.2	29	97	0	121	27	7	6	58	1.50
4217060--4217086	7	3.9	7	100	0	54	55	0	0	44	0.99
4225187--4225228	16	2.6	16	81	11	50	52	4	0	42	1.22
4225556--4225590	17	2.1	17	88	0	52	28	0	0	71	0.86
4225909--4225963	17	3.4	16	75	25	53	61	0	0	38	0.96
4226178--4226221	14	2.9	15	83	10	54	54	2	0	43	1.12
4226690--4226730	20	2.0	21	85	4	57	53	4	4	36	1.44
4227162--4227342	51	3.7	48	73	17	126	37	2	2	58	1.23
4227423--4227476	20	2.6	21	80	11	67	77	0	22	0	0.76
4227423--4227474	22	2.6	19	72	21	52	76	0	23	0	0.78
4227783--4227818	12	2.9	12	87	4	54	86	0	13	0	0.58
4228381--4228416	15	2.5	14	91	8	63	86	0	13	0	0.58
4228916--4228962	15	3.2	15	81	3	60	38	0	0	61	0.96
4229070--4229106	15	2.4	16	95	4	67	83	0	16	0	0.64
4229126--4229219	35	2.8	33	83	16	113	35	0	0	64	0.94
4229152--4229220	23	2.8	26	70	18	67	36	0	0	63	0.94
4229191--4229223	15	2.1	16	88	5	50	36	0	0	63	0.95
4229164--4229223	21	3.0	21	72	18	56	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4229557--4229595	20	1.9	21	89	5	62	79	0	17	2	0.84
4229617--4229690	25	3.0	25	75	11	73	28	2	1	67	1.12
4230759--4230808	15	3.4	14	78	13	55	70	0	6	24	1.10
4231243--4231286	22	2.0	23	82	13	56	56	4	2	36	1.32
4232408--4232445	20	2.0	20	89	5	60	42	0	0	57	0.98
4232420--4232491	20	3.9	19	74	18	64	55	0	0	44	0.99
4232477--4232536	11	5.3	11	69	15	50	48	0	0	51	1.00
4233001--4233047	20	2.3	20	80	16	53	48	0	2	48	1.13
4232966--4233062	52	1.9	50	80	4	113	47	2	1	49	1.20
4233176--4233209	10	3.4	10	87	0	50	0	58	0	41	0.98
4244995--4245051	23	2.4	23	79	5	60	57	1	1	38	1.19
4245555--4245604	20	2.3	23	86	13	70	38	0	0	62	0.96
4245501--4245591	41	2.2	41	83	15	116	41	0	0	58	0.98
4245535--4245598	21	3.3	19	78	10	67	40	0	0	59	0.97
4246060--4246086	2	13.5	2	100	0	54	48	0	0	51	1.00
4246456--4246531	27	2.8	27	74	4	73	46	0	0	53	1.00
4246468--4246545	27	2.9	25	72	14	66	42	0	0	57	0.98
4246525--4246564	11	3.5	12	80	19	50	35	0	0	65	0.93
4247000--4247097	18	5.4	18	79	9	83	47	15	0	36	1.45
4246999--4247109	4	27.5	4	84	0	69	47	13	0	37	1.49
4247027--4247101	8	9.4	8	83	0	78	50	14	0	34	1.43
4247018--4247109	12	7.6	12	82	1	94	48	13	1	36	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4248733--4248777	2	22.5	2	95	0	81	48	0	0	51	1.00
4249133--4249197	2	32.5	2	87	0	94	46	3	1	49	1.27
4249627--4249828	69	2.9	69	89	1	298	39	15	7	37	1.75
4254932--4254956	2	12.5	2	100	0	50	48	0	0	52	1.00
4256405--4256437	14	2.3	15	89	5	50	39	0	3	57	1.14
4256459--4256491	13	2.4	14	90	10	59	60	0	0	39	0.97
4258424--4258500	32	2.4	31	84	6	91	41	0	0	58	0.98
4258463--4258541	10	7.6	11	67	22	55	32	0	0	67	0.91
4258447--4258545	43	2.2	42	80	10	99	36	0	0	63	0.95
4258468--4258541	18	4.2	18	75	16	66	32	0	0	67	0.91

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