genome.fa.s11.2.7.7.80.10.50.1000.28.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  28  of  29  ( 3461 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)
4838451--4838512	28	2.2	28	83	13	83	58	0	1	40	1.08
4839896--4839931	2	18.0	2	100	0	72	50	0	0	50	1.00
4842488--4842574	24	3.6	24	80	0	102	28	20	37	12	1.89
4842480--4842574	48	2.0	48	89	0	145	27	20	38	13	1.90
4844401--4844430	2	15.0	2	100	0	60	50	0	0	50	1.00
4845010--4845073	31	2.1	31	96	0	119	67	15	4	12	1.39
4849985--4850020	18	1.9	19	88	5	56	41	2	0	55	1.14
4850382--4850406	2	12.5	2	100	0	50	48	0	0	52	1.00
4851078--4851115	20	1.9	20	89	10	60	50	0	0	50	1.00
4851480--4851531	21	2.3	21	87	9	68	46	1	0	51	1.12
4851472--4851549	23	3.5	21	79	13	68	43	2	2	51	1.29
4852245--4852322	32	2.5	30	77	20	79	52	1	1	44	1.17
4855721--4855771	13	3.8	14	77	12	54	52	0	1	45	1.12
4856558--4856601	15	2.9	15	86	3	61	54	0	0	45	0.99
4857273--4857298	7	3.7	7	100	0	52	30	0	0	69	0.89
4857280--4857348	30	2.3	30	87	0	93	46	2	0	50	1.16
4863138--4863171	12	2.8	12	83	16	52	67	5	26	0	1.13
4863958--4863990	2	16.5	2	100	0	66	48	0	0	51	1.00
4874098--4874134	6	6.2	6	100	0	74	16	35	32	16	1.91
4877488--4877546	6	10.3	6	75	14	54	57	0	0	42	0.98
4877479--4877546	26	2.7	25	85	14	95	55	0	0	44	0.99
4877491--4877538	5	9.0	5	80	11	51	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4877491--4877538	10	4.5	11	82	12	64	60	0	0	39	0.97
4877556--4877596	11	4.0	11	78	18	52	36	0	0	63	0.95
4877536--4877596	33	1.9	30	90	9	95	39	0	0	60	0.97
4877552--4877600	11	4.6	11	75	17	50	36	0	0	63	0.95
4877607--4877650	22	2.0	22	86	4	63	59	2	0	38	1.10
4877607--4877666	21	2.8	20	78	9	57	56	3	0	40	1.16
4888806--4888836	2	15.5	2	93	0	53	48	0	3	48	1.17
4888960--4888989	15	1.9	16	93	6	53	46	10	6	36	1.64
4889085--4889122	11	3.5	11	82	7	51	63	0	0	36	0.95
4889104--4889163	18	3.5	17	78	10	61	55	0	0	45	0.99
4889941--4890457	270	1.9	270	83	3	666	41	9	8	39	1.68
4892492--4892521	3	10.0	3	100	0	60	33	0	0	66	0.92
4895940--4896071	67	2.0	67	90	3	212	38	17	14	29	1.89
4897323--4897351	8	3.8	8	90	9	51	0	13	0	86	0.58
4897323--4897351	15	1.9	15	100	0	58	0	13	0	86	0.58
4899218--4901023	479	3.8	470	81	10	1960	40	11	7	39	1.71
4901723--4901786	6	11.0	6	80	11	55	29	0	0	70	0.88
4901727--4901761	5	6.6	5	96	3	52	22	0	0	77	0.78
4901727--4901765	16	2.4	16	87	12	53	23	0	0	76	0.78
4901808--4901858	19	2.7	19	79	17	61	45	1	0	52	1.12
4901901--4901935	9	3.9	9	100	0	70	77	0	0	22	0.78
4904589--4904617	2	14.5	2	100	0	58	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4910966--4910999	16	2.1	16	88	0	50	32	2	0	64	1.08
4914069--4914124	19	2.9	19	75	0	67	55	0	1	42	1.10
4914051--4914124	38	1.9	38	97	0	139	54	1	1	43	1.17
4914691--4914730	20	2.0	21	85	5	55	55	0	0	45	0.99
4932193--4932222	12	2.5	12	94	0	51	60	33	0	6	1.23
4932662--4932715	26	2.1	25	86	10	74	48	0	0	51	1.00
4932670--4932730	19	3.0	22	81	9	67	50	0	0	49	1.00
4932739--4932799	22	2.8	22	81	16	74	37	0	0	62	0.96
4932973--4933037	23	2.9	21	78	21	62	56	0	1	41	1.08
4938226--4938287	31	2.0	31	96	0	115	46	25	11	16	1.80
4939428--4939464	2	19.5	2	89	10	60	51	0	0	48	1.00
4939428--4939464	19	1.9	19	94	0	65	51	0	0	48	1.00
4953278--4953351	33	2.3	31	88	4	103	50	5	0	44	1.25
4953926--4953981	2	28.0	2	85	0	58	48	5	3	42	1.43
4954676--4954717	17	2.4	19	80	15	54	50	0	0	50	1.00
4957801--4957890	27	3.2	27	81	15	87	40	1	0	58	1.05
4957853--4957899	14	3.0	15	75	22	51	42	2	0	55	1.12
4957800--4957898	17	6.2	16	66	26	59	40	1	0	58	1.05
4957881--4957938	23	2.5	24	78	10	68	44	0	0	55	0.99
4957879--4957974	38	2.5	39	80	13	110	42	1	0	56	1.06
4957904--4957951	13	3.9	13	80	17	50	39	2	0	58	1.10
4958265--4958305	22	1.9	21	90	5	64	60	0	0	39	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4960100--4960149	21	2.4	22	83	9	61	42	0	0	58	0.98
4960110--4960160	20	2.4	22	84	15	72	43	0	1	54	1.11
4962193--4962229	2	18.5	2	100	0	74	0	48	0	51	1.00
4968424--4968448	3	8.3	3	100	0	50	64	0	0	36	0.94
4969898--4969983	42	2.0	42	82	4	102	51	1	0	47	1.08
4971313--4971373	20	3.4	18	72	23	58	60	1	0	37	1.07
4975873--4975903	2	15.5	2	100	0	62	51	0	0	48	1.00
4985698--4985839	71	2.0	71	97	0	266	26	13	14	45	1.82
4992644--4992684	15	2.7	15	88	3	55	56	0	2	41	1.13
4992699--4992743	18	2.5	17	82	10	54	66	0	2	31	1.04
4992896--4992965	20	3.5	20	79	13	65	42	0	0	57	0.99
4992896--4992947	18	2.7	19	85	8	61	42	0	0	57	0.98
4992919--4992968	18	3.0	18	77	16	63	44	0	0	56	0.99
4992921--4992972	15	3.3	15	76	17	52	42	0	0	57	0.98
4992976--4993017	22	1.9	22	85	0	57	33	2	0	64	1.07
4993029--4993068	18	2.2	18	90	0	62	50	7	7	35	1.59
4993086--4993130	2	22.5	2	100	0	90	51	0	0	48	1.00
4993708--4994198	251	2.0	250	97	0	894	41	7	8	42	1.62
4994620--4994660	2	20.5	2	100	0	82	0	48	0	51	1.00
4995505--4995530	2	13.0	2	100	0	52	50	0	0	50	1.00
5007382--5007409	2	14.0	2	100	0	56	50	0	0	50	1.00
5007759--5007829	10	7.3	10	72	15	51	33	0	1	64	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5007728--5007801	31	2.4	29	79	16	78	32	0	1	66	1.00
5007814--5007860	21	2.2	21	92	0	76	31	2	4	61	1.27
5007954--5008011	15	3.8	15	76	17	57	70	1	27	0	0.97
5007954--5008002	17	3.2	14	76	18	53	69	0	30	0	0.89
5007970--5008023	17	3.2	17	77	12	58	70	1	27	0	0.98
5008034--5008107	31	2.4	29	79	16	78	32	0	1	66	1.00
5007561--5008177	306	2.0	307	98	0	1200	39	5	11	43	1.66
5008120--5008166	21	2.2	21	88	0	67	31	2	6	59	1.34
5009588--5009653	17	3.8	17	86	8	71	46	1	0	51	1.10
5009613--5009653	17	2.4	17	95	0	73	48	0	0	51	1.00
5009638--5009689	20	2.5	20	78	9	61	42	0	0	57	0.98
5009610--5009739	60	2.3	58	79	14	144	41	0	0	57	1.04
5009718--5009751	11	3.2	11	83	8	52	29	0	0	70	0.87
5009642--5009751	21	5.4	20	69	20	77	36	0	0	62	1.01
5009849--5009883	4	9.0	4	87	6	54	77	0	22	0	0.78
5009850--5009885	16	2.2	17	95	5	65	80	0	19	0	0.71
5009915--5009983	25	2.7	24	82	10	84	31	1	1	65	1.11
5010057--5010094	17	2.2	17	86	13	51	47	0	5	47	1.24
5012343--5012398	11	5.4	10	78	21	62	66	1	0	32	1.03
5013364--5013390	13	2.1	13	100	0	54	44	11	22	22	1.84
5014468--5014508	21	2.0	21	85	0	55	41	0	2	56	1.13
5014474--5014506	17	2.0	16	94	5	57	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5014708--5014820	29	4.0	29	75	12	110	58	0	0	39	1.10
5018830--5018863	2	17.0	2	100	0	68	50	0	0	50	1.00
5019765--5019802	6	6.3	6	100	0	76	50	15	0	34	1.45
5021591--5021626	2	18.0	2	100	0	72	50	0	50	0	1.00
5024115--5024167	26	2.0	26	81	7	61	35	1	0	62	1.06
5024721--5024760	20	2.0	21	85	9	57	50	0	0	50	1.00
5025085--5025302	34	6.5	34	85	5	282	40	27	7	24	1.82
5025083--5025302	67	3.3	67	88	1	323	40	27	7	24	1.82
5029368--5029430	19	3.3	19	90	0	90	34	19	17	28	1.94
5029735--5029950	34	6.4	34	83	5	260	40	26	7	25	1.82

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