genome.fa.s3.2.7.7.80.10.50.1000.21.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  21  of  32  ( 3795 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)
3441759--3441797	6	6.5	6	93	0	51	23	0	0	76	0.78
3441761--3441795	3	11.7	3	87	0	52	25	0	0	74	0.82
3442836--3442860	3	8.3	3	100	0	50	36	0	0	64	0.94
3443360--3443423	25	2.5	25	80	12	67	50	0	0	50	1.00
3443383--3443438	22	2.4	25	82	11	75	53	0	0	46	1.00
3443449--3443503	18	3.2	18	77	12	62	38	1	0	60	1.08
3451977--3452081	49	2.2	49	91	1	167	23	25	18	32	1.97
3452617--3452680	20	3.1	20	82	13	85	60	0	0	39	0.97
3455599--3455635	17	2.4	17	86	13	53	32	0	0	67	0.91
3455598--3455636	15	2.6	15	80	15	53	33	0	0	66	0.92
3458430--3458482	28	1.9	28	88	3	81	52	0	0	47	1.00
3460407--3460464	9	5.8	9	77	18	53	36	0	1	62	1.06
3460380--3460465	11	8.3	10	75	23	72	38	1	3	56	1.24
3460386--3460469	9	8.0	11	70	28	51	39	1	2	57	1.20
3460453--3460508	27	2.0	27	86	10	78	50	1	7	41	1.40
3462921--3463009	27	3.3	27	77	12	78	52	2	4	40	1.34
3464501--3464918	142	3.0	142	98	0	793	31	16	13	38	1.87
3466054--3466104	13	3.8	13	76	5	57	54	0	0	45	0.99
3470414--3470461	25	2.0	24	83	4	60	50	0	10	39	1.37
3470705--3470798	10	9.6	10	72	18	56	34	1	5	59	1.27
3470705--3470790	19	4.5	19	76	13	79	32	1	5	60	1.28
3470712--3470798	11	8.5	11	73	16	53	34	1	5	58	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3470835--3470885	21	2.4	22	81	15	63	33	3	9	52	1.53
3474447--3474480	2	17.0	2	93	0	59	50	2	0	47	1.16
3480477--3480692	34	6.4	34	88	1	292	24	7	27	40	1.83
3480477--3480694	67	3.2	67	88	1	319	24	7	27	40	1.82
3480993--3481049	19	3.0	19	86	0	78	33	17	15	33	1.92
3480994--3481056	19	3.3	19	82	8	74	30	17	17	34	1.93
3485122--3485339	34	6.5	34	88	1	296	24	7	27	40	1.82
3485122--3485341	67	3.3	67	88	1	323	24	7	27	40	1.82
3486656--3486695	16	2.5	17	80	11	50	42	0	2	55	1.13
3487984--3488049	31	2.2	30	83	8	80	46	0	0	53	1.00
3488551--3488595	18	2.4	18	85	10	56	51	0	0	48	1.00
3489636--3489664	13	2.3	13	94	5	51	37	0	0	62	0.96
3490009--3490097	27	3.3	27	70	9	81	28	12	30	29	1.93
3493055--3493115	32	2.0	32	83	6	81	32	0	4	62	1.17
3493055--3493115	15	3.9	15	79	10	61	32	0	4	62	1.17
3493837--3493876	6	6.7	6	83	11	55	15	2	65	17	1.39
3494355--3494420	24	2.7	24	81	13	73	33	3	1	62	1.20
3494407--3494452	23	1.9	25	91	8	78	28	2	0	69	1.00
3494407--3494442	12	3.1	12	84	8	56	27	0	0	72	0.85
3494635--3494662	2	14.0	2	100	0	56	50	0	50	0	1.00
3494660--3494724	4	17.5	4	75	12	50	75	0	21	3	0.94
3494666--3494724	23	2.7	22	81	5	66	76	0	20	3	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3494654--3494724	19	3.8	19	80	7	67	73	0	23	2	0.97
3495514--3495550	9	4.1	9	85	0	56	29	0	0	70	0.88
3496376--3496409	16	2.0	18	88	11	54	17	17	0	64	1.29
3500637--3500670	2	17.0	2	100	0	68	50	0	50	0	1.00
3505803--3505841	21	1.9	21	84	5	53	30	0	33	35	1.58
3521630--3521654	13	1.9	13	100	0	50	12	0	0	88	0.53
3527965--3528005	22	1.9	21	95	5	73	19	12	4	63	1.46
3528978--3529022	21	2.2	20	84	4	54	44	4	0	51	1.21
3530136--3530166	4	7.5	4	92	7	53	51	0	0	48	1.00
3530945--3530988	22	2.0	22	86	8	63	63	0	0	36	0.95
3538437--3538492	29	1.9	29	88	0	85	60	8	1	28	1.37
3541331--3541356	2	13.0	2	100	0	52	50	0	0	50	1.00
3544719--3544748	2	15.0	2	92	0	51	50	0	3	46	1.18
3545205--3545234	2	15.0	2	92	0	51	46	0	3	50	1.18
3545585--3545614	2	15.0	2	100	0	60	50	0	0	50	1.00
3545684--3545714	15	2.1	15	100	0	62	41	12	6	38	1.69
3546075--3546334	50	5.2	50	88	1	319	28	17	19	34	1.94
3546075--3546334	100	2.6	100	88	2	362	28	17	19	34	1.94
3551947--3551994	19	2.5	19	83	13	62	47	0	0	52	1.00
3567982--3568298	72	4.4	72	86	4	399	12	4	46	36	1.61
3567982--3568622	36	17.8	36	75	7	291	15	4	40	39	1.69
3568641--3568710	36	1.9	36	82	0	86	18	5	31	44	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3568723--3568821	36	2.8	36	88	0	144	19	4	33	43	1.69
3572164--3572205	13	3.2	13	80	10	50	69	0	0	30	0.89
3574766--3574808	3	13.7	3	90	9	52	69	0	0	30	0.88
3574929--3574980	27	2.0	26	85	11	70	53	3	3	38	1.37
3578900--3578952	2	26.5	2	100	0	106	49	0	0	50	1.00
3579414--3579542	42	3.1	42	85	3	163	30	33	9	27	1.88
3583612--3583708	48	2.0	48	95	0	176	32	19	7	40	1.79
3584998--3585057	28	2.1	28	90	0	93	61	10	11	16	1.55
3586066--3586092	3	9.0	3	100	0	54	33	0	66	0	0.92
3586450--3586500	11	4.5	11	83	11	52	66	0	0	33	0.92
3586450--3586501	18	2.7	20	76	11	63	65	0	0	34	0.93
3586513--3586576	18	3.6	18	72	19	55	56	0	0	43	0.99
3586521--3586575	18	3.2	17	79	20	62	58	0	0	41	0.98
3595191--3595224	2	17.0	2	93	0	59	47	0	2	50	1.16
3597338--3597395	27	2.2	25	85	11	73	51	0	0	48	1.00
3597685--3597713	2	14.5	2	100	0	58	48	0	0	51	1.00
3600155--3600246	13	6.5	14	72	15	73	44	2	0	53	1.12
3600149--3600257	44	2.6	40	75	14	96	46	1	0	51	1.11
3602340--3602384	7	6.4	7	100	0	90	28	31	26	13	1.94
3607956--3608034	41	1.9	41	97	0	149	35	25	12	26	1.92
3610538--3610564	2	13.5	2	100	0	54	48	0	0	51	1.00
3612089--3612220	64	2.1	64	95	0	237	31	15	18	33	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3620217--3620302	42	2.0	43	82	14	108	54	0	1	44	1.07
3621237--3621268	2	16.5	2	93	6	57	50	0	0	50	1.00
3627739--3627781	2	21.0	2	90	4	68	46	0	4	48	1.22
3627910--3627947	20	2.0	20	89	5	60	44	0	5	50	1.24
3627914--3627956	20	2.1	20	86	4	59	48	0	9	41	1.35
3629046--3629085	6	6.7	6	85	0	53	40	15	15	30	1.87
3629563--3629587	2	12.5	2	100	0	50	52	0	0	48	1.00
3631148--3631197	25	2.0	25	84	7	66	60	0	0	40	0.97
3635711--3635756	19	2.4	19	82	10	58	54	0	0	45	0.99
3638097--3638138	19	2.2	20	79	12	52	59	0	0	40	0.97
3644433--3644458	2	13.0	2	100	0	52	50	0	0	50	1.00
3645703--3645738	11	3.2	11	88	4	54	61	0	0	38	0.96
3645885--3645932	2	24.0	2	82	0	60	41	0	8	50	1.33
3645888--3645945	14	4.3	14	80	8	66	37	0	12	50	1.40
3645888--3645945	18	3.2	18	87	0	89	37	0	12	50	1.40
3645885--3645932	22	2.2	22	100	0	96	41	0	8	50	1.33
3645886--3645940	10	5.3	10	78	8	56	38	0	10	50	1.37
3646223--3646257	3	11.7	3	100	0	70	68	0	0	31	0.90
3647761--3647837	1	77.0	1	100	0	154	0	0	100	0	0.00
3648928--3648953	13	2.0	13	100	0	52	30	7	15	46	1.74
3653042--3653088	3	15.7	3	100	0	94	68	0	31	0	0.90
3654687--3654740	4	13.5	4	88	0	54	48	9	1	40	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3654687--3654740	6	9.0	6	79	0	54	48	9	1	40	1.46
3654740--3654766	2	13.5	2	100	0	54	51	0	48	0	1.00
3655173--3655221	9	5.9	9	78	21	54	40	0	0	59	0.98
3655182--3655222	13	3.1	13	82	3	55	36	0	0	63	0.95
3655186--3655234	18	2.9	18	88	8	68	36	0	0	63	0.95
3655187--3655250	19	3.3	18	76	18	58	39	0	1	59	1.07
3655215--3655263	25	2.0	25	83	0	62	40	0	2	57	1.10
3655200--3655298	32	3.2	31	78	16	91	42	0	1	56	1.06
3655245--3655306	18	3.7	17	75	22	60	45	0	0	54	0.99
3655279--3655338	21	3.0	21	81	15	67	35	0	0	65	0.93

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