genome.fa.s74.2.7.7.80.10.50.1000.16.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: Scaffold74
Parameters: 2 7 7 80 10 50 1000
Length:  4633657

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   

This is table  16  of  24  ( 2862 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)
3226494--3226549	18	2.9	19	76	7	60	64	1	0	33	1.04
3226478--3226548	24	2.9	24	76	4	61	63	1	0	35	1.03
3226581--3226623	21	2.2	19	87	8	59	65	0	0	34	0.93
3227002--3227088	26	3.5	25	72	19	83	37	0	0	62	0.96
3227371--3227402	16	1.9	17	93	6	57	62	0	0	37	0.95
3227372--3227427	19	2.9	18	82	10	67	58	0	0	41	0.98
3227846--3227886	17	2.3	19	91	8	68	53	0	2	43	1.13
3227977--3228015	17	2.2	18	86	9	53	56	0	0	43	0.99
3228753--3228779	4	6.8	4	100	0	54	0	25	0	74	0.83
3231759--3231801	20	2.2	19	87	4	59	53	0	0	46	1.00
3233466--3233513	24	2.1	22	81	14	53	54	0	0	45	0.99
3233424--3233513	18	5.1	17	67	16	58	56	0	1	42	1.06
3234292--3234321	2	15.0	2	100	0	60	50	0	0	50	1.00
3235603--3235656	27	2.0	27	88	0	81	53	14	18	12	1.72
3240961--3240986	7	3.7	7	100	0	52	38	0	0	61	0.96
3240958--3240992	14	2.6	13	82	8	52	31	0	0	68	0.90
3241038--3241098	27	2.3	27	81	10	72	40	0	4	54	1.22
3241077--3241149	37	2.0	36	86	7	103	41	0	1	57	1.07
3241227--3241268	9	4.9	9	85	2	52	76	4	0	19	0.96
3241388--3241441	25	2.1	25	82	3	63	53	1	0	44	1.11
3241634--3241667	5	6.6	5	86	6	50	41	0	0	58	0.98
3241663--3241725	10	6.3	10	77	14	51	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3241661--3241700	20	2.0	20	90	0	62	65	0	0	35	0.93
3241668--3241716	20	2.5	20	80	16	57	69	0	0	30	0.89
3241857--3241902	23	2.0	23	83	8	58	50	0	2	47	1.13
3248664--3248820	74	2.2	71	85	5	210	38	3	12	45	1.58
3248682--3248821	74	1.9	74	95	0	253	40	2	12	45	1.55
3258874--3258903	2	15.0	2	92	0	51	53	0	0	46	1.00
3258870--3258902	10	3.3	10	95	0	57	57	0	0	42	0.98
3260424--3260481	16	3.6	16	71	15	57	55	1	1	41	1.20
3266486--3266515	2	15.0	2	100	0	60	50	0	50	0	1.00
3266793--3266829	2	18.5	2	100	0	74	48	0	0	51	1.00
3267145--3267257	45	2.4	48	72	25	109	50	0	0	48	1.06
3268377--3268414	20	1.9	20	88	0	58	36	0	0	63	0.95
3268405--3268438	13	2.7	12	86	13	50	23	0	0	76	0.79
3269034--3269070	3	12.3	3	100	0	74	35	0	0	64	0.94
3269554--3269619	24	2.4	29	76	21	70	43	0	1	54	1.09
3269561--3269614	27	2.1	27	86	10	78	44	0	0	55	0.99
3269554--3269620	27	2.5	27	78	4	73	43	0	1	55	1.09
3273816--3273870	28	2.0	26	89	6	83	43	0	1	54	1.10
3273851--3273909	12	4.8	12	73	8	55	37	1	1	59	1.18
3273896--3273989	20	5.0	19	70	21	65	55	0	0	44	0.99
3273922--3273967	17	2.8	16	78	15	58	60	0	0	39	0.97
3273904--3273989	37	2.3	36	79	14	95	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3274026--3274078	27	1.9	27	84	3	70	45	1	1	50	1.23
3274055--3274094	19	2.1	19	85	4	53	42	2	0	55	1.13
3274610--3274645	2	18.0	2	100	0	72	0	50	0	50	1.00
3277232--3277274	2	21.5	2	100	0	86	0	48	0	51	1.00
3281279--3281317	2	19.5	2	94	0	69	0	51	0	48	1.00
3281627--3281666	15	2.4	17	88	12	57	60	2	0	37	1.11
3281669--3281703	15	2.3	15	90	0	52	45	2	0	51	1.16
3283058--3283186	63	2.0	63	86	8	181	42	3	2	51	1.33
3283052--3283165	32	3.6	31	78	4	122	43	1	2	51	1.25
3283636--3283665	14	2.1	14	100	0	60	36	0	0	63	0.95
3283768--3283803	2	18.5	2	94	5	65	50	0	0	50	1.00
3286804--3286836	12	2.8	12	86	4	50	66	0	0	33	0.92
3286817--3286871	24	2.3	25	81	9	71	52	0	0	47	1.00
3286857--3286907	16	2.9	17	81	18	61	54	0	0	45	0.99
3286842--3286907	16	4.1	17	73	22	54	54	0	0	45	0.99
3286821--3286936	24	5.0	23	72	15	69	56	0	0	43	1.05
3292113--3292175	7	8.7	7	76	13	65	76	0	4	19	0.96
3292161--3292237	24	3.3	23	75	10	75	70	2	9	18	1.26
3292119--3292210	37	2.5	37	83	3	114	73	1	6	18	1.10
3292327--3292362	13	2.9	12	88	8	54	44	0	0	55	0.99
3300672--3300701	12	2.5	12	94	0	51	30	10	10	50	1.69
3303972--3304015	22	1.9	24	86	9	65	59	0	0	40	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3308656--3308726	26	2.9	26	72	16	71	43	1	0	54	1.08
3308672--3308725	21	2.5	23	82	11	62	46	1	0	51	1.11
3308796--3308842	15	3.4	14	80	16	53	65	0	0	34	0.93
3308799--3308840	14	3.1	14	83	10	52	66	0	0	33	0.92
3308805--3308842	13	2.9	13	84	11	51	68	0	0	31	0.90
3311078--3311108	2	15.5	2	100	0	62	51	0	48	0	1.00
3311214--3311372	79	2.0	79	98	0	309	34	22	16	26	1.95
3318952--3318996	20	2.2	20	88	4	63	51	4	8	35	1.54
3320557--3320586	2	15.0	2	100	0	60	50	0	0	50	1.00
3324441--3324810	188	2.0	188	93	1	643	29	9	14	46	1.76
3325323--3325360	19	2.0	19	85	10	51	55	13	2	28	1.51
3325806--3325834	14	2.0	15	93	6	51	31	0	6	62	1.22
3325914--3326003	25	3.6	25	74	21	91	47	0	7	44	1.32
3326155--3326212	18	3.1	18	78	9	62	53	0	1	44	1.10
3326406--3326482	9	9.1	8	74	20	59	37	0	1	61	1.05
3326416--3326547	9	17.6	7	70	22	58	34	0	2	63	1.07
3326398--3326531	18	7.6	18	73	17	79	35	0	2	61	1.13
3326416--3326491	25	3.1	25	81	10	77	38	0	2	59	1.12
3326502--3326550	17	2.8	17	84	3	62	28	0	0	71	0.86
3326509--3326547	19	2.1	19	85	9	53	28	0	0	71	0.86
3326488--3326548	24	2.7	23	82	5	70	27	0	1	70	0.97
3326488--3326550	22	2.8	21	77	13	63	28	0	1	69	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3326446--3326560	52	2.2	51	77	12	115	33	0	2	64	1.07
3326906--3326932	11	2.5	11	100	0	54	92	0	7	0	0.38
3326708--3327037	165	2.0	164	95	0	597	45	10	9	35	1.71
3328633--3328668	17	2.0	19	89	10	58	61	0	2	36	1.11
3329136--3329171	18	2.1	18	89	5	56	38	0	2	58	1.13
3329133--3329185	24	2.2	24	83	6	63	47	0	1	50	1.12
3341715--3341748	2	17.0	2	100	0	68	50	0	50	0	1.00
3344254--3344352	22	4.5	21	72	17	67	43	1	1	54	1.13
3344795--3344824	2	15.0	2	92	0	51	46	0	0	53	1.00
3345734--3345792	30	2.0	28	87	6	82	50	1	1	45	1.21
3349978--3350020	12	3.4	12	81	9	50	55	0	0	44	0.99
3356542--3356575	11	3.0	11	83	8	50	58	0	0	41	0.98
3364816--3364845	15	1.9	16	93	6	53	36	0	0	63	0.95
3365872--3365945	24	3.0	25	79	15	91	44	0	0	55	0.99
3365881--3365954	26	3.1	24	76	17	75	44	0	0	55	0.99
3365912--3365961	20	2.7	19	72	9	50	50	0	0	50	1.00
3367300--3367339	14	2.9	15	85	10	50	65	0	0	35	0.93
3372305--3372347	16	2.6	16	88	3	59	79	6	4	9	1.06
3373302--3373533	127	1.8	127	88	0	356	55	6	5	33	1.47
3374169--3374193	2	12.5	2	100	0	50	48	0	0	52	1.00
3374397--3374441	23	1.9	23	81	4	54	55	0	0	44	0.99
3376099--3376145	2	23.5	2	100	0	94	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3380284--3380326	2	21.5	2	100	0	86	48	0	0	51	1.00
3383346--3383376	14	2.2	14	94	0	53	61	3	0	35	1.12
3384124--3384416	50	5.9	50	86	0	354	29	17	20	33	1.95
3384111--3384414	100	3.0	99	86	0	419	28	16	19	34	1.94
3384654--3384690	19	1.9	19	88	0	56	24	24	21	29	1.99
3384653--3384697	19	2.4	19	80	0	54	26	22	20	31	1.98
3388787--3389036	50	5.0	50	90	1	349	31	19	16	32	1.94
3390282--3390324	18	2.4	18	81	14	54	74	0	6	18	1.04
3390282--3390324	16	2.5	16	88	11	59	74	0	6	18	1.04
3394641--3394740	40	2.5	39	77	6	110	35	4	8	53	1.49

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