genome.fa.s1.2.7.7.80.10.50.1000.33.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   

This is table  33  of  52  ( 6211 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)
5681086--5681115	2	15.0	2	100	0	60	0	50	0	50	1.00
5681718--5681779	2	31.0	2	96	0	115	48	0	1	50	1.10
5682002--5682039	18	2.1	18	85	9	51	60	0	0	39	0.97
5682132--5682173	17	2.4	18	84	11	61	50	0	0	50	1.00
5683332--5683362	2	15.5	2	93	0	53	48	3	0	48	1.17
5683405--5683435	15	2.1	15	93	0	53	41	12	9	35	1.76
5685088--5685125	19	2.0	19	85	10	51	34	7	5	52	1.53
5686752--5686810	25	2.3	25	80	11	66	52	0	0	47	1.00
5687745--5687798	21	2.6	21	82	2	65	53	3	1	40	1.29
5690434--5690467	2	17.0	2	100	0	68	50	0	0	50	1.00
5691829--5691874	3	15.3	3	100	0	92	67	0	0	32	0.91
5696095--5696159	22	3.1	20	72	18	53	36	0	3	60	1.13
5696653--5696729	28	2.7	29	76	13	79	45	3	2	48	1.34
5696758--5696784	2	13.5	2	100	0	54	0	0	51	48	1.00
5702603--5702711	57	1.9	57	96	0	200	22	16	20	41	1.90
5704491--5704528	15	2.4	17	82	13	53	44	0	2	52	1.14
5704522--5704586	26	2.8	23	76	17	71	50	0	1	47	1.10
5705032--5705132	32	3.5	27	76	18	89	52	0	0	46	1.07
5706698--5706752	27	2.0	27	85	3	74	54	0	0	45	0.99
5709166--5709213	18	2.7	16	77	22	51	45	0	0	54	0.99
5710274--5710326	26	2.0	27	81	3	63	37	1	1	58	1.20
5710305--5710373	18	4.1	18	78	16	76	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5710316--5710386	6	12.0	6	74	14	67	63	0	0	36	0.95
5710317--5710369	26	2.0	26	89	7	81	62	0	0	37	0.96
5711049--5711086	19	2.0	19	85	10	51	50	0	0	50	1.00
5711026--5711079	23	2.3	24	78	6	67	48	0	0	51	1.00
5711312--5711378	11	6.0	11	70	8	55	34	0	0	65	0.93
5711302--5711384	23	3.7	22	71	16	55	34	0	0	65	0.93
5711304--5711378	29	2.7	29	80	12	93	34	0	0	65	0.93
5711307--5711375	23	2.9	23	80	6	66	34	0	0	65	0.93
5711359--5711419	20	3.1	20	79	15	74	40	0	0	59	0.98
5711304--5711389	34	2.7	32	76	18	81	34	0	0	65	0.93
5711367--5711435	29	2.4	29	83	11	97	42	0	1	56	1.08
5711775--5711857	28	3.0	28	71	11	82	40	0	1	57	1.06
5711783--5711838	14	3.9	15	79	13	55	42	0	1	55	1.10
5711782--5711838	15	3.9	15	76	17	57	42	0	1	56	1.10
5711869--5711915	16	2.8	16	75	18	51	42	0	0	57	0.98
5712264--5712305	20	2.3	19	84	12	52	40	0	0	59	0.97
5712276--5712312	20	1.9	19	89	10	58	43	0	0	56	0.99
5714920--5714970	24	2.1	24	89	7	77	33	7	1	56	1.39
5715643--5715765	31	4.0	31	71	22	114	40	0	1	57	1.08
5715636--5715751	57	2.0	60	86	11	168	40	0	2	56	1.13
5717110--5717233	7	15.6	8	71	20	66	70	1	0	27	1.02
5717118--5717283	71	2.3	69	80	10	183	69	1	1	27	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5717126--5717225	8	12.9	7	70	19	58	69	2	0	29	1.00
5717126--5717267	30	4.9	28	74	18	80	67	1	1	29	1.07
5717110--5717281	43	3.9	42	79	16	170	68	1	2	27	1.09
5717110--5717274	9	18.6	9	73	19	134	67	1	1	29	1.08
5717311--5717444	25	5.5	24	67	21	82	31	1	2	64	1.14
5717359--5717398	17	2.4	17	87	8	55	37	0	2	60	1.11
5717303--5717482	9	21.2	9	68	18	102	32	1	2	63	1.13
5717328--5717456	42	3.1	43	83	8	144	31	0	2	65	1.11
5717326--5717475	16	9.1	16	66	18	67	32	0	2	64	1.13
5717328--5717445	8	14.7	7	71	20	56	30	0	2	66	1.11
5717359--5717482	42	2.9	44	81	11	125	33	0	2	64	1.07
5717392--5717483	10	9.4	10	72	24	56	30	0	2	67	1.03
5717401--5717506	51	2.1	51	83	10	130	31	0	3	64	1.18
5718038--5718064	14	1.9	14	100	0	54	29	0	0	70	0.88
5718560--5718609	22	2.4	20	83	9	64	40	0	0	60	0.97
5718747--5718790	13	3.1	14	80	9	54	59	0	0	40	0.98
5719174--5719227	15	3.7	15	80	5	65	48	0	0	51	1.00
5719175--5719222	14	3.5	13	78	13	51	50	0	0	50	1.00
5719190--5719280	35	2.4	36	80	12	103	43	1	0	54	1.07
5719233--5719324	16	5.7	16	69	15	55	51	3	0	45	1.17
5722606--5722633	2	14.0	2	100	0	56	50	0	0	50	1.00
5723978--5724082	25	4.2	24	67	21	65	47	0	0	50	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5724047--5724104	18	3.2	18	79	15	57	50	0	1	48	1.11
5724817--5724873	25	2.3	25	78	9	62	52	0	0	47	1.00
5725107--5725144	19	2.0	19	85	10	51	39	2	2	55	1.28
5725188--5725247	19	3.2	20	76	11	63	50	3	3	43	1.35
5725311--5725349	19	2.0	20	90	5	62	35	2	10	51	1.50
5728152--5728191	21	1.9	21	100	0	80	25	17	10	47	1.78
5731612--5731728	62	1.9	62	82	3	146	45	6	5	42	1.53
5731744--5731823	7	10.9	7	71	18	56	52	2	3	41	1.33
5732958--5733045	32	2.8	32	86	6	108	60	0	1	38	1.04
5732976--5733023	13	3.7	14	78	15	59	60	0	0	39	0.97
5732982--5733028	14	2.9	16	75	18	53	59	0	0	40	0.97
5733016--5733063	17	2.7	19	75	21	50	58	0	0	41	0.98
5733778--5733822	20	2.2	20	84	8	54	57	0	2	40	1.11
5733790--5733827	20	2.0	20	89	5	60	57	0	0	42	0.98
5734002--5734052	23	2.2	24	85	3	68	50	0	0	49	1.00
5734066--5734104	2	19.5	2	94	0	60	43	0	5	51	1.24
5734765--5734802	14	2.5	16	83	12	53	52	0	0	47	1.00
5735681--5735731	8	5.6	9	80	15	52	41	0	1	56	1.10
5735680--5735724	19	2.5	19	82	7	58	40	0	2	57	1.11
5737700--5737741	17	2.5	17	84	3	50	66	2	0	30	1.04
5737814--5737842	14	2.1	14	100	0	58	27	6	6	58	1.50
5738851--5738938	19	4.7	18	72	16	72	63	0	0	36	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5738866--5738952	14	6.1	14	70	17	63	60	0	0	39	0.97
5738872--5738969	28	3.4	29	76	18	98	60	0	1	38	1.04
5738871--5738971	29	3.6	27	73	22	84	59	0	0	39	1.04
5747940--5748009	35	2.0	35	97	0	131	20	8	30	41	1.82
5751633--5751665	16	2.1	16	94	0	57	54	0	0	45	0.99
5752198--5752236	17	2.3	17	86	0	51	38	0	0	61	0.96
5752238--5752269	15	2.1	16	88	11	50	53	0	6	40	1.26
5752583--5752626	13	3.5	12	79	11	52	40	0	2	56	1.11
5753271--5753316	24	1.9	24	90	0	74	32	10	2	54	1.47
5753355--5753411	19	3.0	20	76	5	55	33	5	1	59	1.30
5754873--5754920	21	2.3	21	96	3	89	50	0	0	50	1.00
5755404--5755573	86	2.0	87	89	2	261	48	2	4	45	1.34
5755740--5755774	16	2.3	15	90	5	52	34	0	0	65	0.93
5755740--5755788	15	3.2	15	85	2	53	32	0	2	65	1.04
5756258--5756312	18	2.8	19	76	15	58	52	1	7	38	1.40
5758986--5759029	11	3.8	12	82	17	58	61	0	0	38	0.96
5758986--5759021	12	3.1	11	92	8	54	61	0	0	38	0.96
5759641--5759668	7	4.0	7	100	0	56	42	0	0	57	0.99
5759643--5759692	14	3.6	14	76	10	57	34	0	0	66	0.92
5760250--5760325	15	4.8	17	74	19	65	65	0	0	34	0.93
5760262--5760344	23	3.6	23	72	18	73	59	0	2	38	1.11
5760275--5760349	15	4.8	15	69	19	55	56	0	2	41	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5760261--5760330	28	2.6	28	78	17	76	60	0	0	40	0.97
5760275--5760341	28	2.3	29	80	14	75	58	0	2	38	1.14
5760952--5761002	24	2.1	24	82	7	59	31	0	1	66	1.03
5761026--5761134	29	3.9	28	71	12	80	40	6	1	51	1.38
5761026--5761136	28	4.0	27	70	17	75	41	6	1	50	1.38
5761202--5761243	17	2.5	17	88	3	59	35	4	0	59	1.19
5761704--5761744	21	2.0	21	90	0	64	26	0	4	68	1.10
5761820--5761862	19	2.1	21	91	8	72	32	0	0	67	0.91
5761809--5761855	24	1.9	24	87	12	69	29	0	0	70	0.88
5761819--5761871	21	2.3	23	75	21	58	33	0	0	66	0.92

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   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52