genome.fa.s1.2.7.7.80.10.50.1000.34.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  34  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)
5762329--5762380	21	2.3	24	78	18	58	55	0	1	42	1.10
5763791--5763834	23	1.9	23	90	0	70	61	0	6	31	1.22
5763799--5763836	12	3.2	12	81	7	51	63	0	2	34	1.09
5763815--5763851	17	2.2	16	95	4	65	62	0	5	32	1.18
5763899--5763941	21	2.0	21	83	16	54	44	2	0	53	1.13
5763897--5763955	20	3.1	19	75	18	52	50	1	0	47	1.11
5763922--5764020	46	2.2	45	82	12	123	64	2	0	33	1.05
5764251--5764289	6	6.2	6	91	8	60	64	0	35	0	0.94
5764251--5764289	19	2.1	19	90	9	62	64	0	35	0	0.94
5764251--5764289	13	3.1	12	92	7	60	64	0	35	0	0.94
5765596--5765633	2	19.5	2	89	5	51	44	0	5	50	1.24
5767357--5767407	19	2.9	17	81	13	59	41	1	0	56	1.10
5767605--5767637	2	16.5	2	100	0	66	51	0	0	48	1.00
5769573--5769652	5	15.4	5	76	17	74	63	0	0	36	0.94
5769568--5769690	32	3.8	31	71	25	94	63	1	0	34	1.04
5769573--5769690	15	7.3	17	73	21	103	63	1	0	34	1.05
5769573--5769691	19	5.8	20	73	13	100	63	1	0	35	1.05
5769573--5769690	11	10.5	11	70	18	64	63	1	0	34	1.05
5770368--5770409	16	2.7	16	85	3	59	73	0	0	26	0.83
5770398--5770463	32	2.1	32	82	5	80	51	0	4	43	1.22
5770474--5770523	21	2.4	22	80	10	59	66	0	0	34	0.92
5770486--5770524	10	4.0	10	86	6	62	69	0	0	30	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5771655--5771705	22	2.3	21	80	9	57	66	1	0	31	1.03
5772131--5772174	21	2.0	21	82	8	52	45	0	0	54	0.99
5772250--5772324	26	2.8	26	75	18	73	45	2	0	52	1.15
5772617--5772657	14	2.9	15	85	7	50	58	2	2	36	1.24
5773160--5773188	15	2.0	15	93	6	51	68	0	0	31	0.89
5773187--5773228	17	2.5	17	77	14	52	30	0	0	69	0.89
5773233--5773299	3	22.3	3	84	0	89	61	1	5	31	1.29
5773452--5773504	15	3.6	15	78	12	65	43	0	1	54	1.11
5773485--5773538	21	2.7	20	85	2	72	42	0	0	57	0.98
5779396--5779439	15	2.8	16	82	6	54	68	0	0	31	0.90
5782371--5782436	11	5.7	11	72	19	55	39	3	1	56	1.24
5782828--5782872	16	2.8	16	80	9	56	40	2	0	57	1.11
5784191--5784235	21	2.1	22	84	12	58	46	2	2	48	1.26
5785036--5785115	5	15.4	5	76	17	74	63	0	0	36	0.94
5785031--5785153	32	3.8	31	71	25	94	63	1	0	34	1.04
5785036--5785153	15	7.3	17	73	21	103	63	1	0	34	1.05
5785036--5785154	19	5.8	20	73	13	100	63	1	0	35	1.05
5785036--5785153	11	10.5	11	70	18	64	63	1	0	34	1.05
5786092--5786128	1	37.0	1	88	0	56	5	0	94	0	0.30
5786090--5786128	8	5.0	8	90	6	62	7	0	92	0	0.39
5786136--5786174	13	2.9	13	80	3	51	35	0	64	0	0.94
5787369--5787419	22	2.3	21	80	9	57	66	1	0	31	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5788328--5788369	14	3.0	14	83	10	50	57	2	2	38	1.25
5791162--5791214	18	2.9	18	81	13	56	67	0	0	32	0.91
5791199--5791273	15	4.8	15	69	19	55	56	0	2	41	1.13
5791182--5791233	18	2.9	17	82	5	59	65	0	0	34	0.93
5791185--5791254	28	2.6	28	78	17	76	60	0	0	40	0.97
5791199--5791265	28	2.3	29	80	14	75	58	0	2	38	1.14
5791867--5791935	30	2.3	28	77	18	68	30	1	2	65	1.16
5792105--5792146	17	2.5	17	88	3	59	35	4	0	59	1.19
5792582--5792638	21	2.8	20	75	5	60	31	0	3	64	1.10
5792714--5792752	21	2.0	21	90	10	64	30	0	0	69	0.89
5792700--5792745	24	1.9	24	91	8	76	30	0	0	69	0.89
5792706--5792761	24	2.3	24	81	9	60	33	0	0	66	0.92
5795038--5795083	20	2.3	20	78	14	51	21	6	6	65	1.39
5795245--5795278	17	2.0	17	88	0	50	26	0	8	64	1.22
5799885--5800008	20	5.7	20	70	19	95	42	12	14	30	1.82
5800800--5800874	20	3.8	20	74	0	60	30	12	12	45	1.77
5800890--5800941	20	2.6	20	96	0	95	28	9	15	46	1.77
5807329--5807494	51	3.3	51	83	4	201	32	12	25	29	1.93
5807482--5807550	28	2.5	29	83	9	90	27	20	27	24	1.99
5807460--5807672	110	1.9	110	82	3	268	35	14	23	26	1.93
5810348--5811761	55	24.9	55	82	10	1404	26	27	20	25	1.99
5811403--5811543	28	5.1	27	62	16	65	27	29	19	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5811854--5811950	42	2.3	42	77	8	101	16	28	12	42	1.84
5812604--5812664	19	3.6	18	75	25	69	36	13	16	34	1.87
5812602--5812672	32	2.2	32	97	0	133	33	12	18	35	1.89
5812696--5812762	34	2.0	33	85	2	89	25	13	13	47	1.79
5815109--5815493	52	7.4	52	71	11	225	30	26	11	31	1.91
5815215--5815289	27	2.7	28	85	6	100	25	32	18	24	1.97
5815477--5815553	28	2.8	28	82	7	86	23	35	19	22	1.96
5815109--5815604	263	1.9	262	88	2	762	28	27	12	31	1.93
5815482--5815739	107	2.4	107	94	0	444	24	30	16	27	1.97
5815587--5815660	28	2.6	28	85	4	96	24	36	18	20	1.95
5815536--5815711	51	3.4	51	65	23	139	26	29	15	28	1.96
5815142--5815719	263	2.2	259	82	5	626	28	28	12	30	1.93
5821937--5821983	16	3.1	16	79	17	55	70	10	14	4	1.31
5823296--5823964	28	24.2	28	86	5	805	23	31	15	29	1.95
5823295--5823912	55	11.3	54	88	4	846	22	32	14	29	1.94
5823295--5823912	27	22.6	27	88	4	846	22	32	14	29	1.94
5823932--5824112	28	6.4	28	83	4	211	29	26	17	26	1.97
5823931--5824311	96	4.2	87	83	7	338	30	29	18	22	1.97
5823985--5824393	32	13.2	32	84	5	400	30	29	17	21	1.97
5824425--5824545	49	2.6	45	79	7	116	19	27	22	31	1.97
5825617--5825666	14	3.4	15	78	18	52	76	0	22	2	0.89
5825634--5825668	16	2.1	17	89	5	54	82	0	17	0	0.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5825620--5825670	20	2.6	20	84	3	59	78	0	19	1	0.85
5825613--5825666	24	2.2	24	83	6	65	75	0	22	1	0.89
5825640--5825670	10	3.1	10	95	0	53	87	0	12	0	0.55
5828769--5828829	13	5.2	13	70	22	53	40	13	16	29	1.86
5828781--5828818	20	1.9	20	88	0	58	39	15	18	26	1.91
5828769--5828851	33	2.5	33	86	0	112	40	15	15	27	1.88
5828720--5828931	115	1.8	115	90	0	343	41	15	15	27	1.88
5828884--5828913	13	2.3	13	94	0	51	40	10	16	33	1.82
5829656--5829909	83	3.0	84	79	13	261	42	11	25	19	1.85
5829872--5830238	61	6.1	60	79	8	354	30	19	24	25	1.98
5829877--5830259	122	3.2	116	80	6	394	28	19	24	27	1.99
5830279--5830393	61	1.9	61	90	0	185	26	19	27	26	1.99
5830277--5830525	55	4.4	55	79	6	250	25	19	26	28	1.99
5830008--5830629	266	2.3	268	83	4	772	27	18	26	27	1.98
5831614--5831674	1	61.0	1	76	0	59	3	1	6	88	0.67
5831625--5831674	18	2.7	18	87	3	73	4	0	6	90	0.57
5841995--5842021	4	6.8	4	100	0	54	77	0	0	22	0.76
5844110--5844278	51	3.3	51	80	4	171	30	11	27	30	1.91
5846947--5847029	33	2.5	33	90	0	121	40	14	15	28	1.87
5846991--5847040	20	2.5	20	86	0	73	44	18	14	24	1.86
5846979--5847007	13	2.2	13	100	0	58	41	17	13	27	1.87
5851503--5851659	49	3.2	49	79	0	190	35	16	22	25	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5851449--5851659	101	2.1	97	85	4	269	35	16	24	24	1.95
5854676--5855133	27	16.7	27	80	5	467	24	29	14	31	1.94
5854645--5855245	110	5.4	109	79	8	504	25	29	14	30	1.95
5854676--5855246	137	4.2	136	81	6	584	25	30	14	30	1.95
5854746--5855245	54	9.1	56	76	10	246	24	30	15	30	1.95
5855064--5856175	28	38.1	28	82	7	973	30	30	16	22	1.96
5854746--5856198	28	50.5	28	80	7	345	28	30	15	25	1.96
5855248--5855749	32	16.5	32	84	4	353	31	30	17	20	1.96
5855229--5855873	157	4.3	156	83	6	544	31	30	17	21	1.96
5855390--5856190	230	3.4	228	86	4	998	30	30	16	22	1.96

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