genome.fa.s1.2.7.7.80.10.50.1000.38.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  38  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)
6240296--6240343	16	3.3	15	85	11	64	54	2	0	43	1.12
6241061--6241088	14	2.0	14	100	0	56	21	0	0	78	0.75
6242054--6242102	2	24.5	2	100	0	98	51	0	0	48	1.00
6242476--6242542	29	2.3	30	86	2	100	41	0	1	56	1.08
6242486--6242549	29	2.2	29	85	2	83	40	1	0	57	1.08
6244037--6244106	23	3.2	23	78	13	60	42	1	0	55	1.08
6247386--6247431	2	23.5	2	91	4	76	54	0	0	45	0.99
6250026--6250055	15	1.9	16	93	6	53	26	0	60	13	1.34
6263360--6263456	23	4.1	21	69	24	59	43	2	3	51	1.29
6263362--6263411	23	2.0	23	85	11	64	48	2	4	46	1.32
6263580--6263635	30	1.9	29	82	7	69	39	16	1	42	1.58
6263697--6263762	29	2.3	29	89	0	96	46	7	10	34	1.67
6264902--6264956	16	3.6	15	77	20	60	36	1	0	61	1.06
6265480--6265513	17	2.0	17	88	11	52	47	0	0	52	1.00
6265461--6265513	18	3.1	18	81	5	56	49	0	0	50	1.00
6268620--6268652	2	16.5	2	100	0	66	51	0	0	48	1.00
6268926--6268967	3	14.0	3	94	0	75	30	0	2	66	1.04
6269684--6269752	29	2.4	30	76	7	72	52	1	0	46	1.09
6269873--6269924	22	2.4	22	80	6	61	32	0	1	65	1.04
6269907--6269951	19	2.4	18	82	10	54	55	0	0	44	0.99
6269923--6269962	20	2.1	19	85	4	53	60	0	0	40	0.97
6270855--6270916	26	2.4	25	81	7	70	54	4	8	32	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6275506--6275599	42	2.2	42	86	0	125	46	5	14	32	1.67
6284481--6284520	3	13.3	3	94	0	71	0	32	2	65	1.06
6288182--6288237	16	3.5	16	80	9	78	35	8	8	46	1.67
6288172--6288237	32	2.0	33	97	2	125	30	9	10	50	1.68
6290491--6290544	21	2.6	19	81	16	63	53	0	0	46	1.00
6290495--6290560	33	2.0	33	85	8	91	57	0	0	42	0.98
6295824--6295862	19	2.1	19	90	9	62	30	0	0	69	0.89
6297294--6297324	3	10.3	3	100	0	62	32	0	0	67	0.91
6299598--6299636	20	1.9	20	84	5	51	46	2	0	51	1.14
6300885--6300926	21	2.0	20	86	4	57	40	0	0	59	0.97
6302798--6302831	17	2.0	17	100	0	68	41	23	11	23	1.87
6302998--6303053	21	2.8	20	81	5	67	64	3	1	30	1.21
6305550--6305604	2	27.5	2	92	0	83	50	5	0	43	1.25
6306309--6306343	2	17.5	2	100	0	70	48	0	0	51	1.00
6308183--6308245	15	4.1	15	74	11	56	47	3	4	44	1.40
6309459--6309496	10	3.8	10	92	0	58	34	0	0	65	0.93
6310129--6310171	17	2.4	18	92	3	70	41	0	0	58	0.98
6310555--6310615	29	2.0	30	84	6	79	47	8	6	37	1.59
6310705--6310748	14	3.2	13	80	3	52	59	2	0	38	1.10
6310899--6310971	39	1.9	39	88	5	114	58	4	1	35	1.25
6312257--6312292	15	2.4	15	90	0	54	13	2	66	16	1.36
6313883--6313915	15	2.2	15	89	10	50	0	0	12	87	0.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6313889--6313913	13	1.9	13	100	0	50	0	0	12	88	0.53
6315954--6315999	2	23.0	2	100	0	92	50	0	0	50	1.00
6322775--6322801	2	13.5	2	100	0	54	51	0	48	0	1.00
6323149--6323173	11	2.3	11	100	0	50	40	0	36	24	1.55
6323476--6323518	18	2.5	17	85	7	52	48	0	0	51	1.00
6325807--6325871	32	2.0	33	85	5	89	58	0	0	41	0.98
6326768--6326806	18	2.2	17	86	13	53	33	0	0	66	0.92
6327790--6327818	2	15.0	2	92	7	51	48	0	0	51	1.00
6328556--6328717	78	2.0	83	84	8	217	45	3	4	46	1.40
6330055--6330129	35	2.1	36	83	9	93	56	1	0	42	1.08
6334775--6334813	12	3.3	12	82	17	55	41	0	0	58	0.98
6334770--6334813	22	2.0	23	90	4	72	40	0	0	59	0.98
6334775--6334819	22	2.0	22	87	8	65	46	0	0	53	1.00
6335311--6335362	21	2.5	21	84	6	61	51	0	0	48	1.00
6335336--6335380	15	3.0	15	83	6	56	62	0	0	37	0.96
6335759--6335851	48	1.9	49	85	10	129	44	0	2	53	1.12
6335790--6335876	27	3.1	28	79	14	83	41	0	1	57	1.06
6336014--6336047	4	8.5	4	100	0	68	76	0	0	23	0.79
6336611--6336655	20	2.2	20	96	0	81	66	4	6	22	1.33
6339620--6340031	204	2.0	204	94	0	718	37	23	20	18	1.94
6340492--6340532	2	20.5	2	100	0	82	48	0	0	51	1.00
6342519--6342673	80	1.9	80	92	2	258	40	14	9	35	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6343767--6343796	12	2.5	12	94	0	51	40	0	0	60	0.97
6344091--6344130	17	2.4	17	87	4	64	62	0	0	37	0.95
6345684--6345738	27	2.1	26	86	3	74	60	0	1	38	1.08
6346438--6346622	89	2.0	91	81	12	211	51	0	1	46	1.14
6349367--6349412	6	7.0	6	81	18	56	34	0	4	60	1.16
6349367--6349412	13	3.5	13	87	3	65	34	0	4	60	1.16
6352009--6352036	2	14.0	2	100	0	56	50	0	0	50	1.00
6352428--6352461	13	2.5	13	90	4	50	32	5	44	17	1.73
6356404--6356448	13	3.5	13	81	6	56	35	6	42	15	1.73
6356719--6356747	11	2.5	12	94	5	51	72	0	0	27	0.85
6356683--6356745	25	2.6	24	73	9	65	66	1	1	30	1.10
6360531--6360577	21	2.2	21	78	14	53	46	2	0	51	1.13
6361277--6361509	50	4.6	50	93	0	376	30	21	20	27	1.98
6365888--6366121	50	4.7	50	91	0	360	31	20	19	29	1.97
6370666--6370711	20	2.3	20	84	0	56	34	4	47	13	1.62
6375225--6375270	20	2.3	20	84	0	56	34	4	47	13	1.62
6375886--6375941	26	2.2	26	90	6	87	46	21	1	30	1.62
6382396--6382425	13	2.3	13	94	0	51	23	3	10	63	1.40
6382982--6383035	23	2.4	24	90	9	87	55	0	0	44	0.99
6383051--6383117	29	2.3	28	78	12	73	59	1	1	37	1.16
6385233--6385278	18	2.5	19	76	16	51	30	0	2	67	1.03
6387639--6387671	2	16.5	2	100	0	66	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6388008--6388049	2	21.0	2	100	0	84	50	0	0	50	1.00
6389314--6389353	16	2.4	18	80	19	52	45	0	2	52	1.14
6391488--6391554	31	2.2	31	88	0	98	23	10	23	41	1.85
6391561--6391622	31	2.0	31	81	6	72	38	12	19	29	1.89
6394814--6394850	2	18.5	2	100	0	74	51	0	0	48	1.00
6394850--6394880	2	15.5	2	100	0	62	51	0	48	0	1.00
6398867--6398891	13	1.9	13	100	0	50	64	4	0	32	1.12
6399695--6399729	18	2.0	18	94	5	63	40	14	0	45	1.45
6404986--6405018	17	1.9	17	93	0	57	57	0	0	42	0.98
6404986--6405021	18	2.1	17	89	5	54	58	0	0	41	0.98
6406314--6406355	21	2.0	21	95	0	75	38	11	9	40	1.75
6411788--6411898	30	3.7	30	77	4	107	42	9	1	46	1.45
6417342--6417388	2	24.5	2	79	16	55	44	2	0	53	1.12
6417330--6417389	23	2.6	23	86	7	77	46	1	0	51	1.10
6417814--6417879	21	3.0	21	75	14	71	63	0	0	36	0.95
6417813--6417873	11	5.8	10	75	7	50	65	0	0	34	0.93
6417824--6417896	21	3.4	20	71	15	56	64	0	0	35	0.94
6417821--6417917	33	3.0	33	75	11	94	61	0	0	38	0.96
6417883--6417936	25	2.2	24	84	12	74	53	0	0	46	1.00
6417920--6417964	24	2.0	22	91	8	72	46	4	0	48	1.22
6420892--6421022	66	2.0	66	98	1	253	54	11	3	31	1.52
6423118--6423158	20	2.0	21	86	13	59	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6435032--6435061	2	15.0	2	100	0	60	50	0	0	50	1.00
6441155--6441190	19	1.9	18	88	5	54	25	0	2	72	0.98
6442480--6442549	25	2.9	23	78	14	70	44	0	0	55	0.99
6442740--6442785	24	1.9	24	82	8	58	50	0	2	47	1.13
6442761--6442793	18	1.9	17	88	11	50	42	0	3	54	1.15
6443561--6443604	22	2.1	21	87	8	63	45	0	0	54	0.99
6443838--6443908	25	2.8	25	84	4	79	61	0	1	36	1.05
6443870--6443920	5	10.2	5	76	16	52	60	0	0	39	0.97
6443867--6443903	17	2.2	17	90	9	58	64	0	0	35	0.94
6443874--6443934	18	3.2	18	84	13	61	57	0	0	42	0.98

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