genome.fa.s25.2.7.7.80.10.50.1000.34.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   53   54   55   56   

This is table  34  of  56  ( 6609 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)
5809652--5809733	39	2.1	39	100	0	164	53	2	14	29	1.54
5809984--5810028	17	2.6	18	82	10	58	48	4	0	46	1.22
5813059--5813513	79	5.8	79	68	12	236	29	24	12	34	1.92
5813135--5813250	51	2.3	51	83	0	151	31	24	10	33	1.89
5813240--5813310	28	2.6	27	86	8	90	23	32	16	26	1.96
5813186--5813388	107	1.9	107	83	8	261	28	25	13	32	1.94
5816577--5816633	16	3.5	17	73	7	55	38	17	5	38	1.72
5816586--5816655	17	4.2	17	76	9	63	41	12	5	40	1.67
5817608--5817657	12	4.2	12	73	19	50	68	0	4	28	1.08
5819462--5819515	22	2.5	21	73	8	54	46	0	3	50	1.19
5820198--5820238	2	20.5	2	89	0	64	48	2	2	46	1.28
5820397--5820427	2	15.5	2	100	0	62	48	0	0	51	1.00
5825205--5825276	16	4.6	15	81	8	81	36	2	2	58	1.27
5828595--5828646	18	3.1	17	77	20	56	76	5	13	3	1.10
5835757--5835799	20	2.1	20	82	4	50	9	27	44	18	1.80
5836239--5836276	13	2.9	13	92	0	58	34	15	15	34	1.90
5840182--5840226	21	2.1	21	84	8	56	22	20	4	53	1.63
5842447--5842471	13	1.9	13	100	0	50	32	16	16	36	1.90
5845031--5845068	13	2.9	13	92	0	58	34	15	15	34	1.90
5848974--5849018	21	2.1	21	84	8	56	22	20	4	53	1.63
5851239--5851263	13	1.9	13	100	0	50	32	16	16	36	1.90
5852614--5852668	21	2.6	21	88	0	74	43	3	20	32	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5854036--5854557	258	2.0	258	99	0	1035	35	13	19	31	1.90
5865891--5865959	25	3.1	21	70	23	61	44	4	24	26	1.72
5867684--5867735	21	2.5	21	87	6	70	34	3	25	36	1.74
5868404--5868592	103	1.8	105	88	2	292	25	33	6	34	1.81
5868404--5868617	52	4.1	52	84	1	232	26	32	7	34	1.83
5872147--5872512	183	2.0	183	100	0	732	36	7	16	39	1.76
5876274--5876324	20	2.5	20	87	6	68	35	11	11	41	1.78
5877495--5877527	10	3.3	10	95	0	57	21	0	6	72	1.05
5877896--5878000	40	2.7	40	80	12	103	39	0	2	57	1.20
5877897--5877976	39	2.1	39	83	6	101	41	0	2	56	1.13
5877971--5878037	12	5.2	12	77	13	62	37	2	1	58	1.23
5877971--5878037	26	2.6	25	83	4	71	37	2	1	58	1.23
5878501--5878539	16	2.4	16	82	0	51	30	7	12	48	1.69
5879141--5879165	2	12.5	2	100	0	50	52	0	0	48	1.00
5879173--5879280	27	4.0	27	75	9	94	53	2	1	41	1.26
5888139--5888168	12	2.5	12	94	0	51	23	0	0	76	0.78
5888140--5888201	24	2.6	24	82	5	72	30	3	0	66	1.08
5891267--5891334	33	2.1	32	88	2	100	33	13	17	35	1.89
5891375--5891427	20	2.6	21	82	8	65	30	16	15	37	1.90
5891415--5891439	13	1.9	13	100	0	50	36	16	16	32	1.90
5891751--5891784	2	17.0	2	100	0	68	50	0	0	50	1.00
5893495--5893897	178	2.2	182	78	4	415	38	13	18	29	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5896013--5896095	29	2.9	27	79	15	87	36	19	6	38	1.76
5896229--5896270	23	1.9	21	90	9	66	38	0	2	59	1.10
5896663--5896696	12	2.8	12	81	0	50	26	5	11	55	1.58
5900908--5900954	23	2.0	24	88	12	71	27	4	0	68	1.08
5902766--5902798	14	2.4	14	90	10	50	60	3	0	36	1.12
5907525--5907573	14	3.4	15	78	21	52	75	0	22	2	0.90
5907548--5907577	9	3.2	9	95	4	51	86	0	13	0	0.57
5907949--5907979	14	2.2	14	100	0	62	41	0	6	51	1.27
5915384--5916556	27	43.0	27	91	1	1887	23	34	14	27	1.93
5915384--5916556	136	8.6	135	91	1	1887	23	34	14	27	1.93
5915384--5916556	163	7.2	162	92	1	1887	23	34	14	27	1.93
5916539--5916884	32	10.8	32	92	1	552	31	33	18	16	1.93
5918140--5918188	14	3.4	15	78	21	52	75	0	22	2	0.90
5918163--5918192	9	3.2	9	95	4	51	86	0	13	0	0.57
5918563--5918593	14	2.2	14	100	0	62	41	0	6	51	1.27
5924187--5924267	38	2.1	38	86	4	110	27	9	16	46	1.78
5928438--5928476	20	2.0	19	85	5	51	12	0	7	79	0.93
5929554--5929611	20	2.9	20	89	0	80	34	15	13	36	1.87
5939477--5939641	84	2.0	84	82	7	201	24	19	3	52	1.62
5941418--5941443	13	2.0	13	100	0	52	38	15	15	30	1.88
5941400--5941463	32	2.0	33	90	3	103	39	18	14	28	1.90
5941901--5941967	37	1.9	35	88	11	102	32	11	25	29	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5949784--5949833	24	2.1	24	85	7	66	30	4	6	60	1.39
5951345--5951388	21	2.1	21	83	8	54	52	20	18	9	1.72
5956643--5956700	1	58.0	1	75	0	53	87	6	5	0	0.65
5956643--5956700	10	5.9	10	83	4	73	87	6	5	0	0.65
5956643--5956701	29	2.0	30	87	9	86	86	6	6	0	0.71
5956648--5956700	19	2.7	19	85	2	70	88	5	5	0	0.62
5958626--5958675	24	2.1	24	85	7	66	30	4	6	60	1.39
5960592--5960625	11	3.2	11	91	4	52	91	8	0	0	0.43
5960589--5960636	19	2.6	17	81	12	60	83	14	2	0	0.74
5961866--5962761	28	31.6	28	86	2	1108	29	30	16	23	1.96
5961866--5962761	57	15.8	57	86	2	1241	29	30	16	23	1.96
5961868--5962791	113	8.1	114	87	3	1252	29	29	16	23	1.96
5961866--5962791	85	10.8	85	85	3	1207	29	30	16	23	1.96
5966963--5966995	16	1.9	18	88	11	52	42	12	0	45	1.41
5967020--5967067	22	2.2	21	79	17	53	45	2	4	47	1.33
5967025--5967068	22	1.9	24	86	9	65	47	2	2	47	1.27
5973695--5973746	24	2.1	26	85	7	72	61	15	0	23	1.33
5973695--5973746	25	2.0	26	85	3	70	61	15	0	23	1.33
5974430--5974468	20	1.9	20	84	5	51	48	0	0	51	1.00
5976252--5976295	13	3.3	13	77	3	52	25	0	4	70	1.06
5976247--5976312	27	2.5	26	80	7	62	25	1	4	68	1.18
5981504--5981546	13	3.4	12	78	9	50	53	0	2	44	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5985102--5985162	11	5.3	11	74	18	52	11	9	0	78	0.96
5995812--5995840	14	2.0	15	93	6	51	48	10	0	41	1.37
5999479--5999540	22	2.9	21	80	15	65	75	8	11	4	1.16
6000831--6002089	27	45.7	27	83	5	977	24	30	15	29	1.95
6000831--6002089	55	22.9	54	79	6	949	24	30	15	29	1.95
6000963--6002119	388	3.0	383	83	3	1313	25	30	15	28	1.95
6001629--6001705	29	2.7	28	89	2	109	29	35	18	16	1.93
6001597--6001752	28	5.5	29	75	8	99	26	30	15	27	1.96
6002029--6002409	28	13.1	29	84	6	352	29	28	19	22	1.98
6002186--6002518	32	10.8	32	78	6	221	28	27	19	24	1.99
6002186--6002518	63	5.4	63	77	7	224	28	27	19	24	1.99
6002543--6002653	45	2.4	47	83	6	127	19	25	18	36	1.94
6002906--6002978	21	3.3	21	76	19	62	78	2	4	15	1.02
6002905--6002978	31	2.3	32	78	17	82	77	2	4	16	1.04
6005652--6005727	20	3.8	20	89	0	107	31	13	13	42	1.82
6005652--6005727	40	1.9	40	91	0	125	31	13	13	42	1.82
6005693--6005809	51	2.3	51	93	0	198	27	19	11	41	1.85
6022431--6022480	16	3.1	17	83	13	61	54	0	0	46	1.00
6022783--6022886	31	3.4	30	70	16	72	25	16	18	39	1.91
6029055--6029138	38	2.2	38	85	6	109	39	19	17	23	1.92
6029055--6029160	38	2.8	38	81	5	99	34	19	17	27	1.95
6034581--6034605	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6034676--6034702	13	2.1	13	100	0	54	40	14	14	29	1.86
6043427--6043476	20	2.5	20	87	9	68	42	16	16	26	1.88
6048892--6048965	28	2.6	29	76	10	80	22	24	12	40	1.88
6050867--6050909	11	3.7	11	76	11	50	51	0	0	48	1.00
6050900--6050962	31	2.0	32	87	3	92	42	0	1	55	1.09
6052072--6052104	13	2.5	13	95	0	57	45	6	39	9	1.61
6052188--6052258	27	2.6	27	84	6	90	45	23	8	22	1.80
6054142--6054187	21	2.1	22	84	4	58	19	30	19	30	1.97
6056639--6056672	13	2.6	13	100	0	68	44	5	41	8	1.60
6056755--6056825	27	2.6	27	88	6	99	46	23	7	22	1.76

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   53   54   55   56