genome.fa.s6.2.7.7.80.10.50.1000.118.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  118  of  168  ( 20060 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)
34353257--34353331	19	4.0	19	70	20	68	36	1	26	36	1.65
34361719--34361761	22	2.0	22	100	0	86	37	13	25	23	1.92
34362630--34362658	14	2.1	14	100	0	58	37	6	0	55	1.27
34366076--34366156	27	3.0	27	87	0	108	11	39	22	27	1.87
34385957--34385994	18	2.2	17	86	13	51	39	5	0	55	1.23
34386619--34386655	17	2.3	16	90	9	58	48	0	2	48	1.15
34387759--34387846	39	2.2	40	84	6	108	35	5	19	39	1.75
34388020--34388102	39	2.2	39	82	6	98	18	21	22	37	1.94
34388051--34388151	45	2.2	45	92	0	166	19	17	20	41	1.90
34388131--34388179	6	7.8	6	84	6	62	20	18	14	46	1.83
34388324--34388349	2	13.0	2	100	0	52	50	0	0	50	1.00
34388874--34388899	13	2.0	13	100	0	52	76	0	0	23	0.78
34391076--34391127	27	1.9	27	88	0	77	7	15	55	21	1.64
34391522--34391566	21	2.1	21	95	0	81	24	28	15	31	1.96
34397059--34397092	18	1.9	17	88	5	50	35	5	0	58	1.22
34398154--34398215	26	2.2	28	86	8	83	58	3	4	33	1.36
34403139--34403310	9	18.4	9	67	17	75	66	2	1	29	1.14
34403136--34403301	28	5.9	28	83	12	198	65	2	1	30	1.13
34403230--34403310	28	2.9	28	76	12	85	67	2	2	27	1.15
34403496--34403559	19	3.3	20	76	12	71	23	9	3	64	1.38
34403555--34403602	19	2.5	19	75	3	51	37	4	0	58	1.18
34406363--34406407	3	15.0	3	100	0	90	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34406910--34407093	96	1.9	95	94	1	323	32	10	8	48	1.68
34408710--34408780	27	2.6	27	84	0	97	40	16	19	22	1.91
34409179--34409238	29	2.0	32	87	9	90	31	15	15	38	1.88
34410908--34411028	60	2.0	61	90	1	190	41	8	6	43	1.60
34414532--34415087	114	4.9	113	78	10	519	23	22	25	27	2.00
34414533--34415087	229	2.4	226	80	9	610	23	22	25	27	2.00
34415755--34415839	31	2.6	32	79	5	91	21	1	40	37	1.61
34416622--34416711	39	2.3	39	86	5	130	17	2	40	40	1.62
34419782--34419844	22	2.7	23	79	18	69	46	0	3	50	1.17
34419776--34419856	12	7.5	11	71	25	50	45	0	2	51	1.14
34419979--34420321	9	39.7	9	67	21	182	44	21	0	32	1.57
34419976--34420059	43	2.0	43	85	0	114	48	25	0	26	1.51
34420083--34420208	19	6.5	19	68	17	64	45	19	0	34	1.57
34420064--34420321	78	3.3	75	77	16	255	44	20	0	34	1.57
34420236--34420263	13	2.2	13	100	0	56	39	25	0	35	1.56
34428037--34428071	18	1.9	18	88	0	52	25	17	14	42	1.86
34431035--34431082	23	2.1	23	100	0	96	25	16	27	31	1.97
34432748--34432811	3	21.3	3	85	6	85	62	1	4	31	1.25
34438050--34438130	40	2.0	40	90	0	126	22	23	19	34	1.96
34442393--34442542	59	2.5	59	83	8	182	44	9	4	42	1.55
34442444--34442481	20	1.9	20	94	0	67	52	10	0	36	1.36
34442878--34442925	11	4.3	11	81	2	51	12	10	4	72	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34442866--34442925	22	2.7	22	84	7	68	11	11	5	71	1.28
34442860--34442925	23	3.0	22	80	8	71	13	10	4	71	1.29
34445189--34445286	26	3.7	25	71	17	74	66	3	8	22	1.33
34446333--34446367	3	11.7	3	100	0	70	31	0	0	68	0.90
34447007--34447094	13	6.7	13	82	11	99	34	1	6	57	1.32
34447007--34447090	40	2.1	39	86	2	114	33	1	7	58	1.33
34447263--34447294	16	2.0	16	100	0	64	37	6	6	50	1.53
34448225--34448446	115	2.0	112	90	2	345	33	22	13	29	1.93
34449188--34449220	10	3.3	10	87	12	50	48	27	0	24	1.51
34451294--34451342	10	4.8	10	84	2	62	8	0	6	85	0.73
34451294--34451342	25	2.0	24	88	4	71	8	0	6	85	0.73
34451775--34451815	21	1.9	21	85	5	55	26	2	7	63	1.33
34463960--34464319	132	2.7	133	86	3	528	29	18	23	28	1.98
34463963--34464344	133	2.9	132	84	4	518	28	19	23	28	1.98
34463908--34464401	89	5.6	89	76	7	414	30	19	23	27	1.98
34463960--34464399	133	3.3	132	82	2	490	29	19	23	27	1.98
34464092--34464506	222	1.9	223	82	2	530	29	18	22	28	1.98
34465750--34465783	5	6.8	5	86	0	50	14	0	5	79	0.91
34466215--34466270	21	2.7	20	78	10	58	28	5	5	60	1.41
34466300--34466389	26	3.6	26	72	13	89	40	6	3	50	1.45
34469633--34469657	8	3.1	8	100	0	50	64	36	0	0	0.94
34472758--34472786	9	3.2	9	100	0	58	68	0	0	31	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34472897--34472954	16	3.3	16	77	17	62	41	0	36	22	1.54
34473320--34473356	9	4.1	9	89	0	56	29	13	10	45	1.77
34473409--34473439	9	3.4	9	100	0	62	41	22	12	22	1.88
34474353--34474389	9	4.1	9	85	0	56	48	13	8	29	1.71
34475044--34475069	5	5.2	5	100	0	52	19	19	19	42	1.90
34475343--34475386	23	1.9	23	86	9	63	59	0	2	38	1.10
34477877--34477903	2	13.5	2	100	0	54	48	0	0	51	1.00
34478171--34478258	46	1.9	46	81	4	106	28	3	9	59	1.44
34479826--34479887	21	2.8	21	80	11	63	41	8	0	50	1.32
34485540--34486234	370	1.9	371	96	0	1275	40	12	19	27	1.87
34490283--34490341	22	2.7	22	84	5	75	79	0	20	0	0.73
34490285--34490343	20	3.1	18	80	11	64	77	0	22	0	0.76
34490274--34490340	26	2.6	26	77	13	75	82	1	16	0	0.75
34491587--34491887	44	6.8	44	67	17	142	30	18	23	26	1.98
34491722--34491899	88	2.0	88	79	8	193	30	17	23	28	1.97
34491606--34491887	132	2.1	132	91	0	447	31	17	24	26	1.97
34491925--34492084	50	3.2	50	73	3	178	32	20	20	26	1.97
34493587--34494301	50	14.3	49	69	5	401	31	22	21	24	1.98
34493583--34494301	100	7.2	100	91	0	1073	31	22	21	24	1.98
34496078--34496113	3	12.0	3	100	0	72	33	0	0	66	0.92
34496475--34496507	17	1.9	17	93	0	57	33	3	9	54	1.47
34496631--34496711	35	2.3	36	85	8	105	37	7	2	53	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34496662--34496800	51	2.8	51	75	15	137	33	10	2	53	1.49
34501082--34501180	51	1.9	51	97	0	189	50	19	5	25	1.67
34503007--34503082	22	3.5	22	96	0	134	32	14	23	28	1.94
34507155--34507202	19	2.5	19	80	12	53	43	4	0	52	1.20
34522656--34522681	11	2.4	11	100	0	52	69	15	0	15	1.20
34541385--34541525	64	2.2	64	80	2	158	19	30	21	27	1.98
34541407--34541570	64	2.6	64	75	5	154	25	25	21	27	2.00
34543397--34543442	15	3.1	15	80	0	65	30	21	19	28	1.98
34547029--34547062	15	2.3	15	100	0	68	35	14	5	44	1.70
34547248--34547298	20	2.3	23	83	9	63	74	7	1	15	1.13
34547248--34547298	10	4.8	10	76	21	50	74	7	1	15	1.13
34547409--34547486	27	2.9	27	92	0	120	21	23	37	17	1.94
34547413--34547502	27	3.3	27	85	3	92	22	24	36	16	1.94
34547934--34548010	40	2.0	37	82	9	93	36	3	9	50	1.52
34553687--34553716	16	1.9	15	93	6	51	26	3	0	70	1.03
34554241--34554388	35	4.3	32	69	16	93	0	31	0	68	0.95
34554294--34554397	5	21.2	5	70	14	56	0	32	0	66	0.98
34554240--34554328	36	2.5	37	85	7	114	0	30	0	69	0.89
34554240--34554413	31	5.2	32	77	15	126	1	30	0	68	0.97
34554296--34554384	43	2.1	42	89	4	135	1	32	0	66	0.99
34554233--34554389	38	4.4	37	74	19	124	0	31	0	68	0.95
34554540--34554565	12	2.2	12	100	0	52	0	0	7	92	0.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34557512--34557561	3	16.7	3	100	0	100	32	0	0	68	0.90
34557860--34557918	19	3.0	19	76	11	57	52	0	6	40	1.28
34562320--34562353	3	11.3	3	100	0	68	35	0	0	64	0.94
34562352--34562377	3	8.7	3	100	0	52	34	0	30	34	1.58
34562585--34562688	37	2.8	36	73	15	95	38	9	1	50	1.46
34565648--34565881	36	6.7	33	74	20	158	32	26	19	20	1.97
34565728--34565840	38	3.0	38	93	5	187	36	26	17	19	1.94
34565735--34565855	36	3.4	35	91	7	183	37	28	15	19	1.92
34565835--34565887	27	1.9	28	88	3	81	28	28	20	22	1.99
34565810--34566065	103	2.5	102	87	3	363	32	26	17	22	1.97

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168