genome.fa.s6.2.7.7.80.10.50.1000.18.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  18  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)
4871527--4871574	17	2.7	18	80	6	53	50	14	4	31	1.62
4871579--4871639	17	3.6	17	77	16	72	52	4	11	31	1.58
4878424--4878692	113	2.4	113	87	4	380	26	23	22	28	1.99
4878424--4878741	114	2.8	113	85	2	406	25	22	22	29	1.99
4879362--4879401	20	2.0	20	85	5	53	17	2	27	52	1.57
4879396--4879478	7	11.9	7	78	5	60	9	1	48	40	1.44
4879364--4879472	21	5.2	21	67	9	53	13	1	40	44	1.55
4879450--4879479	15	2.0	15	93	0	51	10	0	53	36	1.35
4879942--4880446	232	2.2	232	93	0	859	29	18	20	31	1.96
4880711--4880755	19	2.4	19	80	0	54	35	40	2	22	1.66
4883291--4883498	113	1.8	114	91	1	346	48	7	4	40	1.51
4883288--4883963	57	11.6	57	76	13	442	44	9	4	41	1.57
4883288--4883482	20	10.2	20	69	15	101	48	6	4	40	1.50
4883344--4883927	206	2.8	208	95	0	1037	44	9	5	41	1.58
4883587--4883688	20	5.2	20	73	11	86	48	6	4	40	1.52
4883614--4883816	94	2.2	94	80	1	237	43	10	5	40	1.62
4883795--4883952	20	8.2	20	72	16	145	47	7	4	40	1.52
4883664--4883873	94	2.2	94	80	6	239	43	10	4	41	1.59
4883612--4883932	151	2.1	151	81	5	373	44	9	4	41	1.59
4883978--4884201	9	25.4	9	74	11	187	47	19	1	31	1.58
4883759--4884028	114	2.4	114	83	7	282	47	10	3	38	1.56
4884088--4884208	61	2.0	61	82	10	151	49	20	0	29	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4883984--4884171	104	1.8	104	89	2	297	45	20	1	31	1.61
4889683--4889749	21	3.2	20	78	4	71	32	17	43	5	1.74
4890112--4890235	41	3.0	42	84	7	144	25	18	20	35	1.95
4892272--4892321	21	2.5	20	81	12	59	64	6	0	30	1.18
4892285--4892347	20	3.2	20	84	6	85	55	4	0	39	1.21
4897396--4897502	41	2.6	42	74	4	101	17	26	22	33	1.96
4897549--4897660	41	2.7	41	79	8	129	18	23	23	34	1.96
4897471--4897660	78	2.4	78	81	5	202	17	23	22	36	1.95
4898185--4898223	15	2.7	14	80	7	51	20	0	38	41	1.53
4898158--4898224	14	4.9	14	77	14	59	26	0	31	41	1.56
4899609--4899660	27	1.9	27	84	0	68	42	0	9	48	1.36
4900536--4900562	11	2.5	11	100	0	54	25	18	0	55	1.43
4902380--4902430	21	2.4	22	80	9	70	47	0	1	50	1.12
4902518--4902558	13	2.8	15	85	14	59	46	19	0	34	1.50
4902641--4902926	9	32.8	9	70	17	185	45	20	3	30	1.69
4902662--4902817	34	4.5	34	85	9	199	46	21	1	30	1.59
4902601--4902869	43	6.2	43	70	15	164	48	19	2	28	1.62
4902734--4902883	62	2.4	62	86	4	214	46	18	5	30	1.71
4909049--4909378	43	7.6	43	83	6	299	23	23	23	28	1.99
4909049--4909364	86	3.7	86	80	5	334	24	24	23	28	2.00
4909125--4909364	129	1.9	129	86	0	345	25	24	22	27	2.00
4909049--4909534	43	11.3	43	77	8	292	24	23	23	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4909558--4909637	40	2.0	40	100	0	160	22	22	25	30	1.99
4912252--4912300	24	2.1	24	88	3	73	30	2	2	65	1.15
4912592--4912724	3	44.3	3	98	0	257	66	0	33	0	0.92
4921372--4921527	78	2.0	78	98	0	303	30	21	15	32	1.94
4922225--4922318	41	2.3	41	77	15	95	37	17	14	30	1.90
4922580--4922646	3	22.3	3	100	0	134	32	0	0	67	0.91
4924501--4924567	25	2.7	25	72	9	73	20	23	17	37	1.94
4924501--4924595	50	1.9	50	82	4	120	20	23	20	36	1.95
4925380--4925484	7	15.0	7	81	0	93	40	0	30	29	1.57
4929267--4929322	29	1.9	29	92	0	94	39	5	7	48	1.54
4931991--4932040	20	2.5	21	80	9	59	58	0	2	40	1.10
4931990--4932095	20	5.2	20	66	17	56	58	0	3	37	1.16
4938093--4938243	25	6.1	25	71	11	98	16	26	21	35	1.94
4937947--4938139	104	1.9	104	85	2	271	20	27	21	31	1.98
4938093--4938236	73	2.0	73	82	5	175	16	25	20	36	1.94
4940455--4940503	20	2.5	19	83	6	62	8	12	4	75	1.16
4943778--4943821	21	2.1	21	82	0	52	36	25	27	11	1.90
4947835--4947952	34	3.4	34	69	11	114	37	17	11	33	1.85
4947838--4947991	69	2.2	69	92	0	263	32	17	11	38	1.85
4947868--4947987	35	3.5	35	69	6	100	31	18	10	40	1.84
4952418--4952447	14	2.1	14	100	0	60	33	16	13	36	1.88
4953735--4953987	125	2.0	125	94	1	445	28	16	24	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4954242--4954289	25	1.9	25	100	0	96	39	14	0	45	1.45
4954257--4954347	48	2.0	47	86	6	132	50	12	0	37	1.40
4954274--4954432	48	3.1	48	69	22	149	49	11	1	37	1.50
4954410--4954467	25	2.3	25	91	5	91	44	12	0	43	1.41
4954382--4954512	70	1.9	70	96	0	244	49	12	0	37	1.41
4954941--4954980	18	2.2	18	86	0	53	42	5	27	25	1.75
4956806--4956903	51	1.9	51	87	4	144	45	3	23	27	1.67
4956865--4956919	11	4.9	11	75	20	60	41	1	29	27	1.66
4956865--4956919	22	2.5	21	83	16	67	41	1	29	27	1.66
4957305--4957476	89	1.9	89	86	1	247	46	5	22	25	1.74
4958067--4958372	164	1.9	164	84	8	417	30	13	18	38	1.89
4961245--4961310	34	1.9	35	90	3	107	30	12	7	50	1.67
4966458--4966483	5	5.2	5	100	0	52	61	0	0	38	0.96
4971506--4971540	18	1.9	18	88	0	52	37	14	2	45	1.59
4973093--4973142	25	2.0	25	84	3	66	18	14	6	62	1.51
4973906--4973981	3	25.3	3	100	0	152	67	0	0	32	0.91
4976701--4976751	10	5.3	10	77	17	54	47	0	0	52	1.00
4976681--4976732	18	2.8	18	82	5	59	40	0	0	59	0.97
4976729--4976754	10	2.6	10	100	0	52	53	0	0	46	1.00
4976744--4976782	16	2.3	17	86	13	62	41	0	0	58	0.98
4976744--4976791	18	2.5	17	83	16	51	45	0	0	54	0.99
4976984--4977298	165	1.9	159	82	8	384	31	14	18	35	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4985317--4985403	38	2.3	38	80	5	97	48	3	1	47	1.26
4985377--4985444	22	3.3	20	77	20	61	63	0	4	32	1.14
4991157--4991475	165	1.9	166	86	1	453	31	14	16	37	1.89
4993177--4993242	29	2.3	29	97	0	123	33	4	6	56	1.44
4994137--4994176	18	2.2	19	95	4	73	32	10	10	47	1.70
4995225--4995249	13	1.9	13	100	0	50	24	8	28	40	1.83
5001539--5001569	9	3.4	9	90	0	53	25	12	22	38	1.90
5011901--5012543	46	14.0	46	86	1	851	23	15	30	31	1.95
5011901--5012543	274	2.3	275	89	0	1000	23	15	30	31	1.95
5014061--5018271	46	90.5	46	78	6	2835	22	15	28	28	1.94
5014469--5014547	38	2.1	38	90	0	122	25	12	34	27	1.92
5015086--5018271	183	17.1	182	78	5	2896	23	16	28	28	1.95
5016259--5018271	137	14.6	137	86	1	2713	23	17	29	29	1.97
5037281--5039266	46	43.3	46	87	1	2820	24	16	29	29	1.96
5042971--5043018	2	24.0	2	100	0	96	50	0	0	50	1.00
5043333--5043365	16	2.0	17	88	5	50	39	3	6	51	1.42
5052698--5052753	28	2.0	28	100	0	112	35	14	14	35	1.86
5059569--5059653	36	2.3	36	84	6	109	7	23	11	57	1.58
5063161--5063354	30	6.5	29	85	3	226	37	19	2	41	1.63
5063535--5063570	18	2.1	17	90	10	56	86	2	11	0	0.68
5075321--5075363	18	2.4	18	80	7	52	32	9	4	53	1.53
5081883--5081931	14	3.9	13	77	22	52	77	8	0	14	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5081890--5081988	18	5.5	18	73	17	64	73	9	2	15	1.16
5082923--5082972	7	7.0	7	82	17	59	70	0	16	14	1.18
5082924--5082954	13	2.3	13	94	5	53	74	0	12	12	1.08
5082923--5082974	15	3.6	15	82	15	65	69	0	17	13	1.19
5084363--5084639	43	6.5	43	80	4	303	17	33	31	16	1.93
5084363--5084636	85	3.2	86	82	4	331	16	33	32	17	1.92
5084363--5084636	128	2.1	128	87	1	397	16	33	32	17	1.92
5084667--5084724	21	2.8	22	82	15	70	55	3	1	39	1.27
5085646--5086002	176	2.0	176	97	0	669	37	17	18	27	1.93
5088112--5088175	29	2.2	29	81	10	76	31	26	6	35	1.81

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