genome.fa.s6.2.7.7.80.10.50.1000.143.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  143  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)
42173981--42174017	17	2.2	17	90	9	58	2	18	0	78	0.87
42174545--42174593	26	1.9	25	84	12	64	10	10	2	77	1.07
42177819--42177888	16	4.4	16	75	22	76	1	28	0	70	0.96
42177803--42177906	47	2.2	47	94	0	181	0	30	0	68	0.96
42177879--42177961	6	13.5	6	74	14	62	3	20	4	71	1.20
42177823--42177906	17	5.1	17	72	17	79	1	28	0	70	0.95
42177819--42177895	22	3.4	22	75	10	91	1	28	0	70	0.96
42177842--42177919	29	2.7	28	79	11	77	0	26	2	70	1.00
42178602--42178685	6	13.5	6	76	16	73	3	19	3	73	1.12
42178589--42178640	22	2.3	23	83	9	63	0	23	1	75	0.91
42178589--42178632	16	2.6	17	86	13	65	0	25	0	75	0.81
42178652--42178716	23	2.8	23	81	11	62	15	13	0	70	1.16
42180993--42181043	21	2.4	21	96	0	93	54	5	29	9	1.56
42198243--42198293	17	2.8	18	82	5	68	70	1	1	25	1.08
42198242--42198295	28	2.0	28	85	3	74	68	1	1	27	1.10
42198242--42198322	36	2.2	38	86	4	121	65	2	3	28	1.22
42198245--42198302	17	3.3	17	75	13	55	67	1	3	27	1.17
42198474--42198570	9	10.6	9	74	18	76	28	4	1	65	1.17
42198475--42198580	19	5.7	18	73	13	74	26	3	1	67	1.17
42198475--42198581	9	11.4	9	69	19	60	26	3	1	68	1.17
42198548--42198589	18	2.3	19	79	4	50	19	4	2	73	1.12
42198646--42198687	21	2.0	20	86	4	57	30	2	0	66	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42207265--42207289	11	2.3	11	100	0	50	16	36	0	48	1.46
42207269--42207305	11	3.2	12	88	7	51	27	24	0	48	1.51
42209574--42209691	49	2.4	49	94	0	200	45	2	9	42	1.49
42212790--42213202	125	3.3	125	91	0	628	30	18	18	33	1.94
42216190--42216225	17	2.1	17	94	0	63	41	8	0	50	1.33
42216313--42216348	17	2.0	19	89	10	58	72	5	5	16	1.23
42216982--42217051	23	3.0	23	89	2	95	62	0	1	35	1.04
42229334--42229371	18	2.2	18	86	9	53	68	2	7	21	1.28
42230798--42230847	24	2.2	24	85	7	68	6	6	10	78	1.10
42232985--42233035	25	2.1	25	85	7	70	56	11	0	31	1.35
42233890--42233919	11	2.7	11	94	0	51	60	3	26	10	1.45
42234361--42234466	33	3.2	33	91	0	158	18	26	38	16	1.91
42243297--42243341	23	2.0	23	81	0	54	22	0	15	62	1.33
42243750--42243796	22	2.1	22	84	0	58	38	2	2	57	1.23
42243768--42243794	8	3.4	8	100	0	54	37	0	0	62	0.95
42243817--42243860	23	1.9	23	85	0	61	38	6	2	52	1.41
42244039--42244085	3	15.7	3	100	0	94	34	0	0	65	0.93
42244874--42244918	19	2.3	20	81	7	58	26	20	6	46	1.75
42251119--42251149	16	1.9	16	93	0	53	19	32	6	41	1.77
42252992--42253306	44	7.2	44	78	2	220	35	16	19	28	1.94
42252918--42253070	81	1.9	81	81	8	186	33	16	20	29	1.94
42252995--42253395	88	4.5	88	76	6	295	33	16	19	29	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42253210--42253390	94	1.9	95	84	5	242	30	18	20	29	1.96
42253100--42253410	44	7.0	44	74	13	145	33	17	20	29	1.95
42254901--42254934	4	8.5	4	86	0	50	23	5	0	70	1.09
42254971--42255011	17	2.6	16	82	17	50	21	4	4	68	1.28
42255006--42255057	24	2.2	24	82	6	61	19	3	5	71	1.22
42263171--42263207	12	2.9	13	84	15	51	32	0	0	67	0.91
42264032--42264184	22	7.0	22	90	0	225	32	14	26	26	1.94
42265826--42265873	23	2.1	23	100	0	96	35	12	16	35	1.87
42268171--42268304	59	2.3	57	83	8	173	42	16	19	21	1.89
42269341--42269446	37	3.2	32	75	19	108	44	0	1	53	1.11
42269403--42269444	15	2.8	15	78	10	50	50	0	0	50	1.00
42275000--42275051	27	2.0	27	88	11	81	59	3	3	32	1.33
42278708--42279241	125	4.3	126	86	1	745	29	18	22	29	1.97
42278708--42279241	250	2.1	250	92	0	879	29	18	22	29	1.97
42282455--42283763	22	60.6	22	69	15	438	21	0	28	48	1.56
42282446--42282476	16	2.0	16	93	6	55	22	0	32	45	1.53
42282420--42282486	14	4.6	15	73	12	59	25	0	28	46	1.53
42282657--42282722	29	2.3	29	84	2	80	19	1	28	50	1.57
42282713--42282765	14	3.7	14	80	5	61	22	0	26	50	1.49
42282807--42282876	15	4.7	15	74	12	63	21	0	27	51	1.48
42282984--42283763	21	36.6	21	68	15	270	22	0	28	48	1.56
42283319--42283367	15	3.3	15	80	2	55	20	0	28	51	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42283311--42283374	29	2.2	29	77	2	67	20	0	31	48	1.50
42283593--42283668	15	5.1	16	70	13	63	18	0	27	53	1.44
42283315--42283853	235	2.3	235	86	3	764	21	0	29	48	1.53
42283585--42283776	86	2.2	86	85	2	251	19	0	29	51	1.51
42283746--42283807	33	1.9	32	83	9	81	29	0	27	43	1.55
42283802--42283853	22	2.3	22	93	3	86	17	0	32	50	1.47
42283812--42283859	22	2.2	22	92	0	78	16	0	31	52	1.45
42283819--42283890	37	1.9	37	86	5	101	19	0	27	52	1.46
42283857--42283905	22	2.2	23	85	3	64	16	2	26	55	1.52
42283799--42283914	59	1.9	61	91	6	193	20	0	28	50	1.55
42283879--42283971	22	4.3	22	80	1	98	18	1	25	54	1.50
42283847--42284005	44	3.7	44	75	6	130	22	1	27	49	1.57
42284073--42284123	21	2.4	21	80	0	57	17	1	27	52	1.55
42284059--42284259	22	9.4	22	72	11	114	19	1	29	48	1.58
42284094--42284262	42	4.0	42	85	7	209	20	1	30	47	1.57
42284116--42284261	21	6.9	21	75	5	132	21	1	29	47	1.60
42284473--42284518	21	2.2	21	84	7	58	2	28	39	30	1.69
42286664--42286756	22	3.9	22	69	19	60	47	1	23	27	1.59
42293844--42293887	3	14.7	3	100	0	88	68	0	0	31	0.90
42294147--42294180	16	2.1	16	88	0	50	44	2	2	50	1.32
42294251--42294298	25	1.9	25	100	0	96	47	8	4	39	1.53
42295648--42295743	38	3.0	29	73	25	93	55	22	7	14	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42295611--42295730	38	3.2	38	91	3	181	55	24	6	14	1.63
42295686--42295743	29	2.0	29	93	3	98	56	22	6	13	1.61
42299861--42299891	9	3.4	9	90	0	53	25	12	22	38	1.90
42299945--42299981	9	4.1	9	92	0	65	45	13	10	29	1.77
42301649--42301682	2	17.0	2	100	0	68	50	0	0	50	1.00
42308158--42308243	35	2.4	35	80	16	97	48	1	3	46	1.26
42308254--42308323	5	13.4	5	79	10	52	72	4	22	0	1.01
42308601--42308636	18	1.9	19	88	5	56	38	0	27	33	1.57
42309141--42309274	40	3.4	40	78	7	157	25	16	25	32	1.96
42314040--42314092	20	2.6	20	85	8	63	56	5	0	37	1.23
42314125--42314170	21	2.2	21	84	3	58	69	0	8	21	1.15
42315936--42316255	106	3.0	106	82	0	388	32	18	17	30	1.95
42316350--42316447	44	2.2	45	89	3	146	70	10	3	16	1.27
42316356--42316439	25	3.6	23	68	22	59	70	9	3	16	1.28
42316693--42316746	27	2.0	27	82	13	67	53	3	11	31	1.53
42316787--42316814	2	14.0	2	100	0	56	50	0	0	50	1.00
42319548--42319644	3	31.7	3	81	10	108	63	3	3	29	1.24
42328172--42328203	5	6.4	5	92	0	55	56	0	3	40	1.15
42340759--42340823	31	2.1	32	85	5	89	38	12	6	43	1.67
42340759--42340824	30	2.2	31	83	8	82	39	12	6	42	1.67
42350479--42350511	12	2.8	12	86	4	50	63	0	36	0	0.95
42351093--42351138	18	2.3	20	82	17	69	43	8	41	6	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42351102--42351138	18	2.1	18	100	0	74	37	10	45	5	1.62
42351376--42351454	33	2.4	33	91	0	131	26	17	26	29	1.98
42356447--42356509	25	2.5	25	97	0	117	38	4	0	57	1.20
42356451--42356530	25	3.4	23	85	8	99	38	3	0	57	1.17
42356498--42356535	11	3.5	11	85	0	58	47	0	0	52	1.00
42356701--42356746	2	23.0	2	95	0	83	52	0	0	47	1.00
42360557--42360586	4	7.5	4	100	0	60	23	0	0	76	0.78
42361651--42361688	15	2.6	15	87	4	51	34	2	0	63	1.09
42361648--42361688	14	2.9	14	85	3	55	34	2	0	63	1.08
42364177--42364205	14	2.1	14	100	0	58	13	6	6	72	1.26

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