genome.fa.s13.2.7.7.80.10.50.1000.196.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   

This is table  196  of  199  ( 23770 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)
57095267--57095306	3	13.3	3	100	0	80	32	32	0	35	1.58
57101696--57101941	111	2.2	111	86	4	327	38	21	16	23	1.93
57103756--57103802	3	15.7	3	100	0	94	34	0	0	65	0.93
57105200--57105257	21	2.9	20	82	10	57	43	3	0	53	1.17
57105488--57105548	13	4.7	13	83	0	59	37	24	8	29	1.84
57105485--57105548	26	2.5	26	81	0	83	35	23	7	32	1.84
57105809--57105849	20	2.0	21	86	9	59	19	0	7	73	1.07
57106632--57106698	29	2.3	29	76	7	73	44	11	4	38	1.62
57107006--57107105	31	3.3	31	87	5	125	44	17	13	26	1.84
57121185--57121240	28	2.0	28	92	0	94	39	8	12	39	1.75
57121842--57121901	30	2.0	30	100	0	120	33	16	16	33	1.92
57121849--57121898	15	3.3	15	69	20	50	36	14	16	34	1.88
57131294--57131357	33	1.9	33	93	0	110	42	7	21	28	1.81
57142430--57142474	21	2.1	21	88	8	65	31	0	11	57	1.33
57144899--57144995	42	2.4	41	80	14	103	42	4	1	52	1.27
57150597--57150621	2	12.5	2	100	0	50	48	0	0	52	1.00
57150876--57151038	86	1.9	86	89	0	254	27	14	17	40	1.88
57153965--57154035	30	2.3	32	80	7	83	60	0	0	39	0.97
57154002--57154044	21	2.0	21	82	13	52	60	2	0	37	1.10
57154163--57154219	15	3.5	15	71	17	51	50	1	1	45	1.22
57157096--57157125	13	2.3	13	94	0	51	80	0	20	0	0.72
57158306--57158342	6	6.2	6	100	0	74	83	0	16	0	0.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57159978--57160006	6	4.8	6	100	0	58	34	0	17	48	1.47
57163971--57164024	24	2.2	25	83	6	65	61	3	1	33	1.25
57164005--57164035	11	2.7	11	95	5	53	58	0	3	38	1.15
57172095--57172150	28	2.0	28	100	0	112	39	14	17	28	1.89
57188709--57188747	20	2.0	20	89	0	60	28	0	5	66	1.12
57190820--57190874	15	3.7	15	77	15	60	65	0	3	30	1.10
57198569--57198646	29	2.6	29	83	4	93	47	14	14	24	1.80
57198594--57198667	29	2.5	29	86	4	94	50	16	13	20	1.78
57229232--57229265	12	2.8	12	86	0	50	61	0	0	38	0.96
57233446--57233483	14	2.9	13	81	11	51	28	0	0	71	0.87
57245049--57245080	2	16.0	2	100	0	64	50	0	0	50	1.00
57249062--57249089	2	14.0	2	100	0	56	50	0	0	50	1.00
57259337--57259496	77	2.1	77	93	0	284	33	22	8	35	1.85
57264397--57264430	16	2.1	16	88	0	50	20	17	17	44	1.87
57276563--57276613	26	1.9	27	84	11	70	64	7	3	23	1.37
57284802--57284830	14	2.1	14	93	6	51	0	13	0	86	0.58
57285213--57285244	13	2.5	13	100	0	64	25	6	21	46	1.74
57291375--57291417	17	2.6	16	78	10	50	34	0	0	65	0.93
57292529--57292571	21	2.0	21	82	8	52	51	2	0	46	1.13
57293007--57293087	37	2.2	37	93	0	144	44	7	12	35	1.70
57298802--57298906	33	3.3	33	77	8	126	27	20	31	20	1.97
57298802--57298919	33	3.7	32	74	13	116	27	22	29	20	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57301595--57301640	24	2.0	24	95	4	85	67	0	2	30	1.03
57301595--57301648	24	2.3	23	84	9	72	64	0	1	33	1.04
57302510--57302539	8	3.6	8	95	4	51	23	3	0	73	0.98
57302511--57302547	15	2.3	17	86	9	51	24	5	0	70	1.08
57306088--57306141	24	2.2	24	87	6	74	35	14	16	33	1.90
57306244--57306310	20	3.3	20	85	8	100	38	14	14	31	1.87
57315863--57315919	22	2.6	21	80	5	60	38	0	3	57	1.16
57315885--57315953	35	2.0	35	88	5	104	42	0	1	56	1.08
57315910--57315968	21	2.8	21	84	7	75	38	0	1	59	1.08
57315921--57315968	21	2.2	22	92	3	80	39	0	0	60	0.97
57316233--57316316	11	7.8	12	65	31	57	59	0	0	40	0.97
57316263--57316338	20	4.1	19	71	25	65	60	0	0	39	0.97
57316236--57316326	32	3.0	32	89	10	138	59	0	0	40	0.97
57316258--57316317	12	5.4	12	77	20	60	61	0	0	38	0.96
57316371--57316412	8	5.2	8	83	8	50	83	0	4	11	0.79
57316370--57316431	23	2.7	23	80	11	65	77	1	6	14	1.04
57316370--57316431	24	2.7	22	80	11	63	77	1	6	14	1.04
57320900--57320950	3	16.7	3	95	4	93	31	1	0	66	1.03
57327264--57327303	18	2.2	18	95	0	71	65	0	5	30	1.14
57327660--57327694	18	2.0	17	88	5	52	20	25	0	54	1.45
57331118--57331146	14	2.0	15	93	6	51	41	13	13	31	1.84
57333775--57333831	24	2.4	23	82	8	71	36	15	12	35	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57333936--57333996	20	3.0	20	83	9	88	37	14	16	31	1.89
57344668--57344704	12	3.0	12	96	4	65	64	8	0	27	1.21
57344668--57344706	13	3.1	13	88	7	62	64	7	0	28	1.21
57344668--57344717	25	2.0	25	84	7	66	64	8	2	26	1.32
57349639--57349664	2	13.0	2	100	0	52	50	0	0	50	1.00
57351520--57351559	16	2.5	16	87	0	53	32	0	35	32	1.58
57360384--57360438	19	2.9	19	88	0	92	45	5	16	32	1.70
57373047--57373332	143	2.0	142	92	2	475	41	14	26	17	1.87
57377052--57377104	18	2.8	20	80	13	67	32	11	7	49	1.67
57377256--57377325	19	3.8	19	76	16	76	34	21	5	38	1.77
57381311--57381354	16	2.6	18	82	13	58	50	18	11	20	1.77
57386324--57386382	22	2.6	22	74	12	57	44	0	0	55	0.99
57387025--57387053	11	2.7	11	94	5	51	58	20	0	20	1.39
57387213--57387342	65	2.0	65	92	0	215	33	13	11	41	1.81
57390611--57393321	398	6.8	398	96	0	4771	35	14	13	35	1.86
57390611--57393321	795	3.4	796	95	0	4807	35	14	13	35	1.86
57393551--57393604	28	1.9	28	92	0	90	31	18	14	35	1.91
57399475--57399499	11	2.3	11	100	0	50	32	24	0	44	1.54
57407745--57407815	14	4.8	14	76	20	65	74	2	19	2	1.07
57410762--57410808	24	2.0	23	84	12	60	29	14	4	51	1.62
57425621--57425655	12	2.8	12	91	4	52	85	2	0	11	0.69
57434256--57434318	31	2.0	31	100	0	126	46	9	15	28	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57443788--57443830	4	10.8	4	100	0	86	51	25	0	23	1.49
57444006--57444033	4	7.0	4	100	0	56	50	25	0	25	1.50
57446444--57446481	3	12.7	3	100	0	76	34	0	0	65	0.93
57447411--57447436	11	2.4	11	100	0	52	88	0	11	0	0.52
57449312--57449376	21	3.2	21	67	22	57	24	10	0	64	1.25
57449587--57449624	19	2.0	19	89	0	58	63	0	5	31	1.17
57469503--57469545	19	2.2	21	88	12	65	62	2	0	34	1.08
57469512--57469554	10	4.6	9	80	11	50	67	2	0	30	1.03
57469512--57469554	19	2.3	19	84	8	52	67	2	0	30	1.03
57469773--57469858	30	2.8	32	84	7	97	45	3	5	45	1.44
57470107--57470140	17	2.0	17	88	0	50	35	0	0	64	0.94
57470101--57470138	18	2.1	19	85	5	51	28	0	0	71	0.87
57470103--57470165	29	2.1	29	88	8	90	36	1	0	61	1.05
57470132--57470190	22	2.7	22	82	14	70	42	1	0	55	1.09
57471483--57471507	4	6.2	4	100	0	50	76	0	0	24	0.80
57481118--57481228	4	26.2	4	75	12	80	23	3	29	43	1.71
57485763--57485841	33	2.4	32	79	6	86	34	15	22	27	1.94
57485732--57485951	107	2.1	101	85	6	280	32	16	23	27	1.96
57487788--57487867	11	6.5	12	74	17	67	58	0	2	38	1.11
57487773--57487918	21	7.3	20	67	22	85	61	0	2	35	1.10
57487767--57487916	41	3.7	39	86	10	180	60	0	2	37	1.11
57487767--57487908	50	3.0	50	84	12	176	59	0	2	38	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57487773--57487908	11	13.1	11	68	24	57	61	0	2	36	1.12
57489423--57489460	19	2.0	20	89	5	60	60	15	2	21	1.47
57491274--57491324	27	2.0	25	88	7	75	25	3	5	64	1.33
57497698--57497744	3	15.7	3	90	0	76	31	0	2	65	1.04
57501104--57501730	241	2.6	238	84	4	816	37	18	15	28	1.91
57509538--57509581	23	2.0	23	90	4	72	34	6	0	59	1.24
57510091--57510120	12	2.5	12	94	0	51	33	26	10	30	1.89
57515838--57515862	12	2.1	12	100	0	50	52	0	8	40	1.31
57517083--57517110	4	7.0	4	100	0	56	25	25	25	25	2.00
57517108--57517145	4	9.5	4	100	0	76	26	0	23	50	1.50

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199