genome.fa.s1.2.7.7.80.10.50.1000.55.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  55  of  187  ( 22383 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)
16312287--16312996	148	4.7	149	82	7	795	35	20	16	27	1.94
16312292--16312999	75	9.3	73	79	9	656	35	20	16	27	1.94
16313854--16313893	13	3.3	13	73	20	50	7	15	5	72	1.24
16313848--16313898	23	2.2	23	100	0	102	7	11	3	76	1.13
16313892--16313967	1	76.0	1	73	0	53	1	5	7	85	0.79
16313860--16313967	23	4.8	22	76	13	87	2	8	6	82	0.93
16313906--16313953	8	5.9	8	92	2	78	0	2	12	85	0.69
16319573--16319616	19	2.2	19	84	8	52	34	9	9	47	1.67
16319578--16319672	37	2.6	36	80	12	95	44	9	10	35	1.72
16319690--16319725	16	2.2	16	90	9	56	47	11	8	33	1.69
16319669--16319911	38	6.2	37	66	24	108	44	11	11	32	1.76
16319773--16319839	17	3.8	17	78	7	80	40	11	17	29	1.86
16319773--16319961	18	10.3	18	68	14	102	43	9	15	31	1.78
16319990--16320057	18	3.8	18	76	5	66	36	8	20	33	1.84
16319969--16320046	35	2.3	35	86	2	113	41	8	17	32	1.81
16319807--16320033	18	12.6	18	66	15	92	44	9	15	31	1.78
16320011--16320098	44	2.0	44	84	0	113	43	12	17	27	1.84
16320173--16320222	18	2.8	17	82	8	64	42	6	16	36	1.72
16320474--16320553	13	6.2	13	77	14	76	1	25	0	73	0.90
16320693--16320731	17	2.2	17	86	9	51	0	15	17	66	1.25
16321197--16321222	6	4.3	6	100	0	52	80	0	0	19	0.71
16325816--16325853	18	2.1	18	95	0	67	23	34	0	42	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16330413--16330471	23	2.6	23	80	0	82	44	10	6	38	1.65
16332626--16332689	3	21.7	3	96	3	121	34	0	0	65	0.93
16332710--16332743	5	6.8	5	100	0	68	41	0	17	41	1.50
16332717--16332760	15	2.9	15	86	0	52	43	0	11	45	1.40
16333727--16333780	25	2.2	25	90	6	83	18	24	18	38	1.93
16338381--16339694	438	3.0	437	89	1	1977	26	22	17	32	1.96
16350032--16350063	2	16.0	2	100	0	64	50	0	50	0	1.00
16364374--16364416	12	3.5	13	81	18	56	44	0	2	53	1.13
16364381--16364433	17	3.3	17	80	17	60	43	0	0	56	0.99
16364367--16364439	23	3.0	25	73	15	62	45	0	2	52	1.15
16364400--16364429	15	2.1	15	93	6	53	43	0	0	56	0.99
16369320--16369361	18	2.3	19	84	12	52	57	9	7	26	1.56
16381262--16381396	40	3.3	40	81	5	146	25	16	26	31	1.96
16382147--16382229	23	3.5	24	86	4	125	32	14	18	34	1.91
16387671--16387714	23	2.0	23	86	8	65	63	0	2	34	1.07
16387694--16387724	16	1.9	16	93	0	53	64	0	3	32	1.09
16388259--16388300	15	2.8	15	75	13	50	7	9	4	78	1.08
16389691--16389716	2	13.0	2	100	0	52	50	0	0	50	1.00
16392698--16392796	23	4.3	23	93	0	162	22	21	24	32	1.98
16392926--16392998	38	1.9	37	86	8	103	45	1	21	31	1.61
16394412--16394523	25	4.5	25	80	3	111	23	23	23	30	1.99
16397376--16397410	15	2.2	16	90	5	54	45	14	22	17	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16398046--16398142	50	1.9	50	85	0	131	41	17	7	34	1.77
16401499--16401541	18	2.5	18	88	7	63	30	0	4	65	1.13
16401840--16401881	21	2.0	21	90	0	66	19	7	33	40	1.78
16407707--16407767	31	1.9	33	90	6	99	34	1	0	63	1.04
16407693--16407779	31	2.7	32	78	8	97	34	1	1	63	1.10
16409335--16409738	125	3.3	126	83	10	572	32	20	21	25	1.98
16409505--16409718	110	1.9	110	96	0	392	35	19	21	24	1.96
16411418--16411459	22	1.9	22	100	0	84	21	26	14	38	1.91
16412485--16412575	28	2.9	33	74	15	111	51	7	10	29	1.65
16412459--16412594	61	2.5	50	70	23	130	50	8	8	32	1.63
16412455--16412575	61	2.0	61	86	0	170	52	7	9	30	1.60
16412615--16412706	34	2.6	34	76	10	96	50	3	5	41	1.42
16412839--16412887	21	2.4	20	77	12	55	8	20	38	32	1.82
16413779--16413810	7	4.6	7	100	0	64	56	15	0	28	1.40
16414932--16414988	29	2.0	29	92	0	96	54	3	1	40	1.28
16414985--16415047	22	2.8	23	83	13	78	44	0	26	28	1.55
16414985--16415040	11	5.2	10	85	14	76	44	0	28	26	1.54
16416750--16416793	21	2.0	21	86	4	61	31	0	0	68	0.90
16416906--16417558	87	7.5	86	90	1	907	45	9	12	32	1.74
16417666--16417707	22	1.9	22	90	0	66	64	7	0	28	1.20
16418957--16419014	30	1.9	31	89	3	91	60	1	0	37	1.07
16429373--16429526	83	1.9	83	87	0	227	41	14	7	37	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16429808--16429863	29	1.9	29	85	0	76	28	14	19	37	1.91
16430115--16430160	10	4.6	10	75	20	51	34	28	0	36	1.58
16430079--16430149	22	3.2	22	88	7	108	33	26	1	38	1.65
16430120--16430178	30	2.0	30	93	0	100	32	33	0	33	1.58
16430098--16430200	52	2.0	51	84	5	136	33	31	0	33	1.65
16430150--16430191	22	1.9	22	90	0	66	33	33	0	33	1.58
16430237--16430297	29	2.1	29	87	6	88	39	0	1	59	1.08
16430388--16430421	15	2.3	15	90	5	52	26	0	5	67	1.13
16444906--16444986	24	3.3	23	70	21	65	67	2	27	2	1.15
16444897--16444995	51	1.9	51	93	0	171	65	3	27	4	1.25
16444920--16444995	23	3.1	23	72	17	71	64	2	28	3	1.25
16447414--16447447	5	6.8	5	100	0	68	41	0	0	58	0.98
16448611--16448648	18	2.1	19	90	5	60	52	0	0	47	1.00
16448636--16448666	16	1.9	16	93	0	53	41	9	0	48	1.36
16448762--16448806	18	2.5	19	76	20	51	40	2	2	55	1.24
16452860--16452890	13	2.3	14	94	5	55	67	0	6	25	1.14
16453138--16453191	26	2.1	26	82	6	65	61	0	5	33	1.19
16462043--16462121	13	6.5	13	72	16	71	45	12	1	40	1.50
16462043--16462121	36	2.2	36	93	4	133	45	12	1	40	1.50
16462079--16462130	23	2.3	23	89	0	86	48	13	0	38	1.43
16473773--16473851	39	2.1	38	83	7	97	49	3	10	36	1.55
16480966--16481026	20	3.2	19	71	15	54	22	4	4	67	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16485586--16485619	16	2.1	16	94	0	59	38	0	0	61	0.96
16486199--16486254	21	2.7	21	91	0	85	8	3	23	64	1.38
16488377--16488435	27	2.2	27	84	0	73	30	13	33	22	1.92
16488389--16488442	27	2.0	27	88	0	81	31	14	31	22	1.94
16488395--16488454	27	2.2	27	84	0	75	36	16	25	21	1.94
16490552--16490613	28	2.2	28	91	2	99	14	38	9	37	1.79
16491195--16491234	2	20.0	2	100	0	80	50	0	0	50	1.00
16493836--16494161	37	7.6	45	80	14	245	27	21	14	36	1.93
16494045--16494080	18	2.0	18	100	0	72	22	11	16	50	1.77
16494008--16494117	55	2.0	55	90	0	175	26	18	14	40	1.89
16495954--16495993	21	1.9	21	89	0	62	35	0	25	40	1.56
16496122--16496163	21	2.0	21	81	9	50	30	0	14	54	1.40
16496656--16496726	25	2.9	23	71	23	56	21	23	15	39	1.91
16496712--16496780	27	2.7	25	78	15	61	23	23	26	27	2.00
16500243--16500296	26	2.2	25	81	12	60	59	0	9	31	1.29
16501113--16501145	17	1.9	17	93	0	57	12	15	30	42	1.83
16501391--16501532	25	5.8	25	69	5	94	19	26	19	33	1.96
16508812--16508836	3	8.3	3	100	0	50	0	32	0	68	0.90
16516442--16516515	13	5.7	13	86	0	103	21	8	31	39	1.83
16521933--16521975	23	2.0	23	86	9	63	55	13	20	9	1.66
16523125--16523158	11	2.8	13	82	17	54	64	0	0	35	0.94
16523131--16523158	11	2.5	11	100	0	56	71	0	0	28	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16525058--16525097	22	1.9	20	85	10	53	37	0	20	42	1.52
16541082--16541117	2	18.5	2	94	5	65	50	0	0	50	1.00
16542541--16542662	2	61.0	2	100	0	244	50	50	0	0	1.00
16544149--16544173	13	1.9	13	100	0	50	40	24	4	32	1.73
16545845--16545897	22	2.4	22	78	6	54	50	3	7	37	1.49
16549708--16549759	15	3.2	15	73	19	50	44	0	1	53	1.11
16549786--16549819	15	2.2	16	89	5	52	61	0	0	38	0.96
16552067--16552145	13	6.5	13	75	16	80	40	0	11	48	1.39
16552067--16552144	36	2.2	36	95	0	138	41	0	10	48	1.37
16552103--16552147	23	2.0	23	100	0	90	44	0	8	46	1.34

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