genome.fa.s1.2.7.7.80.10.50.1000.61.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  61  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)
17883316--17883386	28	2.6	27	86	10	99	29	12	26	30	1.93
17884323--17884675	47	7.5	47	94	1	539	27	12	15	44	1.83
17884598--17884672	23	3.3	23	72	18	75	25	13	18	42	1.87
17893984--17894034	2	25.5	2	100	0	102	50	0	0	49	1.00
17902324--17902389	35	1.9	34	87	9	98	51	1	7	39	1.40
17908919--17909073	79	2.0	79	90	0	247	27	10	18	43	1.82
17923387--17923411	2	12.5	2	100	0	50	48	0	0	52	1.00
17930842--17931010	59	3.0	57	80	5	173	32	21	17	28	1.96
17930842--17930974	29	4.6	29	85	3	169	33	21	15	30	1.94
17932788--17932832	9	5.3	9	81	7	51	15	0	28	55	1.41
17938711--17938792	25	3.4	25	71	19	93	53	6	13	26	1.63
17938698--17938791	46	2.0	46	97	0	179	51	8	12	27	1.69
17944041--17944140	33	3.1	32	85	4	128	19	32	12	37	1.88
17953294--17953335	21	2.0	21	95	0	75	42	26	14	16	1.86
17954238--17954267	15	2.0	15	93	0	51	56	13	3	26	1.52
17962471--17962539	16	4.7	15	69	20	56	39	8	13	39	1.75
17963503--17963574	37	2.0	36	83	8	92	38	5	1	54	1.33
17963503--17963584	20	4.3	19	72	17	62	40	4	2	52	1.36
17964490--17964519	5	6.0	5	100	0	60	40	0	0	60	0.97
17966485--17966599	37	3.1	37	89	2	169	33	24	8	33	1.86
17966821--17966923	41	2.5	41	89	6	138	30	21	20	28	1.98
17972252--17972289	19	2.0	19	100	0	76	36	10	26	26	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17972612--17972737	61	2.1	58	86	4	171	40	3	3	51	1.39
17972624--17972757	58	2.3	58	82	8	146	41	3	4	50	1.40
17974177--17974228	4	11.5	4	77	22	50	44	11	0	44	1.40
17974183--17974235	10	5.5	10	82	8	65	43	13	0	43	1.43
17974177--17974235	19	3.2	19	95	2	102	44	11	0	44	1.41
17982095--17982204	22	5.0	22	86	0	139	30	29	0	39	1.63
17982241--17982296	28	2.0	29	92	3	96	37	0	1	60	1.07
17982241--17982304	28	2.2	29	88	2	94	37	0	1	60	1.06
17982395--17982428	15	2.3	15	90	5	52	26	0	5	67	1.13
17984565--17985022	23	18.3	23	75	17	380	45	22	0	31	1.59
17984603--17985170	23	21.7	28	74	18	369	44	23	0	31	1.60
17984565--17985163	51	11.6	51	81	7	644	44	23	1	31	1.60
17984990--17985039	18	2.6	19	84	12	59	44	32	0	24	1.54
17985021--17985139	62	1.9	63	91	5	197	42	26	1	30	1.65
17988451--17988715	124	2.1	125	87	2	381	31	23	15	29	1.95
17990161--17990210	25	2.0	25	84	7	66	34	0	2	64	1.05
17990575--17990612	2	19.0	2	100	0	76	50	0	0	50	1.00
17997487--17997520	16	2.2	16	89	5	52	55	35	5	2	1.39
18012399--18012457	28	2.1	28	93	0	100	40	0	23	35	1.55
18013532--18013637	18	5.8	18	70	22	69	52	3	2	40	1.34
18013564--18013638	36	2.1	36	83	14	93	54	2	2	40	1.28
18015250--18015280	16	1.9	16	93	0	53	74	9	6	9	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18018269--18018337	27	2.5	27	81	11	79	68	0	4	27	1.09
18029274--18029335	28	2.2	28	91	0	97	51	0	6	41	1.27
18030884--18030916	7	4.7	7	92	0	57	18	0	39	42	1.50
18054579--18054631	25	2.1	25	82	0	61	60	7	7	24	1.50
18057711--18058337	211	3.0	210	90	1	988	41	17	18	22	1.90
18061003--18061046	22	2.0	22	86	0	61	56	2	6	34	1.38
18064059--18064122	3	21.3	3	90	6	103	32	0	1	65	1.02
18065128--18065272	76	1.9	76	89	0	227	43	20	4	31	1.73
18068321--18068537	89	2.4	90	80	5	242	34	24	15	25	1.95
18080081--18080132	24	2.2	24	100	0	104	19	30	17	32	1.95
18086561--18086603	15	2.7	15	85	7	50	60	4	6	27	1.43
18089083--18089148	6	11.0	6	85	0	69	51	4	4	39	1.43
18089083--18089148	4	16.5	4	85	0	69	51	4	4	39	1.43
18091800--18091867	33	2.1	33	97	0	127	17	23	13	45	1.84
18094391--18094750	27	13.4	27	84	4	408	17	16	23	42	1.89
18103667--18103760	32	2.8	32	87	4	89	25	7	9	57	1.57
18103695--18103760	32	2.1	32	100	0	132	25	9	9	56	1.60
18105129--18105182	17	3.2	17	78	5	65	20	3	9	66	1.35
18113906--18113936	2	15.5	2	100	0	62	51	0	0	48	1.00
18115566--18115592	13	2.1	13	100	0	54	0	55	7	37	1.28
18120172--18120316	41	3.5	41	89	0	218	24	28	19	28	1.98
18120795--18121034	114	2.1	114	92	0	408	41	14	3	40	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18122012--18122036	13	1.9	13	100	0	50	68	24	0	8	1.16
18127714--18127860	41	3.6	41	89	1	224	23	30	19	27	1.98
18127796--18127919	40	3.1	40	80	5	99	26	29	20	24	1.99
18128326--18128575	114	2.2	113	88	6	396	41	14	3	40	1.64
18128542--18128568	11	2.5	11	100	0	54	55	7	7	29	1.55
18130906--18130966	26	2.4	25	81	8	68	54	1	3	40	1.27
18131030--18131079	4	13.0	4	76	16	52	72	0	26	2	0.96
18133078--18133117	21	1.9	21	84	0	53	20	5	22	52	1.65
18134422--18134474	27	2.0	27	92	0	88	49	13	9	28	1.73
18145143--18145219	38	2.0	38	94	0	136	29	0	37	32	1.58
18149372--18149441	23	3.0	23	100	0	140	30	8	17	44	1.78
18149327--18149441	46	2.5	46	84	4	135	34	7	16	40	1.77
18163188--18163262	31	2.4	31	84	0	87	20	13	13	53	1.72
18164464--18164508	2	22.5	2	100	0	90	48	0	0	51	1.00
18171101--18171125	13	1.9	13	100	0	50	8	16	4	72	1.24
18173644--18173701	30	1.9	31	85	3	82	41	6	17	34	1.76
18173942--18174128	50	3.7	50	75	15	179	24	17	27	31	1.97
18173937--18174120	101	1.8	101	89	4	291	23	17	27	31	1.97
18174346--18174377	16	2.0	16	93	0	55	59	0	15	25	1.36
18181567--18181622	20	2.7	21	84	10	71	55	1	0	42	1.10
18184107--18184149	20	2.2	20	91	0	68	25	23	11	39	1.88
18191268--18191305	15	2.6	15	83	4	51	21	5	0	73	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18191268--18191330	26	2.4	27	79	15	69	23	4	0	71	1.05
18191312--18191340	4	7.2	4	100	0	58	24	0	0	75	0.80
18196603--18196634	9	3.7	9	91	8	57	34	12	21	31	1.91
18196687--18196723	9	4.1	9	85	0	56	45	5	10	37	1.62
18196932--18196991	30	2.0	31	83	9	79	20	38	0	41	1.52
18197246--18197274	9	3.2	9	100	0	58	31	0	0	68	0.89
18199256--18199316	27	2.2	27	80	8	70	55	0	9	34	1.33
18202619--18202680	27	2.3	26	80	2	70	37	19	14	29	1.91
18202698--18202831	24	5.6	24	83	3	153	26	7	20	44	1.78
18202922--18202973	26	2.0	26	88	0	77	15	21	26	36	1.93
18202976--18203306	32	10.4	32	80	6	307	20	18	22	38	1.93
18202976--18203286	96	3.2	96	81	6	353	20	18	22	38	1.93
18203523--18203627	28	3.9	28	86	3	135	20	24	22	32	1.98
18204414--18204454	21	2.0	21	90	0	64	48	21	12	17	1.79
18222971--18223007	2	18.5	2	100	0	74	51	0	0	48	1.00
18223685--18223719	18	2.0	17	88	5	52	62	8	0	28	1.24
18224156--18224194	14	2.7	15	84	4	53	48	0	0	51	1.00
18224838--18224924	11	8.3	11	67	19	60	21	31	2	44	1.65
18224849--18224948	51	2.0	51	86	4	139	24	28	2	46	1.64
18227681--18227869	36	5.0	36	83	12	234	37	11	20	30	1.88
18227643--18227958	82	3.9	81	82	14	366	35	13	22	29	1.92
18227684--18227915	118	2.0	118	94	0	410	36	12	21	29	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
18227833--18227958	46	2.8	46	92	3	204	32	15	23	27	1.95
18228571--18228619	24	2.0	24	100	0	98	40	38	0	20	1.53
18229259--18229300	6	7.0	6	97	0	75	30	0	0	69	0.89
18230227--18230275	26	1.9	25	83	4	62	51	4	4	40	1.40
18232590--18232625	18	2.0	18	88	0	54	22	25	0	52	1.47
18234660--18234729	34	2.1	34	97	0	131	24	10	8	57	1.59
18236611--18236746	50	2.7	50	86	1	173	27	22	29	21	1.99
18246402--18246430	2	15.0	2	92	7	51	51	0	0	48	1.00
18246389--18246441	13	4.2	13	83	9	56	52	0	3	43	1.19
18246464--18246500	15	2.3	17	86	9	51	72	8	2	16	1.19

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