genome.fa.s1.2.7.7.80.10.50.1000.41.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  41  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)
12672694--12672747	22	2.3	22	87	9	72	48	11	0	40	1.39
12672704--12672754	22	2.4	22	90	3	86	49	9	0	41	1.36
12672725--12672834	34	3.2	34	86	1	139	45	13	1	39	1.54
12672787--12672929	25	5.9	25	71	14	84	44	15	2	37	1.61
12672818--12672937	16	7.9	16	66	23	64	44	16	2	36	1.62
12672629--12672942	9	36.2	9	66	22	95	45	13	1	38	1.55
12678517--12678682	66	2.5	66	79	3	165	41	16	27	14	1.87
12678659--12678771	21	5.4	21	85	0	118	35	16	42	5	1.71
12679122--12679307	43	4.3	43	80	4	196	20	17	30	31	1.95
12679129--12679329	86	2.3	86	81	3	235	23	17	30	28	1.97
12679315--12679500	43	4.3	42	77	2	183	31	31	18	18	1.95
12679315--12679500	86	2.2	86	90	0	282	31	31	18	18	1.95
12679658--12679700	22	2.0	22	90	0	68	44	27	18	9	1.80
12682083--12682226	73	2.0	73	92	0	243	34	17	19	28	1.94
12682943--12683009	21	3.3	21	75	12	86	53	4	5	35	1.46
12682964--12683046	18	4.3	19	77	13	80	57	4	3	33	1.37
12682943--12683027	39	2.2	39	100	0	170	55	4	4	35	1.42
12682964--12683046	21	4.1	21	71	20	70	57	4	3	33	1.37
12683755--12683798	23	1.9	23	90	0	70	70	9	11	9	1.34
12683816--12683905	43	2.1	43	97	0	171	18	15	6	58	1.58
12688272--12688447	41	4.3	41	94	0	307	23	28	19	28	1.98
12688624--12688715	41	2.2	41	98	0	175	22	28	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12691167--12691411	50	4.8	51	72	6	178	32	25	15	26	1.95
12691178--12691407	101	2.3	100	82	6	268	32	25	15	26	1.95
12694859--12694921	19	3.3	19	68	24	60	23	3	22	50	1.63
12694856--12694933	38	2.1	38	100	0	156	25	5	20	48	1.70
12694876--12694936	19	3.2	19	66	25	56	26	6	21	45	1.76
12695515--12695558	2	22.0	2	100	0	88	50	0	0	50	1.00
12696508--12696741	41	5.7	41	92	1	369	27	20	28	23	1.99
12696912--12696954	22	2.0	22	100	0	86	23	25	13	37	1.92
12698337--12698378	18	2.3	19	83	4	50	19	9	4	66	1.38
12698345--12698383	19	2.1	19	85	9	53	17	7	7	66	1.40
12711309--12711487	50	3.6	49	72	6	173	32	25	19	22	1.97
12711254--12711528	98	2.8	98	87	1	379	32	23	21	22	1.98
12712105--12712140	5	7.2	5	93	0	63	19	2	0	77	0.88
12713151--12713268	3	40.0	3	82	3	150	32	1	4	61	1.25
12713240--12713274	18	1.9	18	88	0	52	31	5	8	54	1.54
12713318--12713424	2	55.0	2	76	5	85	45	3	2	47	1.35
12713334--12713427	37	2.6	37	89	5	138	44	3	3	48	1.34
12713893--12713921	2	14.5	2	100	0	58	48	0	0	51	1.00
12714853--12714888	18	2.0	18	100	0	72	22	16	27	33	1.95
12734550--12734634	26	3.4	25	75	8	75	60	7	4	28	1.43
12734573--12734638	24	2.6	26	78	4	73	60	7	4	27	1.43
12734762--12734826	25	2.6	25	97	2	121	63	3	6	27	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12736284--12736394	44	2.5	43	82	4	123	23	21	23	31	1.98
12736318--12736410	44	2.1	44	83	0	114	23	24	22	29	1.99
12736396--12736741	174	2.0	174	93	0	584	27	24	19	28	1.98
12736747--12737654	45	20.2	45	84	3	1103	31	24	15	28	1.96
12736444--12736802	86	4.2	86	70	9	271	27	25	18	28	1.98
12738648--12738703	7	8.4	7	75	11	55	0	16	1	82	0.76
12738647--12738708	13	4.8	13	73	15	58	0	17	1	80	0.79
12738649--12738709	18	3.3	17	82	13	68	0	18	1	80	0.80
12739139--12739191	23	2.3	22	81	18	63	5	5	5	83	0.93
12743023--12743079	27	2.1	28	86	3	80	66	3	5	24	1.28
12743181--12743206	2	13.0	2	100	0	52	50	0	0	50	1.00
12746715--12746759	22	2.0	22	100	0	90	17	28	4	48	1.66
12761237--12761298	28	2.2	28	85	5	90	41	4	3	50	1.40
12761368--12761400	2	16.5	2	93	0	57	48	0	0	51	1.00
12761421--12761469	14	3.4	14	85	2	53	57	2	0	40	1.10
12762014--12762050	18	2.1	18	94	0	65	54	5	0	40	1.24
12763812--12763851	19	2.0	20	85	4	55	47	10	20	22	1.79
12767077--12767136	3	19.7	3	96	3	111	65	0	1	33	1.03
12768436--12768509	36	2.1	36	100	0	148	37	5	21	35	1.77
12778328--12778364	3	12.3	3	100	0	74	32	0	0	67	0.91
12790001--12790050	20	2.6	19	78	6	64	52	6	2	40	1.38
12790001--12790107	20	5.8	19	72	18	61	56	3	1	38	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12790053--12790121	36	1.9	37	85	5	97	59	4	1	34	1.26
12791548--12791575	10	2.8	10	100	0	56	57	0	32	10	1.33
12809533--12809563	6	5.0	6	96	4	53	64	16	0	19	1.29
12810599--12810638	21	1.9	21	94	0	71	42	0	0	57	0.98
12810729--12810776	19	2.5	19	79	3	51	27	2	0	70	0.98
12810756--12810809	24	2.2	25	78	18	60	44	3	0	51	1.19
12813158--12813239	40	2.0	40	100	0	164	17	32	24	25	1.96
12815006--12815148	45	3.2	45	87	1	198	37	21	20	19	1.94
12816990--12817067	33	2.4	32	83	12	97	25	7	19	47	1.76
12817078--12817152	20	3.8	20	75	10	75	42	4	0	53	1.19
12819852--12819884	6	5.7	6	89	7	50	36	0	63	0	0.95
12819852--12819887	11	3.2	11	88	4	54	38	0	61	0	0.96
12822018--12822064	14	3.2	15	82	11	53	74	6	0	19	1.03
12823486--12823513	7	4.0	7	100	0	56	14	0	42	42	1.45
12824207--12824598	45	8.5	45	76	9	290	33	17	18	29	1.94
12824205--12824598	141	2.8	140	81	3	427	33	17	18	29	1.94
12831371--12831413	21	2.0	21	100	0	86	37	18	4	39	1.72
12833279--12833356	42	1.9	40	89	5	120	39	17	14	28	1.89
12843421--12843462	22	2.0	22	85	4	59	59	7	14	19	1.57
12847181--12847238	16	3.5	16	75	9	62	48	0	8	43	1.34
12847732--12847833	3	33.0	3	87	7	143	62	0	1	34	1.13
12848382--12848406	13	1.9	13	100	0	50	16	16	0	68	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12851585--12851640	25	2.2	26	83	6	78	46	5	8	39	1.58
12853275--12853999	44	16.3	44	77	4	598	28	24	16	30	1.96
12853247--12853999	89	8.5	89	85	2	802	28	24	16	30	1.96
12855273--12855319	20	2.3	21	88	3	69	14	17	0	68	1.22
12855281--12855320	7	5.7	7	88	11	64	12	15	0	72	1.12
12856230--12856272	22	2.0	22	85	0	59	67	6	11	13	1.41
12858639--12858673	17	2.1	17	94	0	61	42	20	17	20	1.89
12860262--12860303	18	2.4	18	84	4	59	71	0	14	14	1.15
12862029--12862887	89	9.7	88	89	2	656	28	23	16	30	1.97
12862075--12862887	178	4.6	178	89	2	1188	28	24	16	30	1.97
12862075--12862887	267	3.0	267	88	1	1186	28	24	16	30	1.97
12864167--12864199	13	2.3	15	85	15	52	12	15	0	72	1.12
12864167--12864199	7	4.7	7	85	14	50	12	15	0	72	1.12
12864251--12864281	13	2.3	14	94	5	55	38	19	19	22	1.93
12868114--12868152	18	2.2	18	86	4	53	74	0	15	10	1.07
12868194--12868249	25	2.2	26	81	12	71	42	5	10	41	1.62
12869881--12871485	89	18.2	88	81	5	746	28	23	17	30	1.97
12869927--12871466	178	8.7	177	84	5	1410	28	23	17	30	1.97
12869927--12870921	267	3.7	267	88	0	1438	27	23	17	30	1.97
12870804--12871024	120	1.8	120	89	1	345	29	24	17	28	1.97
12870715--12871130	209	2.0	209	88	0	616	29	23	18	28	1.98
12870922--12871482	267	2.1	267	87	2	822	30	22	16	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12872765--12872797	13	2.3	15	85	15	52	12	15	0	72	1.12
12872765--12872797	7	4.7	7	85	14	50	12	15	0	72	1.12
12873732--12873771	19	2.1	19	90	0	62	67	7	12	12	1.41
12877974--12878016	20	2.2	20	82	0	50	58	0	9	32	1.30
12880240--12880277	18	2.2	18	90	4	60	63	10	5	21	1.46
12881534--12881581	24	2.1	23	88	7	71	47	4	2	45	1.33
12882530--12882572	19	2.3	18	80	11	50	34	9	0	55	1.32
12885976--12886040	27	2.4	27	97	2	123	43	6	0	50	1.27
12886401--12886440	20	2.1	19	85	4	53	42	5	7	45	1.54
12888022--12888053	2	16.0	2	100	0	64	50	0	0	50	1.00

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