genome.fa.s1.2.7.7.80.10.50.1000.182.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  182  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)
54673738--54673834	29	3.4	29	80	10	110	38	2	0	59	1.09
54673776--54673843	11	6.6	11	73	23	51	38	1	0	60	1.06
54673814--54673843	12	2.6	11	94	5	51	43	0	0	56	0.99
54673695--54673857	38	4.5	37	76	18	157	36	2	0	60	1.10
54673696--54673850	68	2.3	68	84	10	217	36	2	0	60	1.10
54677061--54677137	31	2.5	31	82	2	102	46	6	5	41	1.52
54678129--54678205	29	2.6	29	83	4	91	48	14	12	24	1.79
54685319--54685344	13	2.0	13	100	0	52	38	38	0	23	1.55
54687203--54687236	17	2.0	17	88	0	50	76	0	23	0	0.79
54689760--54689787	3	9.3	3	100	0	56	32	0	0	67	0.91
54697702--54697735	14	2.3	15	90	5	52	2	5	14	76	1.09
54698028--54698112	2	42.5	2	95	0	152	1	0	47	51	1.08
54703357--54703408	23	2.4	21	82	17	70	25	1	5	67	1.23
54704875--54704910	2	18.5	2	94	5	65	50	0	0	50	1.00
54713777--54713928	41	3.7	41	96	0	277	21	28	20	29	1.98
54713781--54713951	41	4.2	41	90	3	245	23	27	19	29	1.98
54714751--54714777	2	13.5	2	100	0	54	51	0	0	48	1.00
54715784--54715808	13	1.9	13	100	0	50	40	24	4	32	1.73
54721357--54721431	24	3.2	24	62	27	61	32	6	32	29	1.83
54721353--54721491	46	3.0	46	93	0	242	35	8	27	28	1.86
54721810--54721852	2	21.5	2	100	0	86	48	0	0	51	1.00
54724901--54724942	20	2.0	21	86	13	61	30	7	9	52	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54727663--54727711	22	2.2	22	82	13	57	4	16	10	69	1.32
54730317--54730341	13	1.9	13	100	0	50	56	8	16	20	1.65
54730360--54730422	20	3.1	20	64	28	51	39	11	4	44	1.61
54731131--54731176	15	3.1	15	76	17	51	23	10	19	45	1.82
54732343--54732415	36	2.0	36	100	0	146	24	17	24	32	1.97
54734423--54734474	15	3.6	15	80	12	56	44	0	1	53	1.11
54734402--54734587	54	3.2	54	67	21	151	43	1	4	50	1.33
54734315--54734595	120	2.4	119	91	3	451	42	2	5	49	1.40
54734719--54734828	45	2.7	40	80	8	114	31	27	5	35	1.80
54734807--54734852	16	2.9	16	90	0	65	32	32	0	34	1.58
54734809--54734858	16	3.1	16	88	0	64	36	32	0	32	1.58
54735217--54735423	102	2.0	102	100	0	414	34	18	14	32	1.91
54735720--54735775	23	2.7	19	75	19	67	48	12	10	28	1.74
54735727--54735771	23	1.9	24	95	4	83	53	11	11	24	1.68
54735867--54735943	35	2.2	35	92	0	127	31	41	16	10	1.82
54736845--54736953	46	2.4	44	84	13	134	37	4	3	54	1.39
54736880--54737006	45	2.8	45	81	11	134	40	7	2	49	1.45
54736877--54737006	24	5.7	21	74	19	84	39	7	2	50	1.44
54737182--54737243	27	2.3	27	80	2	70	29	3	4	62	1.31
54740112--54740187	10	7.8	10	85	8	61	48	0	0	51	1.00
54740118--54740184	5	13.4	5	87	0	71	49	0	0	50	1.00
54740379--54740426	22	2.2	22	82	14	55	70	8	20	0	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54740783--54740827	22	2.0	24	91	8	76	57	2	17	22	1.50
54742412--54742445	2	17.0	2	100	0	68	50	0	0	50	1.00
54746549--54746615	27	2.4	27	80	7	73	35	4	2	56	1.35
54747106--54747143	19	2.0	19	85	10	51	44	0	0	55	0.99
54752183--54752281	23	4.3	23	96	0	171	30	29	21	19	1.97
54758527--54758643	49	2.2	54	77	14	145	45	10	3	41	1.55
54758540--54758644	49	2.1	50	87	1	149	46	10	3	39	1.56
54759950--54759985	18	2.1	18	94	5	65	52	5	0	41	1.24
54759950--54760016	25	2.6	24	75	11	62	44	4	1	49	1.31
54762570--54762712	8	17.0	8	67	18	51	57	1	2	39	1.19
54762622--54762712	43	2.1	42	82	8	103	58	2	1	38	1.18
54762614--54762751	26	5.2	25	73	11	100	56	2	1	39	1.20
54762666--54762767	37	2.8	37	71	10	93	59	1	2	35	1.23
54764852--54764945	47	2.0	47	100	0	188	31	12	14	40	1.84
54767385--54767675	17	16.8	17	76	11	261	44	11	13	30	1.79
54767384--54767688	69	4.4	68	94	2	502	43	11	13	31	1.79
54767385--54767693	34	8.9	33	78	8	312	43	11	13	31	1.79
54768613--54768654	12	3.5	12	78	9	50	0	23	0	76	0.79
54768605--54768653	11	4.4	11	78	12	55	0	20	0	79	0.73
54769244--54769373	29	4.4	29	83	7	138	40	3	23	32	1.72
54769237--54769373	58	2.3	58	79	7	152	40	5	24	30	1.77
54770310--54770382	25	2.9	25	93	0	119	34	20	13	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54772158--54772464	140	2.2	140	93	0	524	20	26	29	23	1.99
54774094--54774124	14	2.2	14	100	0	62	74	0	6	19	1.03
54774159--54774231	30	2.5	29	86	6	103	26	24	5	43	1.75
54774783--54774849	32	2.1	32	83	5	82	62	1	32	2	1.19
54775177--54775224	17	2.9	17	87	3	62	33	41	16	8	1.78
54777553--54777631	29	2.7	30	83	12	103	51	3	1	43	1.27
54779047--54779102	26	2.1	26	93	3	94	76	3	0	19	0.93
54779032--54779079	19	2.7	18	81	9	55	77	4	0	18	0.93
54779060--54779102	18	2.4	17	77	11	50	79	4	0	16	0.90
54783178--54783230	22	2.4	23	75	12	67	50	0	0	49	1.00
54786087--54786145	31	1.9	31	92	0	100	47	5	11	35	1.62
54786474--54786504	2	16.0	2	93	6	55	51	0	48	0	1.00
54787163--54787187	6	4.2	6	100	0	50	36	32	16	16	1.90
54792034--54792089	24	2.4	22	78	18	60	57	5	3	33	1.39
54793115--54793152	18	2.1	19	90	5	60	28	0	5	65	1.14
54793746--54793853	11	10.4	11	71	22	56	59	0	2	37	1.12
54793720--54793863	40	3.5	40	88	3	207	61	0	2	36	1.08
54799940--54800364	107	4.0	105	88	3	593	34	17	16	31	1.93
54800392--54800436	20	2.2	21	84	11	58	57	6	11	24	1.57
54800426--54800466	22	2.0	21	85	9	57	75	4	7	12	1.16
54800658--54800685	7	4.0	7	100	0	56	85	0	0	14	0.59
54800715--54800741	2	13.5	2	100	0	54	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54802570--54802866	88	3.4	86	73	7	247	30	22	17	28	1.97
54802570--54803037	44	10.8	42	70	11	216	28	22	19	29	1.98
54802849--54803038	41	4.5	41	68	11	139	27	20	22	30	1.98
54802743--54803083	130	2.6	129	82	3	418	27	20	20	31	1.97
54803133--54803720	44	13.4	44	65	16	173	25	26	19	28	1.99
54803086--54803744	132	5.0	132	89	2	975	25	25	19	28	1.99
54804097--54804154	24	2.4	24	88	5	82	36	25	6	31	1.83
54804611--54804938	106	3.1	106	90	0	494	49	9	15	25	1.74
54805199--54805248	20	2.5	20	83	0	64	2	20	2	76	0.99
54809852--54810211	106	3.4	106	89	2	544	33	15	17	33	1.91
54822554--54822622	34	2.0	34	100	0	138	36	11	17	34	1.86
54825695--54825722	2	14.0	2	100	0	56	50	0	0	50	1.00
54825943--54825975	17	1.9	17	88	11	50	33	0	0	66	0.92
54832336--54832408	36	2.0	36	94	0	128	28	31	9	30	1.89
54836502--54836573	22	3.3	22	94	0	117	30	16	27	25	1.97
54838581--54838644	27	2.4	27	87	12	96	50	15	3	31	1.60
54841554--54841606	21	2.5	22	90	3	81	60	3	0	35	1.15
54842381--54842438	28	2.0	30	83	6	75	27	5	12	55	1.58
54845661--54845691	16	1.9	16	93	0	53	64	3	12	19	1.41
54848033--54848111	40	2.0	40	97	0	149	36	7	22	32	1.83
54848265--54848421	44	3.6	44	84	0	190	23	20	21	35	1.96
54848265--54848432	87	1.9	88	85	3	232	23	21	20	34	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54852739--54852784	23	2.0	23	100	0	92	13	17	17	52	1.75
54853002--54853205	106	1.9	106	97	0	390	36	4	18	40	1.72
54857779--54857887	57	1.9	57	90	3	175	30	20	26	22	1.98
54858014--54858145	67	2.0	67	95	0	237	20	18	32	28	1.96
54858844--54858882	2	19.5	2	100	0	78	48	0	0	51	1.00
54870107--54870150	20	2.2	20	95	0	79	27	13	20	38	1.90
54872573--54872602	12	2.5	12	94	0	51	70	0	3	26	1.03
54876174--54876213	21	2.0	21	90	9	66	62	0	0	37	0.95
54891863--54891906	23	2.0	21	86	8	61	56	4	2	36	1.32
54896419--54896470	24	2.2	24	85	0	68	53	9	3	32	1.51

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