genome.fa.s1.2.7.7.80.10.50.1000.104.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  104  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)
30847554--30847618	16	4.2	16	71	7	55	78	1	20	0	0.83
30848030--30848240	19	11.2	19	72	18	106	32	10	10	45	1.73
30848106--30848195	43	2.1	44	85	6	121	23	10	13	53	1.69
30848070--30848234	79	2.1	81	83	4	219	27	11	11	49	1.74
30848030--30848256	18	13.2	18	76	17	182	33	10	10	45	1.73
30848703--30848728	9	2.9	9	100	0	52	46	19	0	34	1.50
30856537--30856975	75	5.8	75	87	4	569	28	17	20	33	1.95
30856532--30857004	152	3.1	151	85	4	612	27	17	19	35	1.94
30857319--30857418	30	3.3	30	78	9	89	33	18	4	45	1.68
30857349--30857417	31	2.3	29	82	7	84	31	18	4	44	1.69
30858013--30858067	27	1.9	29	89	10	87	74	0	25	0	0.82
30858018--30858098	35	2.3	34	85	10	101	70	0	29	0	0.88
30858546--30858601	7	7.7	7	79	13	60	80	0	19	0	0.71
30858546--30858601	15	3.9	14	80	19	62	80	0	19	0	0.71
30858549--30858609	22	2.5	24	76	10	63	80	1	18	0	0.80
30858549--30858611	16	4.0	16	75	4	65	79	1	19	0	0.82
30858753--30858818	29	2.3	29	76	7	73	25	18	12	43	1.84
30859013--30859390	126	3.0	124	88	1	576	28	15	23	32	1.95
30860145--30860233	24	3.5	24	72	18	74	26	0	25	47	1.53
30860107--30860454	86	4.0	87	92	4	560	27	0	25	46	1.56
30860247--30860318	24	3.0	23	80	13	83	27	0	27	44	1.55
30860353--30860436	33	2.6	33	86	1	107	32	1	19	47	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30860435--30860637	13	14.8	13	64	22	69	21	0	31	46	1.56
30860448--30860685	44	5.7	43	81	9	235	22	0	30	46	1.56
30860435--30860564	57	2.3	58	81	6	158	22	0	31	46	1.52
30860484--30860691	42	5.0	41	81	10	228	23	0	30	45	1.57
30860549--30860616	31	2.3	30	85	10	86	22	1	30	45	1.61
30860505--30860679	79	2.3	75	83	9	237	21	0	30	46	1.56
30860578--30860639	12	5.0	12	71	13	54	22	0	30	46	1.52
30860528--30860676	79	1.9	79	91	0	244	21	0	31	46	1.56
30860695--30860807	25	4.7	25	68	18	96	42	13	0	43	1.49
30861895--30861926	7	4.6	7	100	0	64	59	12	0	28	1.34
30863107--30863211	11	9.1	11	69	23	65	44	0	30	24	1.54
30863146--30863201	22	2.5	22	88	2	85	42	0	30	26	1.56
30863162--30863211	10	4.6	11	77	22	61	46	0	34	20	1.51
30863062--30863179	51	2.3	51	85	7	159	46	0	22	30	1.52
30863820--30863867	24	2.0	25	87	4	71	37	8	6	47	1.59
30863858--30863924	19	3.6	19	72	11	59	44	7	10	37	1.67
30863866--30863943	17	4.4	17	73	15	68	43	10	10	35	1.73
30863847--30863994	36	4.1	35	74	8	145	37	10	10	41	1.74
30872518--30872554	7	5.3	7	86	0	56	27	54	0	18	1.44
30872518--30872558	14	2.9	14	88	0	64	29	48	0	21	1.50
30872521--30872582	21	2.9	22	85	4	74	35	41	0	22	1.54
30873646--30873894	41	6.0	41	85	2	284	28	30	20	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30873946--30874037	40	2.3	40	79	3	107	25	23	20	30	1.99
30879521--30879630	44	2.5	44	86	2	150	28	20	21	29	1.98
30892363--30892441	30	2.7	30	82	5	92	54	2	7	35	1.42
30892577--30892631	3	18.3	3	81	7	67	61	1	1	34	1.17
30892576--30892630	27	2.1	27	89	3	85	60	1	1	36	1.18
30893293--30893338	17	2.6	18	82	3	58	8	15	6	69	1.34
30896608--30896652	17	2.8	16	80	6	54	44	0	6	48	1.29
30897987--30898066	32	2.5	32	81	0	97	38	13	23	23	1.91
30898115--30898165	26	2.0	26	96	0	93	35	27	23	13	1.93
30898154--30898218	27	2.5	26	83	14	80	33	26	21	18	1.96
30898281--30898363	24	3.5	23	85	12	114	45	22	8	22	1.79
30898297--30898415	24	5.0	24	84	0	130	44	23	7	24	1.79
30898480--30898576	27	3.6	27	84	1	124	30	21	15	31	1.94
30899508--30899774	133	2.0	133	100	0	534	43	25	11	19	1.85
30900677--30900714	16	2.5	15	87	8	51	60	0	0	39	0.97
30902722--30902764	21	2.0	21	95	0	77	39	11	0	48	1.40
30903511--30903565	17	3.2	17	76	5	58	40	0	3	56	1.17
30907369--30907423	17	3.2	17	76	5	58	40	0	3	56	1.17
30909591--30909620	11	2.6	12	89	10	53	53	13	0	33	1.40
30913440--30913494	17	3.2	17	76	5	58	40	0	3	56	1.17
30914322--30914460	32	4.4	32	81	4	147	37	17	22	23	1.94
30914338--30914460	64	1.9	64	85	3	167	36	17	22	22	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30914467--30914567	27	3.8	26	82	6	96	35	22	23	17	1.95
30914630--30914712	24	3.5	24	88	0	121	45	22	8	22	1.79
30914630--30914729	24	4.2	24	86	0	110	44	23	9	24	1.82
30915304--30915341	19	2.0	20	84	5	51	36	26	15	21	1.93
30918739--30918788	17	2.9	17	87	0	73	44	6	24	26	1.76
30925278--30925310	17	1.9	17	88	11	50	72	6	6	15	1.24
30926507--30926537	14	2.2	14	94	0	53	35	0	3	61	1.12
30927461--30927669	44	4.8	44	68	15	135	26	28	17	27	1.98
30927410--30927681	132	2.1	132	97	0	517	25	27	19	27	1.99
30944134--30944169	14	2.6	14	86	0	54	61	2	0	36	1.11
30949163--30951949	132	21.1	132	91	0	4419	25	24	19	31	1.98
30954210--30955185	132	7.4	132	89	2	1460	25	24	20	29	1.99
30954658--30955105	44	10.2	44	64	14	145	25	23	19	31	1.98
30954210--30955185	263	3.7	263	92	1	1519	25	24	20	29	1.99
30954211--30955185	395	2.5	394	90	1	1481	25	24	20	29	1.99
30956855--30958575	132	13.0	132	90	0	2697	26	23	18	31	1.98
30956855--30957965	44	25.2	44	63	15	247	25	23	19	31	1.98
30958796--30959377	44	13.2	44	62	14	117	25	22	19	32	1.97
30958676--30959523	132	6.4	132	90	1	1342	25	23	19	31	1.98
30970391--30970648	113	2.3	113	78	8	274	27	22	16	34	1.95
30970797--30970826	2	15.0	2	100	0	60	0	50	0	50	1.00
30981415--30981440	13	2.0	13	100	0	52	61	0	15	23	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30982458--30982498	2	20.5	2	94	0	73	46	0	2	51	1.14
30985466--30985528	31	2.0	31	96	0	117	36	17	23	22	1.95
30989994--30990147	63	2.4	63	93	0	272	41	14	20	23	1.89
31003715--31003760	20	2.2	21	84	3	58	28	0	8	63	1.24
31007026--31007064	6	6.5	6	84	0	51	76	5	0	17	0.96
31008684--31008733	17	2.9	17	80	11	57	72	0	12	16	1.13
31008696--31008749	18	2.8	19	74	25	51	68	0	11	20	1.19
31008666--31008772	51	2.1	48	80	10	117	69	2	9	18	1.28
31012635--31012683	12	4.3	11	79	7	53	75	4	2	18	1.06
31017193--31017274	23	3.5	25	74	14	77	47	3	0	48	1.19
31017208--31017274	22	3.0	22	78	8	73	47	2	0	49	1.16
31017646--31017671	12	2.2	12	100	0	52	46	15	0	38	1.46
31020779--31020825	21	2.2	21	92	0	76	36	6	23	34	1.80
31023682--31023734	3	17.3	3	81	11	63	64	1	3	30	1.22
31025256--31025717	86	5.4	85	74	12	300	27	22	20	30	1.98
31025498--31025982	44	10.9	44	72	9	268	28	22	17	31	1.96
31025256--31025933	44	15.5	45	70	10	311	28	22	18	30	1.97
31025499--31025939	89	5.0	88	77	9	387	28	22	17	31	1.97
31025673--31026012	181	1.9	181	89	1	531	28	22	15	33	1.95
31027245--31027365	45	2.5	49	84	9	160	14	24	19	41	1.89
31027881--31027923	21	2.0	21	100	0	86	20	32	9	37	1.85
31028336--31028376	11	3.6	12	77	12	50	0	24	0	75	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31028338--31028381	16	3.0	16	75	18	51	0	25	0	75	0.81
31030274--31030320	19	2.5	20	86	6	62	44	8	19	27	1.79
31032723--31032778	3	18.3	3	82	10	69	64	1	3	30	1.21
31032723--31032789	28	2.3	28	80	10	55	62	1	2	32	1.19
31033533--31033557	13	1.9	13	100	0	50	80	0	4	16	0.87
31033903--31033949	7	6.6	7	81	13	60	10	2	4	82	0.88
31034416--31034468	27	2.0	27	85	7	72	24	30	13	32	1.93
31037605--31037642	18	2.1	18	85	9	51	36	5	0	57	1.21
31045000--31045044	16	2.8	16	96	0	81	24	0	20	55	1.43
31045108--31045154	3	15.7	3	100	0	94	31	0	0	68	0.90

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