genome.fa.s1.2.7.7.80.10.50.1000.50.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  50  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)
14970773--14970943	43	4.0	43	78	13	174	23	16	27	32	1.96
14977009--14977043	18	2.0	18	88	5	54	17	0	8	74	1.06
14979984--14980036	26	2.0	26	100	0	106	26	3	15	54	1.57
14981841--14981892	27	1.9	27	92	0	86	25	26	15	32	1.95
14981841--14981905	27	2.4	26	85	10	78	24	26	15	33	1.95
14981919--14982081	68	2.5	66	80	5	186	20	20	18	39	1.92
14981953--14982082	68	1.9	68	87	3	190	20	23	16	38	1.93
14985464--14985536	28	2.5	30	86	6	105	41	0	5	53	1.24
14986484--14986594	23	4.8	23	87	0	159	23	18	18	39	1.92
14986484--14986605	46	2.7	46	89	2	185	24	18	18	37	1.94
14994007--14994117	31	3.7	30	76	8	100	50	7	1	40	1.40
14994012--14994147	61	2.2	61	90	0	218	50	5	1	42	1.35
14996841--14996966	26	4.9	25	80	4	108	34	7	20	36	1.82
14996859--14996966	25	4.2	25	82	3	126	32	8	21	37	1.83
15008571--15008613	15	2.9	15	80	10	52	60	2	2	34	1.22
15014182--15014225	22	2.0	22	90	0	70	6	18	6	68	1.35
15015729--15015769	3	13.7	3	100	0	82	34	31	0	34	1.58
15017906--15017957	20	2.6	19	84	9	59	48	0	3	48	1.20
15019645--15019697	2	26.5	2	80	0	61	43	5	0	50	1.25
15019726--15019773	20	2.4	20	82	0	60	33	4	0	62	1.14
15019723--15019816	43	2.2	42	85	9	120	34	3	2	60	1.24
15025059--15025098	6	6.7	6	97	0	71	35	27	17	20	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15027793--15027827	12	2.9	12	95	0	61	57	5	0	37	1.23
15030419--15030456	2	19.0	2	88	0	58	5	47	0	47	1.24
15030663--15030700	4	9.5	4	100	0	76	50	0	23	26	1.50
15031612--15031639	14	2.0	14	100	0	56	21	21	7	50	1.72
15037700--15037745	4	11.8	4	82	13	60	23	4	0	71	1.03
15041586--15041634	19	2.6	20	84	9	59	24	18	8	48	1.75
15049468--15049750	51	5.8	51	70	14	220	34	17	19	29	1.94
15049519--15049677	44	3.5	44	75	11	165	30	16	20	32	1.95
15049465--15049787	95	3.4	95	86	5	429	34	17	18	29	1.94
15051286--15051327	4	10.8	4	80	14	52	23	4	0	71	1.05
15051379--15051417	3	13.0	3	100	0	78	33	0	0	66	0.92
15051540--15051599	3	20.3	3	89	3	95	31	0	3	65	1.09
15051609--15051636	4	7.0	4	100	0	56	25	0	0	75	0.81
15062256--15062365	49	2.2	49	95	0	193	40	14	14	30	1.86
15065037--15065128	38	2.4	38	100	0	184	19	8	38	33	1.83
15066046--15066113	32	2.2	32	81	7	86	23	13	20	42	1.87
15066271--15066353	43	2.0	42	85	7	114	21	10	15	51	1.74
15068384--15068687	107	2.9	107	94	0	520	34	20	16	28	1.94
15068910--15068970	10	6.1	10	78	21	74	68	0	1	29	0.99
15068907--15068990	23	3.6	23	83	15	102	69	1	2	27	1.09
15068907--15068992	20	4.8	19	72	17	78	69	1	2	26	1.07
15068907--15068972	3	21.3	3	79	17	73	68	0	1	30	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15070750--15071270	132	3.9	132	90	0	790	27	23	18	30	1.97
15071266--15071513	44	5.6	44	79	6	277	22	22	27	28	1.99
15071274--15071531	88	2.9	89	90	2	412	22	22	26	28	1.99
15072807--15072866	18	3.4	18	80	11	70	1	18	0	80	0.80
15072807--15072860	8	6.6	8	85	12	74	1	16	0	81	0.78
15072824--15072856	15	2.2	15	100	0	66	0	12	0	87	0.53
15072824--15072870	16	3.1	15	82	11	51	0	14	0	85	0.61
15077920--15077954	16	2.2	16	94	0	61	42	20	17	20	1.89
15078878--15079181	107	2.9	107	93	0	520	34	20	16	29	1.94
15079417--15079489	8	8.6	8	75	21	69	72	2	1	23	1.05
15079412--15079464	14	3.9	14	73	16	58	75	0	0	24	0.80
15079400--15079486	27	3.3	25	79	14	79	71	2	3	22	1.13
15079419--15079464	10	4.5	11	76	17	55	73	0	0	26	0.83
15079417--15079490	26	2.8	26	82	9	89	71	4	1	22	1.10
15082964--15083011	24	2.0	25	87	4	71	56	0	2	41	1.11
15083347--15083395	21	2.3	21	100	0	98	26	22	26	24	2.00
15085704--15085762	23	2.6	22	84	10	75	27	10	20	42	1.84
15085727--15085771	23	2.0	23	82	8	56	37	8	17	35	1.81
15089809--15089860	24	2.2	24	89	0	77	36	3	9	50	1.54
15093715--15093750	18	2.0	18	94	0	63	27	13	27	30	1.94
15094012--15094063	24	2.2	24	89	0	77	36	3	9	50	1.54
15095102--15095197	10	10.4	10	69	18	50	36	2	0	61	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15095100--15095181	18	4.6	18	76	8	69	35	1	0	63	1.02
15095196--15095419	95	2.5	93	77	9	232	33	8	20	37	1.82
15095801--15095842	22	1.9	22	85	9	59	73	2	2	21	1.06
15098956--15099026	25	2.8	25	82	2	79	43	11	16	28	1.83
15101648--15101896	127	2.0	127	86	0	345	30	10	23	35	1.89
15104968--15105025	29	2.0	30	83	10	75	41	3	1	53	1.28
15105002--15105032	16	1.9	16	93	0	53	41	3	0	54	1.16
15108943--15108973	9	3.4	9	90	0	53	25	12	22	38	1.90
15121154--15121182	2	14.5	2	100	0	58	48	0	0	51	1.00
15121693--15121749	27	2.1	27	93	0	96	31	0	14	54	1.40
15121702--15121759	27	2.1	27	81	6	64	32	1	13	51	1.51
15122622--15122662	21	2.1	19	86	9	55	46	2	19	31	1.63
15124094--15124131	2	19.0	2	94	0	67	52	0	0	47	1.00
15127924--15127994	35	2.0	35	97	0	133	30	19	18	30	1.96
15134462--15134508	21	2.2	21	77	7	51	36	21	2	40	1.65
15136711--15136742	16	1.9	17	93	6	57	37	21	0	40	1.54
15136903--15137057	43	3.7	42	69	14	131	29	27	18	24	1.98
15139387--15139434	23	2.0	25	84	15	66	10	29	4	56	1.52
15141798--15141828	2	15.5	2	100	0	62	51	48	0	0	1.00
15145865--15145897	2	16.5	2	100	0	66	48	0	0	51	1.00
15148046--15148106	26	2.3	27	75	8	63	24	19	11	44	1.84
15148321--15148356	16	2.3	15	90	4	54	16	2	2	77	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15153135--15153309	23	7.7	23	89	1	271	28	6	21	44	1.76
15153135--15153309	68	2.6	69	97	0	325	28	6	21	44	1.76
15153311--15153570	25	10.7	25	73	16	208	43	14	0	41	1.48
15153311--15153570	121	2.1	121	92	1	441	43	14	0	41	1.48
15153599--15153646	25	1.9	25	87	8	71	37	18	0	43	1.51
15153457--15153638	71	2.6	71	91	3	287	44	13	0	41	1.47
15155903--15156026	51	2.4	51	87	2	178	42	1	25	29	1.65
15156009--15156053	11	4.0	11	91	2	63	51	0	31	17	1.46
15156006--15156052	22	2.1	22	92	4	76	48	0	34	17	1.47
15160367--15160397	15	2.1	14	94	5	53	51	6	0	41	1.27
15160330--15160429	51	1.9	51	82	6	121	55	7	7	31	1.54
15161153--15161228	22	3.5	22	79	15	77	40	15	5	38	1.70
15161150--15161207	22	2.6	22	86	7	82	41	17	3	37	1.66
15161163--15161279	19	5.8	19	86	8	126	38	15	8	37	1.78
15161186--15161279	19	4.8	20	88	10	142	37	14	9	38	1.79
15161186--15161279	40	2.4	38	94	3	161	37	14	9	38	1.79
15167365--15167937	114	5.0	112	78	5	537	25	21	24	27	1.99
15167365--15167930	226	2.5	226	83	5	678	25	22	24	27	2.00
15168205--15168237	15	2.2	15	89	10	50	18	0	45	36	1.49
15168515--15168600	38	2.2	39	85	8	113	20	2	39	37	1.66
15168580--15168622	21	2.0	22	86	13	63	20	0	41	37	1.53
15170837--15170909	30	2.4	31	86	4	112	16	15	20	47	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15171722--15171755	12	2.8	13	86	13	54	50	0	0	50	1.00
15171842--15171871	6	5.0	6	100	0	60	16	0	0	83	0.65
15171867--15171915	26	1.9	25	87	4	71	53	6	0	40	1.26
15171931--15172184	9	29.4	9	73	11	210	45	21	1	31	1.61
15171932--15172157	34	6.6	34	76	10	174	46	21	1	31	1.60
15171932--15171981	16	3.0	16	85	5	64	50	22	2	26	1.60
15171950--15172112	79	2.1	77	85	4	211	47	20	0	31	1.55
15171950--15172180	25	9.0	25	72	15	81	45	20	1	32	1.59
15177684--15177754	21	3.4	20	79	11	72	35	21	40	2	1.68
15178094--15178275	84	2.2	84	87	3	267	36	20	20	21	1.95

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