genome.fa.s1.2.7.7.80.10.50.1000.149.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  149  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)
44457840--44458003	82	2.0	82	98	0	319	23	23	14	39	1.91
44462040--44462100	26	2.3	26	83	8	79	37	19	26	16	1.93
44469874--44469942	26	2.7	25	78	10	68	39	18	26	15	1.91
44473905--44473950	24	1.9	24	91	8	76	36	0	2	60	1.09
44473981--44474183	59	3.3	63	81	14	187	46	8	5	38	1.60
44474017--44474217	59	3.1	67	84	13	287	45	8	4	40	1.57
44474206--44474247	16	2.6	16	96	0	75	45	7	0	47	1.30
44474221--44474276	23	2.5	23	82	2	69	44	1	1	51	1.22
44475841--44475868	2	14.0	2	100	0	56	50	0	0	50	1.00
44477472--44477615	10	15.0	9	66	20	51	59	1	4	34	1.25
44477888--44477922	6	5.5	6	87	12	52	80	2	0	17	0.84
44478029--44478352	9	34.0	9	67	18	106	32	4	3	60	1.33
44478029--44478070	21	2.0	21	85	0	57	38	2	2	57	1.25
44478092--44478142	21	2.3	22	90	6	77	35	0	7	56	1.28
44478184--44478221	19	2.0	20	89	5	60	23	2	0	73	0.95
44478186--44478341	56	2.8	56	75	14	135	27	5	2	64	1.27
44478281--44478340	28	2.1	29	84	6	79	23	3	5	68	1.24
44478270--44478341	28	2.6	27	78	12	74	26	4	4	65	1.29
44478649--44479199	306	1.8	300	91	1	805	44	12	11	31	1.78
44479202--44480093	297	3.0	292	80	6	956	41	10	13	35	1.78
44480262--44480329	22	3.1	21	73	19	75	35	0	1	63	1.04
44483876--44483973	29	3.4	28	78	5	97	23	38	22	15	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44483903--44483997	29	3.3	29	80	0	100	24	36	23	15	1.94
44485473--44485586	23	5.0	23	86	2	158	43	38	2	14	1.60
44493792--44493829	2	19.0	2	88	0	58	0	44	0	55	0.99
44497292--44497358	19	3.5	19	80	10	82	26	25	26	20	1.99
44498284--44498320	3	12.3	3	94	0	65	64	0	32	2	1.07
44498990--44499051	29	2.2	28	82	5	79	59	1	3	35	1.23
44499191--44499251	28	2.3	27	83	13	74	67	1	3	27	1.16
44499224--44499274	23	2.3	22	80	12	52	60	0	7	31	1.25
44499788--44499851	24	2.8	23	73	15	60	35	1	1	60	1.15
44508925--44508966	20	2.1	20	82	8	50	61	9	4	23	1.45
44514390--44514426	15	2.4	16	86	13	51	29	10	13	45	1.77
44520109--44520353	91	2.7	90	86	2	305	33	10	20	36	1.86
44526669--44526735	26	2.6	26	90	4	100	41	7	1	49	1.40
44526799--44526905	27	4.0	27	95	0	160	26	28	29	15	1.96
44527191--44527228	3	12.7	3	100	0	76	34	0	0	65	0.93
44527194--44527338	12	11.8	12	67	15	55	35	0	7	55	1.33
44527959--44528003	18	2.5	18	85	0	63	28	4	46	20	1.69
44530690--44530769	27	3.0	27	90	0	124	15	28	28	27	1.96
44530821--44530880	27	2.2	26	91	8	102	50	0	6	43	1.28
44530823--44530888	27	2.4	27	90	7	89	48	1	7	42	1.40
44536122--44536160	16	2.5	16	95	4	71	38	12	0	48	1.42
44538664--44538729	33	2.0	33	93	0	114	16	25	13	43	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44540522--44540559	18	2.1	19	85	5	51	42	15	15	26	1.87
44543162--44543227	33	2.0	33	93	0	114	15	24	15	45	1.84
44546913--44547172	127	2.0	127	94	1	459	45	13	11	29	1.79
44547911--44548124	41	5.3	41	85	2	254	21	19	21	37	1.94
44547911--44548124	81	2.6	81	86	3	288	21	19	21	37	1.94
44555221--44555255	6	5.8	6	87	12	54	14	2	0	82	0.77
44555834--44555896	31	2.0	32	96	3	119	31	9	15	42	1.79
44560485--44560536	6	8.7	6	86	0	59	26	0	55	17	1.42
44560485--44560538	18	3.0	18	86	0	72	27	0	55	16	1.42
44574876--44574933	24	2.5	24	80	2	64	60	18	1	18	1.45
44576380--44576564	43	4.3	43	84	0	244	33	25	15	25	1.95
44582592--44582933	9	39.1	9	73	9	219	33	0	18	46	1.54
44582599--44582933	70	4.8	70	74	10	292	34	0	18	46	1.54
44582810--44582947	45	3.1	43	73	21	117	32	0	19	47	1.50
44583239--44583277	12	3.5	11	86	13	53	33	2	0	64	1.08
44583485--44583758	123	2.2	123	95	1	487	44	4	8	43	1.54
44584283--44585032	228	3.3	226	77	5	753	31	19	22	26	1.98
44584169--44585032	113	7.6	115	79	4	680	31	20	22	26	1.98
44585197--44585319	7	17.0	7	72	15	81	17	1	39	40	1.60
44585217--44585272	23	2.4	23	96	0	103	14	0	42	42	1.45
44585217--44585317	23	4.5	23	85	4	86	17	0	39	41	1.57
44586534--44586580	22	2.1	22	96	0	85	27	8	23	40	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44586758--44586859	54	1.9	53	88	6	152	26	2	20	50	1.63
44587057--44587086	14	2.1	14	100	0	60	26	13	6	53	1.64
44587623--44587706	45	1.9	43	80	4	96	38	13	2	46	1.56
44588286--44588859	9	67.9	9	65	18	144	46	18	4	30	1.70
44588405--44588514	37	3.0	37	100	0	220	50	16	2	30	1.59
44588500--44588572	34	2.1	34	94	0	128	42	21	6	28	1.79
44588563--44588817	16	16.6	16	64	21	109	45	18	5	30	1.72
44588543--44588850	49	6.6	49	75	12	290	45	19	5	30	1.73
44588532--44588816	90	3.2	90	96	0	516	45	18	5	30	1.72
44588592--44588761	41	4.0	41	77	11	178	46	19	4	29	1.70
44588626--44588673	25	1.9	25	86	0	69	43	25	4	27	1.72
44588716--44588850	25	5.4	25	72	5	76	43	20	5	31	1.73
44594329--44594376	21	2.3	20	89	7	69	35	18	41	4	1.70
44594361--44594400	12	3.3	12	96	0	71	40	17	40	2	1.63
44594821--44595263	42	10.4	42	86	4	498	26	19	20	32	1.97
44594821--44595263	43	10.4	42	86	4	484	26	19	20	32	1.97
44594820--44595263	213	2.1	213	83	7	553	26	19	20	32	1.97
44596893--44596970	41	2.0	39	90	7	122	37	3	5	53	1.41
44597325--44597571	7	34.4	7	68	12	90	45	34	0	19	1.56
44597337--44597378	22	1.9	22	90	0	66	47	30	0	21	1.51
44597472--44597571	41	2.4	41	82	9	107	46	36	1	17	1.55
44597471--44597571	48	2.1	48	81	7	116	45	36	0	16	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44597894--44597980	40	2.2	40	80	0	102	28	22	17	31	1.97
44598073--44598164	40	2.3	40	79	3	96	23	18	22	34	1.96
44598619--44598647	15	1.9	15	100	0	58	27	0	13	58	1.36
44617783--44617855	20	3.7	20	80	14	87	35	23	32	8	1.84
44624272--44624390	60	2.0	60	98	0	229	26	10	31	32	1.89
44632781--44632917	20	7.3	20	64	14	85	33	5	13	48	1.64
44632790--44632924	17	7.4	17	64	14	63	33	4	13	48	1.62
44632785--44632933	37	4.0	37	93	0	253	34	5	14	46	1.67
44632939--44632978	9	4.4	9	87	0	62	35	10	17	37	1.83
44636608--44636648	16	2.7	16	79	20	52	48	9	0	41	1.36
44645418--44645454	12	3.1	12	84	0	56	21	24	21	32	1.98
44650697--44650738	22	2.0	21	90	9	68	57	0	0	42	0.99
44651926--44651975	21	2.3	22	82	3	57	56	6	4	34	1.43
44651927--44651969	13	3.1	14	87	9	54	60	4	2	32	1.30
44652329--44652372	10	4.4	10	82	0	52	45	2	11	40	1.53
44652081--44653152	263	4.3	260	75	14	945	44	7	11	36	1.69
44651835--44652828	508	2.0	504	85	6	1354	45	7	9	37	1.65
44652496--44653076	232	2.5	230	84	4	740	44	7	10	38	1.67
44662777--44662843	18	3.7	18	85	0	98	26	10	25	37	1.88
44662777--44662843	9	7.4	9	82	0	80	26	10	25	37	1.88
44662777--44662842	27	2.4	27	82	9	89	27	10	25	36	1.89
44667476--44667513	14	2.7	14	91	0	58	47	2	10	39	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44667532--44667602	32	2.2	32	85	5	90	30	5	11	52	1.60
44667742--44667788	18	2.4	20	75	17	53	46	4	6	42	1.48
44667930--44667983	25	2.0	26	86	10	74	40	5	5	48	1.50
44668336--44668392	15	3.5	15	71	17	51	47	3	1	47	1.29
44668419--44668457	13	3.0	13	82	10	53	43	0	2	53	1.14
44668984--44669185	89	2.3	89	85	2	262	34	19	9	36	1.85
44669320--44669379	19	3.3	19	72	6	52	61	0	1	36	1.06
44669338--44669399	27	2.3	27	86	10	83	59	1	3	35	1.23
44669414--44669453	21	1.9	21	90	10	64	67	5	2	25	1.23
44671328--44671364	16	2.3	16	90	9	58	27	0	5	67	1.12

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