genome.fa.s1.2.7.7.80.10.50.1000.183.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  183  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)
54900887--54901051	82	2.0	82	95	0	294	28	23	18	30	1.97
54902539--54902586	25	1.9	25	95	0	87	33	31	31	4	1.77
54909489--54909525	17	2.2	17	95	0	65	29	27	2	40	1.70
54913039--54913358	73	4.4	73	91	0	478	28	18	27	25	1.98
54913258--54913573	115	2.8	114	84	3	413	28	19	25	26	1.99
54913372--54913826	187	2.4	188	82	5	544	29	19	25	26	1.99
54913498--54913659	73	2.2	73	82	6	220	27	18	28	25	1.98
54913185--54913762	302	1.9	302	89	3	905	28	19	25	26	1.99
54913681--54913921	72	3.3	73	81	3	297	28	19	25	26	1.99
54914105--54914292	14	13.4	14	67	14	66	20	1	31	46	1.60
54914163--54914215	22	2.4	21	81	6	61	22	0	28	49	1.50
54914163--54914291	7	18.6	7	70	12	52	20	0	31	47	1.56
54914163--54914291	21	6.2	21	72	14	88	20	0	31	47	1.56
54914249--54914292	7	6.3	7	82	10	54	15	0	36	47	1.46
54914360--54914411	26	2.0	26	88	7	79	32	11	19	36	1.87
54914582--54914635	21	2.5	21	80	11	65	24	0	42	33	1.55
54914581--54914643	14	4.4	14	75	11	56	23	0	41	34	1.55
54914579--54914669	22	4.3	21	74	8	87	23	0	41	35	1.54
54914899--54914972	30	2.5	29	82	10	96	51	2	4	41	1.35
54914920--54914956	19	1.9	19	88	0	56	51	2	2	43	1.30
54914904--54914957	10	5.3	10	76	10	56	57	1	1	38	1.20
54915421--54915559	69	2.0	69	97	0	260	39	11	9	39	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54917022--54917089	23	3.0	23	77	12	77	35	8	20	35	1.84
54917947--54918107	42	3.9	42	84	8	206	18	18	28	34	1.95
54919223--54919268	24	1.9	24	95	0	83	34	23	4	36	1.75
54921395--54921443	21	2.3	21	83	10	64	36	16	2	44	1.59
54924472--54924500	6	4.8	6	100	0	58	0	65	0	34	0.93
54931295--54931535	120	2.0	120	96	1	448	24	10	31	34	1.89
54933966--54934014	21	2.3	21	83	10	64	36	16	2	44	1.59
54935659--54935684	6	4.3	6	100	0	52	15	15	0	69	1.20
54935593--54935733	63	2.2	64	88	3	203	26	18	5	48	1.70
54943929--54943969	21	2.0	21	85	4	57	34	2	2	60	1.23
54951242--54951276	2	17.5	2	100	0	70	51	0	0	48	1.00
54951695--54951810	58	2.0	58	98	0	223	43	22	12	21	1.87
54954185--54954241	25	2.3	25	84	6	71	36	17	12	33	1.87
54959150--54959227	26	3.0	25	75	5	77	26	5	8	58	1.49
54961942--54961984	20	2.2	20	86	0	59	13	23	11	51	1.74
54972874--54972906	16	2.1	16	88	11	50	42	0	6	51	1.26
54972869--54973159	93	3.1	92	90	3	424	46	3	4	45	1.40
54972908--54973251	49	7.2	48	70	17	218	47	3	2	46	1.34
54973155--54973233	18	4.4	17	67	19	52	49	1	0	49	1.09
54972884--54973194	93	3.3	92	83	10	321	46	3	3	46	1.37
54973189--54973485	120	2.5	120	92	1	488	44	3	4	47	1.41
54973260--54973450	61	3.2	60	68	19	162	42	3	6	47	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54973264--54973447	59	3.1	59	65	13	133	42	3	7	47	1.47
54973430--54973465	18	2.0	18	88	0	54	44	0	0	55	0.99
54976163--54976187	12	2.1	12	100	0	50	0	0	8	92	0.40
54976646--54976695	15	3.3	15	88	0	64	24	2	12	62	1.40
54976645--54976680	12	3.0	12	91	0	54	22	2	11	63	1.39
54981954--54981991	18	2.2	17	86	9	51	23	5	2	68	1.23
54984479--54984517	18	2.2	18	86	9	53	35	0	0	64	0.94
55002578--55002634	30	1.9	29	86	10	80	61	7	3	28	1.39
55003754--55003792	17	2.3	17	90	0	60	84	5	10	0	0.76
55004409--55004456	17	2.9	17	85	11	57	47	4	8	39	1.53
55005805--55006124	18	17.6	17	68	21	122	41	9	13	35	1.77
55005896--55005977	22	4.0	22	71	16	68	39	6	14	40	1.71
55005896--55005937	21	2.0	21	90	4	66	35	7	16	40	1.76
55005807--55006120	17	17.2	19	69	19	99	41	9	13	35	1.77
55006609--55006650	7	5.9	7	81	15	50	0	16	0	83	0.65
55006609--55006653	22	2.0	22	91	8	74	0	17	0	82	0.68
55006615--55006662	22	2.4	19	86	10	60	0	18	0	81	0.70
55006616--55006663	15	3.2	14	80	13	60	0	16	0	83	0.65
55006662--55006704	14	2.8	16	77	22	56	2	27	37	32	1.70
55006661--55006705	15	3.1	14	81	18	56	2	26	35	35	1.69
55006695--55006754	26	2.3	26	97	0	111	0	26	45	28	1.54
55006764--55006798	17	2.1	17	89	10	54	2	20	48	28	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55006803--55006857	26	2.1	26	83	6	67	0	14	10	74	1.07
55006959--55007030	6	11.8	6	80	14	67	0	22	0	77	0.76
55006972--55007030	13	4.6	13	87	2	75	0	25	0	74	0.82
55006972--55007045	3	25.3	3	78	10	66	0	28	0	71	0.86
55006958--55007040	13	6.0	13	77	16	69	0	24	0	75	0.80
55006962--55007043	16	5.5	15	73	20	66	0	25	0	74	0.82
55006988--55007045	19	3.0	19	76	2	71	0	31	0	68	0.89
55007402--55007514	29	3.9	29	83	4	147	39	5	20	34	1.75
55007393--55007515	58	2.1	59	87	4	178	39	4	20	35	1.74
55008615--55008678	27	2.4	27	86	2	85	53	4	1	40	1.31
55009431--55009472	14	3.2	14	77	16	54	76	9	0	14	1.02
55010700--55010752	18	2.9	18	77	8	54	60	1	1	35	1.19
55010829--55010895	34	1.9	35	87	3	100	44	14	8	31	1.76
55016658--55016870	106	2.0	106	92	0	354	25	15	22	36	1.93
55021067--55021129	17	3.5	17	69	12	54	49	12	3	34	1.57
55021058--55021132	37	2.0	37	94	0	132	45	14	4	36	1.64
55021271--55021369	45	2.2	45	91	5	157	20	1	23	55	1.49
55022279--55022322	23	1.9	23	81	9	54	40	22	6	29	1.80
55028379--55028426	2	24.0	2	100	0	96	50	0	0	50	1.00
55028852--55028884	16	2.0	17	88	5	50	54	18	6	21	1.64
55032773--55032839	3	22.3	3	90	6	109	34	0	1	64	1.03
55036547--55036579	4	8.2	4	100	0	66	24	24	0	51	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55043423--55043831	44	9.0	44	76	11	317	31	20	19	28	1.97
55043504--55043941	138	3.2	138	79	3	472	31	20	20	27	1.97
55044469--55044509	7	5.9	7	94	0	73	43	41	0	14	1.45
55051004--55051042	3	13.0	3	100	0	78	66	0	0	33	0.92
55052579--55052604	7	3.7	7	100	0	52	38	0	0	61	0.96
55060133--55060174	22	1.9	22	85	9	59	50	0	26	23	1.50
55060495--55060595	42	2.4	42	88	3	159	37	21	19	20	1.94
55061029--55061078	21	2.4	21	82	0	64	2	42	18	38	1.61
55066628--55067020	9	42.9	9	75	7	317	33	3	15	48	1.60
55067079--55067116	16	2.4	16	91	4	60	52	5	0	42	1.24
55069136--55069193	23	2.6	23	81	8	66	43	32	0	24	1.55
55069198--55069228	14	2.2	14	94	0	53	32	51	0	16	1.44
55069290--55069333	21	2.1	21	83	8	54	38	36	0	25	1.56
55069526--55069595	21	3.3	21	71	15	63	40	40	1	18	1.60
55069837--55070591	114	6.6	114	87	2	1027	23	21	21	33	1.97
55070762--55070819	29	2.0	29	86	6	82	43	15	8	32	1.77
55073031--55073058	5	5.6	5	100	0	56	39	0	0	60	0.97
55079039--55079094	18	3.0	19	85	10	71	39	1	1	57	1.20
55079165--55079248	45	1.9	43	80	4	96	38	13	2	46	1.56
55079245--55079409	13	12.5	13	74	7	136	40	9	3	46	1.54
55079269--55079414	53	2.8	53	96	0	265	41	10	3	44	1.55
55079860--55080084	9	25.8	9	75	14	213	45	20	1	32	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55079860--55080084	43	5.2	43	75	17	221	45	20	1	32	1.60
55079847--55080043	62	3.2	62	77	13	192	46	20	1	32	1.58
55079847--55080084	25	9.1	25	76	13	173	45	20	1	32	1.59
55082110--55082161	21	2.5	21	90	0	77	30	17	46	5	1.71
55082545--55082668	41	3.0	41	86	2	176	25	18	20	35	1.95
55082552--55082668	42	2.8	41	87	2	171	25	17	19	36	1.94
55083974--55084043	22	3.2	22	93	0	122	31	30	0	38	1.58
55084015--55084073	30	2.0	30	93	0	100	30	35	0	33	1.58
55083993--55084095	52	2.0	51	86	5	145	33	33	0	33	1.58
55084045--55084086	22	1.9	22	90	0	66	33	33	0	33	1.58

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