genome.fa.s6.2.7.7.80.10.50.1000.38.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  38  of  168  ( 20060 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)
10246087--10246271	81	2.3	81	88	3	282	23	23	24	29	1.99
10246784--10246823	15	2.7	14	81	11	53	12	12	20	55	1.69
10248522--10248554	17	1.9	17	100	0	66	24	9	18	48	1.76
10248947--10249218	43	6.3	43	89	0	391	22	17	32	27	1.96
10258973--10259097	27	4.6	27	75	11	112	27	17	24	30	1.97
10258973--10259111	27	5.1	27	77	3	82	26	17	25	30	1.97
10259908--10259950	21	2.0	21	86	8	61	0	32	0	67	0.91
10259908--10259955	16	2.9	15	82	14	51	2	29	0	68	1.01
10261671--10261701	2	15.5	2	100	0	62	48	0	0	51	1.00
10268237--10268283	21	2.2	21	88	0	67	27	36	14	21	1.93
10277210--10277309	50	2.0	50	100	0	200	34	22	10	34	1.87
10280765--10280805	20	2.0	20	85	0	55	39	7	17	36	1.77
10281672--10281737	29	2.2	29	86	2	87	10	31	28	28	1.90
10284753--10284786	18	2.0	16	88	11	50	64	0	0	35	0.94
10291523--10291588	29	2.4	28	81	16	77	40	3	1	54	1.25
10299424--10299606	45	4.1	45	84	2	237	34	27	16	20	1.94
10299430--10299606	89	2.0	88	86	3	248	34	28	16	20	1.94
10308277--10308314	20	1.9	20	89	10	60	39	0	18	42	1.50
10308835--10308994	45	3.6	45	75	6	139	42	19	18	19	1.89
10309453--10309495	21	2.0	21	86	8	61	34	6	11	46	1.67
10311553--10311593	17	2.3	19	91	8	68	31	2	0	65	1.05
10317938--10317964	6	4.5	6	100	0	54	85	0	0	14	0.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10324261--10324433	93	1.9	92	81	6	215	21	23	26	28	1.99
10340363--10340387	13	1.9	13	100	0	50	20	40	8	32	1.81
10342368--10342447	32	2.5	32	93	0	133	40	13	7	38	1.73
10342565--10342712	62	2.4	62	100	0	296	47	8	11	32	1.69
10342890--10342998	44	2.6	41	74	17	98	44	0	4	50	1.29
10342923--10342986	28	2.4	28	86	5	87	43	0	0	56	0.99
10342836--10343095	117	2.3	106	87	10	312	43	1	3	50	1.31
10343042--10343075	17	2.0	17	100	0	68	41	0	0	58	0.98
10343042--10343089	15	3.0	15	81	9	51	41	2	0	56	1.11
10343261--10343299	16	2.4	16	95	0	69	20	35	5	38	1.75
10343714--10343767	27	2.0	28	96	3	101	35	14	16	33	1.90
10343718--10343777	27	2.2	26	88	8	93	33	15	16	35	1.90
10351221--10351295	35	2.1	35	95	0	132	21	8	33	37	1.83
10373574--10373612	20	2.0	20	89	0	60	15	25	2	56	1.52
10373822--10373993	49	3.5	49	84	5	197	23	26	18	31	1.98
10373813--10374106	50	5.8	49	78	8	211	24	26	20	28	1.99
10383990--10384065	39	1.9	39	89	0	116	28	15	15	39	1.89
10393714--10393925	94	2.3	93	83	3	246	26	28	25	18	1.98
10394405--10394447	18	2.4	18	80	7	52	23	4	0	72	1.04
10397004--10397158	77	2.0	77	92	0	256	32	7	25	34	1.84
10408045--10408102	26	2.2	26	81	6	64	63	8	5	22	1.42
10408082--10408125	19	2.3	19	88	7	63	70	2	2	25	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10408090--10408147	29	2.0	29	82	0	71	65	5	1	27	1.23
10414688--10414719	12	2.7	12	95	0	55	18	3	9	68	1.30
10417602--10417639	19	2.0	20	84	5	51	26	13	10	50	1.73
10422550--10422658	51	2.1	51	100	0	218	27	10	33	29	1.89
10430223--10430307	41	2.1	41	84	0	107	17	30	17	34	1.94
10442988--10443022	18	1.9	18	88	11	54	57	0	11	31	1.34
10459116--10459307	98	2.0	98	92	0	321	36	25	10	27	1.89
10460178--10460221	21	2.0	21	82	4	52	52	18	0	29	1.46
10460743--10460774	5	6.4	5	92	0	55	15	0	21	62	1.32
10461167--10461288	44	2.8	44	77	13	135	27	21	20	30	1.98
10463888--10463946	29	2.0	29	100	0	118	44	10	15	30	1.79
10463888--10463963	29	2.7	29	89	4	102	44	7	11	35	1.70
10469869--10470060	98	2.0	98	91	0	312	37	25	10	27	1.88
10470933--10470975	21	2.0	22	86	4	61	48	18	0	32	1.48
10471499--10471530	5	6.4	5	92	0	55	15	0	21	62	1.32
10477725--10477757	16	2.1	16	100	0	66	6	36	0	57	1.23
10485230--10485299	25	2.8	25	77	0	95	25	24	24	25	2.00
10486470--10486497	12	2.3	12	100	0	56	28	42	21	7	1.79
10490724--10490758	18	1.9	18	100	0	70	34	11	17	37	1.85
10491064--10491122	30	2.0	31	86	6	86	22	38	0	38	1.54
10502497--10502687	56	3.4	56	87	2	251	30	10	14	45	1.78
10502497--10502726	111	2.1	114	81	6	274	29	11	15	43	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10505494--10505560	27	2.5	27	83	9	100	26	7	22	43	1.80
10505494--10505560	9	7.4	9	83	9	75	26	7	22	43	1.80
10514699--10514741	3	14.3	3	100	0	86	67	0	0	32	0.91
10517175--10517230	17	3.4	17	97	2	105	50	5	5	39	1.48
10518866--10518895	15	2.0	15	93	0	51	16	6	10	66	1.41
10525844--10525899	27	2.1	27	83	6	69	33	12	28	25	1.92
10530142--10530224	30	2.8	29	78	14	87	36	2	26	34	1.70
10530181--10530238	30	1.9	30	86	6	82	39	5	24	31	1.77
10536509--10536597	44	2.0	44	100	0	178	35	16	17	29	1.93
10543762--10543800	5	8.0	5	91	5	53	25	0	0	74	0.82
10543762--10543798	19	1.9	19	88	0	56	24	0	0	75	0.80
10545274--10545405	71	1.9	71	88	3	203	28	22	25	23	1.99
10548473--10548513	21	2.0	21	85	0	55	26	26	19	26	1.99
10552009--10552110	50	2.0	50	80	0	114	35	6	30	27	1.83
10554972--10555138	23	7.3	23	75	16	168	23	17	25	33	1.96
10554971--10555138	46	3.7	46	93	1	266	23	17	25	33	1.97
10563077--10563113	18	2.1	18	89	0	56	54	0	0	45	1.00
10568091--10568123	16	2.1	16	88	11	50	42	0	0	57	0.98
10568142--10568192	25	2.0	24	85	11	66	50	3	1	43	1.31
10574312--10574537	113	2.0	113	82	1	274	32	11	19	35	1.88
10583721--10583747	9	3.0	9	100	0	54	33	33	22	11	1.89
10587067--10587112	23	2.0	23	84	12	60	6	26	0	67	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10587415--10587457	21	2.0	21	86	0	59	20	34	9	34	1.85
10593869--10594517	320	2.0	320	92	0	1084	36	19	13	30	1.90
10601344--10601380	18	2.1	18	89	0	56	29	5	35	29	1.80
10603830--10603879	19	2.7	19	93	3	84	52	0	16	32	1.44
10604509--10604666	79	2.0	79	94	0	280	27	13	12	47	1.78
10608614--10608643	15	2.0	15	93	0	51	23	16	6	53	1.66
10609407--10609433	13	2.1	13	100	0	54	25	22	14	37	1.93
10613742--10613817	27	2.8	27	87	0	116	35	17	26	21	1.95
10624536--10624564	12	2.4	12	100	0	58	72	0	0	27	0.85
10626259--10626298	21	1.9	21	94	0	71	45	0	0	55	0.99
10634613--10634655	21	2.0	21	91	8	70	32	6	0	60	1.23
10636034--10636073	10	4.3	10	78	18	50	22	0	0	77	0.77
10636033--10636074	8	4.9	8	83	16	57	26	0	0	73	0.83
10644263--10644331	29	2.3	29	85	5	84	49	14	14	21	1.79
10644446--10644478	17	1.9	18	88	11	52	54	0	0	45	0.99
10644958--10644990	15	2.1	16	88	5	50	48	3	0	48	1.17
10648218--10648254	19	1.9	19	88	0	56	59	0	2	37	1.12
10650236--10650275	5	8.0	5	94	0	71	20	0	22	57	1.41
10651998--10652042	20	2.2	20	96	0	81	31	24	22	22	1.99
10659785--10659855	30	2.4	30	82	0	88	23	26	12	36	1.91
10659815--10660059	60	4.2	60	73	9	182	23	28	13	34	1.93
10659815--10659997	90	2.0	90	80	4	199	24	27	12	36	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10659845--10659997	30	5.1	30	76	3	137	24	27	11	36	1.90
10659950--10660050	53	1.9	53	93	0	175	23	29	17	28	1.97
10660016--10660088	29	2.5	30	84	4	96	16	31	15	36	1.90
10661769--10661808	19	2.1	19	86	9	55	17	37	2	42	1.63
10663374--10663419	24	2.0	24	86	4	67	39	2	4	54	1.32
10686761--10686819	30	2.0	30	93	0	100	25	27	30	16	1.97
10688284--10688412	35	3.7	35	77	8	136	30	17	24	28	1.97
10688282--10688430	70	2.1	70	86	0	208	31	16	24	27	1.96
10691423--10691605	87	2.1	88	86	4	262	31	21	12	35	1.90
10694045--10694072	3	9.3	3	100	0	56	67	0	32	0	0.91

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