genome.fa.s4.2.7.7.80.10.50.1000.138.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  138  of  198  ( 23681 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)
43943399--43943441	10	4.3	10	88	5	61	69	2	0	27	1.00
43952172--43952373	74	2.7	75	79	6	185	34	5	19	40	1.76
43952631--43952708	41	1.9	41	91	0	129	24	21	26	26	1.99
43954792--43954835	9	4.9	9	97	0	79	47	6	22	22	1.75
43956590--43956701	19	5.8	19	72	2	62	18	23	29	28	1.98
43956613--43956699	39	2.3	38	79	2	93	16	26	29	27	1.96
43960630--43960718	44	2.0	44	97	0	169	31	19	13	35	1.90
43962709--43962973	132	2.0	132	99	0	521	32	26	9	30	1.89
43964410--43964440	9	3.3	9	95	4	53	58	0	0	41	0.98
43964837--43964870	17	2.0	17	88	0	50	38	2	0	58	1.13
43966169--43966196	5	5.6	5	100	0	56	39	0	0	60	0.97
43966402--43966426	6	4.2	6	100	0	50	84	0	16	0	0.63
43966711--43966751	18	2.3	18	87	8	57	43	0	17	39	1.49
43966948--43967030	21	3.9	21	80	4	87	20	21	22	34	1.96
43971878--43971913	18	2.0	18	94	0	63	30	30	5	33	1.81
43971873--43971919	18	2.9	16	79	14	60	29	29	4	36	1.77
43975354--43975429	30	2.5	30	89	0	107	28	17	22	31	1.96
43977583--43977907	91	3.6	91	82	1	373	32	27	15	24	1.95
43979275--43979571	50	5.8	50	80	3	256	27	20	28	22	1.99
43986385--43986510	61	2.1	61	88	4	184	30	6	19	44	1.75
43989405--43989463	23	2.6	23	81	5	66	37	18	11	32	1.87
43990600--43990633	2	17.0	2	93	0	59	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43996149--43996205	29	2.0	28	83	10	71	29	17	7	45	1.75
43996266--43996375	55	2.0	55	100	0	220	54	7	3	34	1.46
43996748--43996790	22	2.0	22	90	0	68	20	11	9	58	1.61
43997941--43998010	32	2.2	30	82	10	77	51	4	2	41	1.36
43998084--43998126	10	4.3	10	78	0	50	46	0	0	53	1.00
43999296--43999383	29	3.0	29	76	5	79	39	5	21	32	1.77
44002515--44002631	59	2.0	59	96	0	216	54	8	4	32	1.50
44005271--44005296	5	5.2	5	100	0	52	38	0	0	61	0.96
44009062--44009100	21	1.9	21	89	5	62	33	2	0	64	1.08
44009046--44009186	40	3.6	38	70	17	99	30	2	0	66	1.08
44009082--44009142	8	6.4	10	80	16	60	31	1	0	67	1.01
44009071--44009189	39	2.9	40	85	8	152	34	2	0	62	1.15
44011931--44011992	24	2.7	24	81	18	78	54	1	1	41	1.19
44011973--44012004	17	1.9	17	93	6	57	56	0	3	40	1.15
44041424--44041530	10	11.7	9	70	12	67	66	0	4	28	1.18
44041425--44041492	18	3.9	16	80	17	66	69	1	4	25	1.16
44041425--44041530	19	5.7	19	76	13	89	66	0	4	28	1.18
44041527--44041571	21	2.1	21	84	8	56	60	4	8	26	1.46
44041533--44041597	19	3.4	18	71	24	62	58	4	7	29	1.46
44041792--44041844	18	2.8	19	77	8	54	50	0	0	49	1.00
44042380--44042455	31	2.5	28	79	14	64	59	0	3	36	1.16
44044969--44045051	41	2.0	41	100	0	166	31	9	24	34	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44045788--44045823	6	6.0	6	86	0	54	80	0	5	13	0.88
44046931--44047046	57	2.0	57	91	3	189	43	14	12	29	1.83
44050400--44050507	42	2.6	42	78	8	105	41	13	24	20	1.88
44055015--44055198	26	7.1	26	78	2	190	33	27	16	22	1.96
44056039--44056082	22	2.0	22	87	12	65	52	9	0	38	1.33
44056040--44056082	21	2.0	21	91	8	70	53	9	0	37	1.33
44059473--44059538	32	2.1	32	100	0	132	31	9	22	36	1.86
44060257--44060315	23	2.6	23	76	7	57	28	0	5	66	1.13
44068334--44068372	17	2.3	17	100	0	78	15	0	28	56	1.40
44068608--44068648	17	2.4	17	95	0	73	19	24	39	17	1.92
44077757--44077838	20	4.1	20	72	12	69	14	34	20	30	1.93
44077762--44077838	40	1.9	40	84	5	102	14	32	22	31	1.93
44083570--44083609	20	2.0	20	100	0	80	30	0	25	45	1.54
44084393--44084765	27	13.9	27	85	7	440	20	15	18	44	1.87
44088338--44088405	21	3.3	21	70	12	59	29	16	35	19	1.93
44088339--44088483	41	3.5	41	85	0	191	31	15	31	20	1.94
44095996--44096132	69	2.0	69	98	0	265	31	7	19	41	1.79
44096674--44096795	20	6.1	20	67	7	59	16	35	18	29	1.93
44096650--44096735	40	2.2	40	81	8	95	16	33	22	27	1.95
44096642--44096715	20	3.7	20	71	10	62	14	36	22	25	1.93
44104025--44104174	28	5.3	27	69	13	79	28	23	20	28	1.99
44104176--44104205	15	1.9	16	93	6	53	16	10	26	46	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44104423--44104532	53	2.1	54	87	5	161	30	21	9	39	1.84
44107115--44107170	24	2.3	24	84	6	69	64	7	19	8	1.45
44109748--44109800	21	2.5	21	76	14	56	37	3	3	54	1.36
44128755--44128875	37	3.2	37	98	1	233	28	14	14	42	1.85
44129693--44129767	33	2.2	33	86	6	98	10	25	6	57	1.57
44129720--44129773	18	3.2	17	75	15	58	7	25	5	61	1.45
44138055--44138258	68	3.0	68	83	2	239	27	22	12	37	1.91
44138084--44138299	68	3.2	68	82	3	247	26	20	12	39	1.89
44138053--44138299	136	1.8	136	81	1	307	26	21	14	37	1.92
44140904--44140989	43	2.0	43	82	8	104	25	18	2	53	1.56
44152992--44153064	33	2.2	33	85	7	94	9	24	6	58	1.54
44155189--44155235	23	2.0	23	100	0	94	34	25	12	27	1.92
44157379--44157468	41	2.2	41	78	7	94	20	5	15	58	1.56
44159094--44159336	68	3.6	68	78	1	222	26	21	14	37	1.92
44162805--44162890	43	2.0	43	88	4	129	24	20	0	54	1.45
44162805--44162863	15	4.1	15	69	22	54	23	22	0	54	1.45
44164055--44164090	15	2.4	15	90	0	54	36	2	2	58	1.27
44171677--44171704	10	2.8	10	100	0	56	39	50	0	10	1.37
44171965--44172050	42	2.0	42	93	0	145	41	24	13	19	1.88
44178878--44178976	40	2.5	40	88	3	146	36	19	28	16	1.93
44178900--44178957	20	2.9	20	74	7	64	31	18	32	17	1.94
44178915--44178976	20	3.1	20	72	9	63	35	19	32	12	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44192036--44192166	26	5.0	26	90	0	163	20	19	22	37	1.94
44209101--44209158	22	2.7	21	81	7	71	34	3	18	43	1.68
44221975--44222092	5	23.6	5	100	0	236	20	0	19	60	1.37
44228599--44228635	18	2.1	18	100	0	74	51	0	0	48	1.00
44229215--44229254	20	2.1	19	90	4	62	20	5	10	65	1.42
44230320--44230354	18	1.9	18	94	0	61	28	5	25	40	1.78
44231411--44231439	6	5.0	6	91	8	51	0	13	0	86	0.58
44231404--44231439	11	3.2	11	88	7	54	0	16	0	83	0.65
44236603--44236630	9	3.1	9	100	0	56	57	10	0	32	1.33
44236573--44236816	68	3.6	68	99	0	479	45	9	4	40	1.57
44236671--44236698	9	3.1	9	100	0	56	57	10	0	32	1.33
44236739--44236766	9	3.1	9	100	0	56	57	10	0	32	1.33
44236823--44236864	16	2.6	16	92	0	66	42	7	2	47	1.43
44236838--44236892	22	2.5	22	84	0	74	43	1	1	52	1.22
44236877--44236905	6	4.8	6	100	0	58	34	0	0	65	0.93
44242707--44242801	47	2.0	47	100	0	190	20	27	8	44	1.80
44243608--44243649	17	2.5	17	85	11	59	47	0	9	42	1.36
44252986--44253014	11	2.6	11	100	0	58	62	0	17	20	1.33
44253913--44253951	12	3.2	12	86	13	62	82	0	7	10	0.86
44265214--44265414	31	6.5	31	85	1	251	30	8	17	43	1.78
44265214--44265420	92	2.2	93	84	3	231	30	8	17	43	1.78
44265538--44265644	43	2.5	43	86	7	153	25	17	25	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44266327--44266392	31	2.1	32	97	2	125	27	16	18	37	1.92
44267131--44267160	2	15.0	2	100	0	60	50	0	0	50	1.00
44268071--44268182	45	2.5	45	82	5	129	37	11	23	27	1.89
44268340--44268404	27	2.4	27	82	5	78	40	24	15	20	1.91
44269356--44269428	37	2.0	37	100	0	146	19	20	21	38	1.94
44269668--44269714	24	2.0	24	91	0	76	27	17	29	25	1.97
44270965--44271046	23	3.4	23	86	8	94	23	26	21	28	1.99
44272363--44272405	22	2.0	22	90	0	68	9	20	25	44	1.81
44272537--44272619	43	1.9	43	80	4	96	18	20	34	26	1.95
44272597--44272686	43	2.1	43	85	4	119	26	30	20	23	1.98

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   188   189   190   191   192   
          193   194   195   196   197   198