genome.fa.s6.2.7.7.80.10.50.1000.54.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  54  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)
15197215--15197266	26	2.0	26	96	0	95	38	21	15	25	1.92
15199950--15199990	21	2.0	21	85	0	55	51	7	17	24	1.70
15207991--15208039	18	2.7	19	78	9	57	57	4	32	6	1.42
15208007--15208037	9	3.4	9	95	0	53	54	3	35	6	1.42
15211116--15211160	24	2.0	23	82	8	56	42	15	0	42	1.47
15218201--15218238	19	2.0	19	89	0	58	34	5	5	55	1.45
15231298--15231400	41	2.5	41	90	1	163	33	18	30	17	1.94
15231298--15231363	21	3.2	21	69	16	66	31	18	33	16	1.93
15274426--15274455	12	2.5	12	94	0	51	23	26	43	6	1.78
15277968--15278027	30	2.0	30	100	0	120	30	6	23	40	1.80
15280899--15280998	26	3.8	27	81	9	125	43	9	22	26	1.82
15283690--15283774	25	3.4	25	82	9	111	30	21	24	23	1.99
15287405--15287521	22	5.3	22	88	0	162	32	14	25	27	1.95
15289981--15290013	13	2.6	13	90	4	50	21	9	9	60	1.54
15291291--15291521	117	2.0	117	92	0	381	39	19	15	26	1.90
15300367--15300417	23	2.2	23	92	0	84	27	9	21	41	1.84
15304489--15304552	12	5.6	12	78	10	71	6	20	0	73	1.04
15304486--15304552	6	11.7	6	79	6	59	5	20	0	73	1.04
15305637--15305709	37	2.0	37	94	0	128	23	15	0	61	1.33
15305686--15305712	13	2.1	13	100	0	54	22	18	0	59	1.38
15305640--15305718	37	2.1	37	88	4	115	21	16	0	62	1.33
15311285--15311311	2	13.5	2	100	0	54	0	0	48	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15315606--15315650	22	2.0	22	86	0	63	26	2	22	48	1.62
15315721--15315769	19	2.8	17	79	11	53	32	0	0	67	0.91
15316069--15316124	29	1.9	29	88	0	85	41	3	14	41	1.63
15317846--15317873	2	14.0	2	100	0	56	50	0	0	50	1.00
15320443--15320486	19	2.3	18	84	7	52	52	4	18	25	1.64
15320593--15320695	54	1.9	54	83	0	134	24	28	21	26	1.99
15321565--15321691	39	3.3	39	85	2	166	37	18	25	18	1.94
15326745--15326769	12	2.1	12	100	0	50	16	44	16	24	1.86
15327723--15327775	26	2.0	26	85	0	70	24	18	18	37	1.94
15335126--15335171	21	2.3	20	78	14	51	45	17	6	30	1.73
15338508--15338739	79	2.9	79	95	0	419	19	21	39	19	1.92
15339148--15339209	30	2.1	30	81	6	72	51	9	6	32	1.60
15356766--15357070	95	3.2	95	98	0	576	40	17	6	35	1.76
15361555--15361583	11	2.6	11	100	0	58	44	31	10	13	1.78
15361578--15361640	22	2.9	21	76	9	63	36	44	3	15	1.63
15362552--15362672	48	2.5	49	87	2	165	19	20	23	37	1.94
15372002--15372063	22	2.8	22	77	0	61	35	48	1	14	1.54
15377892--15378147	130	2.0	130	91	1	415	21	21	8	48	1.76
15381431--15381669	72	3.3	71	84	3	309	28	23	24	23	2.00
15381574--15381902	115	2.9	113	85	4	455	24	23	26	25	2.00
15381802--15382045	72	3.3	71	83	5	274	27	25	24	22	2.00
15381687--15382163	261	1.8	260	86	3	699	25	23	25	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15381947--15382496	114	4.7	115	82	6	626	25	22	25	27	2.00
15381454--15382277	375	2.2	373	97	1	1535	25	23	25	24	2.00
15388153--15388182	15	2.0	15	93	0	51	50	0	33	16	1.46
15388166--15388194	12	2.4	12	100	0	58	48	0	34	17	1.47
15388546--15388663	42	2.9	40	81	9	125	28	20	27	22	1.99
15394553--15394607	22	2.6	20	75	13	56	30	0	3	65	1.10
15394842--15394893	27	1.9	27	88	7	79	28	0	5	65	1.16
15394849--15394910	26	2.4	26	81	7	65	33	0	4	61	1.17
15397994--15398030	19	2.0	20	89	10	60	72	5	10	10	1.25
15398213--15398250	16	2.3	17	82	17	53	10	5	5	78	1.06
15409005--15409046	15	2.9	15	82	10	52	47	0	0	52	1.00
15409192--15409288	45	2.2	45	85	5	126	32	28	5	32	1.79
15409268--15409300	16	2.1	16	94	0	57	21	33	6	39	1.78
15412489--15412595	36	3.2	36	63	26	97	57	5	10	26	1.53
15412493--15412790	67	4.5	66	88	1	436	54	8	11	26	1.64
15412496--15412790	133	2.2	133	89	1	441	53	8	11	26	1.64
15414069--15414117	20	2.7	18	77	22	57	51	2	2	44	1.24
15419850--15420079	27	8.6	27	91	2	356	36	14	16	32	1.89
15429122--15429228	20	5.8	18	71	18	69	55	2	1	40	1.25
15429156--15429229	12	6.6	11	72	27	50	59	1	1	37	1.14
15430842--15430873	15	2.1	15	94	0	55	68	9	6	15	1.36
15435920--15436199	27	10.4	27	80	6	223	41	21	17	20	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15435919--15436236	80	4.0	81	79	8	310	41	21	17	20	1.91
15435920--15436253	54	6.2	54	78	9	265	40	21	17	20	1.91
15439828--15440180	27	13.1	27	79	5	322	41	22	17	18	1.90
15439843--15440179	81	4.2	81	83	2	374	41	21	18	18	1.90
15441083--15441124	21	2.0	21	90	0	66	66	11	2	19	1.34
15454080--15454117	20	1.9	20	84	10	51	39	0	18	42	1.50
15454709--15454757	20	2.5	20	96	0	89	30	12	20	36	1.89
15460892--15460958	21	3.2	21	72	4	64	22	31	14	31	1.94
15460855--15461078	82	2.7	82	80	6	258	23	26	15	34	1.94
15460855--15461084	41	5.6	41	78	5	216	23	26	15	35	1.94
15461178--15461203	12	2.2	12	100	0	52	7	0	30	61	1.24
15464891--15464916	12	2.2	12	100	0	52	15	0	15	69	1.20
15470487--15470540	28	2.0	26	82	13	65	38	5	14	40	1.70
15482659--15482891	49	4.6	50	75	10	190	23	27	21	27	1.99
15482713--15482891	50	3.5	50	78	9	164	23	29	22	25	1.99
15487279--15487378	46	2.2	46	90	0	155	43	19	17	21	1.89
15488388--15488511	61	2.0	61	96	0	230	30	25	9	33	1.88
15495086--15495137	13	4.0	12	76	16	50	13	9	3	73	1.23
15495088--15495139	27	1.9	27	88	7	79	11	7	3	76	1.12
15495089--15495124	15	2.5	14	86	8	54	8	8	2	80	0.99
15498164--15498204	21	2.0	21	90	0	64	36	7	24	31	1.83
15499224--15499284	26	2.3	26	86	10	81	34	19	4	40	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15499237--15499301	26	2.5	26	78	11	71	36	12	10	40	1.78
15509903--15509951	23	2.1	23	96	0	89	26	18	4	51	1.64
15510383--15510437	26	2.1	26	86	0	74	38	21	18	21	1.94
15510634--15510735	53	1.9	53	91	0	168	18	16	22	42	1.89
15510629--15510742	27	4.3	27	86	2	158	18	16	21	42	1.88
15510629--15510743	53	2.2	53	85	1	167	19	16	21	42	1.89
15511184--15511294	56	2.0	55	91	1	177	27	31	11	29	1.92
15512463--15512528	20	3.3	20	64	26	50	9	30	22	37	1.85
15516010--15516079	32	2.1	32	84	5	86	42	11	15	30	1.82
15516250--15516363	2	57.0	2	94	0	201	50	47	0	2	1.15
15516361--15516395	3	11.7	3	100	0	70	65	34	0	0	0.93
15518299--15518491	50	3.8	50	88	0	287	26	22	30	20	1.98
15522480--15522514	9	3.9	9	84	0	52	60	2	0	37	1.12
15531645--15531678	13	2.7	13	86	4	52	23	5	2	67	1.26
15537566--15537687	43	2.8	43	93	0	199	28	29	19	22	1.98
15537574--15537708	43	3.1	42	91	2	189	32	28	17	22	1.96
15540367--15540391	9	2.8	9	100	0	50	92	0	8	0	0.40
15540492--15540519	12	2.3	12	100	0	56	50	10	7	32	1.64
15541255--15541281	14	1.9	14	100	0	54	14	11	22	51	1.73
15541483--15541528	22	2.1	22	83	0	56	41	2	0	56	1.11
15541537--15541592	26	2.2	26	83	0	67	50	5	5	39	1.48
15541568--15541598	16	1.9	16	100	0	62	45	3	6	45	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15542885--15542923	15	2.6	15	91	0	60	38	41	0	20	1.53
15542883--15542928	22	2.1	22	83	0	56	43	34	0	21	1.53
15542940--15542984	14	3.2	14	90	0	72	46	33	0	20	1.51
15543388--15543551	40	4.1	40	85	1	204	27	21	21	29	1.99
15550089--15550120	15	2.1	15	94	0	55	15	6	9	68	1.36
15551992--15552025	16	2.1	16	88	5	50	61	5	5	26	1.42
15559813--15559846	16	2.1	17	88	5	52	29	32	11	26	1.92
15564417--15564454	17	2.2	17	90	0	58	52	13	5	28	1.61
15564538--15564571	16	2.1	16	88	5	50	61	5	5	26	1.42
15564821--15564872	3	17.7	3	80	4	61	61	1	5	30	1.30

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