genome.fa.s6.2.7.7.80.10.50.1000.80.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  80  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)
23518428--23518472	16	2.8	16	82	0	54	28	0	8	62	1.25
23522595--23522700	38	2.8	37	79	10	108	29	19	13	37	1.90
23522803--23522898	40	2.4	40	83	0	111	18	21	21	37	1.94
23522803--23522898	20	4.8	20	61	0	57	18	21	21	37	1.94
23522841--23522936	40	2.4	40	92	0	156	18	20	19	40	1.91
23528116--23528159	18	2.4	18	76	0	52	50	0	34	15	1.45
23529970--23530070	40	2.6	39	85	3	132	51	7	3	36	1.50
23535490--23535539	17	3.0	17	85	2	75	72	0	12	16	1.13
23536000--23536156	78	2.0	78	100	0	314	42	6	8	42	1.61
23549076--23549126	24	2.1	24	82	7	59	52	5	7	33	1.54
23556642--23556721	28	2.9	28	90	0	124	27	23	25	23	2.00
23561107--23561156	25	2.0	25	100	0	100	20	12	8	60	1.57
23562408--23562451	22	2.0	22	90	0	70	36	13	18	31	1.90
23562719--23562785	34	2.0	34	100	0	134	20	26	25	26	1.99
23564388--23564438	20	2.5	20	83	0	66	11	33	17	37	1.86
23569076--23569145	16	4.4	16	87	7	106	37	2	32	27	1.72
23569127--23569219	44	2.1	46	93	4	163	27	5	31	35	1.80
23569127--23569232	39	2.5	44	85	11	141	29	4	32	33	1.78
23569377--23569413	16	2.2	17	86	13	51	59	0	0	40	0.97
23569370--23569409	14	2.9	15	82	14	50	52	0	0	47	1.00
23569405--23569434	15	1.9	16	93	6	53	50	6	0	43	1.28
23569380--23569562	55	3.2	52	68	21	143	49	3	2	43	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
23569407--23569714	57	5.1	61	68	20	243	49	4	3	42	1.41
23569497--23569533	16	2.2	17	86	13	51	59	0	0	40	0.97
23569365--23569716	120	2.9	120	96	0	650	49	4	3	42	1.38
23569525--23569554	15	1.9	16	93	6	53	50	10	0	40	1.36
23569619--23569653	18	2.0	17	88	5	52	54	0	0	45	0.99
23569645--23569674	15	1.9	16	93	6	53	50	6	0	43	1.28
23574788--23574838	25	2.0	26	92	3	86	33	25	25	15	1.95
23575960--23576030	35	2.0	35	84	10	92	52	9	30	7	1.61
23584460--23584504	22	2.0	22	100	0	90	28	17	17	35	1.93
23587547--23587582	18	2.1	18	89	5	56	16	33	11	38	1.84
23588551--23588603	26	2.0	26	88	0	79	39	20	18	20	1.92
23589734--23589767	17	2.0	17	100	0	68	23	11	35	29	1.90
23589638--23589843	106	1.9	106	98	0	394	41	14	24	19	1.88
23594081--23594124	20	2.2	20	87	0	61	9	36	20	34	1.84
23596452--23596502	25	2.0	26	84	3	68	43	11	7	37	1.71
23596610--23596664	16	3.4	16	73	9	58	43	5	1	49	1.36
23596641--23596711	21	3.1	23	69	18	58	53	2	0	43	1.15
23598973--23599010	19	2.0	19	100	0	76	31	0	26	42	1.56
23608923--23608993	31	2.3	31	100	0	142	50	23	8	16	1.73
23611641--23611934	27	10.9	27	82	3	297	43	19	16	21	1.88
23611641--23611935	54	5.5	54	83	2	344	43	18	16	21	1.88
23611641--23611934	81	3.6	81	86	5	371	43	19	16	21	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
23612174--23612248	26	2.9	26	71	13	73	18	24	24	33	1.97
23612350--23612525	28	6.4	28	84	5	234	22	24	23	29	1.99
23612373--23612525	83	1.9	82	88	4	236	21	24	24	29	1.99
23613703--23613733	16	1.9	16	93	0	53	74	9	6	9	1.23
23614060--23614142	28	3.0	28	87	1	114	26	10	26	36	1.89
23614060--23614154	28	3.4	28	85	2	93	23	12	28	35	1.91
23617127--23617268	29	4.9	29	84	3	169	36	14	28	20	1.91
23617119--23617268	59	2.6	58	82	5	185	36	14	28	21	1.93
23621407--23621442	18	2.0	18	88	0	54	61	0	33	5	1.19
23630331--23630358	3	9.3	3	100	0	56	64	0	0	35	0.94
23630357--23630411	3	18.3	3	100	0	110	34	0	0	65	0.93
23638054--23638121	34	2.0	34	85	5	93	30	23	25	20	1.98
23641839--23641893	26	2.1	26	82	0	65	40	7	5	47	1.54
23642493--23642884	196	2.0	195	97	0	739	44	11	10	32	1.75
23647651--23647786	43	3.2	43	85	2	175	33	30	16	19	1.93
23649208--23649263	27	2.1	27	100	0	112	35	3	12	48	1.58
23651698--23651738	21	2.0	21	85	9	57	29	0	46	24	1.53
23652211--23652239	14	2.0	15	93	6	51	37	41	0	20	1.53
23652244--23652295	21	2.5	21	75	12	52	40	36	0	23	1.55
23652930--23653276	114	3.0	113	90	2	507	26	27	21	24	1.99
23653938--23653984	12	4.1	12	75	10	53	34	0	0	65	0.93
23654779--23654807	2	14.5	2	100	0	58	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
23655196--23655233	18	2.1	18	85	9	51	50	0	2	47	1.15
23656498--23656529	17	1.9	17	93	6	57	53	3	0	43	1.16
23656487--23656576	43	2.0	45	85	10	123	45	3	8	42	1.52
23656487--23656576	46	2.0	43	85	10	119	45	3	8	42	1.52
23658474--23658554	42	1.9	42	85	5	110	16	34	25	23	1.95
23658626--23658694	36	1.9	36	85	5	95	13	34	28	23	1.92
23665449--23665571	62	2.0	62	83	3	158	28	24	18	28	1.98
23666179--23666207	10	2.9	10	100	0	58	82	0	10	6	0.83
23677751--23677836	27	3.2	27	84	0	118	26	20	13	38	1.91
23680829--23680864	8	4.5	8	89	0	54	50	2	2	44	1.31
23681399--23681430	16	2.0	16	100	0	64	43	12	6	37	1.68
23684024--23684071	5	9.4	5	80	13	53	39	14	22	22	1.91
23695987--23696271	40	7.2	40	78	6	256	21	27	15	36	1.93
23695987--23696088	20	5.1	20	67	9	73	17	31	18	32	1.94
23695987--23696261	80	3.5	80	82	1	284	20	27	14	37	1.92
23695986--23696246	120	2.2	120	82	6	305	20	28	14	36	1.92
23706623--23706989	40	9.2	40	82	3	380	19	28	16	35	1.94
23706623--23706980	81	4.5	80	85	2	452	19	28	17	35	1.94
23707765--23707789	11	2.3	11	100	0	50	60	8	8	24	1.52
23708883--23708943	25	2.4	25	77	0	68	26	27	18	27	1.98
23713577--23713761	95	2.0	94	81	1	217	34	22	18	24	1.96
23721465--23721575	57	2.0	56	85	8	154	46	6	15	31	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
23721554--23721584	7	4.6	7	96	4	55	77	0	9	12	0.99
23721554--23721605	14	4.0	13	74	18	54	73	3	11	11	1.23
23721552--23721602	26	2.0	26	84	7	68	72	3	11	11	1.25
23727788--23727838	23	2.2	23	89	6	77	29	5	19	45	1.74
23729094--23729119	11	2.4	11	100	0	52	0	7	0	92	0.39
23729387--23729429	19	2.2	20	84	12	63	32	20	0	46	1.51
23730121--23730243	22	5.4	25	76	17	99	40	17	23	18	1.91
23735119--23735230	39	2.9	39	77	2	120	31	22	21	25	1.98
23738409--23738460	26	2.0	26	84	0	68	34	21	25	19	1.96
23738454--23738518	22	3.0	22	77	4	60	43	18	21	16	1.88
23738538--23738744	32	6.5	32	79	1	191	36	22	21	18	1.95
23738538--23738747	64	3.3	63	76	7	226	36	22	21	18	1.95
23738538--23738744	96	2.2	96	80	3	229	36	22	21	18	1.95
23738788--23738851	27	2.4	27	84	7	78	29	25	25	20	1.99
23738916--23738974	24	2.5	23	83	8	82	47	25	6	20	1.74
23739038--23739203	27	6.2	27	78	4	165	27	18	16	37	1.92
23739038--23739203	54	3.1	54	81	0	190	27	18	16	37	1.92
23745543--23745596	27	2.0	27	100	0	108	25	11	22	40	1.87
23753468--23753497	13	2.2	14	94	5	53	83	0	16	0	0.65
23757360--23757439	38	2.1	38	100	0	160	53	2	38	5	1.36
23762329--23762366	19	2.0	19	85	10	51	21	42	0	36	1.53
23764206--23764244	19	2.0	21	85	10	55	66	7	10	15	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
23768105--23768175	37	1.9	37	88	5	108	38	4	22	35	1.74
23768356--23768531	95	1.9	95	83	4	230	28	18	17	35	1.93
23769695--23769747	26	2.0	26	96	0	97	24	9	28	37	1.86
23774707--23774825	29	4.1	29	78	8	116	24	26	13	35	1.93
23774778--23774866	29	3.1	29	85	6	126	30	25	8	34	1.87
23779383--23779449	34	2.0	34	85	5	91	61	1	0	37	1.05
23780630--23780721	10	9.6	10	72	18	54	55	1	1	42	1.14
23780678--23780722	10	4.4	11	81	13	60	55	0	2	42	1.12
23781050--23781399	124	2.8	124	96	0	628	28	16	22	33	1.95
23784411--23784539	64	2.0	64	98	0	249	50	12	4	32	1.60

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