genome.fa.s8.2.7.7.80.10.50.1000.100.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  100  of  190  ( 22705 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)
30324281--30324327	24	2.0	24	82	0	58	46	4	8	40	1.54
30326090--30326127	18	2.1	18	95	0	67	36	0	0	63	0.95
30326094--30326133	18	2.2	18	86	0	53	37	0	0	62	0.95
30333749--30333803	20	2.8	20	73	13	51	9	34	25	30	1.87
30335911--30335953	22	2.0	22	100	0	86	23	25	13	37	1.92
30337524--30337594	25	2.8	25	91	0	106	22	21	22	33	1.97
30338977--30339032	21	2.6	21	80	2	67	23	21	26	28	1.99
30339968--30340019	20	2.5	21	87	6	88	61	21	0	17	1.34
30340221--30340289	21	3.3	21	85	0	84	2	39	18	39	1.66
30345788--30346086	50	6.0	49	78	8	221	22	27	22	28	1.99
30345884--30346072	99	1.9	101	85	6	265	20	31	23	24	1.98
30345878--30346072	50	3.8	50	87	5	257	20	30	23	25	1.98
30352234--30352285	24	2.2	24	89	0	77	44	0	28	26	1.55
30352765--30352806	20	2.1	20	82	8	50	40	4	16	38	1.70
30360738--30360794	27	2.1	27	100	0	114	36	17	3	42	1.67
30363402--30363473	22	3.3	22	94	0	117	25	27	16	30	1.97
30373057--30373102	3	15.7	3	95	4	85	34	0	32	32	1.58
30377240--30377412	27	6.4	26	86	4	193	43	21	17	17	1.87
30377239--30377412	81	2.1	81	86	0	240	44	21	17	17	1.87
30377236--30377412	54	3.3	54	81	0	221	44	20	16	17	1.87
30379945--30379984	20	2.0	21	90	5	64	55	0	25	20	1.44
30379971--30380014	23	1.9	23	95	0	79	40	0	22	36	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30380303--30380339	9	4.1	9	85	0	56	29	10	10	48	1.72
30396002--30396430	87	4.9	87	89	0	651	24	22	24	29	1.99
30396064--30396375	42	7.2	44	62	11	122	26	22	23	28	1.99
30397640--30397694	7	8.0	7	86	11	78	14	14	0	70	1.16
30397640--30397695	20	2.7	21	78	15	71	14	14	0	71	1.15
30398533--30398632	35	2.9	34	78	15	98	7	10	9	74	1.23
30398553--30398630	29	2.8	29	79	14	83	6	8	8	75	1.18
30416430--30416456	6	4.5	6	100	0	54	29	0	70	0	0.88
30418640--30418676	14	2.6	14	100	0	74	10	8	5	75	1.17
30419282--30419314	17	1.9	17	93	0	57	72	9	0	18	1.10
30431896--30431995	39	2.6	39	85	4	132	38	3	8	51	1.47
30441208--30441255	23	2.1	23	84	7	62	22	20	16	39	1.92
30441302--30441356	26	2.1	26	82	0	65	21	16	16	45	1.85
30442598--30442649	23	2.3	23	93	0	68	19	17	23	40	1.91
30448644--30448682	6	6.3	6	82	5	51	61	2	20	15	1.45
30450041--30450098	28	2.1	28	100	0	116	36	17	10	36	1.84
30450318--30450401	23	3.7	23	85	0	114	44	21	17	16	1.87
30450318--30450407	46	2.0	46	90	0	144	44	23	16	15	1.86
30452799--30452829	9	3.6	9	95	4	55	0	19	0	80	0.71
30452800--30452851	9	5.8	9	77	8	52	1	15	0	82	0.75
30462159--30462355	48	4.1	48	84	2	252	21	28	21	27	1.99
30469375--30469514	48	2.9	49	83	11	175	22	30	20	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30478483--30478561	23	3.4	23	85	0	95	46	26	12	13	1.79
30489702--30489748	2	24.0	2	91	4	78	51	0	48	0	1.00
30489748--30489772	2	12.5	2	100	0	50	0	0	52	48	1.00
30492559--30493273	223	3.0	229	81	10	721	37	10	7	45	1.66
30492991--30493039	16	2.8	17	84	12	55	46	2	10	40	1.49
30497470--30497605	50	2.7	48	86	6	166	18	33	19	28	1.95
30497567--30497643	40	1.9	40	100	0	154	22	37	18	22	1.94
30497664--30497758	44	2.2	44	96	0	172	24	22	12	41	1.88
30499301--30499766	226	2.1	227	86	3	652	38	8	6	45	1.62
30499909--30499995	5	17.2	5	90	7	140	40	0	1	58	1.05
30499850--30499995	30	4.6	31	76	20	119	39	0	3	56	1.21
30502229--30502285	21	2.7	21	78	7	71	40	17	24	17	1.91
30502229--30502340	42	2.7	42	84	2	127	41	16	21	19	1.90
30503266--30503302	16	2.3	16	95	0	65	40	5	2	51	1.39
30507227--30507287	32	1.9	31	90	3	95	57	1	1	39	1.18
30507230--30507303	32	2.3	32	84	6	89	58	1	1	39	1.15
30507231--30507321	18	5.3	17	75	15	80	57	1	2	39	1.18
30510293--30510334	21	2.0	21	95	0	75	42	21	9	26	1.83
30512389--30512453	31	2.1	31	91	0	103	40	15	13	30	1.86
30513743--30513773	14	2.1	15	94	5	55	0	12	0	87	0.55
30516887--30517178	146	2.0	146	100	0	584	35	10	16	36	1.84
30521461--30521543	24	3.5	23	83	4	103	21	7	24	46	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30521606--30521671	27	2.5	27	88	9	100	19	22	24	33	1.97
30521669--30521724	26	2.2	26	83	0	67	16	16	32	35	1.90
30521718--30521904	32	5.8	32	87	2	268	22	19	19	38	1.93
30521914--30521955	22	1.9	22	85	0	57	19	19	16	45	1.86
30527713--30527766	26	2.1	26	89	0	81	25	24	27	22	2.00
30531792--30531900	39	2.8	39	91	4	177	67	0	1	29	1.07
30531881--30531910	8	3.8	8	100	0	60	86	0	0	13	0.57
30539395--30539439	23	2.0	22	84	16	58	35	0	17	46	1.49
30539874--30539914	21	2.0	21	85	9	57	43	0	24	31	1.54
30543528--30543573	24	2.0	24	82	4	58	15	6	17	60	1.55
30548011--30548069	30	2.0	30	96	0	109	27	8	15	49	1.73
30566307--30566507	68	3.2	60	77	13	176	51	5	3	39	1.42
30566307--30566507	61	3.2	58	74	18	181	51	5	3	39	1.42
30581297--30581346	21	2.3	21	80	10	57	20	16	16	48	1.82
30581382--30581443	26	2.4	26	94	0	106	27	24	12	35	1.92
30588746--30588902	81	1.9	81	98	0	305	26	23	20	29	1.99
30595490--30595516	12	2.2	12	100	0	54	66	7	7	18	1.40
30597147--30597194	25	1.9	25	82	0	60	41	14	18	25	1.88
30597204--30597372	24	6.9	24	72	16	125	36	20	26	17	1.94
30597204--30597340	49	2.8	48	81	9	154	35	21	25	18	1.96
30597302--30597366	26	2.5	26	82	5	69	35	21	26	16	1.95
30600482--30600524	22	2.0	22	85	0	59	13	9	6	69	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30601717--30601787	21	3.2	22	84	8	90	28	0	18	53	1.45
30601768--30601806	20	2.0	19	85	14	53	23	0	10	66	1.22
30607372--30607734	180	2.0	180	90	0	564	25	30	20	23	1.99
30608196--30608422	85	2.7	86	81	2	260	32	25	17	24	1.96
30608196--30608422	43	5.3	43	81	3	235	32	25	17	24	1.96
30611298--30611328	9	3.4	9	90	0	53	25	12	22	38	1.90
30611381--30611417	9	4.1	9	92	0	65	45	13	10	29	1.77
30611459--30611516	29	2.0	30	86	3	82	18	34	1	44	1.60
30614548--30614588	15	2.8	15	85	3	57	39	26	0	34	1.57
30614852--30614900	14	3.4	14	88	5	71	42	34	0	22	1.54
30615246--30615685	41	10.8	41	81	2	465	30	28	18	22	1.97
30615253--30615683	81	5.3	81	79	2	427	31	28	18	22	1.97
30618869--30618911	19	2.2	20	83	8	52	32	9	6	51	1.61
30620755--30620833	26	3.0	26	75	8	79	48	3	2	45	1.34
30620846--30620936	31	2.7	33	73	16	89	51	3	2	42	1.30
30620846--30620936	17	5.3	18	67	27	65	51	3	2	42	1.30
30620878--30620953	37	2.1	36	83	11	93	52	2	1	43	1.23
30625684--30625727	21	2.0	22	83	12	56	65	0	4	29	1.12
30625620--30625807	10	20.0	9	66	21	50	62	2	4	30	1.28
30625683--30625755	29	2.4	29	82	8	94	63	0	4	32	1.14
30625977--30626014	19	2.0	20	89	5	60	26	2	7	63	1.35
30625977--30626020	20	2.2	21	84	8	56	25	4	6	63	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30626017--30626059	10	4.6	9	82	8	50	27	6	4	60	1.43
30626007--30626053	19	2.4	21	76	23	57	31	8	4	55	1.49
30626017--30626059	19	2.3	19	87	0	59	27	6	4	60	1.43
30626075--30626131	9	6.4	9	82	8	55	28	0	3	68	1.06
30627334--30627452	56	2.1	56	95	0	211	54	12	11	21	1.69
30629596--30629649	6	9.2	6	79	2	56	75	7	1	14	1.09
30634238--30634293	6	9.3	6	96	0	103	66	16	1	16	1.35
30634290--30634362	3	24.3	3	100	0	146	67	0	0	32	0.91
30634361--30634389	3	9.7	3	100	0	58	68	31	0	0	0.89
30636844--30636889	22	2.1	22	100	0	92	13	17	13	56	1.67

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