genome.fa.s9.2.7.7.80.10.50.1000.103.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  103  of  226  ( 27023 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)
35613460--35613520	15	4.0	15	74	19	54	8	24	3	63	1.37
35613470--35613542	33	2.2	32	80	7	85	6	21	4	67	1.32
35614934--35615027	26	3.6	26	82	0	107	34	20	21	24	1.97
35614997--35615054	27	2.2	27	84	6	75	36	18	22	22	1.95
35624376--35624456	26	3.1	26	83	0	99	34	20	19	24	1.96
35628290--35628328	20	2.0	20	94	0	69	17	25	5	51	1.66
35628530--35628660	49	2.6	49	81	4	138	25	23	19	32	1.98
35628547--35628716	50	3.4	50	79	8	150	23	23	23	29	1.99
35628626--35628724	50	2.0	50	90	4	155	20	29	25	25	1.99
35640773--35640871	39	2.5	39	88	3	146	18	24	24	33	1.97
35655535--35655564	14	2.1	15	93	6	53	10	6	13	70	1.34
35658302--35658395	25	3.8	25	75	0	89	25	21	24	28	1.99
35661741--35661806	27	2.5	27	85	7	82	39	21	19	19	1.93
35661940--35662016	27	2.9	27	92	0	127	27	14	19	38	1.90
35661939--35662026	27	3.3	27	82	4	115	28	12	20	38	1.89
35668490--35668516	13	2.1	13	100	0	54	37	40	0	22	1.54
35669335--35669392	30	1.9	30	89	0	89	41	5	24	29	1.76
35669730--35669922	50	3.8	50	92	0	314	26	22	31	20	1.98
35676820--35676877	30	1.9	30	89	0	89	41	5	24	29	1.76
35677215--35677450	50	4.7	50	91	0	364	27	21	30	20	1.98
35679070--35679157	25	3.5	25	100	0	176	20	27	27	25	1.99
35679069--35679180	50	2.2	50	87	3	163	24	24	25	26	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35680607--35680645	20	2.0	20	90	10	62	15	23	5	56	1.59
35680919--35681041	50	2.5	50	80	0	138	19	28	24	27	1.99
35683691--35683721	11	2.8	11	95	0	53	41	32	9	16	1.80
35698525--35698575	16	3.2	16	85	0	75	29	27	1	41	1.67
35699484--35699600	34	3.5	33	80	5	108	42	17	9	30	1.80
35699736--35699828	46	2.0	46	97	0	177	41	12	13	31	1.83
35700907--35700941	17	2.1	17	88	0	52	77	0	22	0	0.78
35703052--35703280	28	8.2	28	88	0	343	31	23	21	23	1.98
35703019--35703115	33	3.1	34	81	11	91	30	23	22	22	1.99
35703597--35703651	27	2.0	27	82	0	65	34	16	14	34	1.89
35703645--35704001	27	13.3	26	87	3	311	19	17	24	38	1.93
35703643--35704001	81	4.4	81	87	2	452	19	17	24	38	1.93
35703645--35704001	54	6.6	54	89	2	441	19	17	24	38	1.93
35705446--35705483	19	2.0	20	94	5	69	36	10	34	18	1.85
35706563--35706614	27	1.9	27	84	7	70	7	21	5	65	1.40
35711965--35712037	5	14.4	5	78	18	80	58	0	1	39	1.06
35711966--35712035	36	2.0	36	83	10	92	60	0	1	38	1.06
35711965--35712047	14	6.2	13	78	10	71	59	2	1	37	1.19
35717752--35717795	21	2.0	21	87	12	63	2	13	4	79	0.98
35717975--35718043	5	13.6	5	81	14	79	60	1	0	37	1.06
35723937--35724070	50	2.7	50	81	2	153	29	26	17	25	1.98
35726875--35727164	25	11.6	25	77	6	212	30	20	19	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35726902--35727166	75	3.5	74	75	7	241	30	20	18	30	1.97
35726875--35727168	50	5.9	50	78	5	274	31	20	19	28	1.97
35728198--35728260	27	2.4	27	84	7	76	33	23	25	17	1.96
35728212--35728268	27	2.1	27	83	6	71	38	21	22	17	1.93
35728430--35728532	27	3.8	27	88	0	152	27	16	18	37	1.92
35740474--35740526	25	2.1	25	83	13	65	56	0	3	39	1.17
35741814--35742020	32	6.5	32	78	3	193	36	23	20	19	1.95
35741814--35742020	64	3.2	64	75	6	222	36	23	20	19	1.95
35742026--35742076	26	2.0	26	84	0	66	33	23	25	17	1.96
35742317--35742472	27	5.9	27	82	3	190	16	19	23	40	1.91
35742317--35742468	53	2.9	54	84	3	191	16	19	23	40	1.91
35743397--35743456	30	2.0	30	87	6	86	46	11	8	33	1.70
35750971--35750996	12	2.2	12	100	0	52	69	0	0	30	0.89
35772652--35772804	22	7.0	22	90	0	225	32	14	26	26	1.94
35773046--35773188	33	4.2	33	68	24	109	32	30	20	17	1.95
35772955--35773201	102	2.4	103	89	0	370	32	29	19	19	1.96
35774481--35774583	41	2.5	41	87	0	134	26	26	20	27	1.99
35774521--35774598	41	1.9	41	86	0	111	28	25	20	25	1.99
35775170--35775203	2	17.0	2	100	0	68	50	0	0	50	1.00
35775648--35775672	13	1.9	13	100	0	50	40	24	4	32	1.73
35781817--35781919	41	2.5	41	87	0	134	26	26	20	27	1.99
35781857--35781934	41	1.9	41	86	0	111	28	25	20	25	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35782074--35782294	65	3.3	65	74	13	166	42	18	4	35	1.69
35782488--35782517	2	15.0	2	100	0	60	50	0	0	50	1.00
35783464--35783488	13	1.9	13	100	0	50	40	24	4	32	1.73
35789662--35789690	15	1.9	15	100	0	58	31	0	13	55	1.39
35790973--35791151	33	5.3	34	72	9	107	30	13	25	29	1.94
35791005--35791167	33	4.9	33	74	7	123	30	14	25	29	1.95
35790973--35791228	101	2.6	101	85	2	329	30	15	26	27	1.96
35794307--35794429	35	3.5	35	82	4	158	36	31	15	16	1.90
35799302--35799418	27	4.3	27	72	4	92	43	18	18	18	1.88
35799461--35799522	28	2.2	28	88	5	90	27	29	17	25	1.98
35799492--35799557	33	2.0	33	81	0	78	27	25	19	27	1.99
35805345--35805443	27	3.6	27	83	1	126	40	25	19	15	1.90
35816547--35816613	19	3.5	19	91	2	107	37	22	29	10	1.88
35817394--35817420	14	1.9	14	100	0	54	40	0	0	59	0.98
35818293--35818342	23	2.1	23	82	14	57	22	14	14	50	1.77
35828999--35829050	15	3.1	16	84	15	70	30	1	0	67	1.02
35828966--35829050	33	2.6	32	85	5	100	30	4	2	62	1.28
35841614--35841669	23	2.4	23	75	0	67	26	12	21	39	1.89
35841665--35841730	23	2.9	23	69	13	64	25	9	22	42	1.83
35844358--35844538	51	3.6	49	77	11	172	30	27	17	24	1.97
35844345--35844537	101	1.9	102	84	5	248	30	27	17	24	1.97
35847673--35847754	42	2.0	42	85	4	112	31	24	13	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35850404--35850599	51	3.9	50	77	9	202	30	27	17	25	1.98
35850403--35850591	102	1.9	102	85	5	258	30	27	17	24	1.98
35861057--35861109	25	2.2	25	90	10	83	7	1	5	84	0.82
35861073--35861110	20	1.9	20	88	0	58	5	2	7	84	0.86
35861057--35861101	12	3.8	12	91	8	74	8	0	6	84	0.78
35861057--35861109	12	4.3	12	83	9	63	7	1	5	84	0.82
35861661--35861742	42	2.0	42	90	0	128	32	19	8	39	1.82
35861938--35861984	15	3.1	15	76	14	51	34	12	31	21	1.91
35863272--35863367	25	3.9	25	80	14	85	26	21	21	30	1.99
35866182--35866211	16	1.9	16	93	6	53	30	0	20	50	1.49
35877206--35877241	15	2.6	14	91	8	56	52	11	0	36	1.37
35915465--35915528	30	2.2	29	81	10	76	29	28	6	35	1.82
35915472--35915528	30	1.9	30	85	3	80	29	24	7	38	1.82
35923833--35923862	12	2.5	12	88	0	51	10	46	0	43	1.37
35926073--35926435	184	2.0	183	91	1	584	41	9	14	34	1.79
35926847--35926885	21	1.9	20	89	5	60	20	15	17	46	1.84
35927614--35927639	13	2.0	13	100	0	52	23	23	23	30	1.99
35931411--35931502	25	3.7	25	79	1	96	22	26	19	31	1.98
35932763--35932804	17	2.6	16	85	14	59	26	0	14	59	1.35
35934551--35934628	35	2.2	35	81	2	93	41	24	12	21	1.88
35934562--35934643	35	2.3	35	89	2	119	42	24	12	20	1.86
35938213--35938279	31	2.2	31	86	5	91	34	13	8	43	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35939890--35939923	17	2.0	17	94	0	59	41	14	0	44	1.45
35940250--35940300	17	3.1	16	78	13	50	68	1	0	29	1.00
35940587--35940646	25	2.4	25	81	10	77	63	5	6	25	1.39
35941868--35941918	22	2.5	20	84	9	66	31	23	3	41	1.73
35941870--35941912	22	2.0	21	90	4	68	25	25	4	44	1.73
35943088--35943165	11	7.1	11	71	10	61	1	21	3	73	1.07
35943088--35943165	22	3.6	21	73	14	68	1	21	3	73	1.07
35943099--35943169	25	2.7	26	83	14	83	1	21	4	73	1.08
35943088--35943169	33	2.5	33	73	15	80	1	21	3	73	1.06
35943150--35943187	15	2.6	15	87	4	51	10	18	0	71	1.14

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226