genome.fa.s9.2.7.7.80.10.50.1000.224.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  224  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)
69909488--69909527	21	1.9	21	90	10	64	35	2	2	60	1.24
69909496--69909536	21	2.0	21	85	0	55	34	2	2	60	1.23
69910443--69910524	36	2.3	36	84	0	101	36	26	8	28	1.86
69916309--69916451	72	2.0	72	91	2	234	27	20	20	30	1.98
69920791--69920836	15	3.0	15	78	15	58	43	2	0	54	1.12
69921213--69921255	23	1.9	22	85	4	59	60	6	0	32	1.23
69929427--69929788	72	5.0	72	92	1	609	26	18	23	31	1.97
69936303--69936338	2	18.0	2	100	0	72	50	0	0	50	1.00
69938070--69938225	77	2.0	77	94	0	276	23	14	19	41	1.89
69940074--69940111	15	2.6	14	84	15	51	42	2	0	55	1.14
69940073--69940106	16	2.1	17	88	5	52	44	2	0	52	1.16
69942673--69942774	48	2.1	49	90	1	161	40	1	18	39	1.62
69944606--69944631	2	13.0	2	100	0	52	50	0	0	50	1.00
69951786--69952313	72	7.3	72	93	0	867	26	18	22	31	1.97
69952129--69952313	36	5.1	36	60	14	94	26	21	20	31	1.98
69953382--69953424	21	2.0	21	86	8	61	34	0	6	58	1.25
69953723--69953774	16	3.2	16	80	0	59	32	21	3	42	1.71
69956103--69956239	23	5.8	24	78	8	131	55	3	5	35	1.40
69956103--69956239	49	2.9	48	78	9	149	55	3	5	35	1.40
69956135--69956342	24	8.8	24	68	15	80	57	5	5	31	1.43
69956868--69956916	16	2.9	16	77	11	53	28	20	6	44	1.75
69961399--69961619	72	3.1	72	90	2	320	27	19	22	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
69963810--69963852	21	2.0	21	82	8	52	37	0	6	55	1.27
69970610--69970824	72	3.0	72	88	5	310	27	19	25	27	1.99
69973036--69973329	57	5.4	56	78	12	333	39	21	10	29	1.86
69973039--69973329	109	2.7	107	90	2	456	39	21	10	29	1.86
69980329--69980388	13	4.7	13	78	10	70	36	5	20	38	1.74
69980951--69980975	12	2.1	12	100	0	50	40	16	8	36	1.77
69984157--69984189	17	1.9	17	93	0	57	24	3	12	60	1.46
69985745--69985789	3	15.0	3	100	0	90	33	0	0	66	0.92
69988259--69988767	72	7.1	72	90	3	785	26	20	22	30	1.98
69988531--69988643	36	3.1	36	62	22	83	23	22	20	33	1.97
69994515--69994589	7	10.3	7	79	17	73	73	9	2	14	1.19
69994505--69994589	44	1.9	44	95	0	152	72	8	3	15	1.21
69995302--69995375	3	24.7	3	74	0	58	59	6	5	28	1.45
69996270--69996320	20	2.5	20	87	0	66	9	17	50	21	1.74
69996657--69997231	50	11.5	50	70	8	332	23	20	24	32	1.98
69996651--69997296	100	6.5	100	87	1	857	23	19	24	32	1.97
70017167--70017247	40	2.0	40	100	0	162	29	7	25	37	1.83
70035257--70035328	35	2.0	36	83	2	92	40	0	4	55	1.19
70035353--70035394	19	2.2	20	86	4	59	40	0	4	54	1.21
70036413--70036444	2	16.0	2	100	0	64	50	0	0	50	1.00
70036444--70036489	21	2.2	21	100	0	92	52	13	15	19	1.75
70042729--70042770	21	2.0	21	95	0	75	30	14	7	47	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
70046306--70046345	7	5.9	7	97	2	73	0	10	0	90	0.47
70046296--70046344	21	2.3	21	86	6	64	0	14	0	85	0.59
70046765--70046815	23	2.2	24	89	3	77	5	13	1	78	1.02
70049609--70049720	21	5.6	20	73	18	108	37	3	0	58	1.15
70049601--70049777	40	4.4	40	85	7	186	36	3	0	60	1.14
70049674--70049698	9	2.8	9	100	0	50	52	0	0	48	1.00
70049677--70049745	10	6.9	10	73	17	54	42	1	0	56	1.08
70049709--70049742	17	2.0	17	88	0	50	35	0	0	64	0.94
70049735--70049796	32	1.9	32	83	0	79	32	1	3	62	1.20
70053244--70053337	20	4.7	19	75	19	77	40	0	6	53	1.27
70053254--70053300	23	2.0	24	95	4	87	44	0	4	51	1.21
70053279--70053348	20	3.6	19	79	11	72	35	0	7	57	1.26
70053287--70053349	20	3.3	19	82	6	83	34	0	6	58	1.23
70053418--70053457	18	2.3	18	82	4	55	47	12	7	32	1.69
70054741--70054783	2	21.5	2	100	0	86	48	0	0	51	1.00
70055686--70055723	7	5.4	7	100	0	76	42	44	0	13	1.43
70058605--70058636	2	16.0	2	100	0	64	50	0	0	50	1.00
70059904--70059996	48	1.9	48	88	0	141	54	9	25	9	1.63
70061909--70061947	19	2.1	19	85	4	53	46	2	10	41	1.51
70063589--70063623	16	2.2	16	90	5	54	57	17	5	20	1.60
70064651--70064676	11	2.4	11	100	0	52	7	0	7	84	0.77
70065056--70065145	3	30.0	3	97	0	171	33	1	0	65	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
70074420--70074532	56	2.0	56	100	0	226	29	10	14	46	1.78
70074976--70075005	16	1.9	16	93	6	53	40	20	13	26	1.89
70075435--70075469	3	11.7	3	100	0	70	65	0	34	0	0.93
70080611--70080669	28	2.1	28	96	0	109	23	1	18	55	1.51
70082601--70082644	12	3.7	12	78	0	52	6	11	68	13	1.39
70082601--70082644	18	2.4	18	80	0	52	6	11	68	13	1.39
70090687--70090723	2	18.5	2	100	0	74	0	48	0	51	1.00
70091618--70091678	15	4.1	14	72	16	52	40	3	4	50	1.40
70094138--70094316	72	2.5	71	80	7	189	16	26	21	35	1.95
70101776--70101835	8	7.2	8	79	7	57	66	3	0	30	1.07
70102289--70102324	6	6.0	6	96	0	54	0	61	0	38	0.96
70102286--70102320	17	2.1	17	88	0	52	0	60	0	40	0.97
70105303--70105353	24	2.2	24	77	22	56	33	0	5	60	1.21
70107451--70107537	24	3.5	25	75	17	83	51	5	36	5	1.50
70107523--70107572	21	2.4	21	93	0	82	44	0	42	14	1.44
70110126--70110193	15	4.5	15	84	0	82	57	1	39	1	1.17
70110144--70110196	27	2.0	27	85	7	72	60	1	35	1	1.19
70112414--70112498	43	2.0	43	97	2	163	32	4	7	55	1.48
70115974--70116016	20	2.3	19	88	11	63	23	11	4	60	1.50
70127239--70127284	2	23.0	2	100	0	92	50	0	0	50	1.00
70128714--70128778	24	2.7	23	71	15	60	43	0	7	49	1.31
70132237--70132273	16	2.3	16	85	0	56	40	5	10	43	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
70134104--70134159	16	3.5	16	82	0	67	39	8	23	28	1.85
70134145--70134230	44	1.9	44	85	4	118	33	6	23	36	1.82
70134331--70134428	20	5.1	20	72	15	71	56	3	1	39	1.22
70134338--70134448	56	2.0	57	89	1	170	53	3	0	43	1.18
70139837--70139882	20	2.3	20	78	14	51	23	2	4	69	1.17
70140064--70140088	13	1.9	13	100	0	50	32	0	0	68	0.90
70150108--70150149	6	7.0	6	100	0	84	50	16	0	33	1.46
70150139--70150175	16	2.3	16	85	0	56	40	5	10	43	1.63
70155554--70155627	30	2.5	30	84	0	103	27	43	6	22	1.78
70159224--70159249	5	5.2	5	100	0	52	38	19	19	23	1.93
70159198--70159249	26	2.0	26	81	7	61	34	15	26	23	1.94
70160063--70160124	30	2.1	30	87	0	88	41	0	38	19	1.51
70160166--70160202	9	4.1	9	100	0	74	32	10	10	45	1.74
70161419--70161523	35	3.0	36	78	9	101	58	9	4	27	1.50
70164860--70164915	16	3.7	15	76	9	53	26	0	17	55	1.43
70168094--70168155	32	1.9	32	83	6	81	48	17	12	20	1.80
70170160--70170188	10	2.9	10	100	0	58	27	0	0	72	0.85
70170475--70170532	22	2.6	21	81	8	62	37	1	12	48	1.51
70170962--70170999	3	12.3	3	94	5	67	65	0	2	31	1.06
70192673--70192718	3	15.3	3	100	0	92	32	0	0	67	0.91
70194111--70194150	2	20.5	2	94	5	73	50	0	0	50	1.00
70197500--70197562	23	2.7	23	82	0	72	22	12	15	49	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
70204086--70204145	27	2.2	27	93	0	102	31	1	3	63	1.20
70231790--70231821	6	5.3	6	100	0	64	34	0	15	50	1.45
70233658--70233694	17	2.1	18	90	5	58	56	0	0	43	0.99
70234081--70234123	21	2.1	21	87	12	63	25	0	2	72	0.97
70242919--70242959	20	2.1	19	86	13	57	41	2	2	53	1.27
70243871--70243932	31	2.0	32	83	3	81	30	14	4	50	1.64
70248621--70248652	16	2.0	16	93	0	55	25	0	3	71	1.00
70248957--70249035	29	2.6	32	82	9	103	37	8	10	43	1.70
70249211--70249269	29	2.0	30	83	3	75	47	15	6	30	1.71
70251032--70251100	34	2.0	34	94	0	120	46	20	8	24	1.79

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