genome.fa.s9.2.7.7.80.10.50.1000.13.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  13  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)
6198079--6198116	15	2.5	15	84	12	51	42	0	44	13	1.43
6198109--6198156	3	16.0	3	78	8	53	60	0	37	2	1.09
6198095--6198156	18	3.3	18	79	16	63	54	0	40	4	1.22
6198112--6198151	21	1.9	21	94	0	71	60	0	37	2	1.11
6202510--6202558	21	2.3	21	78	0	62	2	30	10	57	1.43
6220815--6220868	27	1.9	28	88	7	83	20	44	0	35	1.52
6222659--6222764	52	2.0	52	94	0	185	26	23	14	35	1.93
6228805--6228931	63	2.0	63	85	0	173	29	22	16	31	1.96
6231485--6231539	21	2.6	21	80	8	58	40	0	0	60	0.97
6237521--6237777	140	1.8	140	84	5	349	43	22	9	24	1.82
6239651--6239680	2	15.0	2	100	0	60	50	50	0	0	1.00
6247050--6247074	2	12.5	2	100	0	50	48	0	0	52	1.00
6250046--6250293	120	2.1	120	100	0	496	41	16	18	23	1.90
6252719--6252750	2	16.0	2	100	0	64	50	50	0	0	1.00
6256976--6257005	15	2.0	15	100	0	60	20	26	6	46	1.75
6261779--6261866	22	4.0	22	87	0	113	29	14	26	29	1.95
6265560--6265599	14	2.9	14	84	0	53	32	7	17	42	1.77
6265568--6265634	35	1.9	35	84	3	91	29	11	13	44	1.79
6265583--6265622	20	2.0	20	85	0	53	25	15	12	47	1.80
6274050--6274107	31	1.9	30	86	10	82	43	1	1	53	1.21
6282222--6282304	27	3.1	27	98	1	159	43	22	15	18	1.87
6287966--6288016	19	2.8	19	82	11	54	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6289458--6289497	14	2.8	15	85	11	57	65	2	0	32	1.06
6294325--6294364	21	1.9	21	94	0	71	0	27	10	62	1.27
6313593--6313664	29	2.4	29	81	4	81	25	9	13	51	1.72
6316382--6316419	18	2.1	18	95	0	67	50	2	0	47	1.15
6319201--6319248	24	2.0	25	83	4	62	68	4	6	20	1.28
6320658--6320713	20	2.7	21	76	15	62	39	3	1	55	1.28
6320660--6320713	21	2.5	22	79	8	67	40	3	1	53	1.29
6321297--6321341	11	4.4	11	78	16	60	35	0	0	64	0.94
6321309--6321350	19	2.2	19	91	0	66	28	0	4	66	1.12
6322704--6322863	76	2.1	74	97	2	302	50	1	6	41	1.37
6331682--6331748	33	2.0	33	97	0	125	26	11	16	44	1.82
6337627--6337669	2	21.5	2	100	0	86	0	48	0	51	1.00
6338707--6338738	16	2.0	16	100	0	64	18	6	25	50	1.70
6361421--6361451	15	2.1	15	93	0	53	19	22	35	22	1.96
6366444--6366469	2	13.0	2	100	0	52	50	0	0	50	1.00
6378213--6378258	9	5.4	9	82	10	53	39	0	0	60	0.97
6380055--6380085	16	1.9	16	93	0	53	16	3	12	67	1.35
6380444--6380480	13	2.8	13	87	0	56	29	10	24	35	1.89
6381072--6381115	22	2.0	21	91	4	70	40	4	13	40	1.65
6381099--6381169	22	3.2	22	63	21	58	38	7	12	42	1.70
6381094--6381187	44	2.1	44	100	0	188	42	6	13	37	1.70
6383664--6383716	26	2.0	26	96	0	97	24	18	20	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6384166--6384536	16	21.6	17	67	22	108	23	13	0	62	1.33
6384230--6384279	13	3.6	13	80	15	64	18	8	0	74	1.06
6384166--6384255	28	3.6	24	72	18	78	26	11	0	62	1.29
6384234--6384324	31	3.0	30	85	9	114	19	9	0	70	1.15
6384230--6384331	15	6.9	14	76	17	82	18	10	0	70	1.15
6384319--6384558	5	44.0	5	68	22	71	23	15	0	60	1.38
6384320--6384401	28	2.9	28	85	8	121	25	19	1	53	1.52
6384378--6384412	12	2.9	12	91	0	61	22	22	0	54	1.45
6384404--6384518	35	3.3	36	78	14	125	19	13	0	66	1.24
6384391--6384556	68	2.4	72	75	13	175	22	13	0	63	1.29
6384415--6384542	21	6.8	20	69	22	82	22	12	0	64	1.27
6384509--6384561	17	3.1	17	83	8	63	30	13	0	56	1.37
6384319--6384556	28	8.5	28	68	18	77	23	15	0	60	1.37
6384533--6384635	33	3.0	35	76	10	113	28	11	0	59	1.39
6384606--6384660	25	2.2	25	90	6	85	38	7	1	52	1.40
6386466--6386512	5	9.0	5	81	9	58	25	19	0	55	1.43
6386504--6386697	101	1.9	101	89	8	304	35	11	0	52	1.42
6389604--6389628	11	2.3	11	100	0	50	76	16	8	0	1.02
6393650--6393709	19	3.1	18	80	9	57	46	3	0	50	1.18
6394540--6394565	6	4.3	6	100	0	52	38	0	0	61	0.96
6398478--6398537	30	2.0	31	96	3	113	45	3	10	41	1.54
6407317--6407366	22	2.2	23	85	3	66	50	2	4	44	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6407342--6407381	16	2.5	16	91	0	62	47	2	7	42	1.45
6407436--6407604	35	4.6	35	67	13	106	39	5	9	45	1.59
6407376--6407615	112	2.1	112	92	1	392	40	7	7	44	1.61
6407743--6407774	15	2.1	15	94	0	55	21	0	25	53	1.46
6407686--6407933	68	3.5	68	75	17	248	21	0	34	42	1.59
6407767--6407795	6	4.8	6	100	0	58	17	0	48	34	1.47
6407781--6407863	21	3.6	25	79	19	83	24	0	34	40	1.55
6407787--6407858	21	3.4	21	88	7	110	25	0	33	41	1.55
6407797--6407861	21	3.1	21	95	0	112	23	0	30	46	1.53
6407895--6407950	15	3.9	15	73	21	66	25	0	32	42	1.55
6416722--6417144	211	2.0	211	99	0	837	27	9	20	41	1.84
6418003--6418052	21	2.4	21	89	0	73	32	32	8	28	1.86
6418170--6418235	29	2.3	29	81	0	78	42	12	6	39	1.67
6423057--6423088	2	16.0	2	93	0	55	50	3	0	46	1.17
6426169--6426200	16	2.1	16	94	5	57	59	0	0	40	0.97
6426161--6426213	24	2.1	26	86	10	74	56	0	0	43	0.99
6426171--6426228	24	2.4	22	78	16	53	55	0	1	43	1.10
6426172--6426230	28	2.1	27	81	12	66	54	0	1	44	1.10
6426445--6426492	22	2.2	22	82	14	55	70	8	20	0	1.12
6427337--6427422	21	4.0	22	80	8	106	17	22	23	37	1.94
6430661--6430699	18	2.2	17	86	13	53	46	20	0	33	1.51
6442256--6442340	28	3.2	28	62	16	72	31	22	7	38	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6442245--6442347	51	2.0	51	98	0	197	27	20	7	44	1.78
6444865--6444891	11	2.5	11	100	0	54	59	0	18	22	1.38
6452563--6452679	62	1.9	62	85	3	164	37	19	13	29	1.90
6453037--6453087	19	2.9	18	86	13	72	62	0	3	33	1.13
6453037--6453091	17	3.3	16	80	16	67	60	0	3	36	1.15
6453123--6453267	75	1.9	78	87	4	215	41	5	2	50	1.40
6453398--6453451	22	2.5	22	76	8	58	59	0	0	40	0.98
6454928--6454967	21	1.9	21	89	0	62	55	0	2	42	1.13
6457348--6457741	87	4.6	87	76	11	375	27	25	15	31	1.96
6457497--6457638	75	1.9	75	85	0	194	26	24	16	31	1.97
6458491--6458575	39	2.2	39	87	4	127	14	20	21	44	1.86
6459100--6459536	213	2.0	213	94	0	766	23	27	15	33	1.95
6468951--6468999	24	2.0	24	96	0	89	12	32	20	34	1.90
6469235--6469281	18	2.6	18	86	0	67	29	34	8	27	1.87
6480652--6480710	17	3.4	17	72	4	64	69	1	3	25	1.13
6480648--6480735	35	2.5	35	96	0	158	68	3	2	26	1.17
6480669--6480725	18	3.2	18	75	5	71	68	3	1	26	1.15
6480669--6480724	17	3.2	17	71	14	60	67	3	1	26	1.16
6505925--6505955	6	5.3	6	96	3	55	0	12	0	87	0.55
6514411--6514456	23	2.0	23	82	4	56	41	2	0	56	1.11
6534081--6534112	2	16.0	2	100	0	64	50	0	0	50	1.00
6540180--6540239	27	2.2	27	80	14	70	56	1	0	41	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6540210--6540255	21	2.4	18	82	13	56	56	6	0	36	1.25
6541035--6541265	9	23.9	9	66	18	58	32	1	6	60	1.29
6541065--6541149	31	2.9	29	75	13	84	34	0	8	57	1.28
6541205--6541261	27	2.1	26	84	12	71	35	1	1	61	1.17
6541844--6541890	20	2.6	18	78	21	53	34	4	0	61	1.15
6542442--6542510	22	3.3	20	78	9	68	39	0	7	53	1.29
6548771--6548851	14	6.3	14	72	18	68	48	6	3	41	1.46
6549325--6549381	29	2.0	29	82	6	71	50	1	1	45	1.22
6549588--6549648	32	1.9	31	87	9	88	55	1	1	40	1.19
6549645--6549708	30	2.1	30	83	11	78	60	0	3	35	1.12

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