genome.fa.s9.2.7.7.80.10.50.1000.131.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  131  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)
43943605--43943633	13	2.2	13	100	0	58	27	17	27	27	1.97
43944600--43944648	20	2.7	18	77	22	57	51	4	2	42	1.32
43945643--43945707	21	3.1	21	71	8	69	33	24	20	21	1.97
43946156--43946191	18	2.1	18	89	5	56	33	25	0	41	1.55
43946824--43946898	30	2.5	29	89	8	107	52	5	1	41	1.33
43947000--43947055	13	4.5	12	74	14	51	51	3	0	44	1.18
43952636--43952687	20	2.6	20	93	0	95	21	26	0	51	1.47
43956050--43956124	37	2.0	38	97	2	143	32	16	26	25	1.96
43967112--43967137	12	2.2	12	100	0	52	42	7	23	26	1.81
43974693--43974744	25	2.1	24	85	3	68	17	21	23	38	1.93
43980149--43980232	25	3.4	25	84	0	114	33	21	21	23	1.97
43980163--43980269	25	4.3	25	82	0	115	36	17	22	23	1.95
43980150--43980257	50	2.2	50	82	0	126	33	21	21	24	1.97
43983990--43984055	26	2.6	25	80	7	78	36	21	24	18	1.95
43984503--43984542	21	1.9	21	90	10	64	45	12	0	42	1.42
43984512--43984553	21	2.0	21	85	0	57	40	19	2	38	1.64
43984687--43984740	28	1.9	29	85	7	76	37	14	5	42	1.69
43989746--43989810	25	2.6	25	82	2	76	33	13	26	26	1.94
43991598--43991622	12	2.1	12	100	0	50	52	32	0	16	1.44
43993488--43993522	18	1.9	18	100	0	70	51	25	11	11	1.71
43997452--43997504	20	2.7	20	82	2	63	39	16	28	15	1.89
43997490--43997553	20	3.2	20	76	8	76	37	15	31	15	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43997476--43997600	40	3.1	40	87	0	178	38	16	28	16	1.90
43999140--43999212	37	1.9	38	88	2	112	31	21	2	43	1.67
43999200--43999243	23	1.9	22	82	17	54	38	22	0	38	1.55
43999417--43999607	51	3.8	51	82	6	244	30	27	16	25	1.97
43999415--43999599	101	1.8	101	91	3	309	30	26	17	25	1.97
43999709--43999742	10	3.5	10	88	4	52	8	23	0	67	1.18
44001374--44001464	45	2.0	45	97	2	175	32	31	10	24	1.90
44001509--44001555	16	2.9	16	72	12	51	42	12	0	44	1.42
44002257--44002363	33	3.5	33	70	23	115	37	12	29	20	1.89
44002343--44002382	20	2.0	20	90	0	62	52	12	22	12	1.72
44005381--44005424	23	1.9	22	82	17	54	38	22	0	38	1.55
44005469--44005557	45	2.0	45	93	0	151	32	23	17	25	1.97
44005632--44005667	17	2.1	17	100	0	72	36	22	16	25	1.94
44005581--44005712	68	1.9	68	86	3	185	33	27	16	22	1.96
44008162--44008218	27	2.1	27	96	0	105	40	15	17	26	1.90
44011998--44012031	16	2.1	16	88	0	50	41	2	20	35	1.68
44013276--44013372	48	2.0	48	97	0	185	26	21	8	43	1.81
44021198--44021229	15	2.1	15	94	0	55	28	6	3	62	1.34
44031799--44032028	43	5.3	43	86	3	320	30	33	16	19	1.94
44032154--44032207	27	2.0	27	82	7	65	57	0	3	38	1.17
44032295--44032385	43	2.1	43	83	2	112	42	10	12	34	1.77
44036653--44036716	30	2.1	31	88	5	94	48	4	1	45	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44036658--44036717	10	5.8	10	76	5	57	45	5	0	50	1.23
44036652--44036725	30	2.5	27	78	18	76	45	6	1	45	1.38
44037117--44037181	27	2.4	27	80	10	78	41	43	3	12	1.58
44038296--44038483	41	4.6	41	92	0	286	30	25	23	20	1.98
44038542--44038686	40	3.6	40	78	9	145	20	19	22	37	1.94
44048804--44048843	20	2.0	21	90	5	64	22	27	15	35	1.94
44051409--44051450	20	2.0	21	90	4	68	23	28	16	30	1.96
44055082--44055125	20	2.2	20	91	0	70	68	2	18	11	1.30
44055120--44055164	22	2.0	23	83	8	58	66	2	26	4	1.22
44055876--44055961	42	2.0	42	100	0	172	29	16	11	43	1.83
44056344--44056385	20	2.0	21	90	4	68	23	28	16	30	1.96
44060188--44060241	27	2.0	27	100	0	108	29	18	14	37	1.91
44072341--44072374	17	2.0	17	88	0	50	47	11	29	11	1.76
44074413--44074437	13	1.9	13	100	0	50	36	0	16	48	1.46
44078865--44078922	28	2.1	28	96	0	107	58	22	13	5	1.55
44080471--44080510	6	6.7	6	97	0	71	0	17	12	70	1.18
44081169--44081223	29	1.9	29	85	10	78	61	3	3	30	1.30
44081808--44081834	6	4.5	6	100	0	54	33	0	0	66	0.92
44082262--44082341	30	2.7	30	76	14	76	45	1	2	51	1.22
44082766--44082809	23	1.9	23	90	0	70	47	0	6	45	1.29
44082897--44082934	17	2.2	17	90	0	58	36	2	5	55	1.37
44084181--44084247	34	1.9	35	87	3	100	44	14	8	31	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44089942--44090003	27	2.3	27	75	10	63	33	17	19	29	1.95
44090131--44090255	35	3.6	35	81	6	146	35	33	12	19	1.88
44092553--44092607	25	2.2	25	83	3	65	63	5	1	29	1.27
44092620--44092675	11	5.1	11	76	8	51	42	0	35	21	1.53
44097186--44097428	116	2.1	116	89	2	373	45	5	8	40	1.58
44097433--44098138	23	31.8	22	80	7	578	27	0	25	46	1.59
44097433--44098142	67	10.7	65	82	8	731	27	0	25	46	1.59
44097433--44098138	44	15.9	44	84	6	611	27	0	25	46	1.59
44098169--44098209	9	4.8	9	88	8	59	58	9	0	31	1.31
44098169--44098209	17	2.4	18	88	8	59	58	9	0	31	1.31
44098684--44098723	18	2.2	18	95	0	71	40	7	30	22	1.81
44099358--44099382	7	3.6	7	100	0	50	60	12	0	28	1.32
44099553--44099590	20	1.9	20	84	10	51	55	7	2	34	1.43
44100484--44100526	11	3.8	12	81	6	54	58	0	0	41	0.98
44102561--44102645	38	2.2	38	83	4	109	63	3	0	32	1.11
44102866--44102897	9	3.6	9	100	0	64	40	0	0	59	0.97
44102870--44102929	23	2.9	21	85	11	72	43	3	0	53	1.17
44103188--44103311	61	2.0	61	89	3	187	37	9	9	42	1.71
44103525--44103587	9	7.8	8	77	19	60	71	0	0	28	0.86
44103526--44103590	8	7.6	9	78	13	57	72	0	0	27	0.85
44103526--44103590	19	3.8	18	73	13	57	72	0	0	27	0.85
44103512--44103611	35	2.8	36	82	8	107	64	2	0	34	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44103558--44103587	14	2.1	15	93	6	53	70	0	0	30	0.88
44103525--44103607	43	1.9	42	83	13	107	67	1	0	31	0.98
44108823--44108849	12	2.2	12	100	0	54	40	11	25	22	1.87
44110531--44110652	59	2.1	59	96	0	226	37	21	13	27	1.90
44134825--44134870	22	2.1	22	100	0	92	21	26	13	39	1.90
44134917--44134976	16	3.7	16	95	4	111	25	0	38	36	1.56
44134957--44135047	45	2.0	45	85	2	121	27	6	28	37	1.82
44135192--44135246	15	3.4	16	80	16	53	54	1	0	43	1.10
44135198--44135246	16	2.9	18	80	20	61	55	0	0	44	0.99
44135099--44135426	156	2.1	156	97	0	611	42	3	6	46	1.47
44135368--44135402	18	2.0	17	88	5	52	54	0	0	45	0.99
44135104--44135544	156	3.1	137	67	19	306	43	3	5	46	1.44
44135294--44135506	67	3.1	67	63	19	152	46	4	3	46	1.38
44135306--44135584	137	2.0	135	82	6	330	45	5	3	45	1.44
44141683--44141708	13	2.0	13	100	0	52	61	7	30	0	1.24
44143515--44143557	13	3.0	15	73	13	54	51	18	4	25	1.66
44144271--44144455	99	1.9	99	91	0	307	45	15	14	24	1.83
44144271--44144455	48	3.8	48	85	7	246	45	15	14	24	1.83
44146764--44146804	19	2.2	19	100	0	82	41	24	7	26	1.81
44152155--44152397	48	5.0	47	81	8	222	45	15	13	26	1.82
44152191--44152266	23	3.2	23	67	20	66	47	14	10	27	1.77
44152170--44152397	98	2.4	96	82	8	282	46	15	13	25	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44152290--44152382	27	3.7	26	67	20	63	47	12	11	27	1.77
44152977--44153062	42	2.0	43	81	2	102	34	24	15	25	1.94
44164436--44164569	27	5.0	27	85	3	155	38	21	19	20	1.93
44164436--44164560	54	2.3	54	83	8	173	40	20	20	19	1.92
44164702--44164782	26	3.1	26	83	0	108	20	19	20	38	1.94
44164916--44164983	33	2.0	34	85	2	93	22	25	26	26	2.00
44178343--44178483	70	2.0	70	98	0	273	31	19	22	26	1.97
44180020--44180116	29	3.4	28	88	5	124	37	17	24	20	1.94
44180018--44180135	58	2.0	59	83	8	152	37	14	26	22	1.92
44180050--44180138	29	3.0	29	90	1	115	34	14	28	22	1.93

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