genome.fa.s1.2.7.7.80.10.50.1000.31.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  31  of  187  ( 22383 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)
9917338--9917382	21	2.1	22	84	12	58	13	2	6	77	1.05
9919919--9919967	22	2.3	21	76	10	55	48	4	14	32	1.62
9921488--9921525	20	1.9	20	84	10	51	42	7	5	44	1.56
9938380--9938417	20	1.9	20	84	10	51	42	7	5	44	1.56
9943179--9943211	2	16.5	2	100	0	66	51	0	0	48	1.00
9946818--9946850	16	1.9	18	88	11	52	30	3	0	66	1.06
9953670--9953721	24	2.2	24	85	0	68	38	3	7	50	1.50
9956236--9956269	17	1.9	18	88	5	52	58	20	2	17	1.51
9956639--9956765	24	5.3	24	69	20	63	59	4	3	32	1.37
9956641--9956722	26	3.2	26	75	14	66	62	4	3	29	1.33
9956758--9956818	24	2.5	24	97	0	113	42	6	11	39	1.67
9960788--9961168	46	8.0	46	80	8	393	30	23	17	28	1.97
9960772--9961203	97	4.5	97	81	5	514	30	23	16	29	1.96
9967264--9967294	2	15.5	2	93	0	53	48	3	0	48	1.17
9968119--9968219	43	2.4	43	86	5	134	21	29	10	37	1.88
9969958--9970080	24	5.0	24	71	15	74	63	3	4	28	1.31
9970047--9970120	23	3.4	22	75	12	55	60	5	2	31	1.33
9972032--9972056	10	2.5	10	100	0	50	52	8	0	40	1.31
9972706--9972732	2	13.5	2	100	0	54	48	0	0	51	1.00
9977660--9977717	5	11.8	5	76	23	61	81	0	18	0	0.70
9977659--9977719	16	3.3	19	78	21	76	80	0	19	0	0.72
9977659--9977717	24	2.4	25	88	5	93	81	0	18	0	0.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9977982--9978303	105	3.0	107	88	3	481	24	18	9	47	1.78
9978770--9978825	24	2.3	24	93	0	94	32	14	21	32	1.93
9979203--9979437	89	2.6	89	81	1	247	30	22	21	25	1.99
9979510--9979839	87	3.8	86	75	9	269	28	22	22	26	1.99
9979510--9979828	174	1.8	174	82	6	405	29	22	21	26	1.99
9979670--9979875	87	2.4	87	78	7	211	29	21	23	25	1.99
9979548--9979870	174	1.9	174	79	6	368	27	22	23	25	2.00
9979972--9980216	45	5.4	45	68	14	135	31	17	23	27	1.96
9981204--9981228	7	3.6	7	100	0	50	12	0	0	88	0.53
9982225--9982249	10	2.5	10	100	0	50	52	8	0	40	1.31
9982490--9982555	32	2.2	28	81	10	69	40	10	6	42	1.64
9983533--9983606	29	2.5	29	86	4	94	21	13	17	47	1.82
9983558--9983631	29	2.5	29	82	4	85	25	14	13	45	1.82
9985419--9985455	2	18.5	2	94	0	65	48	2	0	48	1.15
9989783--9989831	13	3.8	13	78	5	55	38	4	20	36	1.72
9994539--9994609	21	3.4	21	88	0	106	5	46	15	32	1.69
9999288--9999314	14	1.9	14	100	0	54	37	37	0	25	1.57
9999405--9999896	115	4.3	114	84	2	646	28	26	20	25	1.99
9999405--9999896	229	2.2	228	86	2	675	28	26	20	25	1.99
9999800--9999969	73	2.3	73	84	3	218	27	22	22	26	1.99
9999682--10000081	186	2.1	185	86	4	545	26	25	23	24	2.00
10003355--10003380	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10004104--10004321	117	1.9	114	89	4	339	27	8	2	61	1.38
10004187--10004284	52	1.9	51	87	2	142	28	8	1	62	1.30
10011520--10011786	37	7.0	37	86	8	365	37	14	20	27	1.92
10011518--10011871	74	4.4	80	81	14	373	35	15	21	27	1.94
10011482--10011748	119	2.2	120	93	0	455	36	13	21	27	1.92
10011518--10011831	157	2.0	156	93	0	538	35	14	21	27	1.93
10011748--10011871	46	2.8	46	91	3	200	33	16	22	27	1.96
10012762--10013705	483	2.0	483	100	0	1888	36	22	13	26	1.92
10016355--10016385	9	3.4	9	90	0	53	25	12	22	38	1.90
10017489--10017514	5	5.2	5	100	0	52	19	19	19	42	1.90
10019100--10019141	3	14.3	3	82	5	50	61	2	2	33	1.21
10022890--10022935	22	2.0	23	84	12	60	54	10	21	13	1.69
10023919--10023971	23	2.3	22	83	6	70	26	7	0	66	1.18
10024136--10024194	5	11.8	5	100	0	118	38	0	0	61	0.96
10026890--10026929	17	2.4	17	95	0	71	45	7	10	37	1.66
10029705--10029774	18	3.9	18	75	5	61	31	5	1	61	1.28
10030072--10030400	106	3.1	106	83	1	426	30	19	18	31	1.96
10040891--10040929	11	3.5	11	89	6	60	82	0	10	7	0.86
10040890--10040930	12	3.5	12	90	6	66	82	0	9	7	0.83
10041908--10042565	176	3.7	176	94	1	1020	28	15	26	29	1.96
10041880--10042573	44	15.8	45	81	3	698	27	15	26	29	1.96
10044570--10044620	19	2.7	18	84	6	57	35	3	0	60	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10044551--10044620	18	3.9	18	75	15	65	31	5	0	62	1.18
10044918--10045243	106	3.1	105	83	3	393	32	18	17	32	1.94
10044926--10045246	107	3.0	106	83	3	403	32	18	17	31	1.94
10045822--10045990	3	53.7	3	71	9	79	58	4	8	28	1.46
10046079--10046104	7	3.7	7	100	0	52	73	11	0	15	1.11
10046076--10046111	14	2.6	14	83	16	56	72	8	0	19	1.10
10046162--10046187	4	6.5	4	100	0	52	76	0	0	23	0.78
10056580--10056644	3	21.7	3	100	0	130	33	0	0	66	0.92
10060599--10060631	15	2.3	15	89	5	50	51	0	12	36	1.39
10060673--10060709	17	2.2	17	90	0	56	51	5	2	40	1.39
10060797--10060864	30	2.3	29	82	7	75	72	5	2	19	1.19
10061274--10061312	15	2.6	15	95	0	69	51	17	0	30	1.46
10063689--10063731	21	2.0	22	86	4	61	55	23	13	6	1.62
10064889--10065311	51	8.8	50	77	12	388	30	17	16	35	1.93
10064884--10065359	96	5.0	95	86	1	621	29	17	16	35	1.92
10064889--10065488	44	12.9	45	75	12	435	30	17	16	35	1.93
10064884--10065359	191	2.5	191	90	1	740	29	17	16	35	1.92
10075375--10075411	17	2.2	17	90	0	56	51	5	2	40	1.39
10075517--10075576	30	2.0	29	87	9	86	75	3	1	20	1.04
10075653--10075687	12	2.9	12	86	0	52	71	5	2	20	1.19
10078448--10078509	29	2.1	30	82	8	74	48	0	3	48	1.17
10078460--10078519	30	2.1	28	81	6	66	50	0	1	48	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10081562--10082152	44	13.1	44	75	9	168	29	19	17	33	1.95
10081397--10081937	233	2.3	233	85	2	737	30	20	16	32	1.95
10081561--10082152	88	6.6	88	75	8	474	29	19	17	33	1.95
10081819--10082192	132	2.8	131	82	5	432	29	19	17	32	1.95
10093660--10093700	19	2.0	21	86	9	59	51	9	0	39	1.35
10093713--10093750	20	1.9	20	84	10	51	65	5	5	23	1.34
10093884--10093941	29	2.0	30	82	3	73	60	12	6	20	1.54
10098034--10098091	11	5.1	11	74	13	55	74	0	8	17	1.06
10099515--10099968	94	4.8	95	81	6	480	30	19	18	31	1.96
10099514--10099917	186	2.2	187	82	6	471	30	19	18	31	1.96
10116679--10116871	50	3.7	50	83	4	224	26	22	28	22	1.99
10117120--10117158	12	3.2	12	85	0	51	51	5	23	20	1.67
10125275--10125311	2	18.5	2	100	0	74	0	0	51	48	1.00
10125616--10125643	6	4.7	6	100	0	56	14	0	0	85	0.59
10127982--10128020	11	3.5	11	82	6	51	64	5	2	28	1.28
10128300--10128382	11	7.2	11	71	12	51	67	2	6	24	1.25
10142398--10142457	20	3.2	19	75	15	61	58	0	5	36	1.20
10142379--10142495	38	2.9	40	76	14	100	52	0	8	37	1.38
10142409--10142495	40	2.1	41	82	2	104	56	0	5	37	1.23
10142679--10142737	2	29.5	2	100	0	118	50	0	0	49	1.00
10143605--10143636	5	6.8	5	92	7	50	81	0	0	18	0.70
10156039--10156074	6	5.7	6	87	12	54	16	5	0	77	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10159412--10159450	19	2.1	19	90	0	60	30	0	15	53	1.42
10167023--10167102	3	26.7	3	97	0	151	65	0	0	35	0.93
10167846--10167882	15	2.5	14	87	12	56	16	8	0	75	1.02
10168174--10168206	17	1.9	17	100	0	66	66	3	0	30	1.06
10168185--10168227	21	2.0	21	81	0	50	58	6	0	34	1.25
10168320--10168394	3	25.7	3	77	10	75	61	2	2	33	1.24
10170500--10171037	44	12.1	44	74	5	355	33	17	19	29	1.95
10170445--10171060	88	6.9	89	73	6	379	32	17	19	29	1.95
10170550--10171037	132	3.7	131	76	5	431	33	17	19	29	1.95
10171678--10171713	2	18.0	2	100	0	72	50	0	0	50	1.00

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