genome.fa.s4.2.7.7.80.10.50.1000.169.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  169  of  198  ( 23681 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)
53113964--53114058	43	2.2	40	79	15	102	33	2	21	43	1.64
53114039--53114288	26	9.3	26	83	11	317	33	0	18	47	1.55
53114039--53114288	51	4.6	51	85	12	331	33	0	18	47	1.55
53114213--53114294	19	4.5	19	69	27	70	32	0	19	47	1.50
53113996--53114275	88	3.3	88	82	13	349	33	1	18	46	1.57
53114090--53114303	88	2.4	84	83	11	295	32	0	19	47	1.56
53114291--53114376	43	2.0	43	88	0	127	27	0	23	48	1.51
53114843--53114880	18	2.1	19	90	5	60	36	0	7	55	1.29
53114845--53114883	9	4.3	9	81	12	53	43	0	5	51	1.24
53115482--53115563	31	2.6	32	88	5	114	41	23	17	18	1.90
53116263--53116302	20	2.0	20	100	0	80	40	5	45	10	1.60
53119851--53120049	43	4.6	43	85	5	233	20	19	26	34	1.96
53134091--53134187	48	2.0	48	91	0	158	39	9	7	44	1.64
53136496--53136552	25	2.3	25	100	0	114	24	22	17	35	1.95
53136496--53136567	25	2.9	25	89	0	81	25	22	16	36	1.94
53136571--53136627	25	2.3	25	81	3	62	29	24	21	24	1.99
53139344--53139398	28	2.0	28	82	6	69	20	14	7	58	1.60
53146703--53146822	57	2.1	58	87	4	172	45	5	20	28	1.73
53147471--53147604	45	3.0	45	65	12	112	35	17	13	33	1.89
53149366--53149410	23	2.0	23	100	0	90	37	17	22	22	1.94
53151677--53151789	44	2.7	41	78	11	106	67	5	2	24	1.25
53151673--53151729	16	3.7	15	76	17	53	66	1	3	28	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53152083--53152121	20	2.0	21	85	10	55	46	0	0	53	1.00
53153087--53153115	2	14.5	2	100	0	58	51	0	0	48	1.00
53160755--53160875	54	2.2	54	83	2	154	26	21	28	23	1.99
53170658--53170703	3	15.3	3	78	17	51	32	0	2	65	1.05
53175743--53175788	6	7.7	6	83	13	51	82	0	15	2	0.76
53175739--53175788	21	2.3	22	75	6	57	80	0	18	2	0.82
53177309--53177515	100	2.1	101	84	5	269	30	18	24	26	1.98
53177517--53178180	44	15.9	41	67	12	233	33	21	19	25	1.97
53177517--53178233	126	5.7	126	88	1	1046	33	21	19	25	1.97
53177517--53178233	251	2.8	250	89	2	1069	33	21	19	25	1.97
53179332--53179377	3	15.3	3	78	17	51	32	0	2	65	1.05
53179318--53179375	21	2.7	20	84	13	62	32	0	1	65	1.03
53190346--53190444	42	2.4	42	84	0	117	29	16	15	39	1.89
53190380--53190473	42	2.2	42	88	0	134	27	14	15	41	1.87
53191947--53192063	25	4.7	26	75	10	109	32	21	28	17	1.96
53198898--53198950	2	26.5	2	100	0	106	50	0	0	49	1.00
53201677--53201701	13	1.9	13	100	0	50	40	24	4	32	1.73
53204535--53204650	25	4.7	24	74	18	94	31	19	31	17	1.95
53207933--53208005	36	2.0	36	100	0	146	42	8	16	32	1.78
53214031--53214401	123	3.0	124	90	1	582	27	15	23	33	1.95
53216617--53216715	28	3.6	27	81	9	119	31	12	28	28	1.92
53217648--53217764	47	2.5	46	83	5	137	29	13	16	41	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53217648--53217765	23	5.1	23	70	19	93	29	13	16	40	1.86
53220214--53220445	25	9.6	25	75	10	232	45	13	0	40	1.44
53220214--53220491	95	2.9	95	93	0	475	46	13	0	39	1.46
53221598--53221622	7	3.6	7	100	0	50	60	12	0	28	1.32
53222647--53222724	11	7.0	11	80	13	72	43	1	30	24	1.62
53222649--53222724	33	2.3	33	80	13	84	43	1	31	23	1.62
53227179--53227203	12	2.1	12	100	0	50	44	0	8	48	1.32
53228267--53228327	31	2.0	31	83	6	79	31	27	14	26	1.95
53241160--53241256	48	2.0	48	100	0	194	39	18	10	31	1.84
53244722--53244755	10	3.8	9	88	11	52	20	0	0	79	0.73
53257811--53257838	3	9.3	3	100	0	56	67	0	0	32	0.91
53258027--53258064	20	1.9	20	84	10	51	36	0	2	60	1.11
53258711--53258881	88	2.0	87	80	3	191	37	16	9	36	1.82
53259289--53259409	9	12.9	9	67	17	68	25	4	2	67	1.21
53259288--53259378	19	4.8	19	74	16	82	24	4	2	69	1.18
53259287--53259378	37	2.4	36	76	16	89	23	5	2	68	1.22
53259289--53259407	28	4.2	27	77	14	100	25	4	2	68	1.20
53260705--53260792	45	2.0	45	86	4	124	52	2	5	39	1.38
53271478--53271548	25	2.8	25	72	19	67	15	22	25	36	1.93
53271610--53271671	24	2.6	24	77	7	63	16	24	20	38	1.92
53272661--53272689	14	2.1	14	100	0	58	6	20	44	27	1.77
53277084--53277149	35	1.9	34	90	6	107	31	10	13	43	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53280973--53281069	33	2.8	35	72	20	89	45	3	1	50	1.24
53283581--53283615	18	1.9	18	88	0	52	71	8	8	11	1.31
53294034--53294063	15	1.9	16	93	6	53	63	6	13	16	1.50
53298746--53298771	7	3.7	7	100	0	52	0	11	0	88	0.52
53301499--53301547	25	2.0	25	87	0	71	24	28	14	32	1.94
53301504--53301562	25	2.4	25	82	0	73	25	28	13	32	1.94
53316426--53316460	6	5.8	6	93	0	61	51	37	0	11	1.38
53316424--53316461	18	2.1	18	100	0	76	47	42	0	10	1.38
53319743--53319875	42	3.2	41	78	11	144	42	16	24	16	1.88
53319795--53319860	21	3.1	22	70	8	57	45	16	22	15	1.85
53319803--53319867	21	3.1	21	70	12	62	46	15	21	16	1.84
53319800--53319894	42	2.3	42	83	3	120	43	14	23	18	1.87
53321966--53322026	22	2.8	21	70	22	54	54	29	0	16	1.43
53323140--53323320	40	4.5	40	96	0	326	28	23	19	28	1.98
53326921--53326956	6	6.0	6	100	0	72	50	0	33	16	1.46
53332674--53332790	62	1.9	59	84	5	153	51	5	3	39	1.43
53334111--53334159	2	24.5	2	95	0	89	51	0	0	48	1.00
53335748--53335788	15	2.7	16	77	7	50	46	0	14	39	1.45
53344724--53344767	15	2.8	16	76	13	54	36	6	0	56	1.26
53345717--53345768	23	2.2	24	79	6	61	63	5	1	28	1.28
53378478--53378556	41	1.9	41	82	5	97	21	17	25	35	1.95
53381636--53381662	12	2.2	12	100	0	54	51	0	7	40	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53383786--53383842	21	2.7	21	78	13	62	29	7	5	57	1.47
53392892--53393503	133	4.6	133	91	0	920	30	18	23	26	1.98
53392892--53393403	89	5.8	89	75	4	419	31	19	24	25	1.98
53392876--53393503	44	14.2	45	74	5	463	30	18	23	27	1.98
53393629--53393713	44	1.9	45	85	2	118	28	14	27	30	1.95
53395307--53395362	21	2.7	20	78	10	58	28	5	5	60	1.41
53401154--53401179	5	5.2	5	100	0	52	38	19	19	23	1.93
53402098--53402134	9	4.1	9	92	0	65	29	10	13	45	1.77
53402189--53402230	9	4.7	9	84	0	57	35	21	9	33	1.86
53409424--53409527	49	2.1	49	87	0	145	30	8	9	50	1.65
53411233--53411338	44	2.5	41	79	18	135	35	31	3	29	1.75
53411250--53411340	46	2.0	46	93	4	159	38	30	4	26	1.76
53411320--53411356	16	2.3	16	100	0	74	21	35	5	37	1.77
53412026--53412082	29	2.0	29	82	6	71	33	0	1	64	1.04
53413230--53413276	11	4.2	11	78	13	51	21	2	6	70	1.20
53416140--53416168	14	2.1	14	100	0	58	37	27	13	20	1.91
53417051--53417099	19	2.5	20	80	12	57	48	0	0	51	1.00
53417055--53417105	24	2.0	27	88	11	81	52	0	0	47	1.00
53417055--53417119	30	2.3	27	84	7	76	50	0	3	46	1.17
53417253--53417293	3	13.7	3	85	10	57	34	0	2	63	1.08
53421370--53421430	30	2.0	31	96	3	115	45	9	3	40	1.53
53425000--53425043	20	2.2	20	100	0	88	4	20	13	61	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53425746--53425873	60	2.2	58	84	2	166	27	16	14	41	1.87
53431815--53431949	69	2.0	69	95	0	243	28	18	21	31	1.97
53434031--53434068	20	1.9	19	89	5	58	42	0	2	55	1.14
53436877--53436973	50	1.9	50	93	4	169	43	24	6	25	1.77
53438507--53438571	3	21.0	3	72	12	51	61	1	7	29	1.33
53440119--53440808	44	15.4	44	72	5	434	27	21	17	33	1.96
53440164--53440779	89	6.9	88	74	5	385	27	20	17	34	1.95
53440317--53440730	135	3.0	136	86	3	539	27	19	17	35	1.94
53440337--53440597	95	2.8	93	81	4	262	26	19	19	34	1.96
53440327--53440809	135	3.6	135	84	2	513	27	20	16	34	1.95

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