genome.fa.s4.2.7.7.80.10.50.1000.111.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  111  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)
35623513--35623550	11	3.5	11	88	0	58	26	42	2	28	1.69
35625711--35625772	29	2.1	30	93	3	108	24	3	14	58	1.51
35625894--35625923	11	2.7	11	89	0	51	63	3	0	33	1.11
35629362--35629477	61	2.0	60	85	11	159	52	4	2	40	1.35
35629362--35629562	61	3.2	58	70	23	158	51	4	3	40	1.39
35630709--35630896	51	3.7	51	79	10	224	27	16	26	29	1.97
35630713--35630795	26	3.2	26	64	21	66	28	13	25	32	1.93
35630709--35630901	101	1.9	102	84	5	257	27	16	26	29	1.97
35630719--35630933	101	2.1	102	79	5	231	29	14	26	29	1.95
35632284--35632405	54	2.3	54	83	0	154	23	27	25	22	2.00
35634407--35634452	23	2.0	23	82	0	56	23	15	0	60	1.34
35639075--35639113	19	2.0	20	90	9	64	38	5	0	56	1.22
35642388--35642444	26	2.2	26	82	14	73	73	1	1	22	1.02
35643593--35643625	11	3.0	11	91	8	50	63	3	0	33	1.10
35644382--35644422	3	13.7	3	100	0	82	0	31	0	68	0.90
35650908--35650946	15	2.5	17	76	23	50	56	5	0	38	1.22
35655049--35655094	23	2.0	23	100	0	92	39	13	13	34	1.83
35656488--35656527	14	2.9	14	84	0	53	32	7	17	42	1.77
35656510--35656549	20	2.0	20	85	0	53	32	12	12	42	1.80
35656497--35656562	35	1.9	34	87	3	96	33	10	13	42	1.79
35658935--35658966	15	2.1	15	100	0	64	37	12	50	0	1.41
35660515--35660571	29	1.9	30	89	3	89	36	1	43	17	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35662483--35662522	21	1.9	21	85	10	55	17	2	17	62	1.44
35666503--35666566	10	6.3	10	75	15	51	35	0	6	57	1.24
35667884--35667950	25	2.7	25	86	4	82	20	25	25	28	1.99
35670555--35670587	2	16.5	2	100	0	66	48	0	0	51	1.00
35676939--35676993	23	2.4	23	84	0	65	23	18	20	38	1.93
35681308--35681403	19	5.2	19	78	5	106	48	1	12	37	1.48
35681308--35681403	37	2.6	37	93	0	165	48	1	12	37	1.48
35682063--35682127	29	2.4	28	92	7	107	49	0	10	40	1.38
35690611--35690732	27	4.5	27	84	0	118	27	20	15	36	1.93
35690611--35690727	54	2.2	54	82	0	135	28	20	16	35	1.94
35702814--35702882	26	2.8	26	72	22	67	43	21	18	15	1.88
35702919--35702996	26	3.0	26	84	0	84	38	17	20	23	1.93
35702943--35703005	26	2.4	26	89	5	92	34	19	25	20	1.96
35705815--35706063	50	4.8	50	81	3	264	26	22	29	22	1.99
35707591--35707703	42	2.7	42	92	0	181	36	21	19	23	1.95
35708339--35708409	21	3.4	21	82	0	88	4	43	18	33	1.69
35711047--35711101	23	2.4	24	85	11	80	43	0	14	41	1.45
35711077--35711138	31	2.0	32	87	3	90	37	1	17	43	1.59
35711112--35711232	12	10.1	12	72	19	67	34	0	14	50	1.44
35711143--35711214	36	2.0	36	86	5	101	38	0	11	50	1.38
35711082--35711265	96	1.9	95	95	1	332	35	0	15	48	1.49
35711192--35711234	21	2.0	21	86	8	61	34	0	16	48	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35711121--35711280	47	3.4	46	74	13	171	33	0	15	50	1.48
35711290--35711334	19	2.3	19	85	11	56	53	2	0	44	1.13
35711301--35711353	21	2.5	22	78	9	65	56	0	1	41	1.10
35712829--35712905	16	4.9	16	69	20	63	36	18	12	32	1.89
35713369--35713672	148	2.1	148	83	3	380	34	20	18	25	1.96
35714116--35714191	7	10.3	7	74	16	64	43	30	1	25	1.63
35714118--35714184	8	8.9	8	73	15	54	41	32	1	23	1.64
35714116--35714194	15	5.3	15	73	11	72	43	31	1	24	1.62
35714591--35714658	21	3.2	20	74	13	57	44	44	0	11	1.40
35715016--35715656	115	5.6	113	77	5	569	27	23	18	30	1.98
35715042--35715654	229	2.7	226	81	5	637	27	23	18	29	1.98
35717491--35717683	50	3.8	50	90	0	305	20	30	22	26	1.98
35719701--35719768	21	3.2	21	71	8	66	42	19	25	13	1.87
35719866--35719977	24	4.7	24	93	0	188	23	26	7	42	1.79
35724359--35724419	26	2.3	26	82	0	77	32	26	14	26	1.95
35727559--35727617	26	2.2	26	88	11	84	57	0	3	38	1.15
35727577--35727632	18	3.1	18	77	10	69	57	0	1	41	1.09
35727601--35727649	24	2.0	24	88	7	73	53	0	2	44	1.12
35731467--35731495	4	7.5	4	92	7	51	79	0	0	20	0.74
35731944--35731979	18	2.1	18	89	5	56	61	0	2	36	1.11
35734253--35734307	21	2.6	21	85	0	74	60	5	1	32	1.30
35738510--35738546	17	2.2	16	90	4	56	0	16	5	78	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35738534--35738633	33	3.0	33	84	11	116	11	9	4	76	1.15
35738592--35738617	12	2.2	12	100	0	52	15	7	0	76	0.99
35738628--35738695	22	3.2	22	80	17	81	38	0	1	60	1.06
35738628--35738711	22	4.0	21	76	15	77	42	0	1	55	1.07
35738620--35738695	22	3.6	22	78	15	72	36	1	1	60	1.13
35738796--35738859	33	2.0	32	84	9	85	48	1	3	46	1.27
35738772--35738886	45	2.6	43	76	22	112	47	1	1	48	1.22
35738947--35738995	20	2.5	20	80	16	57	59	2	0	38	1.09
35738981--35739028	10	4.6	10	78	19	53	60	2	0	37	1.09
35738946--35739032	22	4.0	23	72	15	69	58	2	0	39	1.11
35739051--35739127	19	4.1	20	73	19	74	72	7	12	6	1.26
35739047--35739127	28	2.9	27	74	5	81	74	7	12	6	1.22
35739045--35739124	37	2.2	36	80	6	90	75	7	11	6	1.20
35746692--35746738	10	4.7	10	78	7	51	63	4	0	31	1.13
35746762--35746786	10	2.5	10	100	0	50	52	12	0	36	1.39
35747099--35747154	20	2.8	19	76	10	67	26	1	1	69	1.08
35747083--35747173	18	4.8	18	75	11	67	27	3	1	68	1.12
35747242--35747309	10	7.3	10	68	25	51	39	0	4	55	1.20
35747243--35747296	18	3.1	17	79	10	63	38	0	3	57	1.17
35749245--35749325	5	15.8	5	73	10	65	40	20	3	34	1.71
35749954--35750045	48	1.9	48	84	0	121	20	38	20	20	1.94
35750195--35750221	5	5.4	5	100	0	54	40	18	18	22	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35750968--35751027	30	2.0	31	86	3	86	40	0	40	20	1.52
35751228--35751264	18	2.1	18	94	0	65	27	8	16	48	1.74
35755525--35755895	51	7.3	51	92	1	566	32	15	23	27	1.95
35759607--35759668	31	2.1	29	84	6	79	43	11	9	35	1.73
35759605--35759671	29	2.3	27	78	14	71	41	10	10	37	1.74
35762616--35762706	25	3.6	25	77	8	94	74	2	0	23	0.92
35762637--35762718	15	5.1	16	72	21	66	76	0	0	23	0.78
35762640--35762671	10	3.3	10	91	8	57	84	0	0	15	0.63
35762616--35762716	50	2.0	53	86	5	145	75	1	0	22	0.91
35762637--35762679	6	7.0	6	89	5	68	83	0	0	16	0.64
35763819--35763875	28	2.1	27	90	3	87	61	15	3	19	1.48
35768580--35768636	17	3.6	15	77	11	60	73	7	0	19	1.05
35768687--35768760	19	3.9	18	76	16	62	63	1	2	32	1.17
35768710--35768779	18	3.7	19	75	16	56	68	1	2	27	1.12
35768698--35768780	29	2.9	28	78	16	82	65	2	2	30	1.18
35774089--35774170	35	2.3	35	93	0	137	25	7	3	63	1.37
35774109--35774166	18	3.3	18	67	13	57	29	5	5	60	1.40
35774108--35774169	19	3.4	19	73	13	76	30	4	4	59	1.39
35774102--35774173	35	2.1	35	100	0	144	27	5	5	61	1.41
35775639--35775699	23	2.5	24	82	12	63	24	22	19	32	1.97
35781502--35781530	9	3.2	9	100	0	58	31	10	10	48	1.71
35785109--35785153	13	3.4	13	82	14	56	40	33	6	20	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35785694--35785810	62	1.9	60	86	5	164	51	3	2	42	1.32
35789342--35789458	47	2.5	47	81	2	128	25	21	17	35	1.95
35790331--35790375	21	2.0	23	83	8	58	51	6	4	37	1.49
35795120--35795236	47	2.5	47	78	0	126	27	20	14	37	1.92
35797861--35797891	5	6.2	5	100	0	62	19	19	19	41	1.90
35799430--35799468	16	2.4	16	84	12	53	56	5	0	38	1.22
35802181--35802697	230	2.2	229	86	3	721	28	17	19	34	1.95
35803028--35803071	19	2.3	19	84	0	61	31	43	2	22	1.66
35805086--35805150	20	3.2	20	73	16	69	44	6	9	40	1.61
35805086--35805256	37	4.5	37	83	3	189	47	8	6	37	1.60

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