genome.fa.s4.2.7.7.80.10.50.1000.127.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  127  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)
40526084--40526324	84	2.9	84	85	3	297	31	10	12	46	1.75
40533824--40533898	37	2.0	37	100	0	150	32	20	5	42	1.74
40539686--40539738	18	3.1	18	75	20	60	28	1	0	69	0.99
40540585--40540640	22	2.5	22	76	2	58	32	1	7	58	1.35
40551020--40551050	4	7.8	4	100	0	62	77	0	0	22	0.77
40552719--40552766	25	2.0	25	91	4	80	6	4	41	47	1.48
40554191--40554235	6	7.2	6	87	7	63	80	2	2	15	0.92
40555742--40555855	44	2.6	45	82	2	149	26	28	14	30	1.95
40556061--40556190	45	2.9	43	73	15	120	26	26	17	29	1.98
40568301--40568325	2	12.5	2	100	0	50	0	48	0	52	1.00
40579387--40579416	2	15.0	2	100	0	60	50	0	0	50	1.00
40587913--40587946	17	1.9	18	88	5	52	29	11	11	47	1.76
40591757--40591861	43	2.5	43	82	4	124	23	31	24	20	1.98
40594907--40594961	27	2.0	27	100	0	110	34	10	21	32	1.89
40597483--40597918	124	3.5	124	90	0	674	32	17	20	29	1.96
40600915--40601128	112	1.9	112	95	0	383	39	7	8	44	1.63
40601195--40601268	21	3.5	21	90	3	121	20	1	33	44	1.60
40601519--40601557	21	1.9	20	84	5	51	5	25	38	30	1.78
40602505--40602530	7	3.7	7	100	0	52	57	15	0	26	1.38
40603656--40603753	51	1.9	51	81	8	119	51	2	20	26	1.59
40603717--40603770	22	2.5	21	77	11	56	50	5	22	22	1.70
40603732--40603764	11	3.0	11	86	13	50	54	9	18	18	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40603913--40603991	40	2.0	40	85	5	106	24	30	24	21	1.99
40610589--40610621	16	2.1	16	88	5	50	57	0	9	33	1.30
40615641--40615699	26	2.4	24	78	13	66	32	10	0	57	1.32
40615899--40615974	38	2.0	38	100	0	152	34	10	13	42	1.78
40616465--40616506	17	2.5	16	75	24	50	66	7	7	19	1.39
40620841--40620878	2	19.0	2	94	0	67	50	2	0	47	1.15
40621475--40621510	18	2.0	18	100	0	72	27	5	22	44	1.75
40625272--40625310	14	2.8	14	92	0	60	23	0	30	46	1.53
40632700--40632780	32	2.4	34	85	8	103	38	12	18	30	1.88
40638476--40638528	27	1.9	28	81	11	65	43	0	3	52	1.19
40639579--40639609	12	2.6	12	89	0	53	29	22	6	41	1.78
40640433--40640483	24	2.1	24	88	0	75	39	5	7	47	1.57
40640443--40640489	24	2.0	24	91	0	76	40	6	8	44	1.60
40644682--40644733	24	2.2	24	89	0	77	36	3	9	50	1.54
40646371--40646401	7	4.4	7	95	0	53	29	35	32	3	1.73
40647500--40647528	4	7.5	4	92	7	51	24	0	0	75	0.80
40653344--40653392	19	2.5	19	83	3	53	46	0	28	24	1.53
40656353--40656386	16	2.1	16	88	0	50	23	0	17	58	1.38
40659167--40659323	42	3.6	44	74	12	130	28	26	19	25	1.98
40664919--40664990	28	2.6	28	86	0	99	30	9	26	33	1.89
40669633--40669743	30	3.6	31	72	9	102	19	14	27	38	1.91
40670682--40670721	19	2.1	20	86	9	57	57	2	35	5	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40674819--40674848	11	2.7	11	94	0	51	56	0	23	20	1.42
40675721--40675879	38	4.2	38	82	4	169	32	28	19	18	1.96
40677833--40677884	27	1.9	27	92	0	86	30	26	7	34	1.85
40677832--40677891	27	2.2	27	84	0	84	30	28	10	31	1.89
40677876--40678120	27	9.1	27	79	7	203	22	22	11	43	1.85
40677876--40678120	54	4.6	53	78	8	237	22	22	11	43	1.85
40679645--40679743	25	4.0	25	82	8	105	30	15	20	34	1.93
40679721--40679834	25	4.5	25	76	7	81	30	18	17	33	1.94
40681542--40681566	10	2.5	10	100	0	50	44	0	0	56	0.99
40688119--40688157	15	2.6	15	83	0	51	66	12	2	17	1.35
40692056--40692081	13	2.0	13	100	0	52	53	7	0	38	1.30
40694486--40694541	3	18.7	3	96	0	103	32	0	35	32	1.58
40695091--40695213	42	2.9	42	92	0	201	47	17	4	30	1.66
40696904--40696937	3	11.3	3	100	0	68	67	0	0	32	0.91
40697291--40697328	18	2.1	19	85	5	51	47	2	15	34	1.60
40697680--40697726	24	2.0	24	84	16	62	31	0	17	51	1.46
40697883--40698022	40	3.5	40	74	10	126	27	18	23	30	1.98
40704386--40704517	49	2.7	50	77	12	130	18	26	18	35	1.95
40704459--40704519	25	2.5	24	78	7	68	16	27	18	37	1.92
40708123--40708188	31	2.2	30	86	5	89	43	13	9	33	1.76
40717578--40717622	24	1.9	24	90	4	74	35	0	2	62	1.08
40717719--40717746	9	3.1	9	100	0	56	57	10	0	32	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40717689--40717898	68	3.1	68	95	1	379	45	9	5	40	1.58
40717887--40717928	16	2.6	16	92	0	66	42	7	2	47	1.43
40719023--40719075	25	2.1	25	82	6	63	20	1	1	75	0.99
40719142--40719200	23	2.5	24	81	15	70	28	1	3	66	1.18
40719116--40719198	27	3.1	27	80	3	87	30	1	4	63	1.22
40719793--40720226	217	2.0	218	96	0	809	30	13	19	37	1.89
40721345--40721377	17	1.9	17	93	0	57	18	36	3	42	1.66
40725078--40725125	23	2.1	23	85	11	64	29	0	22	47	1.51
40730253--40730293	21	2.0	20	86	9	57	31	14	0	53	1.41
40733854--40733941	21	4.2	21	89	0	131	39	18	26	15	1.90
40733843--40733941	42	2.4	42	86	3	139	40	18	26	15	1.89
40734111--40734153	17	2.4	18	80	11	52	51	11	0	37	1.39
40734640--40734686	22	2.2	21	84	3	58	53	10	0	36	1.36
40740083--40740218	68	1.9	71	85	5	188	51	5	2	40	1.39
40751369--40751439	36	2.0	36	94	0	124	47	12	11	28	1.76
40762503--40762531	13	2.2	13	100	0	58	24	10	37	27	1.88
40768775--40768825	26	2.0	26	88	7	79	49	23	5	21	1.71
40771176--40771209	17	2.0	17	94	0	59	44	5	0	50	1.26
40772514--40772565	24	2.2	24	89	0	77	34	3	7	53	1.48
40773971--40774064	24	3.9	24	74	2	71	19	29	18	32	1.95
40774129--40774272	27	5.6	25	82	8	123	21	27	20	31	1.98
40774149--40774261	27	4.4	26	86	5	133	23	28	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40774129--40774247	52	2.3	51	79	12	136	21	26	20	31	1.98
40774304--40774382	39	2.0	39	92	4	133	36	13	17	31	1.89
40779384--40779416	12	2.8	12	95	0	57	42	3	39	15	1.62
40779640--40779681	4	10.5	4	94	0	75	2	0	23	73	0.94
40779684--40779875	74	2.5	75	87	2	260	36	5	11	45	1.65
40780182--40780245	31	2.1	31	91	2	103	25	3	14	57	1.51
40782356--40782401	20	2.3	20	85	7	58	39	17	13	30	1.87
40786978--40787130	72	2.1	72	92	0	252	37	18	13	30	1.89
40788576--40788609	11	2.8	13	91	8	54	44	11	8	35	1.72
40789791--40789987	76	2.6	76	87	0	295	20	19	26	33	1.97
40796685--40796814	39	3.3	39	87	0	188	35	19	11	33	1.88
40799985--40800055	31	2.3	31	80	0	79	29	14	12	43	1.82
40810034--40811333	652	2.0	652	94	0	2271	30	19	20	29	1.97
40812278--40812336	26	2.3	26	82	5	66	61	0	0	38	0.96
40812281--40812331	17	3.2	17	81	8	54	64	0	0	35	0.94
40813899--40813945	16	3.0	16	78	12	53	51	2	0	46	1.13
40813881--40814067	61	3.1	60	68	22	174	50	4	1	43	1.31
40813784--40814096	120	2.6	120	95	0	563	48	6	1	43	1.35
40814044--40814078	18	2.0	17	94	5	61	51	0	0	48	1.00
40818297--40818371	23	3.3	23	80	14	93	53	21	8	17	1.69
40818470--40818504	18	1.9	18	100	0	70	60	22	5	11	1.52
40821787--40821830	21	2.1	21	100	0	88	43	13	9	34	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40834329--40834425	28	3.4	28	77	6	106	48	15	17	18	1.81
40852697--40852739	23	1.9	23	90	4	70	44	0	0	55	0.99
40852695--40852747	23	2.3	23	77	6	63	52	0	0	47	1.00
40858350--40858416	19	3.6	19	79	15	68	4	22	2	70	1.19
40861728--40862022	113	2.6	114	81	4	321	35	17	21	25	1.95
40861934--40862090	75	2.1	75	82	4	183	35	15	21	27	1.94
40861839--40862210	188	2.0	187	82	5	448	34	16	21	26	1.95
40862047--40862609	114	4.9	114	75	11	429	31	18	21	28	1.97
40862044--40862472	229	1.9	227	84	6	580	32	17	22	28	1.96
40862071--40862609	229	2.3	225	80	7	575	31	17	21	28	1.97

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