genome.fa.s5.2.7.7.80.10.50.1000.39.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  39  of  208  ( 24913 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)
10832590--10832648	24	2.4	25	80	11	68	55	5	3	35	1.38
10834902--10834990	24	3.7	23	85	7	97	51	7	3	37	1.48
10837831--10837879	26	2.0	25	84	8	64	46	10	2	40	1.49
10839799--10839949	43	3.5	43	87	0	212	33	28	17	20	1.96
10840075--10840368	43	6.9	43	82	2	326	30	32	17	19	1.95
10840077--10840388	129	2.4	127	85	3	392	31	32	17	18	1.94
10841996--10842037	22	1.9	22	85	0	57	50	4	21	23	1.68
10844830--10844884	15	3.8	14	80	7	56	45	34	0	20	1.51
10845189--10845460	41	6.6	41	93	0	456	29	30	20	19	1.97
10845525--10845637	40	2.8	39	79	9	138	21	20	18	39	1.92
10846420--10846555	4	34.0	4	96	0	254	49	24	0	25	1.55
10847334--10847423	35	2.6	31	76	19	90	42	12	1	44	1.49
10847343--10847435	22	4.4	22	66	21	65	41	12	1	44	1.50
10847370--10847447	39	2.0	41	92	5	133	42	10	1	46	1.46
10847352--10847440	18	4.8	18	79	14	101	43	11	1	43	1.47
10847529--10847603	24	3.2	24	75	11	93	41	4	5	49	1.44
10847616--10847882	9	31.0	9	66	19	83	48	17	1	31	1.58
10847625--10847880	16	16.0	16	65	23	85	49	17	1	31	1.58
10847656--10847725	21	3.2	21	73	15	79	52	14	0	32	1.41
10847653--10847750	44	2.2	43	96	0	160	54	16	0	29	1.43
10847666--10847761	25	4.1	25	71	15	78	53	15	0	31	1.43
10847614--10847833	41	5.3	41	72	16	141	49	18	2	30	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10847616--10847667	25	2.1	25	79	13	54	46	21	1	30	1.62
10849660--10849708	21	2.3	21	96	0	89	26	20	51	2	1.59
10850056--10850154	43	2.3	43	89	0	144	24	17	32	26	1.97
10850301--10850455	73	2.1	73	90	2	240	24	25	23	27	2.00
10850355--10850794	114	3.9	114	91	0	704	25	25	22	25	2.00
10850355--10850794	227	1.9	227	93	0	754	25	25	22	25	2.00
10860910--10861011	51	2.0	51	96	0	186	26	21	19	32	1.97
10864255--10864287	16	2.1	17	88	11	52	39	0	3	57	1.14
10870854--10870917	30	2.2	29	83	5	83	23	3	14	59	1.49
10873659--10873704	3	15.0	3	81	4	56	67	2	2	28	1.14
10873649--10873702	28	1.9	28	88	7	83	66	3	1	27	1.19
10873663--10873710	25	1.9	25	86	0	69	64	2	4	29	1.23
10875355--10875571	86	2.5	86	84	3	283	28	22	19	29	1.98
10875575--10876690	87	12.8	87	82	3	1136	25	22	21	30	1.99
10875572--10878469	174	16.3	174	76	8	1491	25	22	21	30	1.99
10876187--10876505	43	7.3	44	67	8	211	25	24	20	30	1.98
10876690--10878465	87	20.6	87	81	4	1685	26	23	21	29	1.99
10877277--10877437	88	1.8	88	85	5	227	30	19	19	31	1.96
10878431--10878597	88	1.9	88	86	2	219	29	22	17	31	1.96
10878453--10878618	44	3.8	44	90	3	235	28	23	19	28	1.98
10878453--10878618	88	1.9	88	91	0	269	28	23	19	28	1.98
10879231--10879312	41	2.0	40	90	2	128	15	21	18	43	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10881322--10881387	25	2.6	25	83	9	71	59	4	16	19	1.54
10884578--10884624	13	3.7	13	80	2	51	65	2	4	27	1.22
10884575--10884622	19	2.4	19	86	13	62	66	2	4	27	1.21
10884583--10884647	26	2.3	29	79	10	73	61	3	7	27	1.38
10885462--10885545	41	2.0	41	84	4	107	35	13	28	22	1.92
10888815--10888859	15	3.0	15	86	0	63	26	0	6	66	1.16
10888822--10888872	20	2.7	19	85	11	61	27	0	7	64	1.21
10891305--10891360	2	28.0	2	92	0	94	46	0	3	50	1.19
10891714--10891749	14	2.5	15	90	4	56	0	11	44	44	1.39
10891965--10892543	49	11.9	50	69	10	213	21	20	25	32	1.98
10891959--10892594	96	6.5	96	90	4	900	21	20	25	32	1.97
10891959--10892594	193	3.3	193	90	3	911	21	20	25	32	1.97
10905934--10905986	2	26.5	2	96	0	97	47	0	1	50	1.12
10906341--10906376	14	2.5	15	90	4	56	0	11	44	44	1.39
10906744--10906774	7	4.3	7	95	4	53	29	0	0	70	0.87
10912283--10912415	60	2.2	59	81	1	149	39	17	10	32	1.84
10913275--10913312	19	2.0	19	94	0	67	34	15	13	36	1.87
10920884--10921013	42	3.1	42	93	2	210	34	17	24	23	1.96
10920884--10921078	42	4.6	42	87	2	196	35	18	21	24	1.96
10922779--10922996	9	24.8	9	73	13	177	31	1	21	46	1.60
10922804--10922996	34	5.5	34	79	10	155	29	1	21	47	1.58
10922779--10922996	52	4.1	52	79	8	192	31	1	21	46	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10923137--10923191	23	2.4	24	85	11	80	43	0	14	41	1.45
10922982--10923397	32	13.3	32	71	18	206	37	1	14	46	1.53
10923187--10923357	21	8.0	21	65	22	65	35	0	14	49	1.44
10922928--10923356	184	2.3	182	82	8	519	36	1	15	46	1.55
10923091--10923326	96	2.5	96	78	14	231	38	0	13	47	1.47
10923167--10923412	128	1.9	129	95	0	449	36	0	14	49	1.44
10923148--10923355	12	18.1	12	70	21	92	37	0	14	48	1.44
10923167--10923454	128	2.3	128	85	9	387	37	0	13	48	1.45
10923418--10923462	19	2.3	19	85	11	56	53	2	0	44	1.13
10923429--10923481	21	2.5	22	78	9	65	56	0	1	41	1.10
10926073--10926231	73	2.2	74	82	10	202	38	21	13	26	1.91
10926324--10926358	7	5.1	7	86	6	54	45	42	0	11	1.40
10926326--10926350	13	1.9	13	100	0	50	48	44	0	8	1.32
10926559--10926603	22	2.0	23	91	4	74	40	37	0	22	1.54
10927137--10927812	113	6.1	106	76	12	440	26	26	21	25	2.00
10927329--10927812	113	4.3	112	82	5	555	25	26	22	26	2.00
10927187--10927812	227	2.8	223	80	7	657	26	26	21	25	2.00
10933959--10934044	27	3.1	27	80	8	77	52	2	1	44	1.21
10933975--10934016	13	3.2	13	78	18	50	47	0	0	52	1.00
10933978--10934044	29	2.4	29	85	5	84	53	1	1	43	1.19
10933989--10934032	23	2.0	22	90	4	70	50	2	2	45	1.27
10938303--10938408	34	3.1	33	73	10	81	28	23	23	24	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10938894--10939146	81	3.1	80	86	2	348	20	15	19	44	1.86
10938876--10939133	27	9.6	27	84	1	313	19	14	20	44	1.86
10939376--10939430	19	2.9	18	89	10	67	16	38	23	21	1.93
10939385--10939430	19	2.3	20	96	3	85	15	36	21	26	1.93
10939385--10939436	19	2.7	19	90	3	59	17	36	21	25	1.94
10940979--10941012	9	3.9	9	84	7	52	79	0	17	2	0.86
10941458--10941492	16	2.2	16	100	0	70	45	20	11	22	1.82
10941738--10941791	27	2.0	28	86	10	78	27	0	3	68	1.06
10942856--10942904	22	2.3	22	82	10	57	2	30	8	59	1.38
10943264--10943436	63	2.7	63	87	1	231	25	19	27	28	1.98
10944908--10944988	22	3.7	21	70	14	56	55	9	14	19	1.67
10945306--10945396	28	3.3	28	71	9	96	37	3	3	56	1.32
10948347--10948419	25	2.9	25	81	4	74	27	13	12	46	1.79
10952782--10953017	103	2.3	103	87	5	347	32	27	16	22	1.96
10962444--10962474	16	1.9	16	93	0	53	35	0	9	54	1.33
10963921--10963962	22	1.9	22	85	9	59	42	2	0	54	1.13
10971555--10971614	5	12.2	5	84	10	79	36	0	1	61	1.06
10972440--10972504	3	21.7	3	80	0	76	35	0	3	61	1.12
10972440--10972504	27	2.4	27	100	0	130	35	0	3	61	1.12
10979722--10979747	12	2.2	12	100	0	52	15	23	15	46	1.83
10981064--10981120	28	2.0	28	100	0	114	29	17	14	38	1.89
10981788--10981862	36	2.1	36	94	0	132	36	21	22	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10986626--10986650	11	2.3	11	100	0	50	44	36	0	20	1.52
10991189--10991234	23	2.0	23	86	0	65	28	10	13	47	1.76
10991728--10991763	17	2.1	17	100	0	72	38	16	19	25	1.92
10992503--10992556	23	2.3	24	87	3	74	48	0	1	50	1.11
10994447--10994486	20	2.1	18	86	9	53	57	2	2	37	1.26
10994465--10994517	18	2.6	22	77	19	62	71	0	0	28	0.86
10994474--10994518	9	5.0	9	84	10	56	73	0	0	26	0.84
10994483--10994518	17	2.1	18	89	5	56	75	0	0	25	0.81
10999563--10999597	17	2.1	17	100	0	70	65	28	0	5	1.15
11009294--11009329	16	2.2	16	95	0	63	33	13	5	47	1.67

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