genome.fa.s13.2.7.7.80.10.50.1000.168.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  168  of  199  ( 23770 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)
49178884--49178953	24	2.9	23	82	6	68	28	10	4	57	1.50
49184020--49184073	1	54.0	1	79	0	54	88	1	7	1	0.64
49184020--49184070	11	4.8	11	78	9	61	88	1	7	1	0.67
49184021--49184073	20	2.7	20	85	2	72	88	1	7	1	0.65
49186178--49186331	44	3.4	45	76	14	129	27	14	25	31	1.95
49186219--49186890	44	14.8	43	70	12	368	30	17	21	30	1.96
49186305--49186754	92	4.9	91	71	13	329	30	16	21	30	1.96
49186205--49186880	181	3.7	181	87	1	861	30	17	21	30	1.96
49188066--49188093	7	4.0	7	100	0	56	14	0	0	85	0.59
49188336--49188399	29	2.4	25	87	10	83	28	4	0	67	1.11
49188336--49188731	26	15.4	28	68	18	104	28	6	4	60	1.42
49188436--49188495	18	3.1	19	74	18	52	35	5	1	58	1.30
49188459--49188604	57	2.7	55	77	11	147	29	5	4	60	1.37
49188575--49188728	26	6.4	23	77	11	125	28	5	4	61	1.37
49188578--49188626	21	2.3	21	85	3	62	28	4	4	63	1.31
49192399--49192443	22	2.0	22	100	0	90	35	8	0	55	1.31
49192503--49192575	27	2.7	27	86	0	101	27	27	31	13	1.94
49192809--49192840	3	10.7	3	100	0	64	0	0	31	68	0.90
49192991--49193043	27	2.0	27	96	0	97	37	15	26	20	1.92
49197738--49197766	15	1.9	15	100	0	58	20	27	20	31	1.98
49199024--49199063	18	2.4	16	91	8	62	70	2	5	22	1.19
49199290--49199316	6	4.5	6	100	0	54	14	0	0	85	0.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49200676--49200737	31	2.0	30	84	3	79	30	9	12	46	1.74
49201395--49201453	2	29.5	2	100	0	118	50	0	0	49	1.00
49201910--49201952	17	2.5	17	88	7	61	67	0	25	6	1.15
49202877--49202921	3	15.0	3	95	0	81	66	2	0	31	1.04
49209380--49209407	3	9.3	3	100	0	56	32	0	0	67	0.91
49213769--49213795	2	13.5	2	100	0	54	48	0	0	51	1.00
49219884--49220241	69	5.2	69	88	0	466	26	8	18	45	1.79
49219969--49220242	24	11.9	23	68	11	121	27	7	18	46	1.76
49220046--49220242	23	8.5	24	67	18	96	27	6	19	46	1.75
49220182--49220266	23	3.7	23	80	9	75	29	8	20	42	1.81
49221387--49221414	14	2.0	14	100	0	56	42	14	7	35	1.73
49230065--49230099	16	2.2	16	100	0	70	11	37	0	51	1.38
49233413--49233471	30	1.9	31	86	3	84	47	1	22	28	1.61
49235726--49235871	45	3.2	45	93	0	238	19	17	21	41	1.90
49235855--49235903	6	7.8	6	86	2	62	18	20	16	44	1.86
49240694--49240777	43	1.9	43	80	7	98	57	2	1	39	1.20
49240752--49240812	19	3.1	19	77	11	59	59	3	8	29	1.43
49243987--49244287	107	2.8	107	93	1	498	34	17	17	30	1.93
49244326--49244370	20	2.2	21	84	11	58	57	2	11	28	1.45
49244547--49244604	27	2.1	28	84	9	75	53	1	8	36	1.42
49246480--49246772	44	6.6	44	71	12	179	26	22	21	30	1.99
49249808--49250007	45	4.4	45	90	0	292	31	24	16	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49249988--49250419	132	3.3	132	92	0	684	25	26	18	30	1.98
49252827--49252916	31	2.9	30	76	11	92	34	13	14	37	1.85
49267598--49267700	54	1.9	54	100	0	206	53	12	5	28	1.61
49267725--49267786	30	2.1	30	90	0	97	56	12	4	25	1.56
49267817--49267846	14	2.1	14	93	0	51	53	13	13	20	1.72
49268026--49268068	22	2.0	22	85	0	59	55	9	13	20	1.66
49269257--49269298	21	2.0	21	90	0	66	30	11	26	30	1.92
49273049--49273112	29	2.2	29	91	0	101	32	25	1	40	1.65
49283319--49283348	2	15.0	2	100	0	60	50	0	0	50	1.00
49286374--49286406	16	2.1	16	88	5	50	24	3	6	66	1.28
49288148--49288458	106	3.0	106	79	6	355	21	12	19	45	1.84
49290518--49290576	31	1.9	31	82	3	75	35	8	11	44	1.72
49291366--49291404	14	2.8	14	84	0	51	35	12	23	28	1.91
49292882--49293001	54	2.2	54	85	2	161	19	27	26	26	1.99
49293721--49293827	40	2.7	40	91	1	171	31	17	28	21	1.96
49293746--49293811	20	3.3	20	64	8	53	33	15	33	18	1.92
49296453--49296526	38	1.9	38	100	0	148	40	16	5	37	1.71
49300261--49300320	17	3.6	17	72	17	63	45	0	0	55	0.99
49300259--49300319	32	1.9	32	93	3	106	47	0	0	52	1.00
49300270--49300316	8	5.9	8	75	9	51	44	0	0	55	0.99
49301028--49301081	25	2.2	25	100	0	108	38	16	16	27	1.90
49301718--49301754	19	1.9	19	94	0	65	24	29	27	18	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49302008--49302040	17	2.0	17	88	5	50	21	15	3	60	1.48
49303418--49303558	74	1.9	74	88	5	214	36	19	12	32	1.88
49303852--49303902	2	25.5	2	100	0	102	50	0	0	49	1.00
49304355--49304560	89	2.3	89	79	12	210	35	16	10	37	1.83
49304724--49304776	20	2.9	18	75	22	56	54	0	1	43	1.11
49305010--49305058	19	2.6	18	83	6	62	24	6	2	67	1.24
49305135--49305178	20	2.1	21	91	4	72	34	4	0	61	1.16
49305135--49305172	10	3.8	10	85	0	58	31	2	0	65	1.06
49307025--49307065	20	2.1	19	86	13	57	73	2	0	24	0.96
49308856--49308940	9	9.4	9	84	0	98	42	23	8	25	1.82
49308855--49308940	27	3.2	27	86	0	118	43	23	8	25	1.81
49312461--49312560	42	2.4	42	93	0	173	25	27	11	37	1.89
49314291--49314323	17	1.9	17	100	0	66	6	0	15	78	0.93
49315154--49315299	44	3.2	43	69	21	116	30	17	18	33	1.94
49314626--49315644	375	2.8	376	79	7	928	30	18	17	33	1.94
49314591--49315327	94	7.9	94	79	1	688	30	18	17	33	1.94
49315336--49315644	94	3.3	94	84	2	406	28	17	19	34	1.94
49315389--49315649	44	5.7	44	71	17	181	28	18	19	33	1.95
49320328--49320357	8	3.9	8	91	8	53	80	0	0	20	0.72
49320319--49320352	13	2.7	13	95	4	61	79	0	0	20	0.73
49331832--49332128	39	7.6	39	84	2	328	37	28	17	17	1.92
49333296--49333339	2	22.0	2	100	0	88	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)
49334054--49334152	47	2.1	48	96	1	182	38	6	12	43	1.67
49336575--49336599	10	2.5	10	100	0	50	76	0	0	24	0.80
49341691--49341722	14	2.3	14	100	0	64	25	34	9	31	1.87
49343773--49343797	2	12.5	2	100	0	50	52	0	48	0	1.00
49345172--49345212	21	2.0	21	85	9	57	21	21	12	43	1.85
49348645--49348849	32	6.4	32	87	0	284	20	20	18	39	1.93
49348645--49348849	96	2.1	96	91	0	329	20	20	18	39	1.93
49348835--49348864	15	2.0	15	100	0	60	33	13	20	33	1.91
49348803--49348899	50	2.0	47	86	6	131	24	21	19	34	1.97
49356843--49356988	50	2.9	50	82	2	177	22	28	21	27	1.99
49360099--49360133	13	2.7	13	90	0	52	0	20	2	77	0.90
49360094--49360137	20	2.3	18	80	7	52	0	20	6	72	1.07
49360771--49360888	3	40.3	3	71	20	65	28	3	5	62	1.32
49360847--49360890	20	2.1	21	87	4	63	22	2	2	72	1.07
49366842--49366883	22	2.0	22	85	4	59	33	0	2	64	1.07
49367069--49367163	49	1.9	49	89	0	145	37	12	9	40	1.76
49370548--49370598	13	3.8	13	78	2	57	62	5	5	25	1.41
49371064--49371094	9	3.4	9	90	0	53	25	12	22	38	1.90
49371150--49371192	9	4.8	9	91	0	68	44	16	11	27	1.82
49371147--49371192	18	2.6	18	100	0	92	45	15	10	28	1.79
49371228--49371272	21	2.1	21	84	8	56	22	35	0	42	1.54
49371242--49371304	30	2.0	30	85	11	83	15	46	0	38	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49371466--49371498	7	4.7	7	100	0	66	15	69	0	15	1.19
49371626--49371659	13	2.6	13	100	0	68	29	8	29	32	1.87
49371702--49371733	9	3.6	9	95	0	55	37	21	9	31	1.85
49371727--49371760	9	3.8	9	96	0	59	44	14	11	29	1.81
49371719--49371787	18	3.8	18	72	14	61	40	17	11	30	1.85
49371709--49371787	27	2.9	25	76	14	77	39	17	11	31	1.85
49372078--49372149	30	2.4	30	97	0	135	26	25	23	25	2.00
49373306--49373365	10	5.9	10	77	9	59	28	3	5	63	1.31
49387206--49387234	14	2.0	15	93	6	51	68	3	0	27	1.05
49393240--49393264	2	12.5	2	100	0	50	48	0	0	52	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   188   189   190   191   192   
          193   194   195   196   197   198   199