genome.fa.s4.2.7.7.80.10.50.1000.120.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  120  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)
38565212--38565603	46	8.6	46	94	1	621	29	23	13	33	1.93
38565847--38565893	19	2.3	21	85	7	62	42	12	0	44	1.42
38567348--38567379	12	2.6	13	85	14	50	56	6	0	37	1.25
38570527--38570633	53	2.0	53	100	0	214	36	16	13	33	1.88
38571264--38571310	4	11.8	4	100	0	94	51	25	0	23	1.49
38572067--38572113	16	2.9	16	83	0	58	8	19	23	48	1.75
38578243--38578293	18	2.5	20	81	15	61	35	0	0	64	0.94
38578243--38578292	13	3.8	13	78	21	50	36	0	0	64	0.94
38578420--38578700	140	2.0	140	92	2	474	34	14	13	37	1.85
38578879--38578916	19	2.0	19	85	10	51	21	2	5	71	1.19
38579120--38579202	27	3.1	27	100	0	166	26	18	19	36	1.94
38579340--38579408	27	2.6	27	88	0	102	17	34	30	17	1.93
38586330--38586397	27	2.5	27	92	0	118	17	27	33	20	1.95
38595679--38595751	37	1.9	37	84	13	96	32	23	1	42	1.63
38595878--38596009	51	2.6	51	84	4	169	34	26	17	21	1.96
38596033--38596303	51	5.3	50	80	7	271	30	25	15	28	1.96
38596066--38596299	102	2.3	102	95	0	414	31	26	14	27	1.95
38600942--38600987	23	2.0	23	83	8	58	39	10	17	32	1.84
38614799--38614873	35	2.1	35	95	0	132	28	2	33	36	1.71
38616001--38616084	28	3.0	28	79	10	91	36	15	22	25	1.93
38618780--38618914	68	2.0	68	89	4	209	50	6	2	40	1.41
38618772--38618873	20	5.7	18	70	19	63	50	6	1	41	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38627576--38627604	9	3.2	9	100	0	58	20	10	44	24	1.82
38629614--38629658	22	2.0	22	87	8	65	31	2	26	40	1.68
38634566--38634610	22	2.1	21	84	12	56	62	2	6	28	1.33
38635538--38635580	22	2.0	22	100	0	86	37	13	25	23	1.92
38637269--38637298	2	15.0	2	92	0	51	46	3	0	50	1.18
38637277--38637318	13	3.1	14	86	10	52	42	0	4	52	1.22
38637293--38637320	13	2.2	13	100	0	56	39	0	7	53	1.28
38637494--38637912	108	3.9	109	91	4	668	30	17	19	33	1.95
38640056--38640186	60	2.2	60	81	1	147	48	16	13	21	1.80
38640085--38640218	31	4.4	31	72	8	94	45	14	17	23	1.84
38640139--38640218	32	2.5	31	87	2	106	43	11	18	26	1.84
38644206--38644247	2	21.0	2	100	0	84	50	0	0	50	1.00
38647856--38647934	3	26.7	3	94	2	142	64	0	1	34	1.02
38649066--38649106	19	2.2	19	95	0	73	43	12	4	39	1.63
38652771--38652863	42	2.2	42	88	9	138	52	10	3	33	1.52
38652890--38652937	23	2.0	24	92	4	80	41	10	4	43	1.58
38653739--38653765	2	13.5	2	100	0	54	0	0	51	48	1.00
38654000--38654033	7	4.9	7	100	0	68	85	0	0	14	0.60
38661535--38661583	20	2.7	18	77	22	57	51	4	2	42	1.32
38676082--38676172	37	2.4	37	83	5	112	16	10	40	31	1.83
38678594--38678650	28	1.9	30	82	10	73	47	1	21	29	1.61
38678904--38678975	28	2.6	27	71	18	67	29	2	29	38	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38679092--38679187	20	4.8	20	82	0	111	12	31	19	36	1.89
38697711--38697793	20	4.1	21	77	21	81	22	4	0	72	1.04
38697717--38697782	35	1.9	34	87	9	98	22	4	0	72	1.02
38697752--38697785	12	2.8	12	87	12	52	23	5	0	70	1.09
38699937--38699961	9	2.8	9	100	0	50	92	0	8	0	0.40
38705169--38705216	25	1.9	25	91	0	78	37	18	14	29	1.91
38711338--38711378	21	1.9	22	85	14	59	48	7	2	41	1.44
38713157--38713199	18	2.4	18	84	7	52	20	9	4	65	1.40
38717215--38717244	7	4.4	7	91	8	53	13	0	0	86	0.57
38717213--38717244	13	2.5	13	100	0	64	15	0	0	84	0.63
38717215--38717252	20	1.9	20	88	0	58	18	0	0	81	0.69
38717443--38717484	17	2.4	18	84	11	52	38	0	16	45	1.48
38717869--38717916	24	2.0	24	83	0	60	45	8	25	20	1.79
38717992--38718036	21	2.1	21	88	8	65	20	17	17	44	1.87
38718015--38718097	42	2.0	42	85	0	112	18	21	18	42	1.90
38724770--38724824	25	2.2	24	78	9	58	54	0	3	41	1.18
38724813--38724851	20	2.0	20	84	0	51	51	12	0	35	1.40
38727399--38727441	9	4.9	9	80	2	52	46	4	0	48	1.22
38727400--38727441	13	3.2	13	80	16	50	45	4	0	50	1.23
38730099--38730142	23	2.0	21	82	8	52	54	0	11	34	1.36
38730668--38730730	30	2.1	30	90	0	99	25	30	20	23	1.99
38740723--38740774	23	2.2	24	83	10	63	65	5	7	21	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38740740--38740836	5	18.0	5	73	19	72	71	3	3	22	1.15
38740731--38740788	23	2.8	21	76	20	59	70	3	6	18	1.24
38740768--38740837	14	4.9	13	74	22	61	72	1	1	24	1.00
38740772--38740834	34	1.9	31	87	9	90	73	1	1	23	1.01
38745294--38745369	37	2.1	37	94	0	134	26	19	18	35	1.95
38751116--38751159	16	2.8	16	92	0	70	50	9	22	18	1.75
38754777--38754829	22	2.4	22	81	6	63	35	0	16	47	1.48
38767203--38767233	16	1.9	16	93	0	53	48	0	9	41	1.36
38767206--38767247	20	2.2	18	87	8	57	50	0	4	45	1.23
38772296--38772352	17	3.4	17	77	18	73	64	10	3	21	1.39
38772288--38772355	34	2.0	34	100	0	136	64	11	2	20	1.39
38778461--38778502	21	2.0	21	86	4	59	54	2	2	40	1.26
38779325--38779364	16	2.5	16	84	11	55	55	12	0	32	1.38
38779541--38779580	4	9.8	4	94	5	71	47	0	0	52	1.00
38779838--38779905	29	2.3	31	87	5	95	27	7	17	47	1.74
38779855--38779919	29	2.2	29	83	5	78	36	6	15	41	1.72
38787903--38788056	56	2.8	56	86	2	220	43	17	9	29	1.81
38788854--38788896	21	2.0	22	81	4	52	32	2	11	53	1.50
38788864--38788904	22	1.9	21	90	5	64	34	2	2	60	1.23
38788864--38788909	16	2.9	16	75	18	51	36	2	2	58	1.22
38809359--38809429	31	2.2	32	82	2	81	40	12	15	30	1.85
38813290--38813429	51	2.8	50	88	6	212	30	30	15	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38815354--38815391	19	2.0	19	89	0	58	23	44	18	13	1.85
38815611--38815650	19	2.1	19	86	9	55	32	2	5	60	1.32
38821913--38821973	22	2.8	22	92	0	95	34	14	26	24	1.94
38835576--38835613	17	2.3	16	95	4	67	60	2	31	5	1.33
38838977--38839018	22	1.9	22	95	0	75	14	26	16	42	1.86
38852453--38852490	2	19.0	2	100	0	76	50	0	0	50	1.00
38853267--38853442	87	2.0	87	98	0	343	30	21	21	27	1.98
38860490--38860571	40	2.0	40	88	0	119	53	10	15	19	1.71
38860758--38860801	20	2.1	21	91	4	72	6	31	0	61	1.22
38860973--38861000	9	3.1	9	100	0	56	10	46	0	42	1.38
38862734--38862875	27	5.2	27	76	8	117	45	10	18	26	1.81
38862734--38862875	54	2.6	55	76	8	146	45	10	18	26	1.81
38865318--38865358	21	1.9	22	90	5	66	41	4	4	48	1.46
38870166--38870194	8	3.8	8	90	9	51	65	0	0	34	0.93
38874139--38874203	20	3.3	20	69	16	64	38	12	16	32	1.86
38883629--38883683	25	2.2	25	100	0	110	36	12	7	43	1.71
38883754--38883891	44	3.1	43	66	20	102	47	4	3	44	1.40
38886637--38886822	50	3.7	50	86	0	239	33	25	18	21	1.96
38886611--38886821	25	8.5	25	62	5	70	32	26	18	22	1.97
38900845--38900911	34	2.0	34	82	5	82	47	16	11	23	1.80
38906015--38906055	21	1.9	22	90	5	66	73	14	2	9	1.19
38913659--38913718	24	2.5	25	81	13	72	26	21	18	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38914234--38914356	60	2.0	64	87	9	182	46	7	0	45	1.36
38914797--38914843	19	2.5	20	86	6	62	34	2	4	59	1.29
38923170--38923212	21	2.1	21	95	4	79	30	13	11	44	1.80
38926757--38926794	20	1.9	20	84	10	51	13	26	21	39	1.89
38926936--38926964	7	4.1	7	100	0	58	41	0	13	44	1.44
38931022--38931047	12	2.2	12	100	0	52	50	15	15	19	1.79
38952165--38952203	18	2.2	17	86	13	53	46	20	0	33	1.51
38954808--38954840	15	2.2	15	89	10	50	60	0	0	39	0.97
38972292--38972466	45	3.9	44	74	10	140	32	20	20	28	1.97
38972289--38972497	44	4.7	44	71	10	140	31	18	20	30	1.96

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