genome.fa.s1.2.7.7.80.10.50.1000.147.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  147  of  187  ( 22383 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)
43854327--43854378	15	3.3	14	78	19	50	36	7	1	53	1.41
43854777--43854816	20	2.0	19	85	9	53	35	2	5	57	1.34
43857101--43857146	19	2.4	21	79	20	64	50	0	0	50	1.00
43858308--43858350	23	1.9	22	90	4	68	46	2	6	44	1.43
43858322--43858395	37	2.0	37	97	0	139	35	1	10	52	1.45
43861234--43861292	30	2.0	30	87	9	86	45	1	0	52	1.10
43861238--43861293	10	5.6	10	83	12	71	44	1	0	53	1.11
43862408--43862445	18	2.1	18	100	0	76	44	0	15	39	1.47
43879392--43879453	26	2.4	27	84	10	76	41	12	11	33	1.79
43879392--43879467	26	2.9	26	82	7	75	40	10	15	32	1.82
43884969--43885006	3	13.0	3	83	5	51	28	2	0	68	1.03
43896040--43896099	16	3.8	16	95	0	102	33	0	36	30	1.58
43896078--43896187	45	2.6	43	74	9	111	34	5	27	32	1.80
43896361--43896407	15	3.3	15	72	22	55	46	10	0	42	1.38
43896363--43896408	12	3.3	14	74	20	51	45	10	0	43	1.39
43907936--43908291	87	4.1	87	94	0	613	28	22	25	23	2.00
43908392--43908680	44	6.7	44	69	13	152	29	20	23	26	1.99
43909461--43909494	12	2.7	13	86	9	52	0	11	14	73	1.10
43913526--43913718	41	4.7	41	77	3	158	18	17	25	38	1.92
43913507--43913717	82	2.6	82	78	6	205	18	18	25	37	1.94
43921598--43921634	19	2.1	18	85	14	51	29	0	5	64	1.15
43922846--43922900	20	2.7	19	78	15	58	56	10	14	18	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43922905--43922944	20	2.0	21	90	5	64	55	20	12	12	1.69
43923181--43923233	19	2.7	21	75	16	60	52	3	11	32	1.55
43924032--43924072	21	1.9	22	90	5	66	36	0	4	58	1.20
43926064--43926104	21	1.9	22	90	5	66	31	2	0	65	1.05
43928560--43928635	32	2.4	32	91	2	118	17	15	6	60	1.55
43931050--43931113	29	2.2	30	94	2	112	39	12	25	23	1.90
43934655--43934704	24	2.1	24	100	0	100	44	4	20	32	1.70
43934866--43934898	17	1.9	17	100	0	66	39	12	12	36	1.80
43941297--43941339	22	2.0	22	85	0	59	32	23	16	27	1.96
43949838--43950180	189	1.8	189	92	1	580	29	14	15	39	1.88
43950554--43950611	29	2.0	29	100	0	116	27	17	24	31	1.97
43951123--43951198	34	2.3	35	81	6	95	26	11	15	46	1.81
43951372--43951572	97	2.1	97	89	1	305	31	19	13	34	1.91
43952602--43952708	42	2.5	42	77	3	117	24	17	18	39	1.92
43952634--43952837	43	4.8	43	76	6	137	22	18	21	37	1.94
43952613--43952837	86	2.6	85	76	6	222	22	19	20	37	1.94
43964053--43964102	5	9.8	5	91	4	82	0	20	0	80	0.72
43973738--43973780	21	2.0	21	90	0	68	23	23	34	18	1.96
43974482--43974512	15	2.1	15	100	0	62	74	6	0	19	1.03
43975038--43975076	5	7.8	5	100	0	78	17	0	0	82	0.68
43979482--43979587	44	2.4	44	90	3	160	26	32	19	21	1.97
43979859--43979924	33	2.0	33	100	0	132	24	24	18	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43979904--43980159	128	2.0	128	91	3	417	24	22	20	32	1.97
43981384--43981417	6	5.3	6	89	10	50	14	17	0	67	1.23
43981384--43981417	13	2.7	12	86	13	50	14	17	0	67	1.23
43982297--43982387	35	2.6	35	77	11	96	10	9	6	72	1.27
43982326--43982403	29	2.6	31	83	4	88	8	6	6	78	1.10
43982354--43982404	14	3.4	14	81	10	57	11	1	5	80	0.97
43982235--43982517	143	2.0	142	95	0	512	10	11	5	72	1.27
43984534--43984571	20	1.9	20	94	0	67	15	21	5	57	1.57
43986949--43986978	3	10.0	3	92	0	51	66	3	0	30	1.07
43986941--43987004	15	4.3	15	76	11	53	65	6	0	28	1.16
43989514--43989543	9	3.2	9	90	9	51	10	3	0	86	0.67
44007053--44007089	20	2.0	20	84	10	51	5	18	8	67	1.36
44007188--44007239	18	2.9	18	85	8	70	44	0	0	55	0.99
44008841--44008885	3	15.0	3	100	0	90	66	0	0	33	0.92
44008945--44008978	17	1.9	18	88	5	52	76	0	23	0	0.79
44015828--44015884	26	2.2	26	78	6	62	40	5	17	36	1.72
44017329--44017374	19	2.4	19	88	0	74	34	10	28	26	1.90
44021380--44021418	3	13.0	3	100	0	78	66	0	33	0	0.92
44024229--44024289	3	20.7	3	86	3	88	0	29	1	68	0.99
44038316--44038470	47	3.2	47	93	2	256	27	18	34	20	1.96
44041691--44041736	23	2.0	23	100	0	92	56	8	4	30	1.49
44049070--44049113	22	2.0	23	82	13	56	65	4	15	13	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44049230--44049272	22	2.0	22	86	9	61	6	9	9	74	1.22
44050127--44050251	62	2.1	59	86	4	169	30	13	2	53	1.53
44050427--44050451	2	12.5	2	100	0	50	52	0	0	48	1.00
44051117--44051314	107	1.9	106	87	3	290	29	14	19	35	1.92
44064157--44064255	3	33.0	3	95	0	180	32	0	2	65	1.04
44073469--44073522	23	2.3	23	87	0	72	22	29	20	27	1.98
44074285--44074338	2	27.0	2	100	0	108	50	0	0	50	1.00
44076464--44076586	66	1.9	65	80	8	142	39	38	8	13	1.75
44076876--44076924	13	3.8	13	81	5	55	6	16	0	77	0.96
44076874--44076925	25	2.1	25	82	7	61	9	15	0	75	1.05
44076941--44076978	17	2.2	17	90	0	58	15	5	0	78	0.91
44079711--44079754	19	2.3	20	84	7	56	27	20	11	40	1.86
44082457--44082499	6	6.8	6	97	2	68	86	0	13	0	0.58
44082456--44082500	7	6.9	7	94	5	69	86	0	13	0	0.57
44082446--44082499	12	4.6	11	82	15	56	85	0	12	1	0.69
44084504--44084903	85	4.7	85	91	1	604	29	20	24	25	1.99
44084522--44084828	43	7.2	43	66	13	177	28	19	24	27	1.99
44084563--44084869	43	7.2	42	64	13	162	29	21	22	26	1.99
44085704--44086789	88	12.4	88	89	2	1612	27	21	24	26	1.99
44085704--44086789	526	2.1	526	97	0	2055	27	21	24	26	1.99
44087339--44087649	154	2.0	155	96	0	579	34	16	17	32	1.92
44087679--44087787	49	2.2	50	90	1	166	28	11	12	46	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44088622--44088740	60	2.0	60	89	0	184	53	10	0	34	1.42
44088909--44088972	14	4.5	13	76	17	65	0	28	0	71	0.86
44088916--44088950	11	3.4	11	92	7	56	0	31	0	68	0.90
44089100--44089147	24	2.0	25	83	4	62	62	6	0	31	1.20
44089738--44089877	45	3.0	45	91	3	208	15	13	52	17	1.74
44089750--44089877	24	5.5	24	91	5	190	14	14	52	17	1.75
44094798--44094831	16	2.1	16	89	10	52	32	0	0	67	0.91
44096182--44096239	5	11.4	5	88	3	89	41	0	0	58	0.98
44096824--44096868	23	1.9	24	86	13	67	55	2	22	20	1.54
44104799--44104849	17	2.8	19	77	14	54	43	0	7	49	1.32
44136524--44136728	98	2.0	100	88	6	306	31	19	15	34	1.92
44136723--44136781	27	2.2	27	87	0	82	15	28	25	30	1.96
44136831--44136897	29	2.3	29	87	2	91	49	1	7	41	1.40
44142558--44142595	14	2.7	14	91	0	58	36	0	5	57	1.21
44143350--44143426	34	2.3	34	76	0	82	32	6	9	51	1.59
44143490--44143565	28	2.8	26	74	18	75	40	3	5	50	1.44
44143480--44143576	27	3.6	25	68	15	70	38	3	4	54	1.35
44146960--44147004	19	2.4	19	88	3	65	26	11	13	48	1.75
44152153--44152193	21	2.0	21	95	0	73	34	36	0	29	1.58
44156140--44156172	17	1.9	17	100	0	66	48	9	0	42	1.35
44156384--44156448	2	33.0	2	96	3	123	50	0	0	49	1.00
44157781--44157828	5	9.4	5	97	2	87	20	0	0	79	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44170279--44170335	30	1.9	30	96	0	105	19	14	17	49	1.80
44170612--44170669	26	2.2	26	96	0	107	13	25	17	43	1.86
44175577--44175628	26	2.0	26	81	7	61	55	1	0	42	1.10
44176731--44176832	41	2.6	39	89	7	145	30	15	17	36	1.91
44180456--44180484	9	3.2	9	100	0	58	44	0	0	55	0.99
44180455--44180499	18	2.5	18	82	7	56	44	6	0	48	1.29
44181001--44181038	15	2.5	15	91	0	58	50	23	0	26	1.50
44181500--44181537	19	2.1	19	85	5	51	65	5	2	26	1.27
44190150--44190191	3	14.3	3	95	5	77	69	0	30	0	0.89
44198585--44198662	26	2.9	26	78	14	70	57	0	1	41	1.07

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