genome.fa.s1.2.7.7.80.10.50.1000.54.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  54  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)
16070008--16070107	51	2.0	51	90	4	157	26	25	2	47	1.63
16073998--16074040	18	2.4	18	88	0	59	18	27	9	44	1.80
16074281--16074342	21	3.0	21	81	11	65	29	43	20	6	1.77
16075312--16075369	25	2.3	23	81	16	71	27	8	10	53	1.64
16081468--16081669	110	1.8	110	90	2	325	36	29	12	22	1.90
16089399--16089441	20	2.2	20	100	0	86	30	18	0	51	1.47
16090633--16090688	25	2.2	26	84	12	71	0	30	3	66	1.09
16090778--16090824	23	2.0	23	91	0	76	42	10	4	42	1.59
16095058--16095088	8	3.9	8	91	0	53	90	3	6	0	0.55
16095058--16095088	16	1.9	16	100	0	62	90	3	6	0	0.55
16100465--16100524	30	2.0	31	86	3	86	40	0	38	21	1.54
16100808--16100839	9	3.6	9	91	0	55	40	21	12	25	1.88
16101176--16101339	82	2.0	80	82	6	197	29	4	32	34	1.77
16105478--16105806	113	2.9	111	78	11	344	25	23	23	27	2.00
16106413--16106494	14	5.9	14	77	7	60	21	0	42	35	1.53
16106425--16106463	12	3.1	12	88	7	51	17	0	51	30	1.46
16106424--16106463	7	6.0	7	85	11	57	17	0	52	30	1.45
16106425--16106479	19	2.7	20	83	11	67	21	0	47	30	1.51
16106425--16106478	26	2.1	26	82	0	63	22	0	46	31	1.52
16106594--16106656	29	2.2	29	97	0	117	17	0	42	39	1.49
16109452--16110003	9	60.4	9	78	7	578	49	17	2	31	1.59
16112819--16112868	21	2.4	21	96	0	91	32	20	48	0	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16113188--16113437	42	5.9	42	94	1	437	23	21	22	33	1.98
16113188--16113437	85	3.0	84	96	1	446	23	21	22	33	1.98
16113188--16113437	127	2.0	127	96	0	464	23	21	22	33	1.98
16113449--16113544	48	2.0	48	95	0	174	14	18	27	39	1.90
16116469--16116508	3	13.3	3	89	0	62	30	2	2	65	1.19
16129681--16129720	21	2.0	20	85	5	53	30	5	25	40	1.77
16139953--16139996	18	2.4	18	84	0	52	72	11	0	15	1.11
16145775--16145799	8	3.1	8	100	0	50	52	36	0	12	1.39
16146896--16146935	19	2.2	19	90	4	64	42	0	0	57	0.98
16150381--16150424	21	2.1	21	84	12	56	47	0	0	52	1.00
16154055--16154085	14	2.2	14	100	0	62	19	22	12	45	1.84
16157749--16157829	3	26.7	3	97	2	153	32	0	1	66	0.99
16158178--16158439	131	2.0	131	98	0	506	16	40	23	19	1.91
16159515--16159559	24	1.9	23	81	4	54	33	2	11	53	1.49
16160947--16161003	16	3.6	16	95	0	87	29	0	36	33	1.58
16161250--16161284	18	2.0	17	88	5	52	54	0	0	45	0.99
16161209--16161280	28	2.6	28	73	6	65	52	2	0	44	1.15
16174364--16174411	24	2.0	23	84	11	62	50	10	0	39	1.37
16175753--16175783	16	1.9	16	93	0	53	61	3	3	32	1.28
16177876--16177940	25	2.7	24	79	9	69	49	0	4	46	1.22
16180429--16180465	2	18.5	2	100	0	74	48	0	0	51	1.00
16199376--16199434	30	2.0	30	83	9	77	45	5	0	49	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16202715--16202854	47	2.9	47	89	2	217	36	29	5	28	1.80
16208751--16208802	27	1.9	27	100	0	104	30	13	23	32	1.93
16212382--16212413	16	2.0	16	100	0	64	25	6	31	37	1.81
16212361--16212422	25	2.5	25	83	0	70	24	11	27	37	1.89
16216728--16216787	30	2.0	31	83	9	79	20	38	0	41	1.52
16217043--16217080	9	4.2	9	93	0	67	28	0	0	71	0.87
16217758--16217796	21	1.9	20	89	5	60	38	0	2	58	1.12
16220556--16220591	4	8.8	4	87	6	54	25	2	0	72	0.98
16222803--16222887	3	28.0	3	95	2	152	34	1	0	64	1.01
16223018--16223100	43	1.9	43	83	11	107	36	8	4	50	1.54
16223149--16223235	16	5.4	16	70	15	54	41	10	0	48	1.37
16223200--16223226	6	4.5	6	100	0	54	51	14	0	33	1.43
16223264--16223288	4	6.2	4	100	0	50	24	0	0	76	0.80
16228546--16228620	38	2.1	36	82	7	89	20	16	18	45	1.86
16228557--16228632	38	2.0	38	94	0	134	17	17	17	48	1.81
16229983--16230060	27	3.0	27	70	22	67	44	0	2	52	1.14
16229972--16230083	44	2.6	43	75	13	104	45	0	2	50	1.21
16230176--16230268	45	2.1	44	88	9	136	36	25	4	33	1.76
16230250--16230305	16	3.5	16	90	0	85	30	26	7	35	1.83
16230581--16230720	29	5.0	28	73	13	90	60	4	5	30	1.39
16230493--16230720	58	4.3	53	74	16	174	61	5	4	28	1.38
16230444--16230833	26	15.2	26	71	16	199	59	4	6	28	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16230762--16230806	25	1.9	23	82	13	56	66	4	2	26	1.22
16231870--16231907	16	2.4	16	95	0	67	34	7	34	23	1.84
16231887--16231983	44	2.2	44	88	5	142	32	5	29	31	1.80
16232143--16232198	18	3.2	17	85	10	60	53	3	0	42	1.18
16232263--16232308	18	2.6	18	86	6	58	52	2	2	43	1.25
16232120--16232612	120	4.1	120	93	3	839	52	4	1	42	1.28
16232365--16232409	16	2.8	16	80	16	56	60	0	2	37	1.09
16232380--16232417	18	2.2	17	90	4	58	63	0	2	34	1.09
16232502--16232548	18	2.6	18	93	6	78	55	0	0	44	0.99
16232158--16232583	57	7.1	60	67	21	268	52	4	1	42	1.29
16232200--16232623	59	7.1	59	65	12	238	52	4	1	41	1.30
16232610--16232648	20	2.0	20	84	0	51	43	2	12	41	1.56
16235695--16235724	14	2.1	14	100	0	60	40	6	46	6	1.56
16237667--16237701	15	2.2	17	90	10	56	60	0	0	40	0.97
16239251--16239276	2	13.0	2	100	0	52	50	0	0	50	1.00
16246758--16246824	27	2.5	27	97	0	125	31	23	32	11	1.91
16246892--16246943	21	2.4	22	90	6	88	32	0	9	57	1.31
16246892--16246960	21	3.1	22	83	10	70	33	0	8	57	1.29
16246820--16247017	82	2.4	82	96	1	364	32	0	11	55	1.36
16246971--16247038	21	3.2	21	85	2	82	29	0	13	57	1.37
16247110--16247153	16	2.8	16	82	0	61	56	2	2	38	1.24
16247186--16247267	38	2.2	38	97	0	155	39	2	3	54	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16247496--16247630	19	6.8	19	72	20	98	55	11	0	32	1.36
16247496--16247556	21	3.0	21	92	4	99	57	11	0	31	1.34
16247626--16247692	27	2.5	27	97	0	125	11	32	23	31	1.91
16247743--16247785	11	3.7	11	81	6	50	67	2	0	30	1.03
16247745--16247786	10	3.5	12	81	18	52	71	2	0	26	0.98
16250224--16250249	5	5.2	5	100	0	52	23	19	19	38	1.93
16250339--16250384	5	9.2	5	100	0	92	19	19	19	41	1.91
16257883--16257946	29	2.1	29	85	11	83	62	0	0	37	0.95
16257884--16257936	17	3.3	15	75	15	52	60	0	0	39	0.97
16257992--16258036	24	1.9	23	86	4	63	53	0	0	46	1.00
16259115--16259242	22	5.8	22	89	0	184	27	25	14	32	1.94
16275924--16275949	3	8.7	3	100	0	52	69	0	0	30	0.89
16276981--16277025	23	1.9	23	82	13	56	15	8	40	35	1.79
16277067--16277321	123	2.1	124	87	4	363	29	15	23	31	1.95
16279757--16279857	22	4.5	22	84	9	116	42	0	28	28	1.56
16279759--16279857	44	2.2	44	83	5	128	43	0	27	29	1.55
16289202--16289241	20	2.0	20	90	0	62	60	5	0	35	1.19
16289829--16289862	18	1.9	18	88	5	52	52	5	0	41	1.25
16290527--16290561	15	2.3	15	90	0	52	37	42	8	11	1.72
16303196--16303290	45	2.1	46	88	5	140	44	11	11	32	1.77
16305359--16305390	7	4.6	7	100	0	64	56	15	0	28	1.40
16308143--16308200	29	2.0	29	90	10	91	39	12	37	10	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16309920--16309955	16	2.2	16	90	9	56	47	11	8	33	1.69
16310003--16310116	17	6.3	17	70	13	84	40	10	14	34	1.81
16309998--16310142	39	3.8	39	78	9	138	42	10	13	34	1.78
16310003--16310292	18	16.0	18	69	11	137	42	9	15	32	1.80
16310168--16310292	35	3.6	35	82	5	137	41	8	16	33	1.79
16310243--16310330	44	2.0	44	86	0	122	44	12	15	27	1.83
16310406--16310455	18	2.8	17	82	8	64	42	6	16	36	1.72
16311246--16311324	6	12.3	6	80	9	77	0	24	0	75	0.80
16311245--16311324	13	6.2	13	77	10	74	0	23	0	76	0.79
16311465--16311503	17	2.2	17	86	9	51	0	15	17	66	1.25

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