genome.fa.s9.2.7.7.80.10.50.1000.9.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  9  of  226  ( 27023 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)
3865295--3865326	16	2.0	16	93	0	55	71	3	12	12	1.25
3866180--3866997	407	2.0	408	96	0	1503	32	11	23	32	1.91
3867750--3867881	40	3.3	40	86	6	187	65	0	3	31	1.11
3867842--3867866	11	2.3	11	100	0	50	52	0	8	40	1.31
3867733--3867892	40	3.8	40	80	12	162	63	0	3	33	1.10
3868094--3868123	10	2.8	11	90	10	53	20	0	26	53	1.46
3872322--3872359	20	1.9	20	100	0	76	28	0	7	63	1.23
3874296--3874351	28	2.0	28	89	0	85	17	26	17	37	1.93
3887424--3887452	13	2.1	14	93	6	51	6	37	6	48	1.57
3893674--3893733	31	1.9	31	86	0	84	40	15	5	40	1.68
3895972--3896020	2	24.5	2	100	0	98	51	0	0	48	1.00
3896907--3896960	24	2.3	21	77	20	54	46	0	1	51	1.11
3902947--3902981	15	2.3	15	90	0	52	57	0	8	34	1.29
3907265--3907303	18	2.1	19	85	4	53	69	2	0	28	1.02
3907288--3907356	27	2.6	27	81	9	95	39	5	0	55	1.24
3907863--3907972	58	1.9	58	100	0	220	49	0	9	41	1.34
3907872--3907972	18	5.3	20	72	14	88	50	0	9	39	1.36
3908579--3908631	27	2.0	27	88	3	81	35	0	7	56	1.28
3908639--3908677	18	2.1	19	85	4	53	28	0	2	69	1.02
3948135--3948223	25	3.6	25	77	6	83	30	16	32	20	1.95
3948178--3948243	27	2.5	27	85	4	82	30	18	28	22	1.97
3948194--3948250	27	2.1	27	86	0	78	33	14	29	22	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3948260--3948336	24	3.2	23	72	9	73	35	18	31	15	1.92
3959258--3959299	18	2.3	18	80	8	50	54	9	11	23	1.66
3966808--3966854	24	2.0	24	84	16	62	51	17	0	31	1.46
3977236--3977288	26	2.0	26	100	0	106	37	18	16	26	1.93
3980358--3980417	30	2.0	30	93	0	102	28	8	20	43	1.80
3980528--3980558	14	2.3	13	94	5	53	9	0	16	74	1.07
3985405--3985496	26	3.6	26	68	17	68	17	25	23	33	1.96
4000913--4000951	19	2.1	19	100	0	78	25	25	5	43	1.75
4004489--4004538	26	1.9	26	100	0	100	46	0	12	42	1.41
4004759--4004784	2	13.0	2	100	0	52	50	0	0	50	1.00
4022545--4022609	32	2.0	32	100	0	130	27	16	15	40	1.89
4023694--4023784	22	4.0	22	77	9	94	41	20	23	14	1.89
4024860--4024899	5	7.6	5	83	10	53	60	0	0	40	0.97
4024860--4024900	16	2.6	16	92	0	73	60	0	0	39	0.96
4024865--4024894	8	3.8	8	90	0	51	60	0	0	40	0.97
4031637--4031684	16	2.9	16	79	11	53	41	4	0	54	1.20
4035795--4035857	24	2.6	24	80	7	65	61	3	1	33	1.21
4036395--4036434	20	2.0	20	90	0	62	27	10	12	50	1.72
4044306--4044488	50	3.6	49	84	5	215	24	25	31	18	1.97
4048615--4048645	2	15.5	2	100	0	62	51	0	48	0	1.00
4057283--4057326	22	2.0	22	81	4	52	43	6	2	47	1.42
4065737--4065781	22	2.0	22	100	0	90	40	17	13	28	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4076780--4076821	22	1.9	22	95	0	75	50	7	9	33	1.62
4078992--4079225	116	2.0	116	98	0	450	30	21	22	25	1.99
4088590--4088636	2	23.5	2	100	0	94	0	48	0	51	1.00
4097513--4097544	16	1.9	17	93	6	57	68	0	12	18	1.20
4124918--4124993	33	2.3	32	82	6	89	32	19	22	25	1.97
4124813--4125007	105	1.9	105	80	4	232	31	17	25	25	1.97
4128597--4128630	16	2.1	16	94	0	59	23	20	11	44	1.84
4129434--4129499	24	2.8	24	97	0	123	19	25	9	45	1.80
4150025--4150058	15	2.2	15	89	5	50	70	0	0	29	0.87
4180109--4180142	6	5.7	6	96	0	59	17	17	64	0	1.29
4189324--4189360	16	2.3	16	86	13	58	40	0	0	59	0.97
4194332--4194370	4	9.8	4	94	0	69	46	25	0	28	1.53
4194439--4194499	26	2.3	27	94	5	106	40	8	0	50	1.32
4194490--4194527	18	2.1	18	85	14	51	76	15	2	5	1.08
4194560--4194611	27	1.9	27	96	0	95	30	23	32	13	1.93
4194892--4194935	15	2.9	15	72	0	52	47	0	4	47	1.22
4194876--4194935	30	2.0	30	86	0	84	50	0	3	46	1.18
4194829--4195122	134	2.2	137	94	4	524	45	5	6	42	1.52
4195056--4195114	19	3.2	19	80	4	84	49	0	11	38	1.40
4195665--4195716	27	1.9	27	96	0	95	13	32	23	30	1.93
4201913--4201950	20	2.0	20	94	5	69	63	0	0	36	0.95
4208378--4208417	20	2.0	20	90	0	62	27	10	12	50	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4208363--4208429	34	1.9	35	90	3	109	31	8	13	46	1.74
4208357--4208433	14	5.0	15	71	20	52	33	9	14	42	1.77
4228399--4228554	43	3.7	41	84	6	188	29	26	15	28	1.96
4228399--4228554	85	1.8	84	84	5	215	29	26	15	28	1.96
4260073--4260118	2	23.0	2	100	0	92	50	0	50	0	1.00
4261668--4261700	11	2.8	12	86	9	50	48	0	0	51	1.00
4262147--4262186	2	20.0	2	100	0	80	50	0	0	50	1.00
4266861--4266894	2	17.0	2	100	0	68	50	0	0	50	1.00
4268141--4268182	21	2.0	21	100	0	84	33	23	9	33	1.87
4268832--4268891	30	2.0	30	100	0	120	26	10	16	46	1.78
4273722--4273768	9	5.2	9	81	0	58	2	44	2	51	1.25
4273721--4273771	24	2.1	24	88	0	75	1	47	1	49	1.24
4273776--4273822	9	5.2	9	81	0	58	10	38	17	34	1.84
4273774--4273822	12	4.1	12	81	0	53	12	38	16	32	1.86
4273788--4273822	15	2.3	15	95	0	61	8	40	17	34	1.80
4273896--4273935	21	1.9	21	85	10	55	15	32	7	45	1.74
4279111--4279296	93	2.0	93	97	0	354	39	19	9	31	1.84
4284003--4284048	19	2.4	20	82	10	60	45	0	0	54	0.99
4297683--4297716	3	11.3	3	100	0	68	35	0	32	32	1.58
4304660--4304695	2	18.0	2	100	0	72	50	0	0	50	1.00
4310372--4310423	18	2.8	17	77	13	50	48	3	1	46	1.31
4310679--4310731	27	2.0	27	85	7	72	18	7	13	60	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4311873--4311913	21	2.1	19	86	9	55	41	0	0	58	0.98
4312396--4312435	20	2.1	19	90	4	62	25	7	20	47	1.75
4316157--4316184	14	2.0	14	100	0	56	0	0	14	85	0.59
4318050--4318101	24	2.2	24	85	0	68	50	9	5	34	1.59
4320871--4320928	30	1.9	30	89	0	89	41	3	24	31	1.71
4321141--4321171	13	2.4	13	94	0	53	32	0	12	54	1.38
4321270--4321569	56	5.7	53	85	5	337	26	24	28	21	1.99
4321277--4321570	100	2.8	103	84	7	351	26	23	28	21	1.99
4323755--4323787	13	2.5	13	95	0	57	0	27	0	72	0.85
4327364--4327687	162	2.0	162	98	0	621	40	15	12	32	1.83
4347937--4347970	5	6.8	5	96	0	59	20	35	20	23	1.96
4374221--4374246	3	8.7	3	100	0	52	34	0	0	65	0.93
4375541--4375733	96	2.0	96	91	0	314	33	16	24	26	1.96
4386927--4386963	13	2.8	13	83	0	56	24	10	24	40	1.87
4388113--4388157	21	2.1	21	100	0	90	40	24	13	22	1.90
4404615--4404654	22	1.9	21	85	10	55	25	15	37	22	1.93
4407112--4407139	5	5.6	5	100	0	56	42	0	0	57	0.99
4407203--4407250	12	3.9	12	84	10	62	77	0	22	0	0.78
4407900--4407946	24	2.0	24	84	16	62	31	0	17	51	1.46
4408102--4408248	41	3.7	41	76	7	176	24	17	24	34	1.96
4408145--4408316	37	4.4	38	76	7	177	23	18	26	31	1.97
4408105--4408316	78	2.7	78	93	2	347	24	17	25	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4410491--4410530	4	10.2	4	86	5	55	52	0	0	47	1.00
4411354--4411380	13	2.1	13	100	0	54	37	0	14	48	1.45
4411971--4412023	23	2.3	23	100	0	106	37	30	5	26	1.79
4429303--4429415	39	2.9	38	86	3	163	49	24	4	21	1.67
4436891--4436976	42	2.0	42	100	0	172	27	32	9	30	1.88
4449284--4449377	45	2.1	45	93	0	161	26	5	10	57	1.54
4453668--4453712	21	2.1	21	100	0	90	20	28	15	35	1.93
4461605--4461637	5	6.8	5	93	6	59	39	21	21	18	1.93
4464395--4464421	6	4.5	6	100	0	54	85	0	0	14	0.61
4485568--4485605	17	2.2	18	85	4	51	21	2	18	57	1.52

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226