genome.fa.s9.2.7.7.80.10.50.1000.8.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  8  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)
3369521--3369555	11	3.1	11	87	4	52	25	0	0	74	0.82
3369520--3369556	13	3.2	12	81	18	51	29	0	0	70	0.88
3369617--3369678	27	2.3	27	97	0	115	29	22	33	14	1.94
3370984--3371035	26	2.0	26	96	0	95	38	21	3	36	1.72
3372729--3372833	42	2.5	42	77	0	138	16	23	16	43	1.87
3377178--3377210	2	16.5	2	93	0	57	48	3	0	48	1.17
3378053--3378153	43	2.4	43	86	5	134	21	29	10	37	1.88
3380696--3380827	67	2.0	67	93	0	228	21	18	32	26	1.97
3382918--3382984	34	1.9	35	90	3	109	31	8	13	46	1.74
3382933--3382972	20	2.0	20	90	0	62	27	10	12	50	1.72
3382912--3382988	14	5.0	15	71	20	52	33	9	14	42	1.77
3396170--3396228	22	2.7	23	75	17	63	42	6	8	42	1.61
3396913--3396966	20	2.5	21	85	8	65	59	3	0	37	1.15
3396934--3397008	30	2.4	32	88	6	127	60	0	1	38	1.06
3396949--3397016	11	6.4	11	80	13	88	58	0	1	39	1.07
3397040--3397085	18	2.6	17	82	3	56	60	0	0	39	0.97
3414831--3414860	3	10.3	3	92	7	53	33	0	0	66	0.92
3414831--3414857	14	1.9	14	100	0	54	33	0	0	66	0.92
3416869--3416898	16	1.9	16	93	6	53	90	0	10	0	0.47
3423857--3423889	15	2.1	17	88	11	52	42	24	0	33	1.55
3425069--3425103	14	2.4	14	90	4	52	45	0	2	51	1.16
3430164--3430201	5	7.6	5	93	0	67	0	21	0	78	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3434787--3434846	23	2.6	24	84	5	70	46	8	5	40	1.56
3437991--3438046	11	4.9	12	75	16	57	25	26	1	46	1.63
3437995--3438046	22	2.3	23	86	3	79	26	25	1	46	1.63
3439843--3439897	27	2.0	27	86	6	76	27	30	12	29	1.93
3441659--3442132	126	3.8	124	85	3	628	29	21	17	31	1.96
3442992--3443076	31	2.7	31	81	1	98	41	3	1	54	1.25
3450311--3450442	31	4.1	31	74	7	138	52	10	6	31	1.60
3450311--3450507	97	2.1	96	92	2	326	50	10	6	32	1.62
3455621--3455766	71	2.1	71	100	0	292	35	10	18	34	1.86
3467139--3467210	27	2.7	27	74	8	83	29	34	27	8	1.86
3467242--3467283	19	2.2	20	91	4	68	69	0	30	0	0.89
3467248--3467329	30	2.8	29	88	5	112	64	0	35	0	0.94
3467286--3467332	6	8.0	6	92	2	69	55	0	44	0	0.99
3467406--3467444	20	2.0	19	95	5	69	20	0	7	71	1.10
3467632--3467664	17	1.9	17	93	0	57	75	6	9	9	1.18
3469528--3469585	12	4.8	12	78	0	53	24	39	27	8	1.84
3471180--3471326	76	1.9	77	87	4	217	52	11	4	31	1.58
3472580--3472608	13	2.1	14	93	6	51	34	0	0	65	0.93
3472947--3473010	25	2.5	26	77	12	69	18	21	20	39	1.93
3472966--3473057	22	4.0	22	81	9	96	16	22	20	40	1.91
3474564--3474612	18	2.7	18	81	9	55	34	14	10	40	1.79
3478650--3478683	11	3.0	11	91	4	50	88	0	11	0	0.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3478650--3478681	12	2.6	12	95	5	55	90	0	9	0	0.45
3485027--3485100	21	3.5	21	78	9	71	56	0	0	43	0.99
3495624--3495670	24	2.0	24	82	0	58	38	19	10	31	1.86
3500165--3500216	24	2.2	24	85	0	68	34	3	11	50	1.57
3500182--3500228	24	2.0	24	87	8	69	38	8	8	44	1.65
3504605--3504643	16	2.4	16	82	0	51	71	0	15	12	1.14
3512365--3512426	32	2.0	32	90	3	99	50	11	17	20	1.77
3512596--3512639	22	2.1	21	87	8	63	54	22	2	20	1.56
3512623--3512670	21	2.2	23	81	11	64	52	20	6	20	1.68
3512632--3512672	22	1.9	22	95	5	75	48	19	7	24	1.74
3516206--3516418	71	3.0	71	98	0	408	47	14	13	24	1.80
3516309--3516418	37	3.1	37	60	17	86	48	15	13	22	1.80
3523635--3523689	20	2.9	21	82	15	66	69	0	30	0	0.89
3546469--3546496	2	14.0	2	100	0	56	50	0	0	50	1.00
3548766--3548811	23	2.0	23	100	0	92	56	4	13	26	1.55
3556444--3556476	11	2.8	12	86	13	50	63	0	0	36	0.95
3557564--3557645	31	2.7	30	74	9	87	40	9	13	36	1.78
3561400--3561439	2	20.0	2	100	0	80	50	0	50	0	1.00
3561688--3561720	17	1.9	17	88	11	50	72	3	0	24	0.98
3561688--3561721	18	1.9	17	88	5	50	73	2	0	23	0.97
3572281--3572322	16	2.4	18	76	15	52	38	14	9	38	1.78
3598627--3598683	17	3.6	17	75	20	61	50	1	3	43	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3598633--3598682	15	3.3	15	75	13	57	52	2	4	42	1.31
3607146--3607201	22	2.5	22	88	0	85	41	19	26	12	1.87
3607146--3607212	22	3.0	21	79	12	73	40	20	25	13	1.89
3608205--3608237	5	6.8	5	93	6	59	57	0	0	42	0.98
3624788--3624831	14	3.1	14	78	9	54	52	2	2	43	1.26
3626724--3626757	17	1.9	18	88	5	52	55	0	5	38	1.24
3633543--3633574	6	5.3	6	100	0	64	68	0	0	31	0.90
3633543--3633580	18	2.1	18	90	0	58	71	0	2	26	1.00
3634681--3634741	31	2.0	31	87	3	88	50	3	1	44	1.28
3635769--3635798	14	2.1	14	93	0	51	20	13	13	53	1.72
3638056--3638085	15	2.0	15	93	0	51	0	16	0	83	0.65
3641906--3641943	7	5.3	7	82	17	51	84	0	13	2	0.73
3641904--3641942	19	2.1	19	85	9	53	82	0	15	2	0.79
3643641--3643674	17	2.0	17	88	0	50	50	8	14	26	1.72
3678601--3678904	151	2.0	151	99	0	599	26	15	20	37	1.92
3692885--3692940	28	2.0	28	100	0	112	32	7	25	35	1.83
3696300--3696761	111	4.1	111	87	3	620	27	22	27	22	1.99
3698129--3698166	17	2.2	18	90	4	60	84	0	15	0	0.63
3705967--3706011	20	2.2	20	84	4	54	15	20	2	62	1.43
3706141--3706191	15	3.6	16	70	26	51	39	0	0	60	0.97
3720158--3720225	16	4.2	16	96	0	127	23	0	38	38	1.55
3720452--3720486	18	2.0	17	88	5	52	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3725999--3726206	110	1.9	110	83	2	267	33	13	17	35	1.89
3726154--3726270	59	2.0	59	91	3	191	41	7	8	41	1.64
3726385--3726720	107	3.2	107	86	4	452	27	15	13	43	1.84
3727634--3727683	22	2.3	22	89	0	73	24	28	16	32	1.96
3727644--3727686	22	2.0	22	100	0	86	23	25	13	37	1.92
3745215--3745258	16	2.8	16	86	13	56	54	0	4	40	1.21
3756569--3756789	60	3.7	60	95	1	365	28	16	40	15	1.88
3763073--3763180	42	2.6	42	83	0	126	43	19	19	17	1.88
3773488--3773595	53	2.0	53	98	0	207	48	15	23	12	1.80
3773507--3773593	29	3.2	29	63	21	78	48	14	21	14	1.81
3774685--3774775	35	2.6	36	79	10	98	50	1	3	45	1.25
3774783--3774866	6	14.0	6	69	8	55	73	1	22	2	1.01
3776028--3776067	20	2.0	20	95	0	71	42	10	17	30	1.82
3777736--3777782	20	2.4	19	85	3	58	51	4	2	42	1.33
3777736--3777782	19	2.4	20	82	10	53	51	4	2	42	1.33
3777891--3777926	17	2.1	18	89	5	56	33	2	2	61	1.25
3779098--3779134	19	1.9	19	100	0	74	48	2	0	48	1.15
3788291--3788335	3	15.0	3	95	0	63	60	0	40	0	0.97
3793686--3793712	5	5.4	5	100	0	54	18	59	0	22	1.38
3797674--3797713	19	2.0	20	85	4	55	52	0	2	45	1.14
3803764--3804003	122	2.0	123	90	0	383	41	17	13	27	1.87
3812573--3812766	94	2.1	92	80	3	219	27	15	9	46	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3816090--3816132	21	2.1	21	86	4	61	72	2	18	6	1.19
3830455--3830495	20	2.0	20	85	0	55	53	4	4	36	1.44
3833249--3833378	46	2.8	46	92	2	208	39	9	22	29	1.85
3834661--3834691	2	15.5	2	93	0	53	51	0	3	45	1.17
3834757--3834852	3	32.0	3	76	10	81	63	2	4	30	1.24
3834757--3834851	31	3.0	30	77	10	91	63	2	4	30	1.25
3839157--3839181	12	2.1	12	100	0	50	48	0	44	8	1.32
3844349--3844422	29	2.5	30	84	4	87	52	5	4	37	1.43
3856064--3856165	22	4.6	22	87	0	132	31	14	26	27	1.95
3865209--3865241	2	17.5	2	87	12	52	48	0	0	51	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   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