genome.fa.s4.2.7.7.80.10.50.1000.10.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  10  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)
3383819--3383885	34	1.9	35	90	3	109	31	8	13	46	1.74
3383813--3383889	14	5.0	15	71	20	52	32	9	15	42	1.78
3383972--3384010	20	2.0	20	94	0	69	48	2	0	48	1.15
3386600--3386650	18	2.8	18	72	0	57	37	3	45	13	1.63
3389852--3389883	2	16.0	2	100	0	64	50	0	0	50	1.00
3390060--3390154	35	2.7	35	80	8	95	25	13	15	45	1.83
3397363--3397447	42	2.0	42	100	0	170	29	14	21	35	1.92
3402179--3402220	22	1.9	22	100	0	84	38	14	26	21	1.91
3410351--3410415	22	3.0	22	86	0	85	15	29	20	35	1.93
3410506--3410564	31	1.9	31	92	0	100	52	3	22	22	1.61
3417285--3417316	15	2.1	16	94	5	57	46	0	9	43	1.35
3417451--3417538	25	3.6	24	81	9	108	15	26	19	38	1.92
3417622--3417680	31	1.9	31	89	0	91	52	5	22	20	1.65
3458626--3458793	73	2.3	73	95	0	300	19	27	23	29	1.98
3462400--3462496	48	2.0	48	91	0	158	49	11	5	34	1.61
3471773--3471805	6	5.7	6	96	3	59	18	15	30	36	1.91
3474224--3474269	24	1.9	24	86	0	65	28	0	6	65	1.17
3474265--3474318	20	2.7	21	83	11	60	37	0	3	59	1.15
3482035--3482075	11	3.9	11	90	9	68	53	0	0	46	1.00
3482072--3482124	10	5.3	10	75	6	54	73	0	1	24	0.93
3482136--3482175	11	3.5	12	83	10	57	55	0	2	42	1.13
3482048--3482164	30	4.0	30	87	3	159	61	0	2	35	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3482119--3482218	41	2.4	41	85	3	130	61	0	4	35	1.15
3482246--3482282	5	7.2	5	93	3	56	0	37	56	5	1.22
3484211--3484264	20	2.7	20	75	11	56	46	1	0	51	1.11
3487694--3487767	20	3.8	20	73	18	75	64	2	4	28	1.25
3488216--3488271	20	2.6	22	71	13	55	41	1	0	57	1.09
3492667--3492702	2	18.0	2	94	0	63	52	0	0	47	1.00
3499901--3499925	13	1.9	13	100	0	50	32	0	0	68	0.90
3499894--3499981	36	2.5	37	81	10	103	43	1	3	52	1.25
3518606--3518655	26	1.9	26	84	8	66	28	10	10	52	1.67
3519795--3519852	29	2.0	29	90	3	91	36	0	6	56	1.26
3525515--3525545	15	2.1	15	100	0	62	22	19	19	38	1.93
3538192--3538248	28	2.0	29	93	3	98	14	10	8	66	1.44
3538199--3538257	28	2.1	28	84	6	75	16	8	10	64	1.48
3538716--3538786	30	2.4	30	95	0	124	57	11	4	26	1.51
3540352--3540390	19	2.0	20	90	9	64	69	0	0	30	0.89
3547541--3547585	19	2.4	19	82	10	56	37	4	0	57	1.19
3549593--3549622	15	2.0	15	93	0	51	60	3	0	36	1.14
3550672--3550711	21	1.9	21	84	0	53	57	0	0	42	0.98
3552054--3552079	2	13.0	2	100	0	52	50	0	0	50	1.00
3556582--3556647	23	2.8	22	75	11	60	37	18	13	30	1.89
3556832--3556885	12	4.6	12	77	13	58	51	18	12	16	1.75
3556844--3556899	24	2.3	24	93	0	94	50	17	12	19	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3566588--3566639	25	2.0	25	85	14	70	48	1	3	46	1.31
3567369--3567396	3	9.3	3	100	0	56	35	32	32	0	1.58
3568278--3568349	29	2.5	29	82	6	92	29	25	8	37	1.85
3578947--3578980	15	2.3	15	100	0	68	20	23	14	41	1.89
3591852--3591897	17	2.7	17	75	18	51	50	0	0	50	1.00
3601127--3601285	43	3.7	44	79	7	157	28	24	18	27	1.98
3601127--3601296	86	2.0	85	81	7	202	30	24	17	27	1.97
3602845--3602907	30	2.1	30	96	0	117	57	12	3	26	1.51
3611235--3611295	21	3.0	21	83	11	90	52	4	1	40	1.33
3611761--3611823	29	2.3	26	83	8	81	31	3	1	63	1.19
3611808--3611912	55	1.9	54	83	9	133	36	0	2	60	1.18
3611830--3611959	29	4.8	27	70	16	74	34	0	3	61	1.17
3611849--3611921	18	3.8	19	77	15	64	35	1	2	60	1.20
3611893--3611943	16	3.1	16	83	8	50	29	1	1	66	1.13
3611944--3611979	18	1.9	19	94	5	65	25	0	8	66	1.19
3611846--3611978	9	14.4	9	65	24	55	31	0	4	63	1.20
3624801--3624827	14	1.9	14	100	0	54	29	7	0	62	1.22
3625197--3625227	16	1.9	16	93	0	53	61	3	0	35	1.12
3626595--3626632	2	19.0	2	100	0	76	50	0	0	50	1.00
3627460--3627498	17	2.4	16	83	8	51	58	5	0	35	1.20
3629114--3629159	2	23.0	2	81	0	56	43	2	6	47	1.41
3632675--3632700	11	2.4	11	100	0	52	61	7	0	30	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3632686--3632746	28	2.2	28	88	5	88	68	1	0	29	0.99
3632662--3632750	38	2.3	39	81	11	112	66	2	0	31	1.04
3632716--3632758	16	2.6	17	78	10	54	62	0	0	37	0.95
3632889--3632923	18	1.9	18	94	0	61	2	31	51	14	1.57
3640934--3640988	28	2.0	28	100	0	110	40	14	14	30	1.86
3642282--3642309	13	2.2	13	100	0	56	50	21	7	21	1.72
3644490--3644532	20	2.2	20	83	8	52	30	0	16	53	1.43
3644478--3644575	27	3.6	26	76	15	83	33	0	15	51	1.44
3644501--3644561	21	3.0	22	81	15	69	32	0	16	50	1.45
3644482--3644582	14	7.3	14	70	15	59	30	0	17	51	1.46
3645101--3645149	21	2.3	21	100	0	98	22	46	20	10	1.80
3646743--3646785	2	21.5	2	95	0	77	53	0	0	46	1.00
3648156--3648235	31	2.6	30	86	5	99	45	11	8	35	1.71
3653981--3654215	33	6.7	33	71	20	151	30	26	21	22	1.99
3653982--3654190	75	2.8	75	91	1	330	30	26	20	22	1.98
3656578--3656618	21	2.0	20	86	13	57	63	9	21	4	1.44
3660387--3660438	20	2.6	19	84	9	59	63	5	19	11	1.47
3673207--3673235	3	9.7	3	100	0	58	0	65	0	34	0.93
3673460--3673517	18	3.3	18	79	15	59	60	0	1	37	1.07
3673460--3673546	19	4.8	17	74	18	70	59	1	1	37	1.12
3673447--3673546	10	10.8	10	66	24	51	59	2	1	38	1.16
3673447--3673546	36	2.7	38	77	21	115	59	2	1	38	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3682286--3682357	33	2.1	34	82	2	83	63	1	1	33	1.11
3685576--3685606	15	2.1	15	93	0	53	38	16	0	45	1.47
3685803--3685836	2	17.0	2	87	0	50	52	2	0	44	1.16
3685992--3686016	2	12.5	2	100	0	50	48	0	0	52	1.00
3687208--3688037	274	3.0	274	98	1	1567	37	15	11	35	1.83
3688642--3688718	33	2.3	33	97	0	145	23	54	7	14	1.66
3688642--3688732	33	2.8	33	91	3	121	25	51	8	14	1.70
3705108--3705180	12	6.2	12	76	16	64	61	4	5	28	1.37
3706616--3706871	132	1.9	132	92	1	424	27	23	17	32	1.96
3706856--3707413	46	12.1	46	93	0	882	29	28	15	26	1.96
3708515--3708615	45	2.3	43	80	11	116	25	25	13	34	1.93
3708691--3708750	14	4.4	14	78	15	56	1	25	0	73	0.93
3708701--3708796	20	4.9	20	79	14	85	4	15	2	78	1.00
3708732--3708796	10	6.8	9	78	15	51	6	7	3	83	0.91
3708744--3708796	10	5.3	10	86	6	54	5	5	3	84	0.85
3708734--3708786	17	2.9	18	83	13	65	7	7	1	83	0.89
3708744--3708794	18	2.8	18	79	8	50	5	5	3	84	0.87
3711610--3711646	19	1.9	19	89	10	58	29	5	29	35	1.80
3713865--3713898	3	11.3	3	93	0	59	64	0	2	32	1.08
3715502--3715539	13	2.9	13	81	11	51	68	18	7	5	1.34
3715662--3715699	17	2.2	18	85	4	51	2	10	5	81	0.94
3716414--3716495	3	26.7	3	71	20	55	29	4	3	62	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3716414--3716498	12	7.4	11	80	13	75	29	4	3	62	1.32
3719742--3719989	126	2.0	126	93	1	426	32	10	6	51	1.60
3728965--3728989	2	12.5	2	100	0	50	0	0	48	52	1.00
3731008--3731127	52	2.3	52	98	0	231	31	19	8	40	1.81
3731836--3731870	17	2.0	18	88	5	54	42	0	0	57	0.99
3739142--3739222	30	2.7	31	78	12	80	54	1	1	43	1.16
3740752--3740834	42	2.0	42	100	0	166	38	9	19	32	1.84
3744712--3744811	46	2.2	46	96	0	182	27	27	16	30	1.96
3745133--3745187	22	2.5	22	88	5	76	21	12	23	41	1.88
3746972--3747044	23	3.3	23	66	11	71	45	2	4	47	1.36

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