genome.fa.s3.2.7.7.80.10.50.1000.11.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  11  of  150  ( 17918 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)
3142173--3142230	22	2.6	22	78	7	55	39	18	5	36	1.74
3142209--3142262	19	2.8	19	91	0	90	35	16	11	37	1.84
3146331--3146369	21	1.9	20	84	5	51	23	5	5	66	1.32
3147330--3147363	3	11.3	3	93	0	59	64	0	2	32	1.08
3159514--3159576	31	2.0	31	90	0	99	33	9	11	46	1.72
3175294--3175330	19	1.9	19	94	0	65	37	8	16	37	1.78
3176184--3176340	24	6.8	23	70	20	96	33	6	7	53	1.53
3176255--3176305	25	2.1	24	89	10	77	35	3	1	58	1.28
3176473--3176505	2	16.5	2	100	0	66	48	0	0	51	1.00
3183464--3183546	22	3.7	23	91	1	109	33	12	26	27	1.92
3183473--3183546	22	3.4	22	96	0	130	33	13	24	28	1.93
3196032--3196340	59	5.2	58	69	14	216	42	2	3	52	1.31
3196029--3196436	120	3.4	119	92	2	654	43	2	4	50	1.33
3196262--3196295	18	1.9	18	88	5	52	47	2	0	50	1.16
3196485--3196519	6	5.8	6	100	0	70	68	14	0	17	1.21
3196591--3196686	44	2.2	45	84	5	124	35	28	5	31	1.79
3196667--3196702	16	2.2	16	90	0	54	25	30	5	38	1.78
3206164--3206204	13	3.2	13	85	0	55	78	0	4	17	0.93
3206967--3207172	95	2.2	95	91	1	324	33	17	18	30	1.95
3207030--3207210	44	4.0	44	73	17	140	31	21	17	29	1.96
3207453--3207613	87	1.9	87	88	2	243	23	24	22	28	1.99
3207623--3207838	89	2.4	89	86	1	308	24	25	22	28	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3207479--3207854	89	4.3	88	74	11	263	24	24	21	29	1.99
3208211--3208263	24	2.2	24	83	6	63	30	18	15	35	1.92
3209190--3209252	13	4.7	13	75	7	63	4	15	0	79	0.90
3209191--3209229	18	2.1	18	85	4	51	2	17	0	79	0.84
3215767--3215964	98	2.0	98	86	3	274	29	21	16	32	1.95
3216004--3216341	131	2.6	128	75	10	274	28	22	21	28	1.99
3215865--3216429	218	2.6	219	91	1	936	28	21	19	30	1.98
3215873--3216769	44	20.7	42	71	10	454	28	22	18	30	1.97
3216397--3216867	85	5.4	84	73	12	290	29	21	18	30	1.97
3216274--3216775	129	3.9	129	92	2	812	29	21	18	30	1.97
3216697--3216873	98	1.8	98	90	4	286	30	18	18	32	1.95
3216818--3216916	44	2.3	43	80	5	126	29	20	19	31	1.97
3219086--3219184	47	2.0	50	86	5	141	10	10	6	73	1.24
3219145--3219183	7	5.7	7	93	6	62	12	0	7	79	0.93
3234724--3234748	11	2.3	11	100	0	50	32	16	0	52	1.44
3245817--3245857	21	2.0	21	85	4	57	80	7	12	0	0.90
3247298--3247323	12	2.2	12	100	0	52	65	0	0	34	0.93
3248857--3249645	143	5.5	143	89	1	1098	27	21	20	30	1.98
3255161--3255197	13	2.9	12	92	4	56	78	2	0	18	0.87
3255384--3255422	16	2.4	17	83	12	55	66	2	2	28	1.18
3257204--3257233	2	15.0	2	100	0	60	50	0	0	50	1.00
3257823--3257864	8	5.2	8	77	11	50	83	0	16	0	0.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3261093--3261163	32	2.2	33	80	7	83	56	14	12	16	1.68
3262783--3262849	31	2.2	31	97	0	125	46	8	5	38	1.60
3268923--3268979	29	2.0	29	86	6	80	43	0	3	52	1.18
3269038--3269107	31	2.2	32	85	12	92	41	0	4	54	1.20
3269045--3269107	33	1.9	33	87	12	94	42	0	3	53	1.16
3269228--3269283	3	19.3	3	78	14	64	33	0	3	62	1.12
3270333--3270442	38	2.8	39	80	6	125	20	18	27	33	1.96
3279359--3279392	2	17.0	2	100	0	68	50	0	0	50	1.00
3280168--3280232	28	2.3	29	91	2	105	41	9	0	49	1.35
3280493--3280545	18	3.1	18	81	10	67	41	13	0	45	1.43
3280499--3280548	15	3.1	15	85	8	64	44	14	0	42	1.44
3280572--3280647	23	3.3	23	66	10	66	44	1	10	43	1.47
3281287--3281353	28	2.4	28	85	2	100	47	0	8	43	1.34
3287971--3288061	46	2.0	46	95	0	164	32	23	7	36	1.83
3288566--3288610	2	22.5	2	100	0	90	51	0	0	48	1.00
3294383--3294420	19	2.0	19	100	0	76	42	5	15	36	1.70
3300034--3300074	20	2.0	20	85	4	55	36	17	7	39	1.77
3304442--3304475	16	2.1	16	89	10	52	44	0	0	55	0.99
3305403--3305448	20	2.4	19	81	3	56	54	2	10	32	1.47
3306901--3307128	43	5.3	43	87	3	298	32	21	23	23	1.98
3306901--3307172	85	3.2	84	87	4	332	31	21	22	24	1.98
3306901--3307172	42	6.3	43	84	5	320	31	21	22	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3306921--3307163	127	1.9	127	86	5	348	32	20	22	23	1.98
3307618--3307647	12	2.5	12	88	0	51	0	36	20	43	1.52
3313234--3313641	25	16.3	25	70	13	129	30	2	21	45	1.64
3313250--3313749	16	29.9	16	69	16	158	31	2	21	46	1.62
3313250--3313645	34	11.9	34	67	15	132	30	2	21	45	1.64
3313233--3313759	118	4.5	118	92	3	888	30	2	21	45	1.64
3313534--3313786	25	10.7	24	70	16	115	30	1	20	47	1.60
3313454--3313765	34	9.3	34	70	13	132	30	1	22	46	1.61
3319320--3319361	18	2.3	18	84	8	50	78	9	9	2	1.05
3319357--3319494	68	2.0	68	100	0	276	47	20	26	5	1.73
3319785--3319873	18	4.8	18	79	14	101	41	0	12	46	1.41
3319784--3319873	39	2.4	37	85	10	121	41	0	12	46	1.41
3319896--3319986	13	6.8	13	70	18	62	41	2	12	43	1.54
3319896--3319983	40	2.2	40	89	0	131	42	2	11	44	1.53
3320018--3320050	10	3.1	11	86	8	50	36	21	9	33	1.85
3323188--3323222	2	17.5	2	93	0	61	48	2	0	48	1.16
3323624--3323769	7	20.0	7	67	15	55	32	42	0	23	1.60
3323625--3323749	22	5.6	22	79	12	96	32	43	0	24	1.60
3323648--3323690	15	2.8	15	85	3	59	30	41	2	25	1.68
3323681--3323748	29	2.3	29	92	5	111	32	42	0	25	1.55
3323701--3323766	22	3.0	21	78	6	69	31	43	0	24	1.54
3325588--3325724	41	3.3	40	82	4	166	37	23	21	16	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3325716--3325808	40	2.4	39	82	8	109	16	29	24	30	1.96
3326062--3326104	22	1.9	23	90	4	70	39	2	0	58	1.11
3326062--3326109	22	2.2	22	85	7	62	39	4	0	56	1.19
3327415--3327587	10	18.0	9	67	23	61	60	1	0	37	1.07
3327487--3327533	18	2.6	18	93	0	85	68	0	0	31	0.90
3327467--3327514	9	4.9	11	78	21	54	68	0	0	31	0.90
3327539--3327588	9	5.3	9	76	9	55	54	2	0	44	1.11
3331509--3331914	108	3.8	108	83	3	469	41	22	24	12	1.87
3331509--3331914	162	2.5	162	83	4	514	41	22	24	12	1.87
3331691--3331890	27	7.4	27	64	17	94	42	22	24	11	1.86
3331518--3331914	54	7.4	54	85	4	410	41	21	24	12	1.87
3331932--3332030	51	1.9	51	87	4	146	46	20	20	13	1.83
3331983--3332177	63	3.1	63	92	0	318	43	28	14	13	1.83
3333843--3333903	31	2.0	31	83	6	79	22	19	19	37	1.94
3338154--3338180	2	13.5	2	100	0	54	51	0	0	48	1.00
3340127--3340180	23	2.4	23	93	3	92	35	0	11	53	1.36
3343976--3344009	5	6.8	5	86	0	50	32	0	0	67	0.91
3348176--3348220	13	3.6	13	85	8	58	40	4	15	40	1.67
3351150--3351176	11	2.5	11	100	0	54	40	7	0	51	1.30
3351134--3351273	41	3.6	39	82	8	169	35	2	0	62	1.07
3351134--3351284	40	3.7	39	82	10	178	35	1	0	62	1.07
3357163--3357209	23	2.1	22	88	11	69	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3365335--3365366	16	2.1	15	94	5	55	6	15	6	71	1.26
3365804--3365843	17	2.4	17	100	0	80	15	17	42	25	1.88
3373003--3373129	44	2.9	43	82	12	161	29	27	19	23	1.98
3376293--3376534	113	2.1	113	83	6	294	31	19	23	24	1.98
3377352--3377383	14	2.3	14	94	0	55	25	0	25	50	1.50
3377681--3377743	21	3.0	21	83	2	81	23	0	34	41	1.55
3377681--3377793	7	16.1	7	75	3	66	22	0	38	38	1.60
3378100--3378587	251	1.9	251	86	3	696	30	15	20	34	1.93
3380590--3380630	18	2.3	18	95	0	73	46	12	0	41	1.41
3380590--3380630	9	4.6	9	81	0	55	46	12	0	41	1.41

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