genome.fa.s6.2.7.7.80.10.50.1000.11.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  11  of  168  ( 20060 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)
3086354--3086425	19	3.8	19	94	1	128	36	16	9	37	1.82
3087047--3087415	100	3.8	94	86	5	440	27	22	20	29	1.99
3087272--3087415	50	2.9	50	67	4	119	27	22	18	31	1.97
3087359--3087751	167	2.3	170	82	6	446	27	26	18	27	1.98
3087748--3087958	44	5.0	44	84	11	271	30	25	18	26	1.98
3087804--3087870	34	2.0	34	96	0	125	26	23	23	25	2.00
3087760--3087909	78	1.9	78	91	0	246	30	25	19	25	1.98
3089326--3089376	6	8.3	6	76	10	50	3	15	0	80	0.86
3089318--3089378	24	2.6	23	81	5	68	3	19	0	77	0.91
3094010--3094115	43	2.3	47	79	9	114	65	8	8	17	1.45
3094714--3094824	19	5.8	19	92	0	177	36	18	8	36	1.80
3094707--3094824	38	3.2	38	93	2	204	36	18	7	37	1.80
3095815--3096027	69	3.1	69	86	0	300	25	18	23	32	1.97
3098427--3098461	15	2.3	15	90	5	52	57	5	2	34	1.37
3102750--3102843	41	2.3	40	81	1	98	35	5	10	48	1.60
3105119--3105332	43	5.0	42	75	8	148	39	21	19	20	1.93
3112481--3112526	24	2.0	22	83	8	56	50	0	8	41	1.33
3118069--3118144	23	3.3	23	94	0	134	32	26	19	21	1.97
3122453--3122792	170	2.0	171	95	0	610	26	17	26	29	1.97
3128721--3128803	42	2.0	42	83	4	105	50	2	21	25	1.61
3134277--3134334	25	2.3	25	87	0	80	20	22	22	34	1.97
3134297--3134372	25	3.0	25	77	11	75	23	18	26	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3150543--3150767	37	6.3	36	76	9	174	24	22	30	21	1.99
3150623--3150767	71	2.0	71	84	5	186	23	24	31	21	1.99
3154205--3154261	21	2.7	21	80	0	69	17	19	14	49	1.80
3154243--3154342	40	2.5	39	76	6	112	18	19	21	42	1.90
3171237--3171267	2	15.5	2	93	0	53	48	0	51	0	1.00
3173902--3174450	284	1.9	285	94	1	976	41	19	9	30	1.82
3175177--3175232	28	2.0	28	89	3	85	66	0	3	30	1.09
3175459--3175489	16	1.9	16	93	0	53	22	6	3	67	1.28
3175493--3175596	18	6.0	16	79	17	70	38	3	0	57	1.17
3175528--3175596	35	2.0	33	76	20	63	36	2	0	60	1.11
3175511--3175597	18	4.8	18	81	14	108	36	3	0	59	1.14
3175651--3175864	108	2.0	109	85	4	297	28	8	22	40	1.83
3175743--3175787	22	2.0	22	100	0	90	15	8	26	48	1.74
3175967--3176009	18	2.4	19	80	11	54	20	2	2	74	1.04
3176348--3176393	19	2.3	20	85	3	58	60	6	4	28	1.40
3176427--3176466	21	1.9	21	85	10	55	57	2	2	37	1.26
3176525--3176590	31	2.2	29	84	10	87	62	0	0	37	0.96
3176542--3176600	21	2.8	21	69	5	57	61	1	0	37	1.07
3176364--3176590	10	23.4	10	68	15	61	59	3	1	36	1.23
3176525--3176600	32	2.4	31	84	8	91	60	1	0	38	1.05
3180830--3180903	31	2.4	31	88	0	112	20	2	41	35	1.66
3187155--3187198	14	3.1	14	86	3	61	0	22	0	77	0.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3187150--3187198	10	5.0	10	78	12	57	0	20	0	79	0.73
3187833--3187891	27	2.1	28	84	9	77	27	3	5	64	1.30
3193722--3193751	13	2.3	13	100	0	60	73	0	13	13	1.10
3193721--3193760	7	5.7	7	88	11	64	75	0	12	12	1.06
3197218--3197261	18	2.4	18	80	0	61	15	27	0	56	1.40
3197218--3197262	12	3.8	12	78	0	54	15	26	0	57	1.38
3200894--3200945	23	2.2	22	83	12	68	36	1	0	61	1.07
3204391--3204453	29	2.2	29	97	0	117	49	6	3	41	1.44
3204409--3204484	23	3.4	23	70	15	79	50	5	2	42	1.39
3204418--3204501	42	2.1	41	80	10	95	51	7	2	39	1.42
3206572--3206652	22	3.7	22	91	0	117	27	28	14	29	1.95
3206589--3206660	22	3.2	22	90	2	108	26	25	16	31	1.96
3207567--3207650	42	2.0	42	88	4	125	50	5	3	40	1.44
3208992--3209056	21	3.2	20	78	12	71	66	3	0	30	1.07
3208992--3209056	18	3.3	19	80	10	69	66	3	0	30	1.07
3209882--3209951	35	2.0	35	97	0	131	30	24	0	45	1.53
3216794--3216833	20	2.1	19	90	4	62	22	27	0	50	1.50
3218081--3218145	3	21.7	3	93	0	112	30	0	3	66	1.07
3220512--3220564	21	2.6	20	85	8	63	67	7	9	15	1.39
3221298--3221337	3	13.3	3	89	0	62	32	5	0	62	1.17
3221336--3221415	25	3.0	27	71	17	76	35	3	1	60	1.23
3222693--3222774	30	2.7	30	80	0	92	25	14	20	39	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3236916--3236990	20	3.8	20	69	22	59	41	2	10	45	1.53
3247958--3248027	29	2.4	30	83	9	92	17	1	27	54	1.51
3248313--3248368	21	2.8	19	87	10	85	39	10	14	35	1.81
3248313--3248391	19	3.7	22	78	14	69	37	8	15	37	1.78
3248566--3248629	23	3.0	21	74	14	60	20	3	15	60	1.48
3249317--3249358	3	14.0	3	100	0	84	33	0	0	66	0.92
3253750--3253782	17	1.9	17	93	0	57	33	27	18	21	1.96
3253751--3253789	17	2.3	17	86	0	51	38	30	12	17	1.88
3265785--3265911	37	3.6	37	78	11	106	44	1	4	48	1.33
3266005--3266097	45	2.1	44	90	6	143	35	25	5	33	1.79
3266079--3266133	16	3.4	16	92	0	92	29	25	7	38	1.83
3266537--3266598	31	2.0	32	90	3	99	43	12	6	37	1.69
3268868--3268913	16	2.9	16	93	0	74	28	23	6	41	1.79
3281627--3281652	3	8.7	3	100	0	52	69	0	0	30	0.89
3281777--3281890	42	2.7	42	88	0	165	28	13	30	27	1.94
3282822--3282847	11	2.4	11	100	0	52	38	34	0	26	1.57
3283399--3283453	9	6.1	9	86	0	83	41	23	10	23	1.86
3283493--3283521	6	4.8	6	100	0	58	17	0	17	65	1.27
3283477--3283534	18	3.0	20	82	12	66	22	3	12	62	1.45
3283918--3284112	41	4.5	43	73	8	139	26	19	24	29	1.98
3283918--3284189	131	2.1	131	92	0	445	28	20	23	27	1.99
3284001--3284390	44	8.9	44	72	8	260	30	19	23	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3284136--3284428	130	2.2	130	80	6	324	30	19	23	26	1.98
3283831--3284430	174	3.4	174	80	5	608	29	19	23	27	1.98
3284820--3284847	10	2.8	10	100	0	56	75	14	0	10	1.06
3286060--3286097	19	2.0	20	84	5	51	26	2	5	65	1.27
3286102--3286127	2	13.0	2	100	0	52	50	0	0	50	1.00
3287618--3287652	17	2.1	17	89	5	54	14	5	0	80	0.89
3287621--3287662	17	2.4	18	80	15	52	14	2	0	83	0.75
3294148--3294257	56	2.0	56	88	0	166	20	12	14	52	1.73
3297006--3297039	16	2.1	17	94	5	61	23	0	23	52	1.47
3300708--3301018	126	2.5	124	81	6	344	38	23	12	25	1.90
3301674--3301704	6	5.2	6	100	0	62	16	51	0	32	1.44
3303822--3303855	11	3.0	12	83	16	54	32	0	0	67	0.91
3310305--3310391	27	3.2	27	64	20	72	37	12	11	37	1.80
3312643--3312718	24	3.2	24	85	10	102	25	14	17	43	1.86
3314693--3314788	39	2.4	39	86	5	131	48	28	2	20	1.61
3314862--3314920	9	6.4	9	81	11	75	22	10	27	40	1.85
3317033--3317062	11	2.6	12	89	10	53	6	26	6	60	1.47
3317042--3317075	15	2.4	14	90	5	50	5	20	5	67	1.33
3318208--3318300	9	10.3	9	88	0	132	31	9	24	34	1.88
3318208--3318300	27	3.4	27	92	0	159	31	9	24	34	1.88
3320219--3320244	13	2.0	13	100	0	52	38	15	7	38	1.76
3343592--3343636	21	2.1	21	88	8	65	68	0	0	31	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3349331--3349440	21	5.3	21	86	7	138	43	17	22	16	1.87
3352507--3352531	2	12.5	2	100	0	50	52	0	0	48	1.00
3356356--3356381	3	8.7	3	100	0	52	34	34	30	0	1.58
3360011--3360161	77	2.0	77	93	0	257	37	16	19	27	1.93
3365447--3365559	58	1.9	58	85	3	156	35	7	30	26	1.85
3370271--3370311	18	2.2	20	84	16	54	58	0	12	29	1.34
3373443--3373485	3	14.3	3	95	0	77	32	0	34	32	1.58
3378817--3378857	22	2.0	22	90	9	68	51	0	0	48	1.00
3378820--3378865	20	2.3	20	80	0	56	43	2	0	54	1.12
3381112--3381156	18	2.5	18	85	7	56	66	11	20	2	1.33

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