genome.fa.s6.2.7.7.80.10.50.1000.12.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  12  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)
3384750--3384774	13	1.9	13	100	0	50	64	0	4	32	1.12
3389351--3389704	97	3.5	100	77	11	283	31	17	21	29	1.96
3394425--3394449	3	8.3	3	100	0	50	68	0	0	32	0.90
3395774--3395799	13	2.0	13	100	0	52	38	15	7	38	1.76
3396134--3396167	13	2.5	14	85	9	52	58	17	8	14	1.61
3407236--3407301	29	2.2	30	81	2	80	42	15	6	36	1.71
3408358--3408398	20	2.0	20	85	0	55	51	0	0	48	1.00
3413894--3413942	25	2.0	25	83	0	62	18	2	2	77	0.96
3415020--3415044	10	2.5	10	100	0	50	0	0	12	88	0.53
3416041--3416108	16	4.2	16	98	0	127	26	0	35	38	1.57
3416344--3416378	18	2.0	17	88	5	52	54	0	0	45	0.99
3416238--3416548	160	2.0	160	94	1	547	44	3	4	47	1.40
3416484--3416659	59	3.0	57	67	14	158	51	5	0	43	1.28
3421394--3421488	47	2.0	47	93	0	163	28	14	24	32	1.95
3423074--3423178	34	3.1	32	82	10	102	36	32	15	16	1.90
3434443--3434475	15	2.2	15	100	0	66	39	12	6	42	1.67
3436814--3436861	18	2.7	18	80	6	53	58	4	4	33	1.36
3440624--3440682	2	27.5	2	86	13	82	47	6	0	45	1.29
3441567--3441619	22	2.4	21	75	9	52	37	11	1	49	1.50
3443911--3443952	22	1.9	22	90	9	68	59	2	9	28	1.41
3444775--3444817	22	2.0	22	95	0	77	48	11	25	13	1.77
3445486--3445888	44	9.0	44	71	9	190	28	18	21	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3445506--3446029	45	11.6	46	71	10	222	29	20	20	30	1.97
3445593--3445889	133	2.2	133	92	0	477	28	18	21	30	1.97
3445802--3445984	96	1.9	96	81	2	224	29	22	19	28	1.98
3445919--3446028	44	2.5	45	80	1	123	32	23	19	24	1.97
3452437--3452547	53	2.1	53	87	0	159	17	35	20	27	1.95
3453202--3453232	9	3.4	9	90	0	53	25	12	22	38	1.90
3453285--3453321	9	4.1	9	92	0	65	45	13	10	29	1.77
3454307--3454412	52	2.0	52	100	0	212	33	22	13	31	1.92
3454605--3454682	29	2.6	31	74	10	81	25	23	10	41	1.86
3454603--3454812	30	7.0	30	73	11	153	24	24	13	37	1.92
3457091--3457138	25	1.9	25	83	8	62	43	10	6	39	1.64
3463660--3463687	14	2.0	14	100	0	56	57	7	14	21	1.61
3464396--3464461	25	2.7	25	81	6	82	40	7	0	51	1.30
3464399--3464464	24	2.8	23	81	9	71	43	7	0	48	1.31
3464455--3464531	23	3.3	23	66	12	59	33	9	1	55	1.39
3464906--3464961	3	18.7	3	100	0	112	33	0	0	66	0.92
3475210--3475581	27	13.8	26	76	9	203	37	18	19	24	1.94
3475210--3475580	81	4.6	81	83	1	395	37	18	19	23	1.94
3475209--3475581	54	6.9	53	81	5	340	37	18	19	24	1.94
3475787--3475839	26	2.1	25	89	3	79	18	22	24	33	1.97
3475795--3475846	26	2.0	26	88	0	77	13	26	28	30	1.94
3475843--3476045	32	6.3	32	88	0	280	23	19	17	39	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3476042--3476098	22	2.6	21	77	5	60	17	19	19	43	1.88
3480435--3480491	25	2.2	25	84	6	69	38	8	7	45	1.62
3480450--3480505	25	2.2	25	77	3	58	42	8	5	42	1.59
3480705--3480750	23	2.0	24	86	4	67	52	19	8	19	1.72
3481025--3481088	26	2.4	27	84	7	78	56	0	0	43	0.99
3486762--3486805	6	7.2	6	81	2	52	0	56	0	43	0.99
3486762--3486805	18	2.4	18	92	3	70	0	56	0	43	0.99
3486848--3486897	25	2.0	25	92	0	82	4	32	4	60	1.34
3487085--3487110	11	2.4	11	100	0	52	23	0	15	61	1.33
3489754--3489820	33	2.0	33	97	0	125	55	8	10	25	1.63
3489912--3489950	20	2.0	20	89	0	60	46	2	2	48	1.29
3489971--3490057	33	2.7	32	77	12	95	47	17	9	26	1.77
3490033--3490109	14	5.0	15	71	20	52	42	15	9	32	1.78
3490049--3490088	20	2.0	20	90	0	62	50	12	10	27	1.72
3490037--3490103	34	1.9	35	90	3	109	46	13	8	31	1.74
3490072--3490111	14	2.9	14	84	0	53	42	17	7	32	1.77
3496581--3496625	18	2.5	18	88	0	72	15	48	6	28	1.70
3497400--3497434	3	11.7	3	100	0	70	68	31	0	0	0.90
3497498--3497530	10	3.4	10	91	8	59	66	9	0	24	1.20
3497535--3497575	11	3.8	11	90	6	66	0	29	0	70	0.87
3497658--3497722	27	2.4	27	92	5	105	15	29	29	26	1.96
3497658--3497731	27	2.7	27	87	0	103	14	31	28	25	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3497786--3497829	22	2.0	22	90	0	70	59	0	4	36	1.18
3499403--3499488	42	2.0	43	84	2	111	38	1	8	52	1.39
3500078--3500110	14	2.4	14	94	0	57	42	24	6	27	1.78
3501048--3501107	21	2.9	22	72	20	58	43	0	6	50	1.28
3503958--3504152	96	2.0	96	83	3	241	31	22	22	24	1.98
3505143--3505227	42	2.0	42	88	4	127	38	11	1	48	1.48
3505372--3505434	32	2.0	32	87	0	90	34	11	1	52	1.47
3505795--3505845	14	3.6	14	75	15	52	41	19	5	33	1.76
3505846--3505888	21	2.0	21	95	0	77	34	51	0	13	1.42
3505841--3505977	7	20.0	7	72	6	66	36	42	2	18	1.63
3523713--3523742	12	2.6	12	94	5	53	76	10	0	13	1.01
3524399--3524429	15	2.1	15	93	0	53	19	19	29	32	1.96
3524822--3524934	44	2.6	44	87	2	156	32	19	19	28	1.96
3524939--3525527	88	6.7	88	87	3	718	30	25	12	32	1.92
3524939--3525766	44	18.9	44	75	7	612	31	25	12	30	1.93
3525326--3525766	126	3.4	126	86	6	548	31	25	14	29	1.94
3526683--3526732	26	1.9	26	88	8	75	62	8	14	16	1.54
3538919--3538949	15	2.1	15	93	0	53	19	19	29	32	1.96
3544348--3544410	31	2.0	31	100	0	126	46	9	19	25	1.80
3548354--3548423	20	3.5	20	71	11	61	18	2	37	41	1.66
3548351--3548437	41	2.2	39	79	8	93	20	2	35	41	1.65
3548498--3548523	7	3.7	7	100	0	52	38	0	15	46	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3548491--3548524	14	2.4	14	85	0	50	32	0	23	44	1.54
3548519--3548565	14	3.4	14	75	13	53	19	6	29	44	1.75
3548519--3548576	27	2.1	28	87	3	82	17	6	31	44	1.75
3548594--3548674	7	11.1	7	78	16	51	17	0	29	53	1.44
3548634--3548671	7	5.3	7	87	6	58	15	0	28	55	1.41
3548748--3548807	28	2.1	28	81	0	66	20	1	23	55	1.53
3548892--3548991	28	3.6	27	75	14	87	18	4	27	51	1.64
3548895--3548954	21	2.9	21	78	11	61	18	1	23	56	1.50
3548880--3548988	56	1.9	56	81	7	132	16	3	27	52	1.61
3548832--3549233	188	2.1	187	91	3	621	17	3	28	50	1.62
3549083--3549179	28	3.5	27	75	12	88	18	4	23	53	1.62
3549083--3549142	21	2.9	21	78	11	61	20	1	21	56	1.51
3550039--3550097	29	2.0	29	83	0	73	33	8	10	47	1.68
3550429--3550471	19	2.1	22	84	16	58	69	4	0	25	1.07
3556071--3556110	2	20.5	2	87	5	55	45	5	0	50	1.23
3556587--3556643	27	2.1	28	93	3	98	43	7	0	49	1.29
3556805--3556877	18	4.2	18	69	25	59	64	0	35	0	0.94
3556812--3556877	14	5.2	13	68	17	50	65	0	34	0	0.93
3556791--3556855	32	2.0	32	84	0	85	56	0	43	0	0.99
3556815--3556919	10	10.7	10	71	16	60	63	0	35	0	1.01
3556810--3556880	28	2.5	28	75	6	72	64	0	35	0	0.94
3556813--3556921	38	2.9	38	90	2	168	64	0	34	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3557663--3557701	19	2.1	19	90	0	60	23	0	5	71	1.05
3557736--3557805	27	2.7	26	86	8	106	44	10	0	45	1.37
3557804--3557840	14	2.5	15	91	8	58	86	5	2	5	0.78
3560518--3560554	17	2.2	17	100	0	74	29	16	8	45	1.76
3561130--3561181	25	2.1	25	100	0	104	23	21	23	32	1.98
3561546--3561574	14	2.1	14	100	0	58	37	6	0	55	1.27
3565305--3565361	27	2.1	27	93	0	96	24	21	24	29	1.99
3569623--3569657	6	5.8	6	100	0	70	17	31	0	51	1.45
3572580--3572629	18	2.7	18	75	3	55	40	10	14	36	1.79
3578719--3578772	27	2.0	27	100	0	108	33	11	18	37	1.86

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