genome.fa.s6.2.7.7.80.10.50.1000.117.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  117  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)
34098828--34098861	17	2.0	17	100	0	68	58	0	0	41	0.98
34098785--34098980	54	3.4	54	70	17	135	54	3	1	40	1.24
34099023--34099086	32	2.0	32	81	0	74	50	1	0	48	1.10
34100426--34100529	49	2.1	49	87	0	145	50	9	8	30	1.65
34113233--34113295	33	1.9	33	93	0	108	1	33	17	47	1.57
34119440--34119491	21	2.5	20	71	3	50	44	1	1	51	1.23
34123075--34123106	7	4.6	7	96	0	55	40	9	31	18	1.83
34132057--34132137	30	2.7	30	84	7	103	56	1	1	40	1.15
34132058--34132231	40	4.4	38	81	12	165	60	1	1	36	1.15
34132057--34132148	11	8.9	11	71	21	65	56	1	1	41	1.13
34132134--34132195	30	2.1	30	93	3	108	67	0	1	30	1.00
34132145--34132206	29	2.1	30	88	5	92	67	1	3	27	1.15
34132112--34132208	30	3.2	30	81	10	92	63	1	3	31	1.16
34145704--34145750	21	2.2	21	85	7	60	31	2	4	61	1.27
34145709--34145752	21	2.0	22	91	4	72	34	2	2	61	1.21
34146532--34146602	23	2.9	24	82	14	67	26	2	4	66	1.24
34153257--34153288	9	3.6	9	91	0	55	12	0	25	62	1.30
34153397--34153839	127	3.5	125	87	4	617	29	17	23	29	1.97
34156218--34156255	20	1.9	20	84	10	51	55	7	2	34	1.43
34157242--34157296	11	4.9	11	75	20	60	41	1	30	25	1.66
34157242--34157296	22	2.5	22	83	16	69	41	1	30	25	1.66
34158655--34158688	2	17.0	2	93	0	59	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34166174--34166276	41	2.5	41	85	3	127	24	23	23	29	1.99
34171512--34171536	2	12.5	2	100	0	50	52	0	0	48	1.00
34175250--34175381	37	3.6	37	91	2	214	23	22	15	38	1.92
34184094--34184145	23	2.2	23	82	3	59	53	3	1	40	1.30
34185844--34185868	2	12.5	2	100	0	50	52	0	48	0	1.00
34186583--34186708	63	2.0	63	98	0	243	20	15	26	38	1.92
34186708--34186759	23	2.3	23	83	6	61	15	23	23	38	1.92
34187284--34187517	117	2.0	117	94	0	405	27	9	23	39	1.86
34188583--34188680	51	1.9	51	93	0	169	27	5	19	47	1.70
34193315--34193485	58	3.1	57	79	12	153	40	1	3	54	1.25
34193394--34193481	26	3.4	25	68	10	68	42	1	3	53	1.25
34193581--34193667	46	1.9	46	84	13	119	36	24	5	33	1.79
34193649--34193702	16	3.4	16	84	0	72	35	24	1	38	1.66
34193961--34194007	24	2.0	24	82	0	58	57	6	6	29	1.49
34200883--34200930	24	2.0	24	100	0	96	54	16	12	16	1.72
34210592--34210631	20	2.0	20	90	0	62	50	12	10	27	1.72
34210580--34210646	34	1.9	35	87	3	100	46	11	8	32	1.72
34212644--34212682	21	1.9	21	89	5	62	46	2	0	51	1.14
34212649--34212719	29	2.5	27	80	13	79	50	1	0	47	1.09
34212649--34212719	28	2.5	27	82	8	79	50	1	0	47	1.09
34213709--34213755	20	2.3	20	79	13	60	12	8	2	76	1.09
34213734--34213780	25	1.9	24	91	4	76	17	4	4	74	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34213773--34213818	13	3.4	14	80	20	53	19	0	4	76	0.96
34213777--34213812	17	2.1	17	90	10	56	19	0	2	77	0.88
34213773--34213825	9	5.9	9	81	16	65	22	0	3	73	0.99
34213902--34213944	18	2.4	18	76	0	50	48	2	0	48	1.14
34214317--34214356	18	2.2	18	77	0	53	52	0	7	40	1.30
34214339--34214387	16	3.1	16	78	0	53	57	0	4	38	1.18
34214306--34214362	20	3.0	20	79	10	73	52	0	5	42	1.24
34214361--34214410	7	7.1	7	77	8	57	66	0	2	32	1.03
34214361--34214411	13	3.7	13	82	10	57	66	0	1	31	1.03
34214364--34214418	20	2.7	20	78	13	67	65	0	1	32	1.03
34214515--34214629	57	2.0	58	98	1	223	29	0	8	61	1.26
34215076--34215245	71	2.3	76	82	8	206	50	3	4	41	1.40
34215102--34215253	71	2.1	71	91	1	241	50	3	3	42	1.37
34218130--34218206	29	2.6	29	73	17	70	53	1	0	45	1.08
34218190--34218214	13	1.9	13	100	0	50	56	0	0	44	0.99
34218252--34218308	25	2.3	25	84	6	71	59	1	0	38	1.08
34218190--34218378	57	3.3	57	69	22	167	55	4	3	36	1.37
34218390--34218442	21	2.6	21	85	11	74	52	0	0	47	1.00
34218387--34218442	20	2.8	21	84	13	73	50	0	0	50	1.00
34218410--34218507	30	3.1	31	82	7	117	57	1	1	40	1.12
34218836--34218895	19	3.0	21	77	18	65	58	0	0	41	0.98
34218842--34218891	19	2.7	19	84	9	68	62	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34218845--34218965	19	6.6	19	65	25	64	57	1	0	40	1.15
34218856--34218880	13	1.9	13	100	0	50	60	0	0	40	0.97
34218860--34219139	36	8.0	35	75	8	207	53	2	2	41	1.24
34218927--34218973	21	2.2	22	84	3	60	48	2	2	46	1.25
34218978--34219012	15	2.3	15	90	9	54	37	0	2	60	1.12
34219016--34219139	33	3.6	33	78	9	124	57	3	1	37	1.25
34218873--34219140	145	1.9	143	81	9	330	53	2	2	42	1.25
34219195--34219227	9	3.7	9	84	15	50	78	3	0	18	0.87
34219181--34219223	13	3.2	13	90	3	59	74	4	0	20	1.00
34219192--34219260	8	8.2	8	75	9	57	78	2	2	15	1.00
34222182--34222222	5	8.2	5	94	0	55	34	39	7	19	1.80
34247500--34247559	31	2.0	30	90	3	93	33	15	11	40	1.83
34249227--34249287	31	2.0	31	90	0	95	34	11	21	32	1.89
34251619--34251682	32	2.0	32	100	0	128	37	25	9	28	1.87
34256666--34256723	26	2.2	26	84	0	71	20	24	17	37	1.93
34263180--34263262	40	2.1	40	93	4	141	39	10	24	25	1.87
34267919--34267960	19	2.1	20	82	8	50	33	7	4	54	1.49
34270411--34270450	20	2.1	19	90	9	64	45	2	0	52	1.14
34271004--34271039	18	1.9	18	88	5	54	58	2	0	38	1.13
34271051--34271114	26	2.5	25	74	16	60	51	0	1	46	1.10
34271040--34271091	9	6.0	9	78	14	56	46	0	0	53	1.00
34271040--34271134	28	3.4	29	76	15	76	49	0	3	47	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34275674--34275750	29	2.6	30	77	10	86	22	40	16	20	1.91
34279071--34279200	45	3.0	41	67	12	98	33	22	11	33	1.90
34279025--34279200	88	2.0	89	90	1	282	35	21	10	32	1.88
34279141--34279329	100	1.9	99	84	3	254	26	17	16	39	1.91
34279139--34279401	100	2.6	99	76	9	223	26	17	17	38	1.92
34285818--34285888	36	1.9	37	82	5	90	42	4	11	42	1.60
34285937--34285969	13	2.6	13	90	4	50	54	0	0	45	0.99
34287785--34288033	50	4.8	50	83	4	282	20	28	23	27	1.99
34287784--34288033	100	2.4	104	86	5	337	20	28	23	27	1.99
34288371--34288428	30	1.9	30	89	0	89	31	24	3	41	1.71
34291714--34291755	2	21.0	2	100	0	84	50	0	0	50	1.00
34294755--34294782	6	4.7	6	100	0	56	14	17	14	53	1.73
34298018--34298880	432	2.0	434	92	0	1451	31	13	30	23	1.93
34306864--34306949	31	2.9	29	80	5	82	33	6	13	45	1.71
34306899--34306958	29	2.0	30	87	9	88	30	8	13	48	1.71
34307466--34307519	2	26.5	2	96	3	99	50	1	0	48	1.11
34311339--34311388	12	3.9	13	77	12	59	60	2	0	38	1.09
34314437--34314462	12	2.2	12	100	0	52	23	0	46	30	1.53
34318289--34318326	14	2.7	14	80	15	51	44	2	10	42	1.52
34325577--34325667	4	22.8	4	69	12	53	65	1	7	25	1.25
34325558--34325609	23	2.2	24	86	3	70	69	0	5	25	1.10
34327482--34327579	51	1.9	51	87	4	144	31	16	16	35	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34327601--34328167	44	12.5	44	71	8	231	28	20	17	34	1.95
34327396--34327998	95	6.4	95	76	7	462	29	20	17	33	1.95
34327688--34327861	51	3.5	51	75	10	191	28	19	18	33	1.95
34327739--34328213	45	10.4	45	72	7	253	29	21	15	33	1.94
34327836--34328173	89	3.8	89	81	5	326	30	19	15	34	1.93
34327625--34327998	185	2.0	186	81	3	437	27	21	17	33	1.96
34334888--34334970	23	3.7	22	71	9	62	65	2	8	24	1.33
34334940--34335038	4	24.8	4	70	11	51	66	1	8	24	1.25
34334934--34335020	15	5.3	15	69	23	52	66	1	8	24	1.25
34336567--34336593	7	3.9	7	100	0	54	40	0	0	59	0.98

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