genome.fa.s6.2.7.7.80.10.50.1000.39.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: Chr1
Parameters: 2 7 7 80 10 50 1000
Length:  35726063

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   

This is table  39  of  109  ( 13028 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)
12592350--12592391	16	2.6	16	82	14	59	57	0	7	35	1.26
12593282--12593327	24	2.0	24	83	12	60	45	2	10	41	1.51
12603664--12603760	49	2.0	49	85	0	131	44	8	17	29	1.78
12623203--12623240	3	12.7	3	100	0	76	65	0	34	0	0.93
12630346--12630751	215	1.9	215	86	4	586	33	15	13	37	1.86
12631668--12631736	11	6.3	11	79	12	79	43	0	36	20	1.52
12631658--12631744	33	2.7	32	81	10	88	43	1	33	21	1.60
12631672--12631744	22	3.3	22	79	11	69	43	0	32	23	1.54
12631667--12631744	11	7.3	10	75	16	52	43	0	33	23	1.54
12634742--12634793	24	2.2	24	92	0	86	48	9	5	36	1.60
12638016--12638065	25	2.0	25	100	0	100	36	20	24	20	1.95
12638999--12639050	24	2.2	24	89	0	77	50	9	3	36	1.54
12643322--12643433	44	2.5	44	78	5	120	37	16	25	19	1.93
12643322--12643436	22	5.2	22	74	8	83	37	16	26	20	1.93
12644999--12645023	13	1.9	13	100	0	50	32	4	24	40	1.73
12655214--12655309	9	9.9	9	71	15	50	59	3	4	33	1.32
12657320--12657382	20	3.2	20	75	8	67	52	0	1	46	1.10
12657597--12657642	21	2.2	21	81	14	51	39	4	0	56	1.19
12666730--12666886	52	3.0	52	94	0	269	25	10	28	35	1.89
12666889--12667291	125	3.2	125	92	3	645	30	15	22	31	1.95
12669271--12669321	9	5.6	9	75	13	50	64	0	0	35	0.94
12669271--12669320	18	2.7	19	79	11	59	66	0	0	34	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12669278--12669335	29	2.0	29	90	9	93	60	1	0	37	1.07
12669366--12669471	52	2.1	51	85	1	140	33	1	31	33	1.69
12669424--12669492	22	3.1	22	87	0	102	39	1	27	31	1.66
12670563--12670598	18	2.1	16	90	10	54	69	11	0	19	1.18
12679562--12679613	18	2.8	18	82	8	61	50	1	3	44	1.31
12679635--12679923	144	2.0	145	99	0	571	40	14	18	26	1.89
12681882--12682061	91	2.0	91	95	0	324	33	7	23	35	1.83
12687025--12687135	27	4.1	26	72	20	86	59	2	12	25	1.46
12687055--12687138	24	3.2	24	69	18	78	59	3	14	22	1.50
12687044--12687153	54	2.0	55	98	1	213	57	5	14	22	1.58
12687056--12687140	27	3.1	27	71	18	95	58	3	14	23	1.51
12687069--12687153	27	3.1	27	71	18	95	57	7	15	20	1.61
12688670--12689203	44	11.6	44	71	11	333	28	21	17	32	1.96
12688664--12689203	89	5.9	89	79	9	484	28	21	17	32	1.96
12688684--12689203	179	2.8	180	79	9	466	29	20	17	32	1.95
12702103--12702138	19	1.9	18	88	5	54	27	0	0	72	0.85
12704512--12704577	30	2.2	30	88	0	105	19	31	33	15	1.93
12705747--12705809	26	2.4	26	78	0	81	44	30	7	17	1.77
12710598--12710644	14	2.9	16	74	25	53	40	14	21	23	1.90
12714595--12714628	15	2.3	15	100	0	68	32	29	8	29	1.87
12715426--12715491	20	3.3	20	72	8	71	33	22	33	10	1.89
12715866--12715932	20	3.3	21	81	8	68	31	16	32	19	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12715885--12716083	40	5.0	40	78	1	175	34	18	28	19	1.95
12715886--12716083	80	2.5	80	85	4	240	33	18	28	19	1.95
12717046--12717103	29	1.9	31	82	6	75	37	8	13	39	1.76
12734668--12734740	4	18.0	4	87	7	103	21	0	27	50	1.49
12737121--12737151	16	1.9	16	93	0	53	48	6	6	38	1.55
12737254--12737322	20	3.4	20	78	9	77	39	2	0	57	1.13
12737290--12737335	20	2.3	20	85	7	58	45	0	0	54	0.99
12737325--12737360	19	1.9	19	94	5	65	38	0	5	55	1.23
12737331--12737400	19	3.6	20	79	11	74	40	0	7	52	1.29
12737479--12737508	9	3.3	9	90	0	51	30	10	13	46	1.75
12739002--12739026	3	8.3	3	100	0	50	32	0	0	68	0.90
12740603--12740631	5	5.8	5	100	0	58	82	0	0	17	0.66
12740979--12741029	27	1.9	26	88	4	75	17	0	7	74	1.05
12740996--12741029	17	2.0	17	88	0	50	14	0	5	79	0.91
12755255--12755305	27	1.9	26	88	4	75	17	0	7	74	1.05
12755272--12755305	17	2.0	17	88	0	50	14	0	5	79	0.91
12757194--12757301	9	12.5	8	75	17	60	62	1	0	34	1.12
12757199--12757236	7	5.3	7	96	3	67	57	0	0	42	0.98
12757259--12757312	18	3.1	18	79	15	58	66	0	3	29	1.09
12757599--12757633	17	2.0	17	94	5	61	31	0	0	68	0.90
12760946--12760989	23	1.9	23	90	0	70	61	4	2	31	1.28
12760950--12760993	11	3.9	11	80	16	54	63	2	2	31	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12762232--12762366	38	3.4	38	70	15	101	42	2	14	40	1.58
12770673--12770714	14	2.9	15	82	10	52	28	7	0	64	1.20
12780902--12780939	17	2.2	18	85	4	51	68	5	2	23	1.23
12797907--12797935	9	3.0	10	90	10	51	58	0	20	20	1.39
12798148--12798196	26	1.9	25	87	4	71	38	12	16	32	1.86
12799617--12799663	24	2.0	24	83	8	60	17	34	0	48	1.47
12811502--12812343	420	2.0	421	94	1	1476	22	15	18	43	1.88
12814932--12814973	10	3.8	11	80	20	52	54	7	0	38	1.28
12815670--12815725	8	6.9	8	79	16	53	0	14	1	83	0.72
12815674--12815717	4	11.8	4	85	9	58	0	18	2	79	0.83
12815669--12815726	10	5.5	11	82	13	61	0	13	1	84	0.70
12825140--12825211	3	24.0	3	71	13	51	63	1	5	29	1.25
12825160--12825211	15	3.5	16	72	17	58	67	0	3	28	1.08
12825320--12825373	23	2.3	24	81	12	67	68	5	0	25	1.11
12826363--12826396	8	4.1	8	85	7	50	38	0	2	58	1.13
12834960--12834985	12	2.2	12	100	0	52	53	15	7	23	1.67
12837867--12837925	25	2.3	27	79	8	68	66	6	10	16	1.43
12838791--12838869	6	13.2	6	100	0	158	32	0	16	50	1.45
12848793--12848867	19	3.8	19	87	6	105	36	20	10	33	1.87
12849284--12849582	89	3.4	88	87	4	406	30	25	14	29	1.94
12849210--12849581	131	2.8	132	86	3	489	30	25	13	30	1.94
12849212--12849582	44	8.4	44	79	3	388	30	25	14	30	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12849594--12850082	44	11.1	44	67	7	186	24	26	23	25	2.00
12849543--12850397	88	9.7	88	88	0	1154	24	26	23	25	2.00
12849343--12850352	176	5.7	175	82	3	625	26	26	21	26	1.99
12849548--12850371	354	2.3	352	88	0	1216	24	26	23	25	2.00
12856961--12857012	21	2.6	21	93	6	90	38	13	11	36	1.81
12858135--12858169	18	1.9	18	88	0	52	85	5	2	5	0.81
12859221--12859370	9	15.3	9	67	20	54	60	3	3	33	1.30
12859260--12859370	21	5.7	18	68	20	55	59	4	1	34	1.28
12859340--12859398	25	2.6	23	87	12	79	61	1	0	37	1.07
12859325--12859401	12	6.7	12	68	19	56	59	2	0	37	1.11
12868671--12868905	128	1.8	127	85	2	328	22	29	15	32	1.95
12872101--12872148	24	2.0	24	95	0	87	39	25	10	25	1.87
12874018--12874050	17	2.0	17	88	5	50	45	0	9	45	1.35
12893918--12893959	20	2.1	20	100	0	84	50	23	4	21	1.68
12897355--12897693	168	2.0	168	97	0	633	38	8	20	32	1.82
12903777--12903837	14	4.5	14	78	10	56	72	0	24	3	1.00
12915841--12915905	17	3.7	17	76	13	69	21	4	4	69	1.25
12923337--12923378	22	1.9	22	85	9	59	52	2	2	42	1.27
12930842--12931025	99	1.9	98	94	1	323	34	14	11	39	1.82
12936182--12936252	30	2.3	31	78	2	81	35	21	1	42	1.62
12937265--12937316	23	2.3	23	86	6	70	42	21	7	28	1.80
12940472--12940606	64	2.1	64	90	1	209	39	8	5	46	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12943711--12943810	51	2.0	50	86	7	139	45	3	26	26	1.68
12943770--12943846	11	6.9	11	77	21	72	46	1	27	24	1.60
12943770--12943845	34	2.3	34	81	9	93	46	1	27	25	1.61
12958968--12959009	22	2.0	22	86	9	61	35	9	2	52	1.47
12959287--12959385	52	1.9	51	83	2	126	39	10	1	49	1.43
12971349--12971386	16	2.4	16	95	0	67	21	5	26	47	1.71
12972916--12972979	32	2.0	32	100	0	128	34	21	15	28	1.94
12980583--12981041	226	2.0	227	99	0	904	44	3	15	36	1.64
12982121--12982150	15	2.0	15	93	0	51	56	0	0	43	0.99
12983142--12983183	21	2.0	22	85	4	59	35	2	2	59	1.23

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