genome.fa.s12.2.7.7.80.10.50.1000.4.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  4  of  120  ( 14336 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)
1201021--1201146	59	2.1	60	84	5	159	37	18	4	39	1.72
1201779--1201820	20	2.1	20	91	8	68	33	2	2	61	1.21
1202309--1202361	27	2.0	27	96	0	97	26	20	18	33	1.96
1205766--1205797	2	17.0	2	87	12	50	46	0	0	53	1.00
1205866--1205937	5	14.8	5	83	11	87	38	0	4	56	1.18
1207307--1207345	18	2.3	18	86	8	55	64	7	2	25	1.33
1207296--1207345	16	3.0	16	82	5	55	68	6	2	24	1.23
1209230--1209279	21	2.4	21	82	0	64	64	0	6	30	1.18
1211962--1212003	22	1.9	23	85	9	61	52	9	0	38	1.34
1211995--1212032	19	2.1	18	85	9	51	31	0	0	68	0.90
1212040--1212083	23	1.9	23	81	9	54	54	0	20	25	1.45
1212990--1213020	11	2.8	11	95	0	53	64	25	3	6	1.33
1213539--1213662	18	6.9	18	70	24	84	62	0	2	33	1.14
1213539--1213662	9	14.0	8	72	20	54	62	0	2	33	1.14
1213706--1213759	10	5.4	10	76	8	56	68	1	1	27	1.10
1213704--1213759	29	1.9	30	85	10	80	67	1	1	28	1.10
1214228--1214274	20	2.3	21	88	3	78	38	2	4	55	1.31
1214365--1214428	19	3.3	19	84	6	76	31	3	3	62	1.26
1219408--1219442	18	1.9	18	88	0	52	65	2	2	28	1.21
1227118--1227171	25	2.2	25	83	6	65	11	14	16	57	1.65
1246156--1246193	20	1.9	20	84	10	51	57	0	2	39	1.12
1248846--1248879	17	2.0	18	88	11	54	41	11	0	47	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1250817--1250957	73	1.9	73	82	5	178	20	22	22	34	1.97
1250807--1250968	73	2.2	73	76	5	166	19	21	22	36	1.95
1256284--1256318	18	2.0	17	88	5	52	54	0	0	45	0.99
1256171--1256475	155	2.0	157	95	1	551	43	3	5	47	1.42
1256419--1256460	15	2.7	16	82	14	52	52	2	0	45	1.13
1256428--1256469	15	2.9	15	82	10	52	52	0	0	47	1.00
1256447--1256563	29	4.0	29	63	18	71	52	2	3	41	1.31
1256603--1256650	26	1.9	25	84	16	64	52	2	0	45	1.12
1256578--1256786	92	2.3	91	85	6	262	46	3	3	45	1.39
1262786--1262810	9	2.8	9	100	0	50	88	0	0	12	0.53
1262954--1262979	5	5.2	5	100	0	52	80	0	19	0	0.71
1264276--1264364	47	1.9	46	82	8	110	39	1	10	49	1.44
1264779--1264829	17	2.9	17	80	5	66	60	0	0	39	0.97
1264783--1264856	18	4.0	18	73	14	62	58	0	1	40	1.07
1266635--1266686	3	17.3	3	100	0	104	34	0	0	65	0.93
1272683--1272730	22	2.1	23	84	3	62	50	0	6	43	1.27
1278564--1278600	7	5.3	7	100	0	74	29	13	29	27	1.94
1287868--1287902	16	2.1	18	89	10	56	45	2	5	45	1.41
1304729--1304779	20	2.5	19	81	12	57	27	3	3	64	1.28
1304766--1304864	27	3.5	29	77	13	73	30	2	7	60	1.34
1325360--1325411	22	2.3	23	83	6	61	63	1	0	34	1.06
1327997--1328037	12	3.6	12	77	12	50	39	7	0	53	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1328227--1328272	9	5.2	8	82	17	56	78	0	4	17	0.91
1328227--1328262	17	2.1	18	90	10	58	80	0	2	16	0.83
1356283--1356317	15	2.4	15	90	4	54	48	0	8	42	1.33
1361346--1361395	15	3.3	15	74	20	50	44	4	2	50	1.32
1373319--1373398	30	2.7	30	98	0	151	37	23	8	30	1.85
1378422--1378484	32	2.0	32	90	0	99	28	17	15	38	1.91
1391856--1391934	40	2.0	40	87	0	113	43	18	13	24	1.87
1392780--1392816	15	2.3	17	86	9	51	64	2	10	21	1.37
1392780--1392817	16	2.5	15	87	8	51	63	2	13	21	1.42
1394860--1395004	35	4.1	35	81	3	166	27	15	15	42	1.86
1409094--1409137	22	2.0	22	87	12	65	68	2	0	29	1.02
1417937--1418058	45	2.7	45	74	2	120	40	15	22	21	1.90
1418516--1418572	12	4.5	12	79	20	55	47	5	0	47	1.24
1422526--1422587	32	1.9	32	100	0	124	32	20	6	40	1.78
1428200--1428260	32	1.9	32	96	0	113	26	21	9	42	1.84
1428144--1428334	89	2.1	89	82	5	226	25	16	11	46	1.80
1428484--1428547	26	2.4	27	79	10	69	37	3	3	56	1.31
1431743--1431841	23	4.3	23	89	3	146	28	27	21	23	1.99
1434215--1434254	9	4.4	9	83	0	53	52	12	2	32	1.52
1440686--1440719	16	2.0	18	88	11	54	58	2	5	32	1.37
1440776--1440834	25	2.2	28	82	11	70	64	6	6	22	1.42
1440773--1440834	22	2.4	25	78	21	67	66	6	6	20	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1450034--1450110	37	2.1	37	92	0	127	29	12	12	44	1.81
1457305--1457366	30	2.1	30	100	0	124	25	20	22	30	1.98
1457335--1457464	66	2.0	67	96	0	228	26	22	26	24	2.00
1457239--1457432	96	2.0	96	97	0	370	26	21	25	26	2.00
1471261--1471374	4	28.5	4	100	0	228	50	24	0	25	1.50
1472441--1472479	18	2.2	18	85	0	51	64	0	10	25	1.25
1472581--1472703	12	9.8	12	69	11	68	52	8	13	26	1.68
1472586--1472703	25	4.7	24	76	12	103	53	8	12	25	1.67
1472698--1472735	18	2.1	18	85	9	51	60	7	15	15	1.57
1474225--1474291	17	3.9	17	100	0	134	23	28	5	41	1.78
1477526--1477558	17	1.9	17	93	0	57	27	24	6	42	1.78
1478388--1478431	3	14.7	3	100	0	88	34	0	0	65	0.93
1478853--1478879	10	2.7	10	100	0	54	18	0	0	81	0.69
1482405--1482436	2	16.0	2	100	0	64	50	0	0	50	1.00
1482760--1482800	2	20.5	2	100	0	82	51	0	0	48	1.00
1490014--1490129	5	22.6	5	89	5	178	39	0	0	60	0.97
1491051--1491137	39	2.2	39	83	4	104	34	5	20	39	1.77
1491339--1491483	45	3.2	44	92	3	220	21	19	18	40	1.91
1502755--1502809	27	2.0	27	96	0	101	40	12	7	40	1.71
1503391--1503468	41	1.9	41	92	2	131	29	21	15	33	1.94
1507708--1507743	6	5.8	6	96	3	63	0	47	16	36	1.47
1510938--1510979	18	2.3	18	87	0	57	47	7	16	28	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1511713--1511766	21	2.5	21	81	6	54	57	12	9	20	1.63
1520546--1520801	127	2.0	128	90	2	408	40	12	10	36	1.78
1521344--1521383	14	2.9	14	88	0	53	37	30	7	25	1.83
1525587--1525623	18	2.1	18	89	0	56	27	29	8	35	1.85
1526874--1526901	12	2.3	12	100	0	56	28	7	14	50	1.69
1532211--1532262	23	2.3	23	75	15	54	69	1	3	25	1.16
1532954--1533008	22	2.7	21	78	15	62	32	1	1	63	1.15
1533000--1533036	18	2.1	18	89	0	56	48	0	0	51	1.00
1533012--1533050	19	2.1	19	85	4	53	41	0	2	56	1.13
1536539--1536576	13	2.9	13	96	0	67	15	26	21	36	1.93
1536638--1536822	43	4.3	43	82	5	207	27	31	18	23	1.97
1541478--1541525	7	6.9	7	90	0	69	37	58	0	4	1.18
1541470--1541542	7	10.4	7	83	0	65	36	50	0	12	1.40
1542150--1542286	40	3.4	39	78	7	114	19	19	22	37	1.94
1542646--1542676	2	15.5	2	100	0	62	48	0	0	51	1.00
1550626--1550668	21	2.0	21	82	8	52	34	2	6	55	1.39
1550980--1551033	16	3.4	16	87	5	74	29	27	3	38	1.74
1552357--1552436	30	2.6	32	77	13	89	36	15	12	36	1.85
1555716--1555792	14	5.0	15	71	20	52	42	14	9	33	1.77
1555732--1555771	20	2.0	20	90	0	62	50	12	10	27	1.72
1555720--1555786	34	1.9	35	90	3	109	46	13	8	31	1.74
1556184--1556222	20	2.0	20	94	0	69	61	0	5	33	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1559351--1559391	21	2.0	21	90	0	64	34	2	0	63	1.08
1559997--1560054	26	2.2	26	81	6	64	32	1	0	65	1.03
1561990--1562021	10	3.4	10	83	16	50	71	0	0	28	0.86
1562164--1562215	23	2.4	21	83	6	59	38	5	3	51	1.44
1562178--1562234	21	2.7	21	81	10	55	36	3	5	54	1.40
1562242--1562385	9	15.6	9	65	19	57	32	2	3	61	1.27
1562295--1562334	17	2.3	18	86	4	55	27	0	0	72	0.85
1562306--1562365	19	3.2	18	83	9	59	30	1	3	65	1.19
1562327--1562385	19	3.0	19	82	12	66	30	5	3	61	1.34
1564581--1564663	34	2.4	34	80	4	87	55	1	7	36	1.35

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