genome.fa.s3.2.7.7.80.10.50.1000.3.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  3  of  150  ( 17918 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)
693632--693931	153	2.0	151	88	3	442	31	16	16	35	1.91
693792--693977	101	1.8	103	89	2	295	29	13	16	40	1.87
699201--699257	30	1.9	30	85	7	80	45	3	12	38	1.59
706072--706106	4	8.8	4	100	0	70	22	0	0	77	0.78
709012--709036	9	2.8	9	100	0	50	72	0	0	28	0.86
709914--709983	9	7.2	9	75	13	50	42	0	2	54	1.15
709940--709976	19	2.0	19	89	5	58	43	0	2	54	1.14
715764--715789	13	2.0	13	100	0	52	61	15	0	23	1.33
717831--717941	27	4.1	27	82	0	132	36	21	27	14	1.92
717831--717941	54	2.1	54	89	0	168	36	21	27	14	1.92
720357--720415	16	3.1	19	69	20	52	40	3	28	27	1.72
727621--727654	4	8.5	4	93	0	50	44	32	0	23	1.54
732731--732780	22	2.2	23	92	3	84	60	0	0	40	0.97
733307--733367	26	2.3	26	78	18	65	36	0	1	62	1.05
740476--740513	3	12.7	3	94	0	67	0	2	31	65	1.06
741597--741643	24	1.9	25	83	12	62	57	10	10	21	1.62
743255--743298	23	2.0	22	87	12	65	27	6	0	65	1.17
743256--743296	17	2.4	17	84	15	50	26	7	0	65	1.18
750322--750350	4	7.2	4	100	0	58	24	0	0	75	0.80
752534--752567	16	2.1	16	88	0	50	44	23	5	26	1.76
754812--754866	23	2.5	23	82	14	71	30	0	0	69	0.89
754812--754879	23	3.0	23	79	12	61	35	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
759955--760012	4	14.5	4	92	0	98	46	25	1	25	1.62
762775--762834	28	2.1	28	84	6	77	25	15	15	45	1.84
763764--763824	29	2.1	28	85	8	79	45	16	13	24	1.83
765561--765621	32	1.9	32	86	0	86	36	13	6	44	1.69
769955--769994	19	2.1	19	86	9	55	52	2	2	42	1.28
779754--779779	3	8.7	3	100	0	52	69	0	0	30	0.89
779907--780179	133	2.1	133	80	4	300	35	19	17	27	1.94
782717--782942	125	1.8	125	92	1	382	29	15	23	32	1.95
784130--784203	22	3.4	22	94	0	130	37	0	28	33	1.58
785056--785118	23	2.8	22	78	4	63	39	0	6	53	1.26
785074--785120	23	2.0	23	87	0	67	42	0	6	51	1.27
790178--790218	2	20.5	2	100	0	82	51	0	0	48	1.00
790421--790474	3	17.7	3	92	3	90	31	0	0	68	0.90
793202--793257	2	28.5	2	96	3	105	50	0	0	50	1.00
799998--800058	30	2.0	30	87	6	88	4	36	14	44	1.67
802403--802489	43	2.0	43	100	0	174	43	16	11	28	1.82
803238--803314	13	5.9	13	92	0	127	38	28	6	25	1.81
804213--804237	13	1.9	13	100	0	50	16	52	16	16	1.76
819412--819451	21	2.0	21	85	5	55	32	12	10	45	1.75
822197--822241	21	2.1	21	100	0	90	20	22	17	40	1.92
822638--822850	113	1.9	113	87	2	311	43	17	10	28	1.82
826894--826923	2	15.0	2	92	0	51	50	3	0	46	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
829059--829083	2	12.5	2	100	0	50	52	0	0	48	1.00
840868--840912	22	2.0	22	100	0	90	31	28	8	31	1.88
845370--845527	72	2.1	74	88	4	230	13	23	17	44	1.85
845416--845550	72	1.9	72	84	0	180	12	27	17	42	1.85
849797--849948	53	2.9	53	87	0	223	22	19	30	27	1.98
854509--854567	4	14.8	4	100	0	118	50	23	0	25	1.49
854726--854757	16	2.0	16	100	0	64	62	18	6	12	1.50
855838--855894	29	2.0	29	82	6	71	42	1	0	56	1.10
859293--859909	39	16.1	38	80	7	612	9	36	7	46	1.66
859322--859385	30	2.1	30	94	0	110	4	39	9	46	1.57
859352--859909	117	4.8	117	84	3	696	10	36	7	46	1.66
859352--859909	78	7.2	78	84	3	696	10	36	7	46	1.66
871526--871596	32	2.2	32	80	12	83	29	2	9	57	1.45
874437--875449	393	2.6	392	86	3	1427	37	16	15	30	1.90
886386--886417	15	2.1	15	100	0	64	46	6	12	34	1.67
890054--890510	249	1.8	250	88	2	693	34	21	15	28	1.94
890325--890814	203	2.4	202	81	9	541	31	23	14	30	1.94
896602--896643	2	21.5	2	85	4	59	52	0	0	47	1.00
897474--897527	26	2.1	26	89	3	83	55	18	14	11	1.68
907124--907190	29	2.3	30	73	21	79	65	5	5	22	1.37
908741--909236	267	1.8	272	85	6	711	34	16	14	35	1.88
912870--912907	17	2.3	17	81	4	51	23	0	7	68	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
916792--916833	13	3.2	13	75	24	52	30	4	11	52	1.59
924008--924059	27	1.9	27	92	0	86	32	23	32	11	1.90
924579--924642	19	3.4	19	78	4	76	40	7	0	51	1.31
924588--924642	18	3.1	18	76	7	67	40	7	0	52	1.29
925153--925204	27	1.9	27	96	0	95	13	32	23	30	1.93
925155--925213	27	2.2	27	87	0	82	13	28	27	30	1.94
925264--925326	27	2.4	27	83	2	92	47	1	9	41	1.45
938165--938199	6	5.8	6	93	0	61	54	0	14	31	1.40
940903--940940	20	1.9	20	89	10	60	18	2	2	76	1.02
957049--957132	41	2.0	41	100	0	168	48	20	7	23	1.74
960566--960600	2	17.5	2	93	0	61	48	2	0	48	1.16
964914--965174	124	2.1	124	84	4	330	45	6	6	40	1.57
965901--965951	26	2.0	26	88	7	77	25	5	3	64	1.33
972830--972895	34	1.9	34	87	6	98	45	15	7	31	1.74
980267--980297	7	4.4	7	95	0	53	0	22	0	77	0.77
980304--980334	2	16.0	2	93	6	55	51	0	0	48	1.00
996682--996717	18	2.0	18	88	0	54	41	2	0	55	1.14
1002354--1002461	26	3.9	27	73	15	87	18	14	15	50	1.77
1002340--1002525	58	3.4	54	79	10	205	19	16	14	48	1.80
1002376--1002457	27	2.9	28	78	12	87	18	10	17	53	1.72
1002339--1002491	58	2.7	58	86	1	227	18	16	14	50	1.77
1002339--1002480	31	4.9	30	70	20	104	18	16	14	50	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1002628--1002682	25	2.2	24	84	6	74	54	18	9	18	1.69
1003740--1003796	24	2.4	24	76	5	62	52	1	0	45	1.11
1016102--1016161	31	1.9	31	86	0	84	40	11	13	35	1.81
1025579--1025612	15	2.2	16	89	5	52	32	2	0	64	1.08
1026421--1026481	29	2.1	29	84	0	77	49	14	8	27	1.72
1027362--1027394	12	2.6	13	90	4	50	24	0	3	72	0.98
1028050--1028086	2	18.5	2	100	0	74	51	0	0	48	1.00
1031752--1031796	15	3.0	15	93	0	72	0	17	33	48	1.48
1031754--1031794	18	2.3	18	100	0	82	0	14	34	51	1.43
1035378--1035418	21	1.9	22	85	5	57	51	2	2	43	1.28
1050827--1050885	31	1.9	31	92	0	100	33	0	3	62	1.12
1051918--1051951	7	4.7	7	89	7	50	35	0	0	64	0.94
1051918--1051970	15	3.3	15	82	12	54	37	0	1	60	1.08
1053438--1053464	5	5.4	5	100	0	54	81	0	18	0	0.69
1055383--1055445	29	2.2	29	82	0	72	42	3	12	41	1.59
1057451--1057495	22	2.0	22	82	8	54	28	4	2	64	1.25
1060744--1060768	13	1.9	13	100	0	50	56	8	0	36	1.29
1062211--1062275	24	3.0	21	82	12	94	32	24	12	30	1.92
1062274--1062359	45	1.9	45	97	0	163	19	25	29	25	1.99
1062869--1062939	31	2.3	31	87	0	106	39	9	19	30	1.84
1065141--1065180	16	2.5	16	91	0	62	37	7	25	30	1.83
1065162--1065254	44	2.1	44	92	6	152	33	4	25	36	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1065362--1065508	57	2.5	57	81	10	147	51	4	0	43	1.25
1065468--1065525	21	2.6	21	79	17	64	50	8	1	39	1.43
1067644--1067702	27	2.2	26	81	3	73	62	8	5	23	1.43
1067745--1067812	27	2.6	26	85	2	91	17	36	30	14	1.90
1067907--1067944	19	2.0	19	90	10	60	68	0	31	0	0.90
1068445--1068541	33	2.8	35	72	20	89	50	1	3	45	1.24
1069050--1069095	24	1.9	24	86	0	65	45	0	2	52	1.13
1069059--1069115	30	1.9	30	82	13	73	43	1	3	50	1.29
1069729--1069770	7	6.0	7	100	0	84	42	0	0	57	0.99
1070467--1070516	2	25.5	2	95	4	93	48	0	0	52	1.00

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