genome.fa.s3.2.7.7.80.10.50.1000.55.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  55  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)
16561165--16561294	22	6.1	22	78	18	141	40	0	11	48	1.39
16560637--16561360	351	2.1	349	84	9	947	41	0	12	45	1.48
16561231--16561340	56	2.0	56	98	0	211	40	0	10	48	1.45
16565532--16565599	15	4.9	14	71	16	52	41	35	0	23	1.55
16565535--16565572	15	2.5	15	86	0	58	36	42	0	21	1.53
16566080--16566319	41	5.9	40	77	7	178	33	24	25	17	1.96
16566120--16566318	82	2.4	82	88	0	290	33	25	25	16	1.95
16566377--16566473	40	2.5	40	78	6	101	20	28	21	28	1.98
16570194--16570236	22	2.0	22	100	0	86	27	9	20	41	1.83
16582547--16582588	21	2.0	20	86	4	57	59	4	4	30	1.39
16587891--16588261	105	3.6	104	93	1	602	19	19	29	30	1.97
16589759--16589818	30	2.0	30	100	0	120	33	13	30	23	1.93
16590756--16590872	38	3.1	38	83	2	137	38	29	20	11	1.88
16593960--16593998	17	2.3	17	91	8	62	20	5	0	74	1.01
16593942--16594000	30	2.0	30	83	6	75	20	6	3	69	1.26
16595157--16595565	137	3.0	135	83	4	514	40	8	5	45	1.57
16598999--16599050	24	2.2	24	89	0	77	36	3	9	50	1.54
16606752--16606982	45	5.1	45	93	1	383	24	25	22	27	1.99
16608124--16608197	27	2.7	27	97	0	139	18	2	50	28	1.61
16611361--16611450	41	2.2	40	84	9	112	34	5	1	58	1.28
16611352--16611447	38	2.5	35	78	16	102	34	6	1	58	1.30
16616120--16616179	3	20.0	3	72	6	50	33	1	5	60	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16616522--16616583	28	2.2	27	80	11	72	35	3	0	61	1.12
16622427--16623497	44	24.4	44	88	1	1504	31	20	25	22	1.98
16623492--16623631	44	3.2	41	69	10	100	30	23	20	26	1.98
16623535--16623696	43	3.7	43	71	4	135	27	23	25	22	2.00
16623492--16623709	89	2.5	88	88	4	316	29	22	23	24	1.99
16625113--16625172	3	20.0	3	72	6	50	31	3	5	60	1.35
16625157--16625194	16	2.2	18	86	9	53	31	0	7	60	1.25
16625515--16625576	28	2.2	27	80	11	72	35	3	0	61	1.12
16632775--16632801	2	13.5	2	100	0	54	51	0	0	48	1.00
16634160--16634198	17	2.1	20	86	13	57	46	5	17	30	1.70
16645367--16645437	32	2.2	32	92	0	115	39	4	29	26	1.75
16645367--16645429	16	3.9	16	87	0	99	39	3	30	26	1.72
16645599--16645962	120	3.0	120	95	0	656	50	4	1	43	1.30
16647349--16647452	49	2.1	49	92	3	174	51	9	6	31	1.60
16649887--16650059	73	2.3	75	97	2	323	52	8	6	31	1.59
16651190--16651258	21	3.1	21	82	15	93	57	18	5	17	1.59
16651180--16651267	25	3.6	25	85	13	121	56	20	6	15	1.62
16658869--16658895	5	5.4	5	100	0	54	18	0	0	81	0.69
16659864--16659900	19	1.9	19	94	0	65	27	2	0	70	1.01
16659879--16659937	13	4.6	14	74	16	56	28	8	0	62	1.24
16660126--16660155	16	1.9	15	93	6	51	26	10	0	63	1.26
16660843--16660875	16	2.0	17	88	5	50	45	0	6	48	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16661174--16661240	28	2.3	30	75	17	77	35	2	16	44	1.63
16661619--16661674	10	5.7	10	75	12	62	32	0	1	66	1.03
16661615--16661674	19	3.1	19	88	11	95	30	0	1	68	0.99
16661622--16661684	19	3.3	19	80	4	72	28	0	4	66	1.12
16663516--16663566	23	2.2	23	89	0	75	43	19	9	27	1.82
16666334--16666477	32	4.5	32	82	3	182	43	10	9	36	1.72
16674594--16675243	230	2.8	228	83	5	749	30	22	22	25	1.99
16674645--16675233	115	5.1	113	66	12	308	31	22	21	24	1.99
16675250--16675631	190	2.0	191	81	7	447	31	20	21	26	1.98
16676078--16676114	14	2.4	16	78	17	51	16	0	35	48	1.46
16678908--16679163	43	5.6	42	69	20	160	45	12	3	37	1.60
16679045--16679100	9	6.8	9	73	19	59	48	16	0	35	1.46
16678919--16679203	93	3.1	93	90	4	466	45	12	3	37	1.61
16679054--16679103	16	3.2	16	94	2	84	48	16	0	36	1.46
16678961--16679095	31	4.4	31	67	25	88	45	13	1	39	1.52
16679012--16679100	40	2.1	43	85	6	121	48	12	1	38	1.48
16678962--16679203	50	5.1	49	70	20	192	46	13	3	36	1.60
16679147--16679188	16	2.7	15	85	7	66	45	14	0	40	1.45
16682187--16682258	21	3.4	21	88	0	99	36	19	41	2	1.66
16689868--16689911	18	2.4	18	92	0	70	40	40	2	15	1.60
16693095--16693144	16	3.2	16	72	13	50	48	2	2	48	1.24
16694091--16694115	9	2.8	9	100	0	50	76	0	0	24	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16695687--16696473	262	3.0	263	85	4	1058	31	13	18	35	1.90
16697394--16697522	64	2.0	63	93	1	222	25	24	8	41	1.83
16699697--16699749	27	2.0	27	81	7	63	60	1	1	35	1.19
16699898--16699945	24	2.0	24	100	0	96	25	16	4	54	1.60
16702459--16703005	273	2.0	269	89	3	830	43	6	8	41	1.61
16702929--16702980	24	2.2	24	85	0	68	36	0	5	57	1.23
16709035--16709077	13	3.2	13	78	15	52	76	2	9	11	1.10
16709179--16709228	7	7.1	7	84	8	66	72	0	4	24	1.02
16709920--16709967	11	4.4	11	75	0	51	12	12	14	60	1.59
16709911--16709953	22	2.0	22	90	0	68	9	11	18	60	1.57
16709917--16709967	22	2.3	22	82	0	57	13	11	13	60	1.59
16710920--16710960	17	2.4	17	100	0	82	19	26	31	21	1.97
16714672--16714764	37	2.5	37	85	1	116	35	31	15	18	1.91
16719001--16719091	26	3.5	26	79	8	103	34	20	12	32	1.90
16719237--16719289	23	2.3	23	86	0	70	24	20	26	28	1.99
16723430--16723555	40	3.2	40	70	0	117	34	19	21	23	1.96
16723532--16723577	20	2.3	21	77	11	51	39	23	21	15	1.92
16723452--16723577	40	3.2	39	67	8	101	37	19	20	22	1.95
16723821--16723906	37	2.3	37	95	0	154	44	20	6	27	1.77
16734549--16734666	44	2.7	44	78	2	121	30	20	16	32	1.95
16734661--16735787	128	8.8	128	88	1	1594	25	23	19	32	1.98
16735750--16735861	44	2.5	44	85	2	127	24	25	20	29	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16735788--16735874	44	2.0	44	97	0	165	21	24	21	32	1.98
16738024--16738136	6	19.7	6	81	13	105	12	1	13	72	1.20
16738026--16738128	27	4.1	25	74	17	81	12	1	13	71	1.22
16738023--16738130	16	7.1	15	69	21	57	12	1	12	73	1.19
16738023--16738137	43	2.7	43	83	4	144	12	1	13	73	1.19
16739380--16739407	2	14.0	2	100	0	56	50	0	0	50	1.00
16739715--16739751	3	12.0	3	88	5	56	62	0	2	35	1.10
16740570--16740608	17	2.2	18	90	4	62	82	5	2	10	0.93
16741382--16741543	84	1.9	85	93	1	281	30	24	16	28	1.96
16741391--16741543	44	3.6	44	74	7	170	31	24	16	28	1.96
16741558--16742793	129	9.6	130	91	1	1947	24	23	19	32	1.98
16749550--16749592	3	14.0	3	85	4	59	62	2	2	32	1.20
16750413--16750451	17	2.2	18	86	4	53	79	7	2	10	1.02
16762672--16762702	6	5.0	6	96	4	53	16	0	3	80	0.83
16769859--16769908	12	4.6	11	76	19	52	2	10	14	74	1.16
16773036--16773125	46	2.0	46	97	0	171	34	20	21	24	1.96
16777263--16777331	27	2.6	27	86	4	95	27	24	13	34	1.92
16780264--16780300	10	3.6	10	88	3	56	70	0	29	0	0.88
16780462--16780595	39	3.2	38	76	20	110	32	3	12	50	1.58
16783158--16783367	116	1.8	115	85	6	298	32	11	7	48	1.67
16783269--16783746	158	3.1	153	77	11	518	31	9	7	51	1.62
16783997--16784137	10	14.0	10	65	18	60	0	31	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16784025--16784133	24	4.6	24	68	14	66	0	31	0	68	0.90
16784031--16784138	18	5.7	19	74	15	82	0	31	0	68	0.90
16783997--16784127	38	3.4	36	76	17	113	0	32	0	67	0.91
16783998--16784136	34	4.1	34	75	9	131	0	31	0	68	0.90
16788651--16788765	51	2.3	51	93	0	194	31	15	25	27	1.96
16790152--16790308	43	3.7	42	82	4	145	31	27	16	24	1.96
16790152--16790320	86	2.0	84	82	8	207	33	26	15	24	1.95
16790926--16790952	13	2.1	13	100	0	54	48	22	0	29	1.51
16801348--16801760	125	3.3	125	92	0	646	31	16	20	30	1.95
16802716--16802833	49	2.4	49	98	0	227	42	9	2	45	1.49

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