genome.fa.s6.2.7.7.80.10.50.1000.149.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  149  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)
43960904--43960945	22	1.9	22	95	0	75	40	28	21	9	1.84
43965325--43965375	22	2.3	22	89	0	75	23	27	15	33	1.95
43965336--43965378	22	2.0	22	100	0	86	23	25	13	37	1.92
43969281--43969362	40	2.0	40	100	0	164	25	21	19	32	1.97
43969673--43969729	29	2.0	29	92	0	96	21	26	21	31	1.98
43974855--43974897	21	2.1	20	82	4	50	25	2	6	65	1.30
43976838--43976894	26	2.1	26	83	6	69	28	3	7	61	1.39
43979094--43979118	13	1.9	13	100	0	50	36	8	16	40	1.77
43980498--43980555	30	1.9	30	89	0	89	41	3	24	31	1.71
43980768--43980798	13	2.4	13	94	0	53	32	0	12	54	1.38
43980893--43981085	50	3.8	50	90	0	296	24	23	31	20	1.98
43982964--43983021	21	2.6	23	76	23	77	27	20	8	43	1.81
43983129--43983194	9	7.2	9	77	16	73	56	21	0	22	1.43
43983163--43983194	11	3.1	11	82	17	50	62	18	0	18	1.33
43988605--43988674	25	3.0	23	76	16	63	20	5	1	72	1.12
43988605--43988674	24	3.0	24	79	12	65	20	5	1	72	1.12
43988619--43988675	6	9.3	6	80	14	55	19	3	1	75	1.04
43990295--43990349	21	2.6	21	91	0	92	21	9	40	29	1.84
44002697--44002723	8	3.4	8	100	0	54	11	0	0	88	0.50
44009320--44009363	22	2.0	23	90	4	72	50	2	2	45	1.27
44009360--44009427	34	2.0	34	88	2	102	45	1	1	51	1.19
44009477--44009532	16	3.3	16	72	18	51	44	1	3	50	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44013329--44013355	13	2.1	13	100	0	54	37	0	33	29	1.58
44018086--44018160	9	7.9	9	74	11	60	65	1	5	28	1.22
44018078--44018177	39	2.6	37	79	13	105	65	1	5	29	1.20
44018675--44018767	21	4.8	19	71	23	70	26	1	2	69	1.06
44018667--44018773	28	3.8	29	71	15	80	25	2	1	70	1.11
44018688--44018721	16	2.1	16	88	5	50	29	0	2	67	1.05
44018676--44018774	9	10.7	9	70	17	60	25	2	2	70	1.08
44023304--44023376	19	3.8	19	92	0	128	38	9	15	36	1.80
44023937--44023988	25	2.1	25	85	7	70	32	3	5	57	1.40
44024052--44024107	25	2.1	28	84	15	75	30	0	3	66	1.09
44024637--44024676	19	2.0	20	85	4	55	32	5	10	52	1.56
44024917--44025111	98	2.0	98	89	0	300	30	9	22	37	1.85
44032382--44032470	25	3.5	24	76	13	81	31	20	25	22	1.98
44032328--44032478	24	6.1	25	67	19	84	35	19	25	19	1.96
44032733--44032790	27	2.1	27	100	0	116	27	15	18	37	1.92
44037514--44037561	23	2.1	22	81	11	53	58	4	10	27	1.49
44044631--44044764	26	5.3	26	71	11	93	18	25	23	32	1.97
44044746--44044793	24	2.0	24	83	0	60	18	22	22	35	1.96
44046391--44046438	24	2.0	24	100	0	96	33	20	25	20	1.97
44046649--44046715	26	2.6	26	83	2	91	32	22	25	19	1.97
44046765--44046905	65	2.2	65	86	0	192	32	20	23	23	1.98
44052844--44052884	21	2.0	21	95	0	73	39	24	17	19	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44058906--44059050	71	2.0	71	94	0	254	33	18	18	29	1.95
44060763--44060829	5	14.2	5	78	12	70	38	0	1	59	1.06
44060778--44060814	19	1.9	19	88	0	56	45	0	0	54	1.00
44061869--44061931	3	21.0	3	86	0	90	36	0	3	60	1.13
44062075--44062128	24	2.2	26	83	12	69	46	0	25	27	1.53
44068390--44068421	2	16.0	2	100	0	64	50	0	0	50	1.00
44073324--44073348	4	6.2	4	100	0	50	76	0	0	24	0.80
44086926--44086974	23	2.1	23	85	7	64	44	2	2	51	1.24
44086959--44087053	37	2.5	38	75	16	99	38	2	2	56	1.23
44095721--44095792	35	2.2	33	82	12	85	33	15	33	18	1.92
44095864--44096001	39	3.5	40	91	3	208	36	2	0	59	1.18
44095914--44095994	11	7.8	11	71	19	59	37	2	0	60	1.10
44095925--44095978	28	1.9	28	81	7	65	35	3	0	61	1.14
44095944--44096004	31	2.0	31	87	6	88	39	1	0	59	1.08
44099326--44099411	20	4.3	20	78	0	73	41	15	6	36	1.74
44099326--44099435	40	2.7	39	77	5	112	41	13	6	38	1.70
44099363--44099430	20	3.4	20	80	8	75	44	16	4	35	1.67
44099527--44099674	20	7.2	20	72	11	93	41	11	8	38	1.71
44099582--44099619	12	3.2	12	85	11	51	47	15	7	28	1.74
44099609--44099774	40	4.1	40	80	6	140	40	11	6	40	1.67
44099630--44099734	20	5.2	20	74	4	95	38	11	5	44	1.64
44099618--44099774	60	2.6	59	76	7	156	40	10	6	42	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44099616--44099787	20	8.6	20	69	11	66	40	11	6	41	1.67
44099720--44099781	21	3.0	21	76	2	63	43	11	8	37	1.70
44099796--44099844	20	2.5	20	79	0	53	38	12	6	42	1.67
44099887--44100025	20	7.1	20	67	8	70	43	15	6	35	1.72
44100251--44100380	20	6.4	20	75	10	102	43	13	8	34	1.75
44107163--44107262	30	3.4	28	80	14	112	60	0	3	37	1.12
44107173--44107223	19	2.5	20	90	9	86	58	0	3	37	1.16
44107199--44107322	39	3.2	38	90	6	196	66	0	3	30	1.08
44111841--44111893	21	2.3	23	84	9	65	52	1	0	45	1.11
44131319--44131349	12	2.6	12	94	0	53	70	6	0	22	1.09
44131592--44131676	13	6.3	14	72	10	61	0	35	1	63	1.02
44132742--44132782	21	1.9	22	90	5	66	46	29	0	24	1.53
44134777--44134835	28	2.0	31	83	9	79	50	5	0	44	1.24
44136835--44137033	98	2.0	100	92	3	332	22	22	9	45	1.80
44140817--44140855	15	2.5	15	87	4	51	41	0	2	56	1.13
44140807--44140853	16	2.7	18	78	18	55	44	0	2	53	1.12
44141245--44141345	51	2.0	50	88	9	152	61	3	3	30	1.32
44141466--44141579	51	2.2	52	82	3	133	33	14	8	42	1.77
44141499--44141598	52	1.9	51	83	2	128	34	14	8	44	1.74
44153287--44153344	29	2.0	29	93	0	98	17	34	15	32	1.91
44157381--44157463	18	4.3	18	68	24	62	28	8	1	61	1.33
44158187--44158626	46	10.7	41	76	17	316	29	19	13	37	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44158277--44158590	36	8.0	36	77	15	277	29	18	13	38	1.89
44158231--44158584	123	2.9	123	91	2	565	29	18	13	37	1.89
44158231--44158626	82	4.9	82	75	15	376	29	19	13	37	1.90
44161269--44161319	12	4.4	12	80	9	61	43	3	0	52	1.19
44162948--44162989	23	1.9	21	90	9	66	66	2	4	26	1.23
44162947--44162994	21	2.3	20	83	16	62	68	4	4	22	1.24
44171402--44171434	17	2.1	16	88	11	50	42	24	0	33	1.55
44177073--44177111	16	2.3	16	86	8	51	51	5	0	43	1.24
44177376--44177426	13	3.8	13	75	25	52	60	0	1	37	1.08
44182999--44183052	27	2.0	27	96	0	99	38	9	22	29	1.85
44189199--44189291	37	2.5	37	98	0	177	25	19	18	36	1.94
44189271--44189430	52	2.9	52	81	13	196	26	25	13	33	1.94
44189297--44189429	59	2.3	59	85	2	178	26	27	10	36	1.89
44191809--44191845	6	6.2	6	100	0	74	16	0	18	64	1.29
44215773--44215941	73	2.3	72	78	8	171	35	19	24	20	1.96
44215899--44215991	26	3.7	26	80	5	93	33	18	26	21	1.96
44216350--44216389	21	1.9	21	89	0	62	40	25	0	35	1.56
44217998--44218046	21	2.3	22	96	3	91	44	16	10	28	1.80
44224782--44224832	26	2.0	26	96	0	93	41	17	7	33	1.79
44236220--44236295	28	2.7	27	75	15	73	31	17	0	51	1.45
44236248--44236303	21	2.7	20	83	8	76	30	12	1	55	1.47
44236251--44236324	35	2.1	36	80	16	84	29	13	1	55	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44236235--44236313	21	3.8	20	75	9	50	31	18	1	48	1.57
44237900--44237938	20	2.0	20	84	0	51	46	7	10	35	1.67
44237949--44238022	20	3.8	19	71	5	58	35	16	4	44	1.66
44238126--44238212	20	4.3	20	80	0	102	42	19	5	32	1.75
44238106--44238220	40	2.9	40	84	0	122	41	17	6	33	1.76
44238126--44238255	60	2.2	60	81	5	147	40	17	5	36	1.73
44238333--44238377	20	2.2	20	88	0	63	40	17	4	37	1.70
44238412--44238458	20	2.4	20	85	3	69	46	21	0	31	1.51
44238474--44238512	20	2.0	19	85	5	51	38	20	0	41	1.53
44238560--44238634	20	3.8	20	73	5	62	40	17	5	37	1.72

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