genome.fa.s8.2.7.7.80.10.50.1000.187.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   

This is table  187  of  190  ( 22705 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)
55803897--55804047	40	3.7	41	83	6	182	60	1	2	35	1.19
55804006--55804031	11	2.4	11	100	0	52	53	0	7	38	1.30
55806108--55806144	11	3.2	12	85	11	51	48	5	18	27	1.70
55806124--55806148	11	2.3	11	100	0	50	48	8	28	16	1.74
55806100--55806248	51	3.0	51	77	14	141	46	2	27	24	1.64
55806161--55806248	11	7.5	11	78	18	81	45	1	30	22	1.60
55808640--55808668	15	1.9	15	100	0	58	24	13	13	48	1.79
55815702--55815756	25	2.2	24	81	15	67	30	10	12	45	1.77
55821841--55821889	23	2.1	24	81	7	57	44	2	8	44	1.45
55822156--55822268	19	5.8	19	82	4	145	38	11	15	34	1.83
55822157--55822263	40	2.7	40	89	2	155	39	12	14	34	1.83
55822864--55822903	21	1.9	21	84	0	53	27	7	2	62	1.35
55823311--55823335	9	2.8	9	100	0	50	24	0	8	68	1.16
55823398--55823473	36	2.1	36	100	0	152	26	5	13	55	1.59
55823407--55823486	36	2.2	36	86	0	106	31	6	18	43	1.75
55823587--55823844	98	2.6	97	85	5	252	28	10	23	37	1.88
55823651--55823845	98	2.0	98	95	0	354	28	10	25	35	1.89
55829056--55829085	12	2.5	12	94	0	51	40	13	26	20	1.89
55830092--55830135	22	2.0	23	86	8	65	54	4	2	38	1.33
55837957--55838000	21	2.2	21	92	8	74	31	0	0	68	0.90
55838065--55838126	21	3.0	21	70	13	56	50	1	3	45	1.27
55845598--55845670	21	3.5	21	73	0	65	43	20	21	13	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55845640--55845772	42	3.2	42	82	2	160	42	18	20	18	1.90
55845682--55845746	21	3.1	21	70	0	67	44	18	20	16	1.87
55847791--55847815	13	1.9	13	100	0	50	56	4	8	32	1.47
55848242--55848279	9	4.3	9	83	6	51	42	2	0	55	1.14
55863879--55864056	89	2.0	89	89	0	275	37	8	14	40	1.76
55864118--55864157	20	2.2	19	86	13	57	35	5	25	35	1.78
55865792--55865836	3	15.0	3	100	0	90	66	0	0	33	0.92
55868720--55868770	19	2.8	18	79	11	59	60	9	3	25	1.45
55869241--55869281	20	2.0	20	85	0	55	31	2	2	63	1.20
55871085--55871109	4	6.2	4	100	0	50	28	48	0	24	1.52
55880497--55880524	3	9.3	3	100	0	56	0	32	0	67	0.91
55884863--55884979	60	2.0	60	98	0	225	34	28	11	25	1.91
55886869--55886914	22	2.1	22	100	0	92	45	0	19	34	1.51
55896413--55896467	27	2.0	27	82	0	65	36	16	10	36	1.84
55901700--55901729	2	15.0	2	100	0	60	50	0	0	50	1.00
55923553--55923633	31	2.7	29	83	9	92	38	3	6	51	1.45
55923553--55923634	29	2.8	28	75	18	78	37	3	7	51	1.48
55926057--55926081	8	3.1	8	100	0	50	12	24	12	52	1.72
55932073--55932127	25	2.2	26	86	3	76	30	1	5	61	1.29
55934998--55935051	15	3.7	15	80	5	65	53	9	1	35	1.44
55941425--55941473	25	2.0	25	84	8	64	53	8	6	32	1.55
55946229--55946328	31	3.4	30	71	23	95	26	15	11	48	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55958596--55958670	37	2.0	37	97	0	141	17	29	13	40	1.87
55959279--55959317	14	2.7	15	88	8	62	41	0	0	58	0.98
55960496--55960542	3	15.7	3	100	0	94	31	0	0	68	0.90
55961278--55961326	24	2.0	25	88	4	73	63	2	0	34	1.06
55961301--55961344	20	2.3	20	80	7	56	63	2	0	34	1.07
55961192--55961456	9	27.7	10	66	21	51	60	3	1	35	1.23
55961276--55961381	17	6.1	17	70	22	51	63	2	0	33	1.09
55961389--55961455	19	3.6	19	69	26	54	58	2	1	37	1.23
55961737--55961785	25	2.0	26	92	8	84	75	0	2	22	0.90
55962547--55962815	135	2.0	134	91	0	439	35	17	12	34	1.87
55963277--55963321	21	2.1	22	83	4	56	40	4	6	48	1.49
55963327--55963399	9	7.9	9	73	11	58	38	0	5	56	1.23
55963298--55963381	38	2.2	38	83	10	100	41	0	4	53	1.22
55963366--55963412	18	2.7	17	78	15	51	27	4	8	59	1.45
55963324--55963399	19	4.2	17	70	20	64	39	0	5	55	1.23
55967416--55967546	37	3.5	37	88	3	181	29	28	19	22	1.98
55968512--55968569	22	2.7	22	84	7	66	31	5	0	63	1.16
55968513--55968587	26	3.1	25	81	9	77	34	5	0	60	1.20
55968544--55968601	26	2.2	26	81	6	64	39	5	1	53	1.33
55968635--55968664	15	2.0	15	100	0	60	33	13	13	40	1.83
55969548--55969610	32	1.9	33	83	3	83	22	9	9	58	1.58
55970125--55970169	23	2.0	22	86	4	63	60	6	4	28	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55979351--55979392	22	2.0	21	85	4	57	26	4	14	54	1.59
55988399--55988436	3	12.7	3	89	10	60	65	0	34	0	0.93
55989057--55989098	21	1.9	23	85	9	61	21	11	4	61	1.48
55993048--55993097	21	2.4	21	80	6	57	70	10	2	18	1.25
55998844--55998876	2	16.5	2	100	0	66	0	48	0	51	1.00
55998876--55998904	2	14.5	2	100	0	58	48	0	0	51	1.00
56005394--56005500	46	2.4	46	85	4	148	28	24	13	33	1.93
56005480--56005513	18	1.9	17	94	5	59	23	29	5	41	1.78
56005436--56005561	62	2.0	64	93	6	222	27	24	12	34	1.92
56005498--56005616	46	2.6	46	93	5	199	29	21	14	34	1.93
56005394--56005604	108	2.0	107	93	0	359	28	22	13	34	1.93
56007301--56007342	3	14.3	3	80	5	50	64	4	0	30	1.14
56014418--56014500	40	2.1	40	84	6	107	34	1	0	63	1.02
56014909--56014934	6	4.3	6	100	0	52	19	0	0	80	0.71
56019429--56019469	20	2.0	20	85	4	55	19	4	4	70	1.24
56022039--56022097	29	2.0	29	100	0	118	59	10	16	13	1.61
56022170--56022238	25	2.7	26	77	4	77	69	5	2	21	1.23
56022160--56022238	25	3.1	25	73	8	70	65	6	5	22	1.35
56022260--56022397	27	5.3	27	74	14	114	60	0	5	33	1.23
56025629--56025740	20	5.7	19	73	13	84	26	9	9	53	1.65
56025629--56025742	40	2.9	39	83	6	140	27	10	9	52	1.67
56026908--56026955	11	4.5	11	76	2	53	31	4	8	56	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56026908--56026955	22	2.2	21	85	3	60	31	4	8	56	1.48
56030185--56030240	29	1.9	29	82	13	71	32	10	3	53	1.53
56033755--56033789	2	17.5	2	93	0	61	45	0	0	54	0.99
56038105--56038179	29	2.5	29	79	12	80	54	2	4	38	1.33
56041366--56041423	24	2.5	23	83	8	64	56	5	1	36	1.32
56041392--56041478	41	2.2	38	78	15	95	60	1	3	34	1.21
56041417--56041464	17	3.0	16	80	17	55	62	0	4	33	1.14
56041436--56041464	14	2.1	14	100	0	58	58	0	6	34	1.25
56041428--56041487	23	2.6	23	72	15	61	65	0	3	31	1.09
56056817--56056860	22	2.0	22	81	0	52	40	4	2	52	1.34
56063516--56063578	22	3.0	22	75	22	64	6	41	4	47	1.50
56064061--56064094	2	17.0	2	100	0	68	0	50	0	50	1.00
56074543--56074594	26	2.1	25	82	13	63	21	7	7	63	1.46
56076117--56076161	24	2.0	23	86	8	65	42	2	0	55	1.12
56087503--56087550	24	2.0	25	83	4	62	68	6	6	18	1.32
56095479--56095514	18	1.9	19	94	5	65	33	2	16	47	1.61
56099845--56099921	32	2.2	36	80	19	94	37	18	1	42	1.58
56101218--56101284	35	1.9	34	82	8	82	4	23	4	67	1.28
56101880--56101906	7	3.9	7	100	0	54	55	0	0	44	0.99
56102103--56102163	31	2.0	29	93	6	104	29	0	13	57	1.36
56102291--56102378	31	2.9	32	76	12	89	45	14	5	34	1.69
56102778--56102830	23	2.4	22	81	12	56	47	0	1	50	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56107134--56107160	2	13.5	2	100	0	54	51	0	48	0	1.00
56114157--56114199	11	3.8	11	80	17	52	65	2	2	30	1.18
56114570--56114634	3	21.7	3	100	0	130	33	0	0	66	0.92
56115240--56115300	20	3.0	20	74	6	70	27	4	3	63	1.30
56124452--56124487	16	2.2	16	90	5	54	16	5	11	66	1.40
56125469--56125695	41	5.5	41	73	3	161	26	19	24	28	1.99
56125469--56125695	123	1.8	123	81	1	285	26	19	24	28	1.99
56125544--56125694	82	1.8	82	81	0	185	26	21	26	25	1.99
56125706--56125743	20	2.0	18	90	10	58	26	5	5	63	1.37
56126102--56126134	14	2.3	15	94	5	59	33	0	30	36	1.58

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190