genome.fa.s7.2.7.7.80.10.50.1000.131.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   

This is table  131  of  204  ( 24458 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)
40055471--40055534	26	2.5	26	89	0	92	32	18	7	40	1.80
40063940--40064001	30	2.2	30	85	8	85	29	6	8	56	1.53
40064131--40064155	12	2.1	12	100	0	50	32	0	0	68	0.90
40064371--40064567	95	2.1	97	85	1	263	36	8	8	46	1.64
40064519--40064645	47	2.7	46	74	15	132	44	9	2	44	1.49
40072194--40072250	27	2.2	26	90	6	89	56	3	3	36	1.34
40076529--40076636	9	11.9	9	73	15	73	61	1	0	36	1.13
40076541--40076636	45	2.1	45	83	7	115	61	2	1	35	1.15
40076575--40076633	26	2.3	27	82	8	77	61	3	1	33	1.23
40077029--40077113	10	8.2	10	71	19	50	31	2	3	62	1.25
40077040--40077113	23	3.5	21	75	17	73	29	2	4	63	1.26
40077042--40077509	10	48.8	9	66	20	109	34	1	4	58	1.28
40077241--40077505	17	14.8	18	64	24	64	35	1	4	59	1.24
40077362--40077471	9	11.9	10	67	23	55	35	0	0	64	0.94
40078034--40078062	15	1.9	15	100	0	58	13	10	6	68	1.37
40080669--40080694	2	13.0	2	100	0	52	50	0	0	50	1.00
40094245--40094335	17	5.4	17	66	23	57	40	3	3	52	1.34
40100177--40100286	57	2.0	55	81	3	130	29	20	3	47	1.67
40102179--40102213	17	2.1	17	88	0	52	40	20	5	34	1.76
40104687--40104747	32	2.0	31	87	6	88	37	18	9	34	1.83
40105284--40105351	15	4.6	14	71	10	55	61	1	0	36	1.05
40108444--40109068	44	14.2	44	67	6	264	28	24	18	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40108375--40109124	132	5.7	132	92	0	1212	28	24	18	28	1.98
40109903--40109927	13	1.9	13	100	0	50	56	8	24	12	1.62
40115049--40115090	20	2.1	20	82	8	50	66	2	7	23	1.28
40116803--40116984	68	2.6	69	85	6	222	46	12	1	40	1.48
40117348--40117605	67	3.9	65	85	5	320	42	15	3	39	1.64
40117974--40118239	67	4.0	67	92	0	424	40	15	5	38	1.70
40118078--40118181	30	3.2	32	63	26	81	41	17	3	37	1.68
40118091--40118193	30	3.2	30	64	26	75	40	19	3	35	1.70
40118048--40118163	37	3.3	37	63	24	88	42	14	4	38	1.66
40116780--40118762	633	3.1	630	86	4	2645	39	15	9	35	1.80
40118619--40118762	67	2.1	67	91	2	227	40	16	4	38	1.68
40123223--40123271	15	3.3	15	100	0	98	28	20	26	24	1.99
40129045--40129086	14	3.0	14	86	6	50	35	0	4	59	1.19
40130145--40130221	30	2.6	29	77	6	73	48	3	14	33	1.62
40131415--40131448	17	2.0	17	100	0	68	35	5	23	35	1.79
40138424--40138463	12	3.3	12	78	0	53	20	2	15	62	1.43
40138698--40138901	107	1.9	107	92	0	345	28	20	19	31	1.97
40141200--40141247	1	48.0	1	78	0	51	89	2	8	0	0.56
40141201--40141245	19	2.4	19	92	0	72	88	2	8	0	0.58
40148386--40148426	16	2.7	15	85	7	64	43	21	2	31	1.66
40148545--40149262	131	5.5	131	90	0	1071	28	19	24	26	1.99
40149901--40149939	19	2.1	19	85	9	53	74	5	12	7	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40151090--40151129	12	3.3	12	82	0	53	22	2	12	62	1.42
40155684--40155714	7	4.4	7	100	0	62	70	0	0	29	0.87
40155720--40155746	8	3.4	8	100	0	54	29	0	0	70	0.88
40156222--40156300	31	2.5	31	91	0	131	40	25	6	27	1.80
40156511--40156654	74	1.9	74	95	0	261	18	27	9	43	1.81
40157230--40157563	175	1.9	174	85	1	454	29	16	19	35	1.93
40157485--40157559	31	2.4	32	80	10	84	24	8	22	45	1.79
40158516--40158545	5	5.8	5	92	7	51	83	0	16	0	0.65
40158514--40158545	10	3.0	11	90	9	57	81	0	18	0	0.70
40158516--40158545	16	1.9	16	93	6	53	83	0	16	0	0.65
40158514--40158562	21	2.3	22	85	3	64	77	2	16	4	1.01
40161906--40161945	18	2.2	18	86	0	53	7	17	47	27	1.74
40161919--40161945	6	4.5	6	100	0	54	0	18	48	33	1.49
40161876--40161927	24	2.2	24	89	0	77	9	21	44	25	1.82
40165044--40165103	29	2.1	29	83	0	75	35	25	23	16	1.95
40171164--40171511	116	2.9	119	87	4	517	34	27	10	26	1.90
40172033--40172072	21	1.9	21	100	0	80	17	20	7	55	1.66
40172947--40172984	18	2.1	19	85	5	51	36	0	10	52	1.36
40182214--40182252	15	2.7	14	85	14	53	51	0	0	48	1.00
40182320--40182376	29	2.0	29	89	6	89	52	10	10	26	1.68
40189793--40189896	48	2.2	48	98	0	199	23	22	11	43	1.85
40197279--40197316	20	2.0	20	89	5	60	28	28	31	10	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40198151--40198193	6	6.8	6	81	5	50	81	2	2	13	0.89
40199622--40199687	32	2.1	32	94	0	114	56	12	4	27	1.55
40199888--40199921	12	2.9	12	91	4	52	64	0	2	32	1.08
40202088--40202162	35	2.1	35	95	0	132	44	12	12	32	1.78
40202781--40202830	19	2.6	19	78	9	57	54	16	4	26	1.59
40204887--40204949	30	2.1	30	90	0	99	38	42	0	19	1.51
40213911--40213949	18	2.0	20	85	9	55	41	25	5	28	1.77
40214516--40214607	8	11.5	8	91	0	148	25	11	25	38	1.90
40216674--40216768	49	1.9	49	100	0	190	47	18	6	27	1.73
40217525--40217610	41	2.0	42	86	13	120	61	11	2	24	1.41
40223740--40223797	29	2.0	29	96	0	107	56	13	15	13	1.67
40224246--40224271	3	8.7	3	100	0	52	34	34	0	30	1.58
40225548--40225580	14	2.4	14	90	10	50	36	9	0	54	1.32
40225783--40225825	19	2.3	19	95	0	77	39	16	13	30	1.87
40227661--40227940	27	10.4	27	86	5	345	43	21	16	17	1.87
40227661--40227927	80	3.3	78	85	7	340	43	21	16	17	1.87
40227661--40227943	134	2.1	134	88	2	417	44	21	16	17	1.87
40227661--40227940	54	5.2	53	87	2	380	43	21	16	17	1.87
40231753--40231835	26	3.1	27	75	8	80	36	25	20	18	1.95
40234014--40234193	90	2.0	91	83	3	229	27	17	16	38	1.91
40237259--40237599	146	2.3	146	92	4	539	52	10	12	24	1.71
40237316--40237607	146	2.0	146	98	0	566	49	10	14	25	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40242168--40242203	18	2.0	18	94	0	63	19	11	41	27	1.85
40243414--40244014	81	7.4	81	83	2	672	41	20	17	19	1.90
40243414--40244014	27	22.3	26	80	6	610	41	20	17	19	1.90
40250086--40250143	22	2.5	23	86	8	82	31	15	29	24	1.95
40251098--40251129	11	2.9	11	95	0	55	34	28	12	25	1.92
40251354--40251391	18	2.1	18	90	5	58	50	0	7	42	1.31
40258507--40258601	47	2.0	47	95	0	172	29	28	11	30	1.92
40263878--40263941	31	2.1	31	88	5	94	68	7	23	0	1.15
40264709--40264815	19	5.8	18	70	18	60	51	3	2	42	1.34
40278240--40278272	17	1.9	17	88	11	50	0	30	0	69	0.88
40281928--40282007	39	2.1	39	100	0	160	32	22	17	27	1.96
40281933--40282016	39	2.2	39	93	0	141	32	21	17	28	1.96
40289307--40289363	20	2.8	19	84	5	60	22	33	0	43	1.54
40291541--40291636	42	2.4	39	89	7	138	56	5	0	38	1.22
40291607--40291651	23	1.9	24	86	13	67	57	0	0	42	0.98
40292182--40292232	23	2.3	23	86	3	68	41	7	19	31	1.80
40293109--40293184	21	3.6	21	74	22	79	27	0	5	67	1.12
40293109--40293200	42	2.3	40	80	15	104	30	0	4	65	1.12
40293141--40293200	21	3.5	16	74	22	50	31	0	1	66	1.01
40293148--40293195	21	2.3	21	85	0	69	27	0	2	70	0.98
40293266--40293532	143	1.9	141	82	6	342	52	11	12	23	1.72
40300047--40300158	27	4.2	26	79	5	98	62	5	12	19	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40300047--40300162	54	2.1	54	85	7	155	62	5	12	19	1.49
40300047--40300179	28	4.9	27	83	3	142	60	5	13	21	1.53
40300538--40300759	43	5.2	43	84	3	297	21	27	19	32	1.97
40300467--40300603	71	1.9	71	91	2	222	21	23	21	33	1.97
40300538--40300759	85	2.6	85	85	4	295	21	27	19	32	1.97
40301107--40301177	21	3.4	21	82	0	88	7	45	14	33	1.71
40304505--40305137	270	2.3	268	84	2	777	33	18	13	34	1.90
40304505--40305214	270	2.6	270	82	3	669	33	19	13	33	1.90
40305595--40305663	7	9.4	7	76	7	57	33	42	1	23	1.63
40305596--40305663	15	4.6	14	76	8	73	33	42	1	22	1.62

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204