genome.fa.s1.2.7.7.80.10.50.1000.33.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  33  of  187  ( 22383 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)
10441622--10441651	2	15.0	2	100	0	60	50	0	0	50	1.00
10444154--10444193	15	2.7	15	100	0	80	22	30	37	10	1.87
10444170--10444252	42	2.0	42	87	0	121	27	39	18	14	1.89
10444318--10444597	36	7.8	36	97	0	488	25	38	18	17	1.92
10444339--10444765	144	3.0	142	82	9	460	26	40	16	16	1.89
10444536--10444831	144	2.1	144	97	0	556	28	41	12	16	1.85
10444852--10444945	24	3.9	24	73	5	82	26	43	10	19	1.83
10445533--10445571	6	6.7	6	94	5	71	17	0	0	82	0.68
10445533--10445571	17	2.2	17	95	4	69	17	0	0	82	0.68
10448561--10448599	20	2.0	20	100	0	78	25	17	25	30	1.97
10453305--10453339	3	12.0	3	87	6	54	0	0	28	71	0.86
10454178--10454485	151	2.0	152	91	1	503	30	9	10	49	1.70
10474770--10474830	21	3.0	19	81	11	59	54	1	3	40	1.27
10475393--10475457	33	2.0	33	93	0	112	52	7	12	27	1.66
10475379--10475462	33	2.8	29	79	13	96	50	7	15	27	1.70
10478821--10478933	37	3.1	37	76	13	99	40	1	4	53	1.31
10478821--10478896	11	6.8	11	70	24	52	42	1	2	53	1.23
10478821--10478916	48	1.9	48	81	6	111	41	2	4	52	1.32
10482209--10482239	16	1.9	16	93	0	53	67	6	0	25	1.14
10484180--10484233	22	2.3	24	81	9	67	35	1	7	55	1.39
10507631--10507682	23	2.4	21	81	12	61	63	1	1	32	1.16
10507630--10507682	21	2.5	22	81	3	63	64	1	1	32	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10508316--10508406	42	2.2	42	85	0	119	20	35	17	26	1.95
10508529--10508553	2	12.5	2	100	0	50	48	0	0	52	1.00
10515384--10515411	2	14.0	2	100	0	56	50	0	0	50	1.00
10517444--10517495	24	2.2	24	89	0	77	34	1	11	51	1.49
10521359--10521410	24	2.2	24	92	0	86	36	1	9	51	1.46
10536749--10536777	3	9.7	3	100	0	58	68	0	31	0	0.89
10536993--10537072	22	3.6	22	89	0	106	27	15	27	30	1.96
10545359--10545383	12	2.1	12	100	0	50	52	24	8	16	1.70
10547113--10547156	23	1.9	23	85	0	61	38	13	6	40	1.71
10555870--10555908	3	13.0	3	100	0	78	66	0	0	33	0.92
10576462--10576666	35	5.6	35	67	19	103	20	17	22	40	1.92
10576414--10576776	75	4.9	75	83	3	444	20	19	21	38	1.93
10576568--10576693	40	3.3	39	75	10	134	19	17	22	40	1.91
10583695--10583733	17	2.3	17	86	0	60	25	10	17	46	1.80
10587154--10587213	29	2.1	28	87	3	84	31	1	0	66	1.01
10590180--10590219	21	2.0	21	90	5	64	70	5	0	25	1.08
10591661--10591706	14	3.1	14	81	12	56	30	0	4	65	1.12
10592516--10592541	3	8.7	3	100	0	52	65	0	0	34	0.93
10592540--10592577	3	12.7	3	94	0	67	31	0	2	65	1.06
10595119--10595489	105	3.6	103	93	2	600	30	29	19	19	1.97
10596545--10598183	44	36.6	44	76	6	1178	30	20	16	32	1.95
10596585--10598114	228	6.8	223	76	9	733	30	20	16	32	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10596577--10598194	589	2.8	590	84	3	1969	30	20	16	32	1.95
10600194--10600564	192	1.9	192	93	0	634	36	24	13	25	1.92
10601016--10601072	22	2.6	22	83	2	71	33	17	28	21	1.96
10609456--10609494	18	2.2	18	90	9	62	35	20	15	28	1.93
10612176--10612229	26	2.1	26	100	0	108	44	0	18	37	1.50
10612411--10612452	2	21.0	2	100	0	84	50	0	0	50	1.00
10613148--10613259	41	2.7	41	94	0	188	28	20	28	22	1.98
10619066--10619112	24	2.0	24	82	0	58	34	27	6	31	1.82
10620338--10620371	18	1.9	18	88	5	52	8	38	32	20	1.84
10620902--10620932	15	2.1	15	100	0	62	32	19	12	35	1.90
10621415--10621474	28	2.1	28	90	0	93	55	5	31	8	1.51
10623105--10623176	22	3.3	22	94	0	117	30	16	27	25	1.97
10626420--10626461	22	1.9	22	90	0	66	30	16	30	21	1.95
10627257--10627288	3	10.7	3	100	0	64	68	0	0	31	0.90
10628094--10628119	5	5.2	5	100	0	52	42	19	19	19	1.90
10629227--10629257	9	3.4	9	90	0	53	38	22	12	25	1.90
10632301--10632446	50	2.9	49	82	2	175	35	27	12	24	1.91
10634044--10634183	23	6.1	23	83	0	181	30	24	20	25	1.98
10634409--10634447	18	2.2	17	86	13	53	46	20	0	33	1.51
10645487--10645529	21	2.1	21	82	4	52	62	4	6	25	1.40
10657818--10657876	3	19.3	3	96	3	109	33	0	0	66	0.92
10666080--10666135	18	2.9	19	73	26	55	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10666150--10666196	22	2.2	21	84	3	58	57	0	0	42	0.98
10666150--10666198	21	2.3	22	85	3	64	55	0	0	44	0.99
10666178--10666234	15	3.5	15	73	17	60	49	1	1	47	1.22
10667298--10667337	20	2.0	20	85	4	55	55	0	7	37	1.29
10671169--10671208	16	2.4	16	87	4	53	37	0	0	62	0.95
10679943--10680282	121	2.8	121	86	1	475	21	16	18	43	1.87
10682234--10682258	2	12.5	2	100	0	50	52	48	0	0	1.00
10692350--10692392	2	21.5	2	100	0	86	48	0	0	51	1.00
10695009--10695041	14	2.2	16	89	10	52	45	0	0	54	0.99
10698587--10698648	31	2.0	31	84	6	81	45	8	9	37	1.67
10699558--10699598	21	2.0	21	90	0	64	36	2	14	46	1.58
10701254--10701278	6	4.2	6	100	0	50	16	0	0	84	0.63
10704035--10704096	31	2.0	31	93	0	106	46	11	8	33	1.69
10709563--10709619	19	3.3	19	68	27	63	29	17	8	43	1.79
10709562--10709625	32	2.0	32	100	0	128	31	18	9	40	1.83
10715210--10715244	3	11.7	3	100	0	70	65	0	0	34	0.93
10717361--10717391	7	4.6	7	92	8	55	87	0	0	12	0.55
10717361--10717391	13	2.3	13	94	5	53	87	0	0	12	0.55
10717601--10717637	19	2.1	17	90	10	56	18	24	0	56	1.41
10719231--10719279	23	2.1	23	96	0	89	44	4	32	18	1.68
10719251--10719334	42	2.0	42	97	0	159	46	9	22	21	1.80
10723737--10723827	23	4.1	23	71	16	93	45	6	28	19	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10723757--10723840	42	2.0	42	100	0	168	45	9	23	21	1.81
10727663--10727722	30	2.0	30	83	3	75	21	43	0	35	1.53
10737886--10737952	9	7.4	9	87	0	98	43	20	8	26	1.82
10742728--10742957	45	5.1	45	86	4	311	40	20	18	20	1.91
10742728--10742954	90	2.5	90	89	2	348	40	20	18	20	1.91
10749915--10749974	24	2.5	22	84	10	66	41	10	5	43	1.60
10750996--10751070	22	3.4	22	92	0	114	26	26	13	33	1.93
10764994--10765058	34	1.9	33	84	9	87	38	7	12	41	1.71
10768732--10768789	3	19.3	3	78	7	55	63	0	6	29	1.20
10769678--10769711	17	2.0	17	94	0	59	14	17	52	14	1.74
10770244--10770525	44	6.4	44	85	4	372	29	24	14	31	1.95
10770518--10771280	132	5.8	132	85	4	950	28	23	18	29	1.98
10770518--10771280	396	1.9	395	88	4	1144	28	23	18	29	1.98
10772637--10772677	7	5.9	7	86	11	57	12	14	0	73	1.11
10777623--10777674	3	17.3	3	80	7	52	61	0	7	30	1.24
10778558--10778591	17	2.0	17	94	0	59	14	17	52	14	1.74
10779980--10780010	9	3.4	9	90	0	53	25	12	22	38	1.90
10780064--10780100	9	4.1	9	92	0	65	45	13	10	29	1.77
10783030--10783065	2	18.0	2	94	0	63	52	0	0	47	1.00
10783396--10783445	21	2.4	22	80	16	61	66	6	6	22	1.36
10785354--10785492	44	3.2	42	71	19	122	25	26	23	23	2.00
10785284--10785558	88	3.2	87	84	3	360	24	26	22	26	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10785323--10785465	45	3.2	45	70	18	136	22	25	23	28	1.99
10787246--10787337	43	2.1	44	86	6	125	8	11	4	75	1.18
10791339--10791623	111	2.6	112	89	3	443	32	21	16	29	1.95
10796155--10796196	22	1.9	22	85	9	59	40	16	16	26	1.90
10797790--10797841	25	2.1	25	85	7	70	28	1	3	65	1.21
10798256--10798381	50	2.6	47	78	8	128	32	3	8	55	1.46
10798259--10798381	49	2.5	49	77	6	124	33	3	8	55	1.46
10811225--10811270	19	2.4	19	96	0	83	26	28	19	26	1.99
10812625--10812667	11	4.2	11	82	14	56	20	6	25	46	1.76
10812637--10812702	9	7.2	9	83	10	80	22	9	28	39	1.85

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