genome.fa.s13.2.7.7.80.10.50.1000.33.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  33  of  199  ( 23770 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)
9350340--9350380	9	4.6	9	81	0	55	46	12	0	41	1.41
9350402--9350435	17	1.9	18	88	5	52	38	5	0	55	1.24
9350532--9350836	9	34.6	9	77	9	279	44	17	0	36	1.54
9350575--9350873	158	1.9	157	91	2	492	43	18	1	37	1.58
9356321--9356386	21	3.2	20	86	4	87	34	18	45	1	1.59
9356810--9356891	43	1.9	43	87	5	121	32	19	20	26	1.97
9356863--9357174	42	7.3	43	88	2	418	26	23	20	29	1.99
9356863--9357155	85	3.5	85	89	0	444	25	23	20	30	1.98
9358240--9358288	17	2.9	16	74	14	53	42	0	12	44	1.41
9360424--9361058	104	6.1	104	84	1	752	30	17	15	36	1.91
9360447--9361041	312	1.9	313	85	1	836	30	17	15	36	1.91
9361247--9361353	52	2.1	52	100	0	214	39	21	13	26	1.90
9367252--9367295	19	2.5	18	85	10	56	43	4	0	52	1.22
9372610--9372649	20	2.0	20	90	0	62	50	12	10	27	1.72
9372598--9372664	34	1.9	35	90	3	109	46	13	8	31	1.74
9373452--9373505	21	2.6	21	100	0	108	22	33	18	25	1.97
9375616--9375823	46	4.6	46	91	1	332	34	15	21	29	1.94
9378322--9378486	29	5.8	28	82	4	179	24	13	23	38	1.91
9378326--9378484	86	1.8	86	81	7	198	23	13	24	37	1.92
9385871--9385914	22	2.0	22	100	0	88	63	9	0	27	1.24
9385874--9385922	22	2.2	22	92	0	80	63	8	0	28	1.23
9396865--9396901	6	6.2	6	96	0	56	10	0	5	83	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9397634--9397669	18	2.0	18	88	0	54	41	2	8	47	1.48
9398694--9398751	29	2.0	29	100	0	116	31	10	17	41	1.83
9400548--9400838	50	5.8	50	85	1	343	20	27	22	28	1.99
9407196--9407494	68	4.4	68	80	3	305	33	17	23	26	1.96
9418396--9418436	19	2.1	20	90	4	66	58	4	9	26	1.50
9420564--9420879	45	7.1	45	62	15	136	25	25	22	27	2.00
9420041--9421119	133	8.1	132	92	1	1308	27	24	19	28	1.99
9422430--9422459	8	3.9	8	95	4	53	13	13	0	73	1.10
9422421--9422456	15	2.5	14	90	4	54	13	13	0	72	1.13
9427446--9427479	5	6.8	5	87	12	52	79	0	2	17	0.86
9427651--9427691	19	2.1	20	90	4	66	58	4	9	26	1.50
9431597--9431638	20	2.0	21	86	9	59	26	19	28	26	1.98
9439650--9439702	26	2.0	26	100	0	106	18	26	22	32	1.97
9443986--9444051	33	2.0	33	93	0	114	36	24	10	28	1.89
9445745--9445873	70	1.9	66	84	6	168	43	11	12	32	1.78
9448325--9448406	23	3.6	23	86	0	110	41	25	17	15	1.89
9448325--9448426	46	2.2	46	82	0	123	41	24	17	16	1.90
9448444--9448519	23	3.3	23	72	7	73	40	19	15	23	1.90
9448443--9448688	92	2.7	92	82	5	264	41	21	14	22	1.89
9448467--9448633	23	7.3	23	70	2	111	41	22	16	19	1.89
9448577--9448685	23	4.7	23	76	8	69	42	22	14	21	1.89
9448418--9448685	46	5.8	47	84	1	233	40	22	14	22	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9449989--9450172	87	2.1	87	85	4	246	36	15	25	22	1.93
9449989--9450192	29	7.0	29	77	5	162	37	14	25	22	1.92
9450049--9450192	58	2.5	58	85	3	182	38	14	25	22	1.92
9456084--9456122	18	2.1	18	85	4	51	12	33	12	41	1.82
9461637--9461703	34	1.9	35	87	3	100	31	8	14	44	1.76
9465201--9465252	24	2.2	24	93	3	88	53	23	7	15	1.67
9467204--9467250	18	2.6	18	89	3	67	53	0	46	0	1.00
9470350--9470413	31	2.0	33	93	6	114	39	23	12	25	1.90
9471604--9471689	33	2.6	33	79	0	91	30	10	43	16	1.81
9473490--9473519	12	2.5	12	94	0	51	76	13	3	6	1.11
9473751--9474571	110	7.6	111	87	5	1002	57	14	0	26	1.42
9473751--9474571	222	3.8	218	86	6	1024	57	14	0	26	1.42
9474089--9474571	108	4.6	104	85	6	600	57	14	0	26	1.42
9474986--9475035	24	2.1	24	85	14	68	62	2	2	34	1.18
9475451--9475485	2	17.5	2	100	0	70	48	0	0	51	1.00
9476420--9476498	39	2.1	39	83	11	101	54	2	0	43	1.14
9476472--9476517	9	4.8	9	87	12	65	63	2	0	34	1.07
9476463--9476504	17	2.5	16	79	20	50	64	2	0	33	1.07
9476479--9476537	11	5.8	10	84	11	68	59	3	0	37	1.14
9476472--9476537	22	3.2	20	87	10	82	60	4	0	34	1.17
9476472--9476545	22	3.6	21	80	12	73	60	4	0	35	1.15
9476656--9476680	5	5.0	5	100	0	50	60	40	0	0	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9483643--9483697	11	5.1	11	73	20	53	56	0	1	41	1.10
9503390--9503544	83	1.9	83	94	0	274	28	14	25	32	1.94
9507209--9507304	38	2.5	38	93	0	165	34	18	21	25	1.96
9507209--9507319	38	2.9	37	84	5	143	36	18	19	26	1.94
9513464--9513561	38	2.6	38	80	0	115	38	3	8	50	1.48
9518232--9518258	9	3.0	9	100	0	54	55	0	11	33	1.35
9532044--9532267	119	1.9	119	79	5	256	36	15	16	31	1.90
9533848--9533881	16	2.2	16	89	5	52	5	2	32	58	1.37
9534253--9534349	44	2.2	44	83	0	113	28	20	23	26	1.99
9534281--9534523	129	1.9	129	87	3	355	26	21	22	30	1.99
9534366--9534481	44	2.6	43	77	12	103	26	21	20	31	1.98
9534669--9534948	89	3.1	89	80	7	334	26	26	20	26	1.99
9534730--9534943	45	4.8	44	68	15	134	26	25	21	26	1.99
9542882--9542934	27	2.0	27	96	0	97	18	11	7	62	1.52
9543039--9543063	8	3.1	8	100	0	50	60	0	0	40	0.97
9543269--9543304	17	2.1	17	100	0	72	36	5	5	52	1.48
9545995--9546053	24	2.5	24	94	0	100	42	0	27	30	1.56
9546103--9546200	17	5.4	17	66	13	61	33	3	12	51	1.55
9546094--9546206	37	3.1	37	94	1	192	33	4	13	48	1.62
9546207--9546321	9	12.6	9	86	6	160	22	7	33	35	1.83
9552713--9552745	16	2.1	16	88	5	50	6	3	33	57	1.38
9553862--9553956	17	5.6	17	68	18	54	41	2	4	52	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9553931--9554045	60	1.9	58	86	6	160	40	2	5	51	1.38
9553933--9554065	58	2.3	59	82	10	148	41	2	6	49	1.41
9556109--9556147	18	2.2	17	86	4	51	46	5	5	43	1.48
9556109--9556153	17	2.6	18	85	3	56	42	4	6	46	1.50
9559223--9559254	10	3.1	10	91	8	55	9	18	12	59	1.59
9564485--9564570	43	2.0	43	90	0	136	22	24	2	51	1.60
9565693--9565732	19	2.1	19	86	9	55	2	25	0	72	0.97
9574511--9574545	16	2.2	16	90	10	54	40	5	5	48	1.51
9583440--9583706	27	9.9	27	78	1	241	28	25	21	23	1.99
9583442--9583706	81	3.3	81	81	1	273	29	25	21	24	1.99
9584263--9584342	38	2.1	38	85	0	106	36	30	12	21	1.90
9586247--9586300	3	18.0	3	100	0	108	33	0	0	66	0.92
9586934--9587132	99	2.0	99	97	0	371	38	19	3	39	1.67
9591481--9591514	2	17.0	2	93	0	59	50	2	0	47	1.16
9604466--9604646	27	6.6	27	80	5	166	37	14	24	24	1.92
9604648--9604728	27	3.1	26	73	18	69	30	20	19	28	1.97
9605090--9605121	16	2.0	16	100	0	64	43	6	12	37	1.68
9608987--9609025	18	2.2	17	86	13	53	33	0	20	46	1.51
9609130--9609158	8	3.6	8	100	0	58	24	13	27	34	1.93
9609245--9609343	23	4.3	23	97	0	189	23	21	26	29	1.99
9611356--9611667	137	2.3	137	89	1	457	45	16	17	20	1.86
9611358--9611666	91	3.4	90	90	2	449	44	16	17	21	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9611358--9611667	46	6.8	45	87	2	433	45	16	17	20	1.86
9611359--9611714	45	7.8	45	85	4	218	43	16	18	21	1.88
9612265--9612324	31	1.9	31	100	0	120	33	15	13	38	1.86
9613814--9613935	61	2.0	61	100	0	244	31	18	13	37	1.88
9617083--9617116	8	4.2	8	85	14	52	11	50	0	38	1.39
9617083--9617124	16	2.7	15	89	7	66	9	50	2	38	1.48
9617533--9617591	25	2.4	25	97	0	109	18	10	20	50	1.75
9623981--9624370	132	3.0	131	88	2	575	25	24	19	29	1.99
9623959--9624372	131	3.1	132	85	2	582	25	25	19	29	1.98
9625836--9625934	23	4.3	23	81	2	128	24	19	25	31	1.98

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