genome.fa.s13.2.7.7.80.10.50.1000.13.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  13  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)
4120049--4120080	13	2.3	15	89	10	50	15	6	21	56	1.62
4120455--4120852	54	7.4	53	75	7	252	29	18	13	38	1.88
4120455--4120804	162	2.2	162	80	5	402	29	18	13	39	1.88
4120489--4120908	108	3.9	108	76	7	295	29	19	13	38	1.89
4120501--4120900	162	2.5	162	77	7	377	29	19	13	38	1.89
4121083--4121695	323	1.9	324	92	1	1032	29	16	10	43	1.82
4120780--4121688	55	16.8	54	72	9	397	29	17	11	41	1.84
4127956--4128094	54	2.5	56	85	2	183	28	19	21	30	1.98
4127956--4128096	56	2.6	54	84	4	176	28	19	21	29	1.98
4137297--4137353	30	1.9	30	92	0	96	33	10	22	33	1.88
4152026--4152086	30	2.1	30	81	9	72	34	1	1	62	1.15
4153589--4153623	15	2.3	16	85	14	56	28	0	0	71	0.86
4166614--4166653	21	2.0	20	85	5	53	72	5	0	22	1.04
4166689--4166771	10	8.9	9	70	16	53	32	2	1	63	1.15
4166726--4166781	19	2.8	20	72	5	60	35	1	3	58	1.26
4169453--4169595	50	2.8	50	87	1	205	20	30	23	26	1.98
4184728--4184761	17	2.1	16	88	5	50	17	0	2	79	0.86
4184739--4184792	28	1.9	28	81	7	65	35	1	0	62	1.06
4198277--4198516	109	2.2	107	85	8	333	28	18	16	36	1.92
4200840--4201034	106	1.8	106	84	2	266	34	21	18	25	1.96
4203568--4203595	14	2.0	14	100	0	56	42	7	7	42	1.59
4208288--4208326	4	9.5	4	83	5	51	28	23	0	48	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4209117--4209156	13	3.2	13	82	17	57	75	0	25	0	0.81
4211215--4212094	88	10.0	88	91	1	1361	27	24	23	25	2.00
4212232--4212622	95	4.1	95	90	1	586	30	17	22	29	1.96
4214083--4214142	16	4.1	14	70	17	50	31	1	5	61	1.27
4214112--4214143	3	10.3	3	93	6	55	31	0	3	65	1.08
4214242--4214327	2	44.0	2	72	9	52	45	8	0	46	1.33
4214275--4214374	41	2.6	38	79	6	110	38	9	1	52	1.40
4220047--4220133	27	3.3	27	65	26	69	21	17	11	49	1.78
4220372--4220406	9	3.8	9	92	3	52	14	2	8	74	1.17
4223021--4223074	2	27.0	2	100	0	108	50	0	0	50	1.00
4223213--4223264	2	26.0	2	96	0	95	50	1	0	48	1.12
4223628--4223955	106	3.1	106	83	3	410	31	18	18	31	1.95
4224899--4224963	17	3.8	16	71	18	51	67	3	3	26	1.20
4224926--4224980	25	2.1	27	86	6	78	65	1	5	27	1.25
4224976--4225025	24	2.1	24	81	3	57	60	6	0	34	1.21
4226215--4226267	9	5.7	10	82	10	60	62	1	1	33	1.17
4226215--4226267	18	2.8	19	82	5	72	62	1	1	33	1.17
4226235--4226277	19	2.3	19	84	8	52	65	2	0	32	1.06
4226739--4226781	17	2.6	15	85	14	50	30	2	0	67	1.03
4230163--4230365	102	2.0	102	88	1	300	30	19	13	37	1.90
4233896--4233959	25	2.6	25	82	2	76	68	3	3	25	1.18
4233892--4233975	25	3.1	26	77	10	71	66	2	4	26	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4234013--4234081	22	3.2	21	76	17	63	60	2	0	36	1.11
4234020--4234086	21	3.1	22	78	14	61	56	4	0	38	1.19
4234064--4234136	37	2.0	37	86	0	101	58	2	1	36	1.21
4233996--4234137	10	14.4	10	72	11	62	61	3	0	34	1.18
4233888--4234136	9	26.8	9	70	16	77	62	3	2	32	1.22
4234623--4234742	9	13.6	9	66	21	58	31	2	1	64	1.17
4234689--4234743	17	3.2	17	77	10	58	34	1	0	63	1.05
4235845--4235896	26	2.0	26	82	17	65	50	1	0	48	1.12
4235870--4235904	15	2.2	16	90	5	54	60	2	0	37	1.12
4245278--4245324	3	15.7	3	100	0	94	68	0	0	31	0.90
4252534--4252571	12	3.2	12	85	3	51	68	2	15	13	1.32
4255608--4255677	24	2.9	24	83	8	97	41	2	40	15	1.62
4256775--4256845	33	2.3	31	85	7	99	57	29	0	12	1.35
4267789--4267894	53	2.0	53	94	0	185	6	17	15	60	1.55
4272362--4272505	47	3.1	47	72	16	165	44	2	3	49	1.33
4272347--4272562	91	2.4	91	92	0	351	47	3	3	45	1.36
4272377--4272630	91	2.6	99	73	16	242	46	3	1	47	1.32
4272420--4272587	47	3.7	46	72	15	159	47	4	2	45	1.35
4272569--4272864	120	2.5	120	93	1	486	43	3	4	48	1.39
4272699--4272735	15	2.4	16	82	17	51	54	0	0	45	1.00
4272810--4272844	18	2.0	17	88	5	52	45	0	0	54	0.99
4273003--4273099	45	2.2	44	88	5	142	35	29	3	31	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4280173--4280218	24	2.0	24	83	8	60	32	2	2	63	1.19
4281872--4281897	3	8.7	3	100	0	52	0	30	0	69	0.89
4282404--4282441	17	2.3	17	86	4	51	31	0	2	65	1.06
4300439--4300480	21	2.0	21	82	17	52	30	28	4	35	1.78
4303498--4303522	6	4.2	6	100	0	50	68	0	0	32	0.90
4304473--4304549	14	5.0	15	71	20	52	42	14	9	33	1.77
4304489--4304528	20	2.0	20	90	0	62	50	12	10	27	1.72
4304477--4304543	34	1.9	35	90	3	109	46	13	8	31	1.74
4317184--4317334	76	2.0	76	100	0	302	54	9	3	31	1.50
4318624--4318657	8	4.5	8	85	14	54	11	14	50	23	1.76
4318624--4318675	22	2.4	22	87	6	70	17	11	48	23	1.79
4321024--4321086	30	2.1	29	88	2	90	36	9	6	47	1.62
4321220--4321298	31	2.6	31	82	9	83	40	10	11	37	1.75
4322486--4322853	124	3.0	124	92	0	592	29	16	21	32	1.95
4324493--4324534	11	3.8	11	90	0	57	47	7	26	19	1.74
4324520--4324563	22	2.0	22	82	8	54	40	2	29	27	1.68
4329437--4329477	20	2.1	19	90	4	64	41	0	0	58	0.98
4329441--4329483	19	2.2	20	83	4	52	41	0	0	58	0.98
4331478--4331516	18	2.2	17	86	13	53	33	0	20	46	1.51
4332732--4332984	46	5.6	46	92	1	415	28	23	15	32	1.95
4347739--4347900	66	2.5	66	82	2	182	29	16	24	29	1.96
4350545--4350583	19	2.1	19	85	9	53	53	15	7	23	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4351949--4351977	14	2.1	14	100	0	58	41	13	20	24	1.89
4355304--4355340	6	6.2	6	93	0	65	0	18	0	81	0.70
4360421--4360470	20	2.4	22	76	6	59	60	6	4	30	1.39
4362243--4362294	16	3.4	16	69	15	56	34	0	9	55	1.32
4363601--4363645	24	2.0	24	86	8	67	33	8	6	51	1.59
4367406--4367481	24	3.2	23	76	9	73	48	0	1	50	1.09
4367420--4367463	12	3.7	11	80	14	52	52	0	2	45	1.13
4367443--4367480	14	2.4	17	87	12	55	47	0	0	52	1.00
4367699--4367730	17	2.0	17	88	11	50	62	15	21	0	1.32
4369424--4369476	28	2.0	25	82	10	61	45	3	7	43	1.50
4386114--4386139	6	4.3	6	100	0	52	50	15	0	34	1.45
4386306--4386458	15	10.3	15	70	8	62	18	9	57	15	1.63
4386310--4386458	45	3.3	45	80	4	176	18	8	58	14	1.61
4386331--4386453	30	4.1	31	75	8	92	18	8	58	13	1.61
4394292--4394341	19	2.6	20	81	15	61	32	0	8	60	1.26
4399768--4399817	22	2.3	22	80	10	59	46	2	8	44	1.44
4400024--4400077	2	27.0	2	96	0	99	48	0	1	50	1.11
4400116--4400168	13	3.7	15	80	12	58	60	0	3	35	1.15
4400850--4400913	32	2.0	32	100	0	128	40	21	9	28	1.84
4401204--4401248	23	1.9	24	86	13	67	15	6	33	44	1.73
4403503--4403593	40	2.3	40	83	7	107	38	21	21	17	1.93
4403987--4404065	7	11.4	7	74	8	63	21	0	32	45	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4403987--4404075	14	6.4	14	76	7	83	23	0	30	46	1.53
4404004--4404063	20	3.0	20	72	18	61	25	0	30	45	1.54
4404087--4404146	28	2.1	28	81	6	68	20	1	28	50	1.58
4404861--4405176	43	7.3	43	85	2	402	32	31	17	19	1.94
4405474--4405564	43	2.1	43	84	6	114	42	9	10	36	1.73
4406907--4407197	41	7.1	41	92	1	469	29	27	24	18	1.98
4407245--4407333	40	2.2	39	78	7	99	24	14	20	40	1.90
4407717--4407757	20	2.0	20	95	0	73	24	43	2	29	1.67
4408583--4408614	13	2.5	13	95	5	57	12	6	34	46	1.67
4408548--4408650	52	2.0	52	84	3	136	15	13	23	47	1.81

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