genome.fa.s13.2.7.7.80.10.50.1000.188.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  188  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)
54832852--54832878	6	4.5	6	100	0	54	85	0	0	14	0.61
54832921--54832950	11	2.7	11	94	0	51	76	0	23	0	0.78
54842804--54842835	6	5.3	6	92	0	55	0	18	37	43	1.51
54847676--54847724	24	2.2	24	86	13	70	48	0	2	48	1.12
54847701--54847766	30	2.4	27	75	20	73	48	0	1	50	1.10
54849160--54849205	3	15.3	3	100	0	92	34	0	0	65	0.93
54854475--54854524	2	25.0	2	100	0	100	50	0	0	50	1.00
54864960--54864990	2	15.5	2	100	0	62	51	0	0	48	1.00
54870626--54870658	16	2.1	16	88	5	50	36	3	0	60	1.12
54871077--54871124	23	2.0	25	84	11	66	45	6	8	39	1.59
54874285--54874322	17	2.1	19	85	9	53	21	13	10	55	1.67
54888062--54888094	15	2.2	15	100	0	66	48	6	0	45	1.27
54889515--54889557	19	2.3	18	84	11	52	37	0	0	62	0.95
54890428--54890462	7	5.0	7	100	0	70	28	0	0	71	0.86
54895020--54895059	15	2.7	15	96	0	71	17	50	32	0	1.47
54895015--54895057	15	2.6	17	82	17	63	16	51	32	0	1.45
54898705--54898730	6	4.3	6	100	0	52	69	15	0	15	1.20
54900200--54900266	33	2.0	33	100	0	134	23	2	23	49	1.64
54909105--54909170	18	3.3	19	76	19	80	65	0	1	33	1.02
54909093--54909160	11	6.4	11	72	17	54	61	0	2	35	1.11
54909083--54909150	31	2.2	31	91	0	118	63	0	2	33	1.10
54909133--54909179	10	5.0	10	80	15	64	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54909134--54909200	30	2.4	27	92	7	107	65	0	1	32	1.02
54909134--54909210	30	2.8	26	83	14	93	64	0	1	33	1.01
54909557--54909598	3	14.3	3	95	5	77	64	0	0	35	0.94
54913662--54913701	17	2.4	16	84	12	53	67	2	2	27	1.16
54915138--54915178	5	8.2	5	100	0	82	19	0	0	80	0.71
54917026--54917065	19	2.0	20	86	13	57	60	20	0	20	1.37
54917026--54917067	21	2.0	20	82	13	50	61	19	0	19	1.34
54917682--54917759	2	40.0	2	90	10	126	47	1	0	51	1.09
54923208--54923286	39	2.0	39	95	0	140	54	13	11	20	1.70
54925334--54925368	18	2.1	17	89	10	54	48	0	0	51	1.00
54926347--54926442	29	3.5	27	73	10	70	63	2	0	34	1.06
54926347--54926424	40	2.0	39	87	7	113	62	2	0	34	1.09
54926353--54926440	38	2.3	38	77	14	94	67	2	0	30	1.03
54926408--54926452	15	3.0	16	75	12	51	64	0	0	35	0.94
54927680--54927747	18	3.9	18	78	18	72	33	1	1	63	1.13
54927685--54927747	9	7.2	9	75	21	55	33	0	1	65	1.03
54927663--54927743	33	2.3	37	75	18	91	34	2	2	60	1.23
54934968--54935030	25	2.4	26	84	7	83	39	9	0	50	1.35
54938498--54938565	23	2.7	24	77	13	66	33	0	5	60	1.21
54951356--54951451	31	3.1	31	95	3	174	32	9	12	45	1.74
54952000--54952065	24	2.8	23	77	8	71	77	4	13	4	1.08
54952046--54952079	16	2.1	16	89	10	52	88	5	5	0	0.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54952280--54952308	10	2.9	10	100	0	58	17	10	10	62	1.54
54957669--54957762	31	3.1	30	95	4	170	32	9	12	44	1.75
54958377--54958404	2	14.0	2	100	0	56	50	0	0	50	1.00
54963151--54963191	15	2.7	15	92	0	64	48	0	7	43	1.30
54968308--54968338	16	1.9	16	93	0	53	51	0	0	48	1.00
54977713--54977763	27	1.9	26	88	4	75	54	3	0	41	1.19
54977735--54977782	22	2.0	25	88	11	75	54	4	0	41	1.20
54978509--54978551	22	2.0	21	95	4	77	53	0	0	46	1.00
54982690--54982776	45	1.9	46	88	2	131	19	28	17	34	1.94
54983243--54983288	24	1.9	24	86	8	67	67	6	10	15	1.40
54990021--54990072	11	4.7	11	82	0	59	25	26	1	46	1.63
54990014--54990069	22	2.5	23	82	5	78	26	26	1	44	1.64
54990851--54990925	29	2.6	29	91	0	123	37	22	16	24	1.93
54991585--54991637	26	2.1	26	89	10	83	39	37	5	16	1.73
54992773--54992810	18	2.1	18	95	0	67	23	5	0	71	1.07
55007401--55007433	16	2.0	17	88	5	50	51	9	21	18	1.73
55014684--55014932	50	4.8	50	85	3	300	20	28	23	26	1.99
55014683--55014932	100	2.4	104	87	5	346	20	28	23	26	1.99
55015027--55015058	13	2.5	13	94	0	55	56	12	0	31	1.37
55026564--55026613	25	2.0	25	88	7	75	64	6	0	30	1.18
55030409--55030439	16	1.9	16	93	0	53	32	6	6	54	1.51
55044704--55044775	21	3.0	24	74	15	69	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55045041--55045080	19	2.1	19	85	4	53	47	5	2	45	1.38
55045876--55045914	9	4.4	9	83	6	53	66	2	2	28	1.18
55045876--55045914	17	2.2	18	86	4	53	66	2	2	28	1.18
55046397--55046453	26	2.2	25	81	9	60	59	1	3	35	1.25
55048381--55048481	3	32.7	3	86	11	134	31	2	1	63	1.21
55049029--55049155	67	2.0	64	87	9	188	12	10	14	62	1.53
55049502--55049809	110	2.8	110	90	1	469	31	15	17	35	1.91
55059534--55059610	36	2.2	36	97	2	147	23	12	28	35	1.92
55062987--55063082	9	10.7	9	87	0	129	61	5	1	32	1.25
55062987--55063082	6	16.0	6	90	0	129	61	5	1	32	1.25
55065902--55065945	2	22.0	2	100	0	88	50	0	0	50	1.00
55066410--55066439	2	15.0	2	92	0	51	50	3	0	46	1.18
55073175--55073234	3	20.0	3	92	0	102	30	0	3	66	1.07
55073233--55073363	3	43.7	3	95	0	208	29	32	4	33	1.78
55087029--55087055	14	1.9	14	100	0	54	66	11	0	22	1.22
55097128--55097184	2	28.5	2	100	0	114	0	0	49	50	1.00
55105278--55105312	16	2.2	16	100	0	70	48	17	17	17	1.81
55109321--55109345	13	1.9	13	100	0	50	12	0	8	80	0.92
55113565--55113625	30	2.0	30	100	0	122	29	27	13	29	1.94
55117096--55117193	49	2.0	48	94	2	169	46	10	17	25	1.79
55122847--55122876	13	2.2	14	94	5	53	33	0	0	66	0.92
55123315--55123443	59	2.1	60	92	4	215	45	7	6	40	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55124337--55124393	25	2.2	25	84	6	69	54	1	0	43	1.10
55126144--55126259	30	4.0	30	81	11	102	41	3	0	54	1.23
55126149--55126207	25	2.4	24	83	13	59	44	3	0	52	1.17
55127961--55128001	21	2.0	20	85	4	55	46	2	2	48	1.28
55131260--55131287	2	14.0	2	100	0	56	50	0	0	50	1.00
55140381--55140441	28	2.1	29	87	3	88	29	1	8	60	1.35
55141421--55141446	2	13.0	2	100	0	52	50	0	0	50	1.00
55152709--55152734	4	6.5	4	100	0	52	50	0	0	50	1.00
55153158--55153208	23	2.2	23	85	0	66	29	7	21	41	1.81
55157187--55157294	53	2.0	53	98	0	207	33	20	12	33	1.91
55165346--55165447	45	2.3	45	82	3	134	44	17	14	23	1.86
55165649--55165736	40	2.2	41	87	2	124	40	20	7	30	1.81
55165649--55165716	21	3.3	21	68	15	61	38	20	8	32	1.84
55166543--55166601	25	2.4	25	94	5	104	50	3	0	45	1.18
55166673--55166728	30	1.9	28	85	7	76	48	5	0	46	1.25
55168517--55168972	250	1.8	245	84	3	617	38	11	6	43	1.66
55169120--55169163	17	2.5	19	82	10	58	43	0	2	54	1.12
55173430--55173463	2	17.0	2	100	0	68	50	0	0	50	1.00
55174668--55174716	3	16.0	3	95	4	89	65	0	2	32	1.04
55175415--55175580	3	54.3	3	95	2	287	65	0	2	32	1.06
55181260--55181325	13	5.0	13	75	3	60	34	0	22	42	1.54
55181253--55181351	40	2.5	40	83	0	117	38	1	21	39	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55185553--55185596	23	1.9	22	82	17	54	36	25	0	38	1.56
55185664--55185831	23	7.3	23	91	0	282	30	26	20	22	1.98
55185664--55185830	69	2.4	69	97	0	316	31	26	20	21	1.98
55187226--55187260	18	1.9	18	88	0	52	31	11	2	54	1.51
55188899--55189026	43	3.0	43	79	8	161	23	17	27	31	1.97
55193798--55193823	12	2.2	12	100	0	52	23	7	0	69	1.14
55195017--55195044	5	5.6	5	100	0	56	57	0	0	42	0.99
55197901--55198036	25	5.5	24	82	3	110	34	17	25	22	1.96
55197904--55198044	50	2.8	49	78	4	138	34	17	25	22	1.96
55200077--55200153	28	2.8	27	92	3	127	32	24	20	22	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