genome.fa.s1.2.7.7.80.10.50.1000.113.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  113  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)
33841344--33841391	20	2.5	20	77	16	55	58	6	22	12	1.57
33845081--33845145	18	3.6	18	95	0	121	43	0	3	53	1.16
33848395--33848428	16	2.2	15	89	5	50	55	0	0	44	0.99
33848392--33848438	22	2.2	20	85	14	60	55	0	0	44	0.99
33848489--33848559	30	2.3	32	80	14	94	47	9	7	35	1.64
33853797--33853845	24	2.0	24	96	0	89	38	22	4	34	1.73
33854954--33855148	50	3.9	50	79	2	196	23	28	20	28	1.99
33862549--33862788	50	4.7	50	79	4	214	22	26	21	29	1.99
33875992--33876040	10	5.0	10	77	18	50	8	12	2	77	1.07
33879229--33879278	20	2.5	20	81	9	66	44	2	0	54	1.11
33883718--33883751	6	5.7	6	100	0	68	35	0	32	32	1.58
33884198--33884266	34	2.0	34	97	0	129	27	10	17	44	1.80
33884807--33884836	12	2.5	12	88	0	51	70	13	13	3	1.30
33884872--33884905	3	11.3	3	100	0	68	32	0	0	67	0.91
33890379--33890447	34	2.0	34	100	0	138	28	8	17	44	1.78
33895582--33895742	26	6.2	26	86	1	225	37	9	28	23	1.87
33895582--33895742	77	2.1	78	89	3	245	37	9	28	23	1.87
33895582--33895782	77	2.6	78	84	5	228	35	10	29	24	1.89
33898029--33898067	20	2.0	20	90	10	62	35	2	7	53	1.43
33901448--33901490	14	3.1	13	80	12	50	83	4	0	11	0.78
33908718--33908759	22	1.9	22	85	0	57	30	16	28	23	1.96
33915714--33915832	45	2.6	45	74	4	105	31	18	25	24	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33915930--33916959	44	23.6	44	68	11	167	28	19	24	27	1.98
33915790--33917297	435	3.5	435	89	1	2175	28	18	24	27	1.98
33915789--33917312	218	7.0	218	87	2	2026	28	18	24	27	1.98
33917643--33917685	13	3.3	12	81	15	50	81	4	0	13	0.84
33922153--33922208	17	3.2	17	75	10	51	50	1	0	48	1.11
33923386--33923584	85	2.3	89	79	10	221	29	18	14	37	1.90
33923734--33923766	9	3.7	9	100	0	66	45	0	0	54	0.99
33923725--33923764	18	2.2	18	86	0	53	52	2	0	45	1.14
33923739--33923783	20	2.4	18	85	7	54	51	0	0	48	1.00
33923780--33923824	19	2.4	19	84	0	54	53	2	2	42	1.25
33923794--33923841	19	2.5	19	89	0	69	56	2	4	37	1.30
33923879--33923938	21	2.9	22	78	19	74	60	3	10	26	1.45
33928310--33928371	24	2.4	26	81	10	74	24	35	6	33	1.81
33928578--33928654	29	2.7	29	84	8	86	33	1	2	62	1.17
33928600--33928660	28	2.1	29	81	3	70	36	1	3	59	1.24
33933754--33933796	18	2.4	18	92	0	68	13	41	2	41	1.57
33939401--33939705	102	3.0	101	80	6	348	31	19	9	40	1.83
33941653--33941714	31	2.0	31	96	0	115	30	22	14	32	1.94
33942172--33942288	39	3.0	38	82	5	135	41	12	9	35	1.76
33943866--33943924	25	2.4	25	97	0	109	67	0	6	25	1.15
33946414--33946440	4	6.8	4	100	0	54	77	0	0	22	0.76
33947345--33947413	34	2.0	34	100	0	138	26	13	28	31	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33948903--33948941	21	1.9	21	89	5	62	58	0	0	41	0.98
33948902--33948947	20	2.3	20	81	7	58	63	0	0	36	0.95
33953698--33953726	14	2.0	15	93	6	51	31	0	0	68	0.89
33957952--33957992	19	2.2	19	86	0	55	19	21	17	41	1.90
33958951--33959192	134	1.8	134	80	7	294	38	15	15	30	1.89
33964187--33964351	36	4.5	37	78	6	183	21	12	28	37	1.90
33964187--33964375	73	2.6	71	80	8	209	20	13	28	37	1.90
33965339--33965465	54	2.4	54	83	0	164	24	25	27	22	2.00
33966581--33966611	6	5.2	6	92	0	53	70	0	12	16	1.16
33968060--33968086	14	1.9	14	100	0	54	29	0	7	62	1.22
33970632--33970670	20	2.0	20	90	10	62	17	20	5	56	1.60
33970873--33971052	50	3.6	49	82	3	193	23	25	20	31	1.98
33970922--33971158	50	4.6	50	81	7	180	24	27	18	28	1.98
33985352--33985534	50	3.7	50	85	1	215	27	22	28	21	1.99
33985354--33985534	100	1.8	100	84	2	247	27	22	28	21	1.99
33985456--33985573	49	2.4	50	82	4	141	33	22	22	22	1.97
33994466--33994519	26	2.1	26	82	3	65	29	14	11	44	1.80
34024926--34025104	50	3.6	49	79	8	175	30	24	25	20	1.98
34048443--34048711	46	5.8	46	89	1	423	36	9	24	28	1.87
34049027--34049053	2	13.5	2	100	0	54	48	0	0	51	1.00
34051555--34051615	22	2.8	22	97	0	113	26	26	13	34	1.93
34055488--34055575	25	3.4	25	70	11	88	15	21	30	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34055490--34055602	52	2.2	52	98	0	217	15	20	30	33	1.94
34058314--34058375	18	3.3	18	67	20	54	14	33	8	43	1.75
34058297--34058382	39	2.2	39	97	0	163	12	32	6	47	1.68
34067397--34067453	27	2.1	27	96	0	105	45	12	3	38	1.59
34067668--34067709	22	2.1	19	86	13	57	45	2	0	52	1.13
34068414--34068467	25	2.1	26	83	10	67	29	5	1	62	1.28
34075816--34075961	25	5.8	25	82	3	159	29	12	22	35	1.91
34075815--34075961	50	2.9	50	84	0	186	29	12	23	35	1.91
34078222--34078298	39	2.0	38	80	12	86	29	6	2	61	1.35
34085474--34085704	50	4.6	50	84	2	257	27	20	30	21	1.98
34085471--34085704	100	2.3	100	89	0	342	27	20	29	21	1.98
34085471--34085753	50	5.7	49	82	3	203	27	20	28	22	1.99
34087436--34087466	11	2.7	12	90	10	55	25	0	0	74	0.82
34089758--34089944	51	3.7	51	81	7	211	28	13	27	30	1.94
34089761--34089843	26	3.2	26	65	27	68	30	12	25	32	1.92
34093740--34093782	16	2.8	15	79	13	52	53	27	0	18	1.45
34109217--34109265	20	2.5	20	81	15	66	12	24	6	57	1.58
34109480--34109604	50	2.5	49	81	10	153	20	29	23	26	1.99
34110910--34110964	28	2.0	28	92	0	92	43	18	7	30	1.77
34112417--34112456	14	3.0	14	83	16	50	42	15	5	37	1.68
34119161--34119209	20	2.5	19	79	20	57	53	2	2	42	1.24
34119164--34119205	16	2.6	16	81	7	50	52	2	2	42	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34119213--34119241	15	1.9	15	100	0	58	0	13	0	86	0.58
34119279--34119340	30	2.1	30	87	6	90	48	11	8	32	1.68
34128435--34128467	17	2.0	17	88	5	50	45	0	0	54	0.99
34130800--34130869	27	2.5	29	90	6	110	40	10	1	48	1.45
34130924--34131002	27	2.9	27	90	7	117	27	26	29	16	1.97
34131049--34131164	18	6.5	17	76	13	76	65	0	33	0	0.99
34131051--34131122	10	6.6	10	73	17	54	68	0	31	0	0.90
34131051--34131152	24	4.3	23	71	11	73	66	0	33	0	0.92
34131054--34131127	14	5.1	13	71	25	51	68	0	31	0	0.89
34131054--34131133	34	2.8	28	75	24	85	67	0	32	0	0.91
34131069--34131228	38	4.4	38	83	9	176	66	0	32	1	1.00
34131071--34131171	10	10.5	10	72	16	79	65	0	33	0	1.00
34131911--34131962	19	2.7	19	82	8	61	26	0	7	65	1.20
34135956--34136074	62	1.9	62	85	11	163	53	11	0	34	1.37
34135956--34136088	64	2.1	62	82	12	155	53	12	0	34	1.38
34136080--34136129	3	16.7	3	100	0	100	66	0	0	34	0.92
34136422--34136527	27	3.9	27	91	2	160	16	30	26	27	1.96
34136554--34136582	9	3.0	10	90	10	51	0	0	10	89	0.48
34136556--34136581	9	2.9	9	100	0	52	0	0	7	92	0.39
34136586--34136653	27	2.5	28	85	4	95	48	1	10	39	1.46
34137728--34137790	33	1.9	33	81	12	76	60	1	6	31	1.31
34153810--34153860	17	2.9	17	86	13	61	72	1	3	21	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34153927--34153972	14	3.0	16	76	20	53	39	0	8	52	1.33
34156946--34157004	24	2.5	24	94	0	100	44	13	22	20	1.86
34157007--34157065	29	2.0	29	100	0	118	55	3	20	20	1.57
34159307--34159344	20	2.0	20	94	5	69	31	31	5	31	1.80
34161054--34161101	24	2.0	25	84	12	64	25	8	10	56	1.61
34162889--34163077	95	2.0	97	91	2	310	37	14	17	31	1.90
34167228--34167255	8	3.5	8	100	0	56	60	0	10	28	1.30
34167590--34167671	43	1.9	43	85	5	112	36	19	17	26	1.94
34167641--34167777	42	3.2	41	75	7	123	35	18	21	25	1.96
34169017--34169056	20	2.0	21	85	5	55	50	2	7	40	1.44

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