genome.fa.s3.2.7.7.80.10.50.1000.12.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  12  of  150  ( 17918 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)
3380652--3380685	17	1.9	18	88	5	52	38	5	0	55	1.24
3380800--3381236	9	48.0	9	77	11	410	45	17	0	35	1.54
3380979--3381085	38	2.8	39	88	2	155	43	18	0	37	1.50
3383357--3383422	21	3.1	21	82	0	69	39	21	37	1	1.63
3383856--3383948	43	2.2	43	86	3	125	29	19	24	26	1.98
3383870--3384078	42	4.9	42	82	3	213	27	22	20	30	1.98
3383869--3384076	85	2.4	85	80	4	213	27	22	20	29	1.98
3388171--3388258	40	2.2	40	81	0	104	18	19	35	27	1.95
3406134--3406162	14	2.1	14	100	0	58	44	13	13	27	1.82
3407325--3407360	12	3.2	12	92	7	58	61	0	0	38	0.96
3407307--3407456	39	3.7	40	80	11	155	61	0	2	36	1.12
3407325--3407416	9	9.7	9	70	19	62	63	0	1	35	1.02
3407383--3407414	16	2.0	16	100	0	64	62	0	0	37	0.95
3407414--3407439	11	2.4	11	100	0	52	53	0	7	38	1.30
3409088--3409131	14	3.0	15	75	18	56	20	6	6	65	1.39
3411413--3411453	14	2.9	15	78	7	50	43	7	7	41	1.60
3411422--3411488	34	1.9	35	85	8	93	37	8	7	46	1.64
3422125--3422319	98	2.0	98	96	0	363	36	24	9	29	1.87
3424836--3425433	44	13.8	44	70	12	291	27	22	20	29	1.99
3424771--3425445	217	3.1	217	93	0	1129	27	22	20	29	1.99
3424753--3425304	44	12.7	44	71	16	300	26	23	20	29	1.99
3426661--3426688	6	4.7	6	100	0	56	0	14	0	85	0.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3430777--3430807	13	2.5	13	94	5	55	48	0	0	51	1.00
3437181--3437205	12	2.1	12	100	0	50	24	36	24	16	1.94
3437365--3437450	9	9.4	9	87	2	118	39	27	9	23	1.85
3442828--3442894	27	2.4	28	83	11	77	44	14	2	37	1.61
3444280--3444569	103	2.9	98	87	5	388	32	27	18	21	1.97
3444410--3444489	27	2.7	27	86	11	97	32	27	22	17	1.96
3447367--3447392	11	2.4	11	100	0	52	73	0	7	19	1.07
3449037--3449103	24	2.8	23	70	19	57	74	2	4	17	1.11
3463750--3463777	3	9.3	3	100	0	56	32	0	67	0	0.91
3471445--3471479	17	1.9	17	88	11	52	42	0	0	57	0.99
3471827--3471856	7	4.3	7	95	0	51	30	33	0	36	1.58
3476176--3476201	10	2.6	10	100	0	52	26	0	0	73	0.84
3476950--3477379	108	3.9	108	92	2	650	34	17	17	30	1.93
3477977--3478044	31	2.3	29	82	7	82	61	13	14	10	1.56
3481286--3481353	31	2.2	31	86	2	93	55	0	5	38	1.24
3482343--3482385	21	2.0	22	86	13	63	48	2	0	48	1.14
3482336--3482392	22	2.5	24	78	21	68	50	1	0	47	1.11
3487648--3487728	39	2.0	40	95	2	146	51	11	4	32	1.58
3489874--3489904	15	2.1	15	93	0	53	67	16	0	16	1.23
3490040--3490091	18	2.8	18	82	5	59	76	5	1	15	1.05
3490051--3490093	13	3.2	14	80	9	54	79	4	2	13	1.00
3490134--3490175	15	3.2	13	78	15	50	57	0	2	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3490423--3490461	18	2.1	18	85	4	51	66	5	2	25	1.25
3497957--3497990	12	2.8	12	86	13	52	82	0	17	0	0.67
3498835--3499057	44	4.9	45	74	15	181	29	19	22	28	1.98
3498795--3499037	44	5.2	49	74	19	166	28	18	23	29	1.98
3498775--3498999	94	2.4	94	86	5	296	29	19	22	28	1.98
3498924--3499603	363	1.9	366	83	1	889	31	16	21	30	1.95
3499430--3499641	44	4.8	44	73	9	162	29	19	22	28	1.98
3499681--3499778	41	2.4	41	93	3	162	29	19	18	32	1.96
3499762--3499929	44	3.9	42	76	11	142	31	17	19	31	1.95
3499764--3499959	88	2.2	88	79	7	202	31	17	19	31	1.96
3504962--3505027	27	2.4	27	89	0	105	31	18	18	31	1.95
3505329--3505362	6	5.7	6	92	0	59	32	14	17	35	1.91
3505331--3505367	12	3.2	12	88	3	58	29	10	18	40	1.85
3515557--3515598	21	2.0	21	86	9	59	28	2	2	66	1.16
3515575--3515615	19	2.2	18	86	4	55	24	0	4	70	1.06
3516716--3516757	9	4.4	9	80	19	50	57	0	2	40	1.12
3523893--3524063	46	3.7	46	81	2	200	34	19	19	25	1.96
3536308--3536394	39	2.2	39	95	0	156	33	22	9	34	1.86
3549412--3549439	11	2.5	11	100	0	56	53	17	0	28	1.44
3552888--3552939	27	2.0	27	92	3	88	30	34	21	13	1.92
3552919--3553054	42	3.5	42	71	17	146	33	27	16	22	1.95
3552913--3553091	75	2.4	75	93	0	295	32	27	17	21	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3555270--3555365	25	3.9	24	78	6	93	34	20	23	20	1.97
3555258--3555365	50	2.2	49	83	5	128	33	21	25	19	1.97
3558960--3559241	36	7.8	36	84	4	268	23	41	22	12	1.88
3558960--3559241	72	3.9	72	81	4	309	23	41	22	12	1.88
3558974--3559241	108	2.5	108	84	3	317	23	41	22	13	1.88
3562652--3562709	9	6.4	9	70	21	50	60	1	1	36	1.17
3562736--3562776	9	4.6	9	85	11	57	19	0	2	78	0.87
3562841--3562906	29	2.2	29	97	2	123	31	0	3	65	1.08
3562839--3562923	10	9.2	9	74	15	68	32	1	2	63	1.15
3562837--3562906	10	7.1	10	75	3	70	34	0	2	62	1.10
3568603--3568645	13	3.1	14	84	12	54	60	0	0	39	0.97
3570414--3570446	15	2.3	15	89	5	50	12	3	9	75	1.14
3572419--3572469	13	3.9	13	75	10	59	31	5	25	37	1.80
3578754--3578779	6	4.3	6	100	0	52	84	0	0	15	0.62
3582770--3582822	19	2.8	18	83	8	70	33	0	1	64	1.05
3589446--3589477	16	2.1	16	88	11	50	68	0	3	28	1.04
3589473--3589512	14	2.7	16	81	14	50	57	0	0	42	0.98
3600795--3600827	2	17.0	2	93	6	59	48	0	0	51	1.00
3600833--3600875	18	2.5	17	82	14	52	53	2	18	25	1.56
3601223--3601262	14	2.9	14	84	0	53	32	7	17	42	1.77
3601231--3601297	35	1.9	35	87	3	100	31	10	13	44	1.77
3601246--3601285	20	2.0	20	85	0	53	27	12	12	47	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3604226--3604271	22	2.1	22	100	0	92	39	17	13	30	1.87
3604344--3604496	71	2.1	71	81	13	170	37	9	9	43	1.70
3604431--3604497	20	3.2	23	61	30	58	43	10	8	37	1.71
3607568--3607608	15	2.8	14	85	10	55	58	0	4	36	1.20
3615726--3615750	7	3.6	7	100	0	50	24	0	0	76	0.80
3619667--3619692	3	8.7	3	100	0	52	0	0	30	69	0.89
3620853--3620909	15	3.2	20	65	31	56	50	0	1	47	1.11
3620841--3620909	33	2.1	34	94	2	122	49	0	1	49	1.09
3620925--3620950	6	4.3	6	100	0	52	46	0	0	53	1.00
3620907--3620963	12	4.9	12	74	21	50	35	0	0	64	0.93
3620951--3620999	22	2.2	23	79	17	59	36	2	2	59	1.21
3623112--3623160	22	2.3	22	83	13	66	46	0	0	53	1.00
3629348--3629399	21	2.5	21	80	0	59	30	28	9	30	1.89
3638547--3638593	16	2.9	16	80	3	58	80	10	4	4	0.98
3638551--3638592	15	2.6	16	81	7	50	80	9	4	4	0.99
3654793--3654853	17	3.6	17	77	6	70	32	3	1	62	1.21
3654791--3654852	19	3.5	19	81	16	80	33	3	1	61	1.22
3660386--3660690	90	3.4	90	88	2	400	28	16	23	31	1.96
3660687--3660718	7	4.6	7	96	0	55	31	3	37	28	1.73
3660386--3660690	45	6.8	45	80	5	348	28	16	23	31	1.96
3660737--3660825	45	2.0	45	84	4	117	37	15	19	28	1.92
3662868--3663093	106	2.1	106	88	0	344	31	17	18	32	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3668764--3668803	21	2.0	21	85	5	55	40	0	15	45	1.46
3672285--3672345	31	2.0	32	87	12	92	29	9	11	49	1.71
3675142--3675205	33	1.9	33	90	0	101	25	15	42	17	1.88
3679969--3680011	21	2.0	21	100	0	86	30	9	9	51	1.65
3681054--3681118	3	21.7	3	100	0	130	67	0	32	0	0.91
3683728--3683806	39	2.0	39	97	0	149	25	3	26	44	1.71
3690486--3690519	18	1.9	18	94	5	61	52	2	0	44	1.16
3696492--3696529	19	2.0	19	94	0	67	68	7	15	7	1.37
3700957--3700996	13	3.1	13	92	0	71	40	25	7	27	1.82
3708063--3708231	60	2.8	60	88	0	257	25	49	11	14	1.76

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