genome.fa.s25.2.7.7.80.10.50.1000.18.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   

This is table  18  of  56  ( 6609 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)
3326287--3326408	11	11.2	11	68	18	51	45	2	0	51	1.20
3326281--3326336	22	2.5	22	80	13	71	44	1	0	53	1.11
3326295--3326374	27	3.0	26	74	15	74	46	2	0	51	1.14
3326316--3326363	16	2.8	17	84	9	62	47	4	0	47	1.21
3326402--3326453	27	1.9	28	88	7	81	46	0	3	50	1.20
3326997--3327032	3	12.0	3	93	0	63	0	36	0	63	0.94
3327462--3327513	25	2.0	26	88	3	79	30	0	0	69	0.89
3327467--3327514	12	3.9	12	79	12	53	27	0	0	72	0.84
3333919--3333962	22	2.0	22	86	8	63	45	0	0	54	0.99
3334949--3335735	184	4.3	182	84	4	915	31	22	15	31	1.95
3335985--3336015	14	2.2	14	94	0	53	83	0	16	0	0.64
3336732--3336757	3	8.7	3	100	0	52	0	30	0	69	0.89
3337041--3337074	16	2.1	16	88	0	50	50	0	0	50	1.00
3337732--3337764	12	2.5	14	90	9	52	33	0	6	60	1.21
3337936--3337987	10	5.0	10	74	6	50	55	0	1	42	1.10
3337869--3338035	74	2.3	72	80	13	191	54	1	1	42	1.18
3337870--3338014	76	2.0	71	82	10	170	52	2	1	44	1.21
3338315--3338440	40	3.4	39	67	26	112	37	1	9	51	1.44
3338310--3338656	70	5.0	69	85	7	418	33	1	12	52	1.48
3338364--3338470	30	3.2	30	66	26	81	33	1	11	53	1.47
3338310--3338656	141	2.5	138	82	7	443	33	1	12	52	1.48
3338655--3339427	73	10.7	72	81	6	782	30	1	12	54	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3338684--3339425	291	2.6	287	86	3	1017	30	1	13	54	1.49
3339378--3339427	20	2.4	21	80	9	59	34	0	4	62	1.14
3340932--3341075	40	3.6	40	97	0	263	56	13	0	29	1.37
3341450--3341499	22	2.3	21	83	6	64	40	0	0	60	0.97
3342029--3342058	3	10.0	3	100	0	60	33	0	0	66	0.92
3346631--3346660	15	2.1	15	93	6	53	53	0	0	46	1.00
3347061--3347111	2	25.5	2	100	0	102	49	0	0	50	1.00
3347671--3347714	23	1.9	23	85	0	61	43	0	0	56	0.99
3349945--3349974	2	15.0	2	100	0	60	50	0	0	50	1.00
3350155--3350199	18	2.4	18	85	3	54	31	0	0	68	0.89
3350155--3350228	27	2.9	26	76	11	73	40	0	0	59	0.97
3350825--3350854	14	2.1	14	100	0	60	43	6	6	43	1.57
3351178--3351222	3	15.3	3	95	4	83	31	0	0	68	0.89
3351351--3351386	12	3.3	11	88	11	56	66	0	0	33	0.92
3353185--3353261	17	4.9	16	69	21	56	61	5	1	32	1.26
3353544--3353588	5	9.0	5	90	0	72	42	55	2	0	1.12
3353861--3353901	22	1.9	22	90	5	66	58	0	0	41	0.98
3353933--3354032	41	2.3	44	80	11	109	41	1	0	58	1.05
3357494--3357535	12	3.8	11	87	9	50	47	4	0	47	1.23
3362017--3362043	2	13.5	2	100	0	54	51	0	0	48	1.00
3363061--3363097	2	18.5	2	100	0	74	51	0	0	48	1.00
3363332--3363375	22	2.0	22	82	8	54	54	0	4	40	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3364500--3364530	2	15.5	2	100	0	62	51	0	0	48	1.00
3366757--3366790	16	2.3	14	90	10	50	88	0	11	0	0.52
3377225--3377291	27	2.4	28	76	11	75	40	0	1	58	1.07
3377386--3377420	10	3.5	10	88	0	52	62	0	0	37	0.95
3377676--3377727	24	2.1	26	86	10	74	50	0	17	32	1.47
3381975--3381999	12	2.1	12	100	0	50	52	0	8	40	1.31
3383878--3383943	21	3.4	21	62	23	54	34	27	4	33	1.77
3383870--3383942	36	2.0	36	100	0	146	35	28	5	30	1.80
3386550--3386578	7	4.3	7	91	8	51	72	0	0	27	0.85
3386550--3386578	13	2.1	14	93	6	51	72	0	0	27	0.85
3387656--3387687	14	2.3	15	89	10	50	46	0	0	53	1.00
3388967--3389022	21	2.7	20	74	15	51	42	3	0	53	1.18
3388968--3389058	34	2.7	32	79	14	87	41	3	1	53	1.24
3389069--3389135	28	2.4	27	82	12	82	34	2	0	62	1.10
3395015--3395051	19	1.9	19	89	10	58	35	0	0	64	0.94
3395114--3395163	12	3.9	13	72	15	50	30	0	0	70	0.88
3395117--3395158	8	5.4	8	83	11	52	26	0	0	73	0.83
3395117--3395156	15	2.5	16	84	12	55	27	0	0	72	0.85
3395394--3395463	27	2.5	30	75	17	87	44	1	5	48	1.35
3396030--3396086	21	2.7	20	77	20	62	42	0	1	56	1.10
3396614--3396660	24	2.0	24	84	12	62	61	0	0	38	0.96
3396614--3396660	23	2.0	23	84	12	60	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3396965--3397007	14	3.1	14	78	15	54	48	0	0	51	1.00
3397008--3397058	25	2.0	24	82	14	59	54	0	0	45	0.99
3397400--3397454	26	2.2	26	87	6	78	49	0	0	50	1.00
3397400--3397457	24	2.3	23	83	13	71	50	0	0	50	1.00
3397418--3397476	25	2.3	27	79	8	68	55	3	0	40	1.16
3397442--3397500	30	1.9	32	89	6	95	57	5	0	37	1.21
3397436--3397507	30	2.4	28	78	13	81	55	4	0	40	1.19
3398194--3398232	20	2.0	20	85	10	53	15	2	7	74	1.15
3398183--3398230	24	2.0	25	84	8	64	12	2	10	75	1.14
3399393--3399434	21	2.0	21	86	9	59	45	0	0	54	0.99
3399613--3399655	21	1.9	21	86	13	59	55	0	0	44	0.99
3400639--3400686	16	3.0	16	81	6	62	45	16	10	27	1.80
3400620--3400697	32	2.4	32	80	6	95	48	20	7	23	1.75
3401547--3401584	15	2.6	15	87	4	51	55	23	2	18	1.55
3401641--3401715	7	10.7	7	77	8	64	49	2	1	46	1.24
3401641--3401711	15	4.9	15	73	14	69	49	2	1	46	1.25
3401670--3401722	6	8.2	6	85	8	61	50	1	0	47	1.12
3403038--3403080	18	2.3	19	81	14	54	34	6	0	58	1.25
3403065--3403184	30	4.1	29	81	8	127	36	3	1	58	1.25
3404058--3404104	17	2.7	18	80	12	53	61	2	10	25	1.39
3404677--3404715	20	2.0	20	85	10	53	38	10	0	51	1.36
3411331--3411374	15	3.1	15	87	12	58	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3411359--3411404	23	2.0	23	83	8	58	50	2	0	47	1.13
3411465--3411552	38	2.3	37	81	11	115	32	3	1	62	1.19
3411479--3411546	19	3.6	18	76	11	64	29	1	1	67	1.08
3411475--3411552	38	2.0	40	90	5	124	32	2	1	64	1.15
3411644--3411684	21	2.0	21	85	9	57	41	0	0	58	0.98
3411644--3411715	27	2.7	29	77	18	84	43	0	0	56	0.99
3411650--3411694	22	2.0	22	83	8	56	40	0	0	60	0.97
3412629--3412658	14	2.1	15	93	6	53	46	0	0	53	1.00
3412796--3412852	15	4.0	14	75	8	53	40	0	0	59	0.97
3413269--3413322	24	2.2	24	83	6	65	55	0	0	44	0.99
3413876--3413921	2	23.0	2	100	0	92	50	0	0	50	1.00
3417612--3417646	2	18.0	2	94	5	63	51	0	0	48	1.00
3417834--3417879	17	2.8	16	81	18	51	54	0	0	45	0.99
3422236--3422266	16	2.0	16	93	6	55	29	0	0	70	0.87
3422397--3422434	2	19.0	2	100	0	76	50	0	0	50	1.00
3425697--3425736	3	13.3	3	100	0	80	67	0	32	0	0.91
3426117--3426179	26	2.4	26	97	0	117	41	4	33	20	1.73
3430350--3430400	2	25.5	2	100	0	102	49	0	0	50	1.00
3431146--3431224	23	3.3	23	76	15	72	40	2	0	56	1.12
3431143--3431211	19	3.2	20	80	11	68	37	2	0	59	1.12
3431226--3431270	21	2.1	21	84	12	56	71	0	2	26	0.98
3435067--3435109	15	2.8	15	78	3	50	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3435075--3435106	14	2.3	14	94	0	55	53	0	0	46	1.00
3435267--3435293	7	3.9	7	100	0	54	14	0	0	85	0.61
3435492--3435522	15	2.1	15	93	0	53	64	3	0	32	1.09
3438109--3438140	15	2.1	16	94	5	57	62	0	0	37	0.95
3438146--3438170	2	12.5	2	100	0	50	52	0	0	48	1.00
3438276--3438316	20	2.0	20	85	0	55	80	7	2	9	0.99
3439506--3439536	16	1.9	16	93	0	53	12	16	22	48	1.80
3440163--3440355	97	2.0	97	94	0	341	28	18	17	35	1.94
3442569--3442632	29	2.1	31	88	5	96	39	0	1	59	1.07
3442570--3442619	14	3.5	14	81	5	64	32	0	2	66	1.03

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