genome.fa.s78.2.7.7.80.10.50.1000.4.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: Scaffold78
Parameters: 2 7 7 80 10 50 1000
Length:  2238306

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   

This is table  4  of  15  ( 1751 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)
518172--518789	104	6.0	104	88	5	780	35	11	33	20	1.88
518192--518789	137	4.4	135	88	4	812	35	11	32	19	1.88
518192--518789	34	17.5	35	84	8	727	35	11	32	19	1.88
518772--518849	30	2.6	29	86	10	95	33	16	29	20	1.95
518699--518828	64	2.0	64	82	5	156	36	13	28	21	1.92
518801--518947	57	2.5	61	75	11	146	28	16	31	23	1.96
518808--518953	30	4.9	31	75	10	110	28	16	31	23	1.96
519895--519948	26	2.1	25	86	10	74	0	11	7	81	0.87
519912--519961	16	3.2	16	78	16	61	0	10	10	80	0.92
520212--520241	10	2.9	10	95	5	51	0	0	10	90	0.47
520199--520242	12	3.8	12	90	3	63	0	2	11	86	0.66
527184--527208	13	1.9	13	100	0	50	36	16	16	32	1.90
527825--527932	38	2.8	38	88	0	162	26	14	30	27	1.95
529534--529588	28	2.0	28	100	0	110	18	10	21	49	1.78
534360--534392	16	2.1	16	88	11	50	6	0	12	81	0.85
534355--534393	20	2.0	20	85	5	53	5	0	15	79	0.90
536459--536498	19	2.2	19	86	4	55	15	0	10	75	1.05
536447--536668	76	2.9	74	75	13	175	18	8	9	63	1.47
536586--536739	56	2.7	57	79	5	152	17	7	11	64	1.47
536709--536740	17	1.9	16	93	6	55	18	6	12	62	1.50
536595--536763	57	3.0	56	76	9	146	16	7	11	64	1.48
536809--536851	18	2.4	18	84	7	52	18	4	2	74	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
536824--536861	18	2.0	18	90	10	58	18	7	0	73	1.06
538519--538560	22	2.0	21	86	13	59	42	0	0	57	0.99
538555--538598	18	2.4	18	85	7	54	40	0	6	52	1.28
539912--539954	2	21.5	2	100	0	86	51	0	0	48	1.00
541725--541796	32	2.2	32	82	7	83	43	2	2	51	1.30
544029--544053	2	12.5	2	100	0	50	52	0	0	48	1.00
543997--544111	58	2.0	58	92	0	194	50	8	3	37	1.50
544088--544130	2	22.0	2	90	4	70	53	0	0	46	1.00
546205--546250	22	2.0	23	84	12	60	45	2	0	52	1.13
546515--546583	7	9.9	7	72	12	52	55	0	0	44	0.99
546501--546554	15	3.7	15	82	7	67	44	0	0	55	0.99
546800--546851	20	2.7	19	77	11	61	48	0	3	48	1.20
549429--549494	30	2.2	30	94	0	114	27	7	9	56	1.58
558393--558469	20	3.8	20	77	5	75	44	15	7	32	1.75
558393--558469	40	1.9	40	81	5	93	44	15	7	32	1.75
558419--558470	20	2.6	20	90	0	77	44	15	5	34	1.70
562747--562799	21	2.4	21	84	6	61	41	3	0	54	1.18
563385--563440	21	2.6	21	80	5	58	53	0	0	46	1.00
563907--563946	21	1.9	21	84	0	53	55	0	2	42	1.13
563942--564008	30	2.2	31	81	7	75	37	5	10	46	1.63
564731--564761	7	4.4	7	100	0	62	38	0	0	61	0.96
564719--564760	14	3.1	13	86	10	57	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)
564719--564772	21	2.5	21	82	11	65	46	0	0	53	1.00
567334--567417	29	2.8	29	75	16	82	42	1	5	50	1.34
568050--568101	21	2.5	19	78	12	50	59	0	1	38	1.08
568075--568167	39	2.4	39	75	8	91	54	0	0	45	0.99
571479--571503	1	25.0	1	100	0	50	0	0	100	0	0.00
572433--572683	34	7.4	34	88	0	333	24	6	27	41	1.80
572433--572682	102	2.5	102	89	0	367	24	6	26	41	1.80
574956--575053	27	3.7	27	78	4	94	46	22	6	24	1.74
579412--579445	14	2.4	14	90	0	50	29	5	47	17	1.71
584630--584697	14	4.9	14	71	10	59	39	1	0	58	1.07
585027--585066	16	2.5	16	88	8	55	52	2	0	45	1.14
592376--592437	14	4.1	15	75	17	56	40	3	1	54	1.26
592376--592444	32	2.2	32	84	10	88	40	2	1	55	1.24
593836--593860	12	2.1	12	100	0	50	56	8	8	28	1.57
593939--593984	18	2.5	19	89	7	76	60	0	0	39	0.97
593942--593981	17	2.3	18	86	4	64	60	0	0	40	0.97
593962--593994	12	2.6	13	85	9	50	66	0	0	33	0.92
596526--596567	22	1.9	22	90	9	68	42	7	19	30	1.78
599579--599620	22	1.9	21	81	18	50	40	0	0	59	0.97
599712--599760	15	3.3	14	78	13	53	42	0	0	57	0.99
600949--601001	23	2.3	23	71	12	54	35	0	1	62	1.06
600950--601018	29	2.5	29	84	13	92	34	0	1	63	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
600968--601035	30	2.3	30	80	10	77	44	1	4	50	1.31
601070--601114	23	2.0	23	86	0	63	48	0	4	46	1.22
601486--601522	2	18.5	2	100	0	74	48	0	0	51	1.00
601663--601706	18	2.4	18	85	11	54	72	0	0	27	0.85
602936--602970	16	2.3	15	90	5	52	57	0	0	42	0.99
605306--605351	21	2.2	21	100	0	92	15	21	23	39	1.92
608844--608898	27	2.0	27	86	6	76	47	0	1	50	1.11
613470--613511	22	1.9	22	90	9	68	38	0	0	61	0.96
614373--614420	14	3.4	14	82	5	62	60	6	6	27	1.45
614642--614708	24	2.6	26	82	13	77	46	0	7	46	1.31
614702--614727	11	2.4	11	100	0	52	42	0	0	57	0.98
614663--614730	27	2.4	27	83	9	75	44	0	4	51	1.21
614806--614853	12	4.2	12	73	24	50	54	0	0	45	0.99
614768--614847	21	3.8	21	77	12	76	56	0	1	42	1.07
615224--615251	2	14.0	2	100	0	56	50	0	0	50	1.00
620142--620187	17	2.8	16	77	6	56	32	2	6	58	1.36
620590--620641	22	2.3	23	86	3	70	69	0	1	28	0.99
622869--622894	13	2.0	13	100	0	52	23	23	23	30	1.99
626428--626485	30	1.9	30	85	0	80	34	1	3	60	1.24
627448--627513	33	2.0	34	82	14	84	56	0	3	40	1.15
628876--628965	27	3.2	28	81	9	112	63	1	1	34	1.09
628875--628965	29	3.3	27	83	9	112	62	1	1	35	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
629100--629260	80	2.0	80	87	2	232	36	16	19	27	1.93
629233--629266	2	17.0	2	87	0	50	44	0	2	52	1.16
629318--629360	21	2.0	21	86	4	59	37	2	6	53	1.41
630287--630372	33	2.7	33	84	8	99	55	0	0	44	0.99
630310--630383	20	3.8	20	74	13	57	56	0	0	43	0.99
630306--630362	17	3.4	17	80	7	71	57	0	0	42	0.98
637066--637116	25	2.0	25	85	7	68	45	1	1	50	1.24
638030--638062	2	16.5	2	93	0	57	45	0	0	54	0.99
639630--639656	2	13.5	2	100	0	54	0	51	0	48	1.00
642884--642928	20	2.3	19	81	11	54	57	0	0	42	0.98
642925--642988	30	2.1	31	85	8	87	42	1	0	56	1.09
643405--643437	17	2.0	17	88	5	50	54	0	0	45	0.99
644420--644488	31	2.2	31	82	12	79	56	0	0	43	0.99
644999--645041	14	3.3	14	78	18	56	51	0	0	48	1.00
645150--645206	24	2.5	24	80	8	66	47	0	0	52	1.00
645241--645300	25	2.5	23	76	15	68	41	0	3	55	1.16
645247--645307	23	2.8	23	76	16	67	44	0	3	52	1.17
645727--645801	25	3.1	25	75	7	75	53	0	0	46	1.00
647197--647223	3	9.0	3	100	0	54	66	0	0	33	0.92
648443--648493	16	2.8	19	77	20	63	31	0	0	68	0.90
648747--648897	10	14.8	10	64	22	57	55	1	1	41	1.19
648754--648881	26	5.0	26	71	17	81	53	1	1	42	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
648833--648904	19	3.3	21	78	16	76	56	1	0	41	1.07
648752--648901	53	2.9	52	74	14	127	55	1	1	42	1.16
650438--650477	21	1.9	21	90	10	64	62	0	0	37	0.95
650754--650786	17	1.9	17	93	0	57	51	0	6	42	1.26
650764--650814	24	2.1	25	86	13	72	58	0	1	39	1.09
651255--651329	18	4.2	18	74	6	73	54	1	0	44	1.08
652191--652233	12	3.5	13	78	12	54	58	0	0	41	0.98
654329--654385	29	2.0	29	83	10	73	45	0	7	47	1.30
654397--654442	19	2.3	20	88	7	67	52	0	0	47	1.00
654473--654503	16	2.0	16	93	6	55	41	0	0	58	0.98

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15