genome.fa.s341.2.7.7.80.10.50.1000.4.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: Scaffold341
Parameters: 2 7 7 80 10 50 1000
Length:  1349338

Tables:   1   2   3   4   5   6   7   8   9   

This is table  4  of  9  ( 1050 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)
485083--485155	34	2.1	35	92	2	121	52	5	2	39	1.39
493592--493630	18	2.1	19	90	4	62	76	0	0	23	0.78
494023--494092	34	2.1	34	82	15	83	38	0	0	61	0.96
496382--496427	17	2.6	17	82	3	56	45	0	2	52	1.13
496955--496984	14	2.1	14	93	0	51	0	16	0	83	0.65
497085--497110	13	2.0	13	100	0	52	46	0	0	53	1.00
497175--497223	18	2.5	19	83	12	64	53	0	0	46	1.00
497175--497223	19	2.5	20	87	9	75	53	0	0	46	1.00
497198--497263	24	2.7	26	81	13	77	60	1	0	37	1.06
497275--497315	12	3.8	11	81	12	50	56	0	0	43	0.99
497285--497364	33	2.5	32	76	15	85	55	0	0	45	0.99
503805--503864	5	11.6	5	77	15	52	33	1	1	63	1.14
503811--503889	11	7.7	11	77	14	71	29	1	3	65	1.17
503799--503868	27	2.6	28	82	15	69	32	1	1	64	1.11
503799--503864	21	3.3	21	80	12	68	34	1	1	62	1.14
504960--504989	12	2.4	13	94	5	53	3	6	0	90	0.56
506247--506294	16	3.1	15	80	16	53	47	0	0	52	1.00
506661--506709	17	2.8	18	71	6	55	61	12	6	20	1.52
506760--506809	24	2.2	23	89	7	75	70	14	2	14	1.27
507222--507277	23	2.6	21	78	13	69	21	7	7	64	1.43
507268--507310	17	2.5	17	77	7	52	13	6	13	65	1.46
507248--507362	59	1.9	59	83	0	149	18	10	9	61	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
509891--509932	19	2.3	18	84	12	50	38	7	0	54	1.28
512843--512874	14	2.1	16	88	11	50	56	6	9	28	1.55
513464--513765	166	1.8	167	84	7	416	31	9	10	48	1.69
513390--513765	168	2.2	168	82	6	426	31	11	9	48	1.70
514044--514242	98	2.0	99	96	0	364	34	6	3	55	1.43
521125--521159	2	17.5	2	87	0	52	54	2	0	42	1.15
522318--522360	8	5.1	8	81	10	50	13	4	0	81	0.84
522329--522360	9	3.6	9	91	0	55	12	0	0	87	0.54
522895--523297	62	6.5	65	74	11	163	21	17	30	31	1.96
522890--523297	31	13.2	33	76	11	106	20	17	31	30	1.96
522984--523621	29	21.6	29	80	6	425	21	15	32	29	1.95
522984--523623	57	10.8	57	75	9	475	21	15	32	29	1.94
522979--523442	240	1.9	241	90	0	732	19	16	32	31	1.94
523074--523610	86	6.1	86	76	9	273	21	15	33	29	1.94
523585--523672	27	3.3	26	87	6	122	31	12	29	26	1.93
525049--525120	24	3.1	23	80	8	83	8	11	5	75	1.19
525025--525120	46	2.1	46	82	7	115	7	11	6	75	1.19
528738--528768	15	2.1	15	94	5	55	38	0	12	48	1.42
531060--531114	28	2.0	27	85	3	74	34	20	20	25	1.96
532140--532175	18	1.9	19	88	5	56	13	2	0	83	0.76
532284--532634	176	2.0	175	96	0	648	20	16	14	48	1.81
534369--534417	2	25.0	2	89	4	64	55	0	2	42	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
534363--534393	16	1.9	16	93	0	53	64	0	6	29	1.18
535401--535428	13	2.2	13	100	0	56	0	7	0	92	0.37
536536--536577	21	2.0	22	86	9	61	52	2	0	45	1.13
536541--536581	19	2.0	21	86	9	59	53	2	0	43	1.13
538268--538311	21	2.1	21	87	4	63	43	0	0	56	0.99
538577--538654	40	2.0	40	89	5	122	50	17	6	25	1.70
539446--539473	2	14.0	2	100	0	56	50	0	0	50	1.00
541869--541906	18	2.1	18	100	0	76	39	5	10	44	1.61
542977--543077	51	2.0	51	94	3	177	59	13	9	16	1.60
542977--543056	26	3.1	25	66	24	67	63	11	10	15	1.51
542977--543056	24	3.2	23	66	27	56	63	11	10	15	1.51
544142--544191	3	16.7	3	100	0	100	32	0	0	68	0.90
544396--544434	2	19.5	2	100	0	78	51	0	0	48	1.00
544562--544594	17	1.9	18	88	11	52	27	0	0	72	0.85
546291--546333	12	3.6	12	81	6	52	67	0	2	30	1.03
548925--548951	2	13.5	2	100	0	54	48	0	0	51	1.00
549343--549376	17	1.9	18	88	5	52	35	2	0	61	1.11
549859--549890	15	2.0	17	88	11	50	43	0	0	56	0.99
550905--550982	16	4.6	17	80	12	88	65	1	1	32	1.09
550905--550985	17	4.8	16	79	14	67	64	1	1	33	1.10
550905--550986	8	9.8	8	70	15	58	64	1	1	32	1.09
551050--551086	17	2.2	17	100	0	74	51	5	10	32	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
551437--551548	30	3.5	30	66	20	75	35	1	3	58	1.26
551499--551540	21	2.0	21	85	0	57	28	2	0	69	1.01
552034--552082	22	2.3	21	82	10	55	36	2	4	57	1.30
552901--553017	20	6.3	19	69	18	59	47	0	0	52	1.00
552894--553024	55	2.3	58	79	9	144	47	0	0	52	1.00
552963--553015	19	2.8	18	83	11	70	49	0	0	50	1.00
553007--553050	21	2.1	21	87	4	63	61	0	0	38	0.96
553041--553080	21	2.0	20	85	5	53	60	0	0	40	0.97
556079--556105	2	13.5	2	100	0	54	51	0	0	48	1.00
558090--558121	2	16.0	2	100	0	64	50	0	0	50	1.00
560510--560721	107	2.0	107	96	0	388	33	20	8	37	1.84
563805--563857	22	2.5	21	75	22	56	69	0	3	26	1.05
564265--564370	15	6.6	16	69	20	53	42	0	0	56	1.05
564319--564371	16	3.4	16	74	12	56	45	0	0	54	0.99
564259--564380	25	4.5	26	66	22	74	39	0	0	59	1.03
564329--564431	42	2.5	41	74	13	104	40	0	0	59	0.98
564778--564836	28	2.3	26	83	13	70	66	1	0	32	1.02
564803--564869	19	3.6	18	71	26	50	56	0	1	41	1.08
565259--565321	18	3.3	18	77	16	65	39	1	0	58	1.07
565881--566019	75	1.9	74	88	5	212	16	18	13	51	1.77
566240--566269	15	2.0	15	93	0	51	50	0	0	50	1.00
566248--566296	23	2.1	23	85	7	64	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
566757--566800	22	2.0	22	82	8	54	54	4	0	40	1.21
567467--567540	2	39.0	2	74	15	68	50	4	1	44	1.29
567468--567538	13	5.6	12	75	14	56	50	4	1	43	1.30
568521--568909	157	2.5	157	83	3	453	34	12	24	28	1.92
568539--568909	79	4.7	78	81	2	420	35	12	24	27	1.91
570958--571091	51	2.6	51	85	0	178	42	14	15	27	1.86
572177--572251	4	18.8	4	79	15	75	28	0	1	70	0.95
572245--572315	34	2.1	33	87	7	99	40	1	0	57	1.07
573498--573535	18	2.1	19	90	5	60	57	0	0	42	0.98
577251--577276	2	13.0	2	100	0	52	50	0	50	0	1.00
580192--580230	2	19.5	2	100	0	78	0	51	0	48	1.00
580273--580332	29	2.1	29	93	0	102	41	11	18	28	1.85
582393--582440	15	3.2	15	78	0	51	29	0	2	68	1.01
582473--582514	18	2.3	19	83	8	59	30	2	0	66	1.04
583413--583523	34	3.3	34	81	5	127	22	4	26	46	1.70
583882--583918	19	1.9	19	88	0	56	29	27	16	27	1.97
587990--588071	34	2.4	34	91	0	128	25	6	24	43	1.77
592974--593038	12	5.7	11	71	12	51	66	0	1	32	1.01
593056--593115	25	2.4	23	77	22	68	56	0	1	41	1.09
593057--593118	27	2.4	25	80	15	72	56	0	1	41	1.09
593066--593121	21	2.6	21	75	24	55	57	0	1	41	1.09
593414--593478	34	1.9	34	84	12	89	64	0	1	33	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
593798--593840	13	3.4	13	90	3	61	51	6	0	41	1.29
594913--594953	16	2.5	16	88	4	55	36	2	2	58	1.24
598769--598833	16	4.3	15	75	11	62	38	4	6	50	1.48
602049--602103	13	3.9	14	73	15	51	50	1	0	47	1.11
602041--602103	29	2.2	29	91	0	99	46	1	0	52	1.10
602419--602467	17	2.8	18	75	12	57	34	6	2	57	1.35
602485--602513	15	2.0	15	93	6	51	34	0	0	65	0.93
602452--602508	25	2.3	25	79	11	71	33	1	3	61	1.23
602777--602840	24	2.7	23	73	17	60	62	14	0	23	1.31
604344--604728	209	1.8	209	85	2	549	35	17	13	33	1.89

Tables:   1   2   3   4   5   6   7   8   9