genome.fa.s2.2.7.7.80.10.50.1000.4.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  4  of  38  ( 4457 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)
532108--532457	27	11.7	27	77	15	207	31	14	32	22	1.94
532068--532193	60	2.1	60	90	0	198	34	13	31	19	1.91
532108--532436	93	3.6	87	78	10	354	31	13	32	21	1.93
532133--532436	60	4.9	60	77	12	255	31	13	32	21	1.92
532281--532381	34	3.0	34	86	1	150	34	9	32	22	1.87
532438--533117	33	21.7	33	80	9	732	34	15	27	22	1.94
532438--533124	156	4.4	156	82	7	799	34	14	28	22	1.94
532438--533116	30	21.7	31	81	9	690	34	15	27	22	1.94
534424--534448	13	1.9	13	100	0	50	40	12	16	32	1.84
534372--534470	33	3.0	33	86	2	128	41	14	14	30	1.85
540897--540953	27	2.2	26	84	9	71	21	26	12	40	1.88
540988--541080	32	2.9	32	80	6	109	29	29	21	20	1.98
541167--541729	52	10.3	52	74	10	281	24	23	14	36	1.93
541196--541354	61	2.6	61	93	0	273	23	25	14	37	1.92
541258--541727	217	2.2	217	79	4	543	24	23	14	37	1.93
542560--542635	20	3.7	20	82	6	89	31	14	11	42	1.82
542683--542798	56	2.1	56	96	0	214	24	22	12	40	1.89
545604--545648	22	2.1	22	84	12	58	15	8	11	64	1.49
549358--549387	11	2.7	11	94	0	51	86	13	0	0	0.57
550859--550933	32	2.3	33	88	2	107	29	34	18	17	1.94
550854--550980	33	3.9	33	76	12	111	28	30	18	22	1.97
551060--551859	52	14.7	52	70	12	210	23	24	15	36	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
551097--552019	113	8.3	112	71	14	449	23	24	15	36	1.93
551421--551553	61	2.2	61	82	5	153	24	23	12	39	1.90
551549--552019	52	8.7	52	71	11	166	22	24	16	35	1.95
551603--551862	104	2.5	103	79	6	274	22	25	18	33	1.96
551545--551853	156	2.0	156	85	0	420	22	25	18	34	1.96
551152--552047	382	2.3	387	83	4	1103	23	24	15	36	1.93
555336--555363	13	2.2	13	100	0	56	42	14	14	28	1.84
555665--555903	52	4.6	52	80	2	246	23	25	15	35	1.94
555843--555977	61	2.2	62	89	4	209	21	24	14	40	1.90
559490--559553	32	2.0	33	87	3	94	42	14	14	29	1.84
565616--565640	13	1.9	13	100	0	50	32	20	16	32	1.94
568038--568092	20	2.8	20	88	5	76	40	14	14	30	1.86
568163--568188	13	2.0	13	100	0	52	38	15	15	30	1.88
568145--568208	32	2.0	33	90	3	103	42	15	14	28	1.86
569946--570001	20	2.8	20	75	2	58	32	12	14	41	1.83
577287--577529	28	8.7	28	82	1	272	30	26	17	25	1.98
577577--577924	49	6.9	49	79	6	286	25	27	16	30	1.97
577577--577816	99	2.4	98	80	6	266	25	27	18	29	1.98
578579--578641	19	3.7	18	74	24	64	31	11	19	38	1.86
578598--578622	13	1.9	13	100	0	50	36	16	16	32	1.90
578577--578654	32	2.4	32	93	0	129	33	12	17	35	1.88
578671--578725	20	2.8	20	88	5	76	32	14	12	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
583562--583633	20	3.6	20	96	0	135	26	20	15	37	1.92
583622--583646	13	1.9	13	100	0	50	32	16	16	36	1.90
583604--583665	32	1.9	33	90	3	99	27	17	16	38	1.91
583582--583685	52	2.0	53	83	5	131	29	17	14	38	1.89
591551--591869	78	4.1	77	81	6	336	37	12	22	26	1.90
591609--591889	79	3.6	78	83	8	329	37	12	22	27	1.90
591918--592213	79	3.8	79	74	6	208	35	13	24	26	1.92
591934--592212	78	3.6	76	75	4	220	34	13	25	26	1.93
592176--592236	28	2.2	28	82	5	70	32	16	24	26	1.96
592188--592431	80	3.1	77	77	9	249	37	12	24	26	1.90
592385--592508	64	1.9	65	86	4	180	37	10	24	27	1.88
608037--608061	13	1.9	13	100	0	50	36	16	16	32	1.90
608127--608151	13	1.9	13	100	0	50	32	16	16	36	1.90
608105--608171	33	2.0	33	88	0	98	40	13	11	34	1.81
614055--614138	42	2.0	42	92	0	141	21	15	23	39	1.92
616721--616755	3	11.7	3	87	0	52	25	34	2	37	1.71
616719--616757	9	4.3	9	86	0	51	23	33	2	41	1.68
619459--620088	61	10.4	60	78	4	559	28	18	26	27	1.98
619379--620088	122	5.8	120	78	5	656	29	17	26	26	1.98
619395--620088	242	2.8	243	79	6	724	28	17	26	26	1.98
630141--630166	4	6.5	4	100	0	52	76	0	0	23	0.78
632226--633121	157	5.7	157	79	4	833	35	11	24	29	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
632227--633121	78	11.4	78	77	6	702	35	11	24	29	1.90
635517--635650	39	3.4	39	69	19	123	23	15	22	38	1.92
635496--635674	80	2.2	80	92	0	304	25	15	19	39	1.90
649156--649343	41	4.7	41	77	9	183	21	26	12	39	1.89
649200--649357	76	2.1	76	85	1	210	23	23	12	41	1.88
649160--649423	41	6.6	41	73	12	172	22	25	11	40	1.88
649501--649582	31	2.6	31	80	3	103	31	28	23	17	1.96
649501--649642	61	2.3	62	81	3	162	28	26	23	20	1.99
651088--651657	79	7.2	78	77	6	441	34	12	24	28	1.92
651112--651655	158	3.4	157	84	6	636	34	12	24	29	1.91
651593--651691	51	1.9	51	86	8	139	39	8	21	31	1.82
651516--651787	129	2.1	132	82	7	340	35	10	24	29	1.89
653896--653931	18	2.0	18	100	0	72	16	33	11	38	1.84
654850--655138	42	6.8	42	77	10	237	40	13	25	19	1.89
654890--655084	44	4.5	44	77	10	156	42	12	26	18	1.86
655127--656802	62	27.3	62	82	4	1762	33	18	22	24	1.97
655127--656802	123	13.7	123	82	4	1784	33	18	22	24	1.97
670498--670561	9	7.0	9	85	1	74	81	10	1	6	0.94
670498--670575	18	4.1	18	73	16	68	80	11	1	6	0.94
670510--670570	27	2.2	27	85	8	79	81	11	1	4	0.90
671787--672613	28	29.1	28	83	6	959	29	30	17	23	1.97
671787--672613	114	7.3	114	86	5	1018	29	30	17	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
671787--672610	171	4.8	171	86	5	1044	29	30	17	22	1.97
672669--672791	49	2.6	46	83	7	149	21	26	20	30	1.98
676853--676904	17	3.1	17	81	10	54	7	9	3	78	1.06
676864--676920	25	2.3	23	80	13	69	8	10	3	77	1.11
682377--682421	20	2.3	20	84	3	56	26	15	17	40	1.90
682485--682633	79	1.9	79	94	0	262	32	11	14	41	1.81
683268--683339	21	3.5	20	75	11	65	38	16	13	30	1.88
689400--689676	44	6.3	44	78	5	220	21	19	16	42	1.88
689400--689676	131	2.1	132	82	2	324	21	19	16	42	1.88
697221--697287	28	2.4	28	89	0	98	26	19	29	23	1.98
697275--697665	52	7.5	52	72	14	216	33	11	25	29	1.91
697481--697555	27	2.7	28	87	2	98	21	18	34	25	1.96
697533--697662	51	2.5	51	86	2	170	33	10	23	31	1.89
700013--700076	33	1.9	33	83	0	83	43	14	14	28	1.83
701025--701220	28	7.1	28	61	20	90	20	19	30	29	1.98
701107--701196	26	3.3	26	67	19	76	18	17	33	30	1.95
700951--701722	55	13.3	59	85	6	858	23	20	28	26	1.99
700951--701722	235	3.3	231	86	6	973	23	20	28	26	1.99
702688--702729	15	2.8	15	92	0	66	0	2	7	90	0.53
715522--715547	13	2.0	13	100	0	52	30	15	15	38	1.88
733272--733305	16	2.1	16	89	10	52	5	2	2	88	0.70
736687--736731	21	2.2	20	88	11	74	46	20	13	20	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
737631--737685	20	2.8	20	97	0	101	40	12	14	32	1.84
737654--737716	33	1.9	33	83	0	81	41	11	12	34	1.79
737833--737877	22	2.0	22	95	0	81	20	22	28	28	1.98
738491--738562	32	2.3	32	83	4	85	23	22	26	27	1.99
738621--738929	28	11.0	28	78	7	288	25	17	27	30	1.97
738585--738872	84	3.4	84	79	10	268	26	17	26	29	1.98
740078--740148	1	71.0	1	71	0	52	1	1	11	85	0.72
740088--740147	19	3.2	19	87	0	84	1	1	10	86	0.71
740078--740149	6	11.0	7	77	14	66	1	1	12	84	0.75
743196--743220	13	1.9	13	100	0	50	36	16	16	32	1.90

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