genome.fa.s16.2.7.7.80.10.50.1000.3.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: Scaffold16
Parameters: 2 7 7 80 10 50 1000
Length:  5287347

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   

This is table  3  of  35  ( 4175 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)
395446--395595	64	2.3	64	82	8	180	37	25	15	22	1.93
396498--396547	22	2.3	22	86	6	66	76	10	0	14	1.03
396498--396540	8	5.6	8	81	10	54	74	11	0	13	1.07
396515--396547	15	2.1	16	88	5	50	78	9	0	12	0.95
398832--398937	41	2.6	40	82	5	122	17	24	9	48	1.77
398911--398990	41	2.0	41	87	5	117	16	22	12	48	1.79
398871--399247	82	4.6	82	70	11	207	17	21	12	48	1.81
399074--399163	41	2.1	42	79	8	101	18	21	12	47	1.81
398940--399301	123	2.9	119	75	10	311	17	21	12	48	1.81
399269--399584	147	2.2	146	78	6	343	18	23	11	46	1.81
400877--400931	18	3.0	18	84	10	67	23	1	0	74	0.91
410103--410209	53	2.0	53	98	0	205	26	26	19	28	1.99
411857--411881	13	1.9	13	100	0	50	32	16	16	36	1.90
411869--411921	20	2.6	21	90	3	81	41	15	16	26	1.88
417372--417396	13	1.9	13	100	0	50	32	16	16	36	1.90
417384--417432	20	2.4	21	89	3	73	40	14	18	26	1.89
417972--418038	37	1.9	35	85	11	93	32	10	25	31	1.89
423554--423728	80	2.2	79	86	1	233	30	17	27	24	1.97
423683--423754	28	2.6	28	86	0	90	23	18	36	22	1.95
423764--423911	51	2.9	50	81	6	165	35	12	23	28	1.91
425931--426005	20	3.8	19	82	7	87	42	13	16	28	1.85
428103--428147	21	2.2	21	84	11	58	35	28	8	26	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
428026--428263	112	2.1	111	90	1	368	34	23	12	28	1.92
428188--428239	19	2.6	21	84	6	63	38	28	9	23	1.86
429202--429226	13	1.9	13	100	0	50	36	16	16	32	1.90
429182--429246	33	2.0	33	87	0	94	33	12	13	40	1.82
429289--429316	13	2.2	13	100	0	56	28	14	17	39	1.89
432475--433232	141	5.4	140	74	9	533	38	14	20	25	1.91
432641--432803	69	2.3	68	80	8	159	42	14	17	25	1.87
432877--433232	73	4.9	73	78	6	321	39	14	21	24	1.91
432606--433243	144	4.5	143	75	9	411	38	15	20	25	1.91
434490--434534	19	2.3	20	80	3	56	4	6	6	82	0.95
447541--447579	20	2.0	20	94	0	69	48	15	10	25	1.76
448270--448320	20	2.5	20	87	3	66	39	25	9	25	1.86
448227--448432	112	1.8	113	86	3	299	34	21	12	31	1.90
448402--448440	20	2.0	20	89	0	60	28	25	15	30	1.96
450177--450205	6	4.8	6	100	0	58	31	0	0	68	0.89
452865--452942	31	2.5	31	91	0	129	26	17	15	39	1.90
455520--455650	28	4.7	28	82	0	163	26	30	19	23	1.98
455520--455648	56	2.3	56	95	0	231	26	30	19	24	1.98
455577--455837	109	2.4	109	83	3	328	26	26	14	31	1.95
455686--455754	27	2.5	28	85	4	95	26	27	20	26	1.99
455713--455892	82	2.2	82	82	6	215	30	26	11	32	1.92
456940--457027	25	3.6	24	70	13	63	56	10	1	31	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
456961--457034	25	3.0	25	75	11	73	58	8	1	32	1.36
457307--457343	19	2.0	19	89	5	58	37	0	0	62	0.96
457453--457512	27	2.2	28	88	8	90	38	0	0	61	0.96
459137--459201	33	2.0	33	84	0	85	36	13	16	32	1.89
460783--460823	3	13.7	3	94	0	73	36	0	34	29	1.58
461250--461291	15	2.8	16	82	10	52	52	2	14	30	1.54
465335--465372	12	3.0	13	92	7	69	31	13	15	39	1.86
467234--467263	15	2.0	15	100	0	60	40	0	20	40	1.52
467944--467982	20	1.9	20	89	5	60	43	20	15	20	1.88
468034--468089	20	2.8	20	83	0	67	35	16	17	30	1.92
475234--476204	166	5.8	166	79	7	854	51	9	10	28	1.67
475243--476204	332	2.9	332	81	5	1038	51	9	10	28	1.68
476046--476336	146	2.0	146	81	8	342	51	9	13	25	1.71
476923--476979	19	2.9	19	81	2	69	35	17	10	36	1.84
477907--477941	13	2.7	13	90	0	52	31	8	20	40	1.82
479967--480022	26	2.2	26	96	0	103	58	12	3	25	1.50
480224--480353	63	2.1	63	100	0	260	36	4	24	34	1.76
480665--480720	19	2.8	20	91	2	87	33	17	10	37	1.85
482350--482469	42	2.9	40	71	19	102	44	17	23	15	1.86
482799--483495	44	15.2	46	77	5	380	42	16	20	20	1.89
482897--483483	89	6.4	91	75	8	399	42	16	20	20	1.88
482852--483440	227	2.6	226	79	5	555	42	16	20	20	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
483294--483482	93	2.0	93	80	4	211	39	16	21	22	1.92
485072--485097	13	2.0	13	100	0	52	38	15	15	30	1.88
490782--490807	13	2.0	13	100	0	52	38	15	15	30	1.88
491986--492036	25	2.1	24	82	10	59	1	11	7	78	1.04
492791--492816	13	2.0	13	100	0	52	38	15	15	30	1.88
494862--494904	20	2.1	20	82	4	50	11	30	41	16	1.83
495177--495223	21	2.3	21	82	10	62	44	4	19	31	1.70
495345--495383	13	3.0	13	92	0	60	38	15	15	30	1.88
495544--495583	13	2.9	14	88	7	55	42	25	0	32	1.55
495540--495594	15	3.8	15	73	9	51	49	25	0	25	1.51
501545--501570	13	2.0	13	100	0	52	30	15	15	38	1.88
502787--502820	16	2.1	17	88	5	52	41	8	14	35	1.77
505571--505637	33	2.0	33	88	0	98	34	11	13	40	1.81
505591--505615	13	1.9	13	100	0	50	36	16	16	32	1.90
505711--505834	52	2.4	52	93	4	207	34	18	17	29	1.94
510877--511236	155	2.3	155	79	4	404	39	21	16	22	1.92
512744--512777	13	2.7	13	90	4	52	0	23	0	76	0.79
512744--512785	12	3.4	13	80	12	52	2	26	0	71	0.98
513167--513840	165	4.0	164	78	8	605	51	10	10	27	1.70
514298--514350	20	2.7	20	100	0	106	41	18	15	24	1.89
514443--514468	13	2.0	13	100	0	52	38	15	15	30	1.88
514425--514488	32	2.0	33	87	3	94	40	17	14	28	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
520917--521043	31	4.1	31	90	1	184	33	15	19	30	1.93
520917--521061	62	2.4	62	84	1	193	33	15	20	30	1.94
522222--522262	21	1.9	22	90	5	66	41	0	0	58	0.98
525216--525256	22	2.0	21	90	9	66	36	2	12	48	1.54
526106--526132	13	2.1	13	100	0	54	40	14	14	29	1.86
530362--530429	34	2.0	34	94	0	118	27	27	10	33	1.89
531190--531245	19	2.9	19	83	2	67	33	14	12	39	1.83
532882--532916	15	2.3	15	95	0	61	42	0	28	28	1.56
538215--538240	13	2.0	13	100	0	52	38	15	15	30	1.88
538278--538335	13	4.0	13	74	23	53	32	15	15	36	1.89
538292--538354	19	3.7	18	76	24	73	34	17	12	34	1.88
538279--538354	32	2.4	32	95	0	134	34	17	14	34	1.90
538596--538659	13	4.9	13	86	0	92	34	14	14	37	1.86
538597--538659	26	2.4	26	91	0	108	34	14	14	36	1.86
541305--541376	20	3.6	19	76	14	67	33	19	15	31	1.93
541427--541451	13	1.9	13	100	0	50	36	16	16	32	1.90
542240--542280	21	2.0	21	85	4	57	39	14	14	31	1.87
546285--546386	34	3.0	34	89	1	159	28	25	10	35	1.90
546931--546994	33	1.9	33	90	6	103	32	14	17	35	1.89
548693--548925	105	2.2	106	84	6	296	39	4	10	45	1.59
549805--549857	13	4.5	13	69	26	55	35	16	13	33	1.88
549808--549872	33	2.0	33	90	6	105	33	18	13	33	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
550529--550624	38	2.5	37	88	5	140	35	19	4	40	1.71
551359--551408	21	2.4	21	83	9	59	48	0	20	32	1.50
551366--551408	21	2.0	22	86	4	61	51	0	20	27	1.48
551517--551542	13	2.0	13	100	0	52	38	15	15	30	1.88
558792--558848	19	2.9	19	78	5	60	36	15	14	33	1.88
558833--558859	13	2.1	13	100	0	54	40	14	14	29	1.86
561366--561391	13	2.0	13	100	0	52	38	15	15	30	1.88
569068--569125	26	2.3	26	84	3	73	68	1	5	24	1.19
572873--572924	22	2.4	22	100	0	104	19	44	13	23	1.86
579170--579207	2	19.0	2	100	0	76	50	0	0	50	1.00

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