genome.fa.s194.2.7.7.80.10.50.1000.20.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: Scaffold194
Parameters: 2 7 7 80 10 50 1000
Length:  3945165

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   

This is table  20  of  24  ( 2800 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)
3342080--3342127	22	2.1	23	96	3	89	62	8	10	18	1.52
3343037--3343111	20	3.8	20	80	7	80	41	13	12	33	1.81
3343674--3344820	28	39.8	28	85	5	1409	21	17	32	28	1.96
3343674--3344820	143	8.0	143	88	4	1558	21	17	32	28	1.96
3346057--3346102	1	46.0	1	82	0	56	0	2	6	91	0.50
3346046--3346103	20	2.8	20	92	2	89	1	3	8	86	0.76
3346046--3346103	9	5.9	9	80	15	62	1	3	8	86	0.76
3358703--3358750	22	2.1	23	96	3	89	62	8	10	18	1.52
3359660--3359734	20	3.8	20	80	3	80	40	12	13	34	1.81
3359657--3359734	40	2.0	39	87	2	111	39	12	12	34	1.82
3360002--3360080	22	3.7	22	73	13	65	29	11	10	49	1.71
3360360--3360407	22	2.2	22	88	7	71	33	16	8	41	1.78
3360909--3360955	22	2.1	23	88	4	69	42	4	4	48	1.42
3367405--3367545	52	2.7	52	91	2	230	31	17	17	33	1.94
3367534--3367558	13	1.9	13	100	0	50	36	16	16	32	1.90
3367624--3367648	13	1.9	13	100	0	50	32	16	16	36	1.90
3367602--3367668	33	2.0	33	88	0	98	40	13	11	34	1.81
3367706--3367747	21	2.0	21	90	0	66	35	14	14	35	1.86
3368460--3368851	171	2.3	172	93	1	669	36	14	24	24	1.92
3368738--3369706	52	20.0	52	80	12	732	31	17	25	25	1.97
3368848--3369663	144	5.7	144	83	10	1119	31	17	25	25	1.97
3368698--3369712	288	3.5	288	97	0	1859	31	17	25	25	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3369717--3369809	33	2.8	33	93	6	163	15	19	36	29	1.92
3369816--3371009	34	37.0	34	77	16	872	31	13	33	20	1.91
3369779--3370888	128	8.5	137	79	13	771	31	13	34	20	1.91
3370106--3370977	61	13.9	62	77	16	470	30	13	34	21	1.92
3370201--3370463	28	8.8	28	70	17	120	30	14	32	22	1.94
3370106--3370977	62	13.9	61	75	16	391	30	13	34	21	1.92
3369817--3371009	280	4.1	286	77	15	999	31	13	33	20	1.91
3369823--3371009	283	4.6	247	77	14	807	31	13	34	21	1.92
3370774--3370852	27	2.9	27	96	0	140	18	17	39	24	1.92
3370441--3370885	98	4.6	97	80	13	419	29	13	36	20	1.91
3370234--3370984	125	6.0	122	77	14	547	30	13	34	21	1.92
3370809--3370866	27	2.1	27	83	0	71	31	12	36	20	1.89
3370865--3370979	30	3.9	30	84	10	164	25	13	37	23	1.92
3379223--3379363	52	2.7	52	91	2	230	31	17	17	33	1.94
3379352--3379376	13	1.9	13	100	0	50	36	16	16	32	1.90
3379442--3379466	13	1.9	13	100	0	50	32	16	16	36	1.90
3379420--3379486	33	2.0	33	88	0	98	40	13	11	34	1.81
3379524--3379565	21	2.0	21	90	0	66	35	14	14	35	1.86
3379862--3379886	13	1.9	13	100	0	50	36	16	16	32	1.90
3379931--3379982	13	3.5	13	73	26	50	36	17	13	32	1.89
3379278--3380268	495	2.0	487	85	8	1355	32	19	17	31	1.95
3382805--3382877	22	3.4	22	92	1	121	38	4	21	35	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3383435--3383507	20	3.7	19	83	7	76	28	15	16	39	1.89
3384061--3384152	46	2.0	46	95	0	166	46	16	9	27	1.78
3384359--3384412	19	2.8	19	74	2	54	35	14	14	35	1.88
3389378--3389429	21	2.5	21	90	0	77	46	13	7	32	1.72
3389745--3389842	22	4.5	22	81	0	97	47	17	4	30	1.66
3390272--3390325	22	2.5	22	87	0	90	44	12	7	35	1.71
3390270--3390352	28	3.2	28	73	19	97	43	10	7	38	1.67
3393919--3393993	20	3.8	19	77	10	71	32	12	13	42	1.80
3394899--3394953	22	2.5	22	100	0	110	18	10	9	61	1.54
3394899--3394960	22	2.9	21	90	4	63	20	11	9	58	1.61
3397630--3397685	29	1.9	29	100	0	112	39	25	14	21	1.91
3399128--3399152	1	25.0	1	100	0	50	100	0	0	0	0.00
3400642--3400666	11	2.3	11	100	0	50	52	0	0	48	1.00
3401405--3401435	2	15.5	2	93	0	53	51	0	3	45	1.17
3401970--3402018	26	1.9	25	87	4	71	69	0	4	26	1.06
3402087--3402128	2	21.0	2	100	0	84	50	0	0	50	1.00
3402461--3402503	20	2.2	20	86	0	59	51	2	2	44	1.27
3402800--3402852	12	4.4	12	77	17	56	28	0	0	71	0.86
3403479--3403555	19	3.9	19	71	25	70	71	0	1	27	0.94
3403471--3403526	29	2.0	27	86	13	78	69	0	0	30	0.89
3403481--3403557	14	5.3	14	72	17	50	71	0	1	27	0.94
3403516--3403559	12	3.5	12	82	17	54	70	0	2	27	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3403482--3403564	16	5.6	14	69	18	53	69	0	1	28	0.96
3403475--3403613	31	4.2	33	74	12	117	63	0	0	35	1.00
3403552--3403619	18	3.9	19	68	28	53	57	0	0	42	0.98
3403477--3403620	10	14.7	10	67	19	56	63	0	0	35	0.99
3406603--3406650	18	2.7	19	81	12	57	31	0	2	66	1.03
3406605--3406653	19	2.7	18	81	12	55	30	0	2	67	1.02
3407068--3407102	2	17.5	2	100	0	70	48	0	0	51	1.00
3408080--3408119	3	13.3	3	94	0	71	30	0	2	67	1.04
3408490--3408539	2	25.5	2	78	11	50	50	2	4	44	1.32
3409115--3409154	19	2.2	18	86	4	53	42	0	0	57	0.98
3409106--3409154	20	2.5	20	81	12	50	44	0	0	55	0.99
3409565--3409609	19	2.4	19	81	11	56	51	4	0	44	1.21
3409563--3409697	46	2.9	47	76	15	129	50	2	0	46	1.19
3410358--3410417	16	3.8	16	80	4	59	46	25	16	11	1.81
3410428--3410476	16	3.1	16	78	0	53	46	30	16	6	1.71
3411762--3412537	387	2.0	387	100	0	1552	42	15	8	33	1.78
3416298--3416416	52	2.3	52	95	0	211	29	16	18	35	1.93
3416298--3416436	52	2.7	52	86	4	183	30	16	19	33	1.94
3416425--3416449	13	1.9	13	100	0	50	36	16	16	32	1.90
3416513--3416537	13	1.9	13	100	0	50	32	16	16	36	1.90
3416491--3416557	33	2.0	33	88	0	98	40	13	11	34	1.81
3418556--3418585	13	2.3	13	94	0	51	23	3	0	73	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3418702--3418898	73	2.7	73	93	0	331	36	2	9	52	1.45
3419157--3419276	16	7.5	16	77	7	109	38	30	18	12	1.88
3419157--3419276	48	2.5	48	82	2	152	38	30	18	12	1.88
3419235--3419302	16	4.3	16	79	1	66	41	35	16	7	1.76
3419510--3419547	20	1.9	20	100	0	76	44	5	42	7	1.56
3419628--3419698	27	2.6	27	84	6	81	46	22	8	22	1.78
3421582--3421627	21	2.1	22	84	4	58	19	30	19	30	1.97
3424214--3424284	27	2.6	27	88	6	99	46	23	7	22	1.76
3424927--3425001	20	3.8	20	76	0	78	34	14	12	38	1.83
3424927--3425004	40	2.0	39	84	2	102	34	14	12	38	1.84
3432194--3432531	49	6.9	49	84	3	455	24	26	17	31	1.97
3432173--3432531	146	2.4	148	83	3	461	24	26	17	31	1.97
3432173--3432579	49	8.1	53	81	7	302	25	26	16	31	1.96
3433379--3433445	33	2.0	33	88	0	98	34	11	13	40	1.81
3433399--3433423	13	1.9	13	100	0	50	36	16	16	32	1.90
3433486--3433510	13	1.9	13	100	0	50	32	16	16	36	1.90
3437737--3437763	10	2.7	10	100	0	54	0	0	22	77	0.76
3447452--3447561	1	110.0	1	73	0	76	85	8	2	3	0.80
3447452--3447561	17	6.7	16	76	11	98	85	8	2	3	0.80
3447452--3447553	22	4.8	20	76	15	89	85	7	2	3	0.82
3447452--3447553	21	4.8	20	75	18	91	85	7	2	3	0.82
3447493--3447561	21	3.3	21	82	9	88	86	11	0	1	0.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3449005--3449451	29	15.4	28	76	11	296	29	29	17	24	1.97
3449064--3449117	27	2.0	28	88	3	83	33	35	16	14	1.90
3449035--3449451	30	14.3	30	74	15	128	29	30	17	23	1.97
3449214--3449451	113	2.1	116	85	6	315	32	29	17	20	1.95
3449214--3449467	85	2.9	85	87	7	343	32	29	18	19	1.96
3449467--3449700	48	4.8	49	83	10	293	26	25	16	31	1.97
3449563--3449657	43	2.2	44	94	3	165	27	26	16	29	1.97
3449565--3449633	22	3.2	22	62	25	56	26	26	17	30	1.97
3449609--3449745	53	2.5	54	81	6	154	24	24	16	35	1.95
3452010--3452052	15	2.9	15	82	3	52	62	9	6	20	1.48

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