genome.fa.s42.2.7.7.80.10.50.1000.21.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: Scaffold42
Parameters: 2 7 7 80 10 50 1000
Length:  3911082

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  21  of  24  ( 2843 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)
3178316--3178439	19	6.6	19	73	15	98	35	15	12	37	1.84
3178307--3178417	32	3.2	32	74	17	114	35	16	13	35	1.88
3178346--3178439	40	2.3	40	92	0	152	35	13	11	39	1.82
3178366--3178439	21	3.6	21	81	7	98	33	14	12	39	1.84
3184951--3185340	101	3.9	99	83	5	401	33	17	25	23	1.96
3185052--3185607	49	11.9	49	74	15	408	31	18	25	24	1.98
3185001--3185340	153	2.3	149	83	3	421	32	17	26	23	1.97
3185302--3185538	39	5.6	39	73	16	204	27	20	27	25	1.99
3185254--3185602	87	4.0	87	92	1	556	29	19	25	25	1.99
3185476--3185553	39	2.0	39	87	5	113	24	21	24	29	1.99
3185624--3185718	29	3.3	30	75	10	90	16	15	33	33	1.91
3185732--3185872	27	5.0	27	72	11	111	31	14	31	22	1.94
3185876--3185932	27	2.1	28	83	3	71	31	15	33	19	1.93
3185902--3186427	33	16.8	33	77	14	499	32	13	33	19	1.91
3185752--3186153	60	6.6	61	83	9	462	32	13	34	19	1.91
3186125--3186427	60	4.9	60	82	8	376	31	14	33	20	1.92
3186374--3186524	34	4.6	34	83	7	179	33	15	27	22	1.95
3187171--3187344	20	8.8	20	68	24	93	27	17	14	40	1.88
3187255--3187324	33	2.1	33	94	0	122	27	20	12	40	1.88
3187277--3187305	13	2.2	13	100	0	58	27	13	17	41	1.87
3189747--3189823	28	2.8	28	86	7	95	24	29	18	27	1.98
3189809--3189925	51	2.3	52	86	4	157	30	24	11	33	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3189775--3190112	130	2.6	130	78	7	362	28	24	12	34	1.92
3191575--3191611	1	37.0	1	91	0	56	94	0	2	2	0.36
3191573--3191610	19	2.0	19	100	0	76	89	0	5	5	0.59
3191575--3191612	20	1.9	20	100	0	76	92	0	2	5	0.47
3191616--3191672	21	2.7	21	97	0	105	33	10	19	36	1.86
3191728--3191795	19	3.9	19	78	21	85	35	11	14	38	1.83
3191749--3191773	13	1.9	13	100	0	50	36	16	16	32	1.90
3191730--3191792	32	2.0	32	96	0	117	34	12	15	36	1.86
3194509--3194573	15	4.4	15	82	3	69	86	4	9	0	0.71
3194509--3194557	1	49.0	1	79	0	53	89	6	4	0	0.57
3195539--3196326	55	14.3	55	91	4	1170	28	30	20	20	1.98
3196919--3196956	18	2.1	18	100	0	76	78	0	5	15	0.91
3196959--3197015	21	2.7	21	97	0	105	33	10	19	36	1.86
3197071--3197138	19	3.9	19	78	21	85	35	11	14	38	1.83
3197092--3197116	13	1.9	13	100	0	50	36	16	16	32	1.90
3197073--3197135	32	2.0	32	96	0	117	34	12	15	36	1.86
3197178--3197203	13	2.0	13	100	0	52	30	15	15	38	1.88
3197158--3197224	33	2.0	33	88	0	98	25	14	16	43	1.86
3199671--3199743	27	2.7	27	87	6	94	23	34	21	20	1.97
3199726--3199896	51	3.3	51	78	4	189	29	25	11	33	1.91
3199879--3199960	28	2.9	28	82	7	96	24	31	17	26	1.97
3201556--3201618	21	3.0	22	79	9	76	1	6	14	77	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3205252--3205276	13	1.9	13	100	0	50	36	16	16	32	1.90
3205232--3205298	33	2.0	33	88	0	98	32	11	14	40	1.83
3205339--3205363	13	1.9	13	100	0	50	32	16	16	36	1.90
3205352--3205552	52	3.9	52	91	0	330	34	19	16	29	1.94
3212133--3212238	20	4.8	20	69	24	70	38	11	16	33	1.84
3212268--3212331	19	3.7	19	72	23	77	35	17	12	34	1.87
3212255--3212330	32	2.4	32	95	0	134	35	17	13	34	1.88
3218328--3218403	21	3.7	21	77	7	75	43	11	15	28	1.83
3218426--3218482	20	2.8	21	78	7	64	36	12	17	33	1.87
3227354--3227388	2	17.5	2	100	0	70	48	0	0	51	1.00
3228155--3228205	20	2.5	21	90	9	79	39	11	19	29	1.87
3228155--3228228	21	3.6	21	82	10	64	40	10	17	31	1.84
3233635--3233689	20	2.8	20	97	0	101	36	20	10	32	1.87
3233783--3233841	20	3.3	20	69	30	69	38	15	13	32	1.86
3233751--3233841	33	2.8	33	93	1	148	40	16	12	30	1.85
3234786--3234817	12	2.7	12	95	0	55	31	28	9	31	1.88
3242497--3242551	20	2.8	20	91	0	92	36	18	10	34	1.86
3242537--3242563	13	2.1	13	100	0	54	40	14	14	29	1.86
3242611--3242674	32	2.0	32	90	3	103	37	14	15	32	1.87
3245268--3245491	79	2.8	78	84	8	267	28	31	9	30	1.88
3248191--3248242	12	4.5	11	75	20	52	57	1	0	40	1.10
3249363--3249387	10	2.5	10	100	0	50	0	0	8	92	0.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3251497--3251536	3	13.3	3	100	0	80	32	0	0	67	0.91
3252029--3252078	9	5.7	9	73	21	52	60	0	2	38	1.09
3254334--3254404	20	3.6	19	81	11	72	32	11	15	40	1.83
3262655--3262698	7	6.3	7	100	0	88	29	29	27	13	1.94
3263228--3263294	33	2.0	33	88	0	98	34	11	13	40	1.81
3263248--3263272	13	1.9	13	100	0	50	36	16	16	32	1.90
3263368--3263491	52	2.4	52	94	1	214	35	18	17	28	1.94
3271544--3271573	7	4.3	7	100	0	60	30	30	26	13	1.94
3272245--3272278	14	2.4	14	100	0	68	32	29	23	14	1.94
3274978--3275043	21	3.1	21	82	8	71	50	0	1	48	1.10
3275049--3275082	16	2.0	16	88	11	50	41	0	0	58	0.98
3278415--3278472	28	2.0	29	83	12	75	55	5	5	34	1.45
3278615--3278683	28	2.4	27	74	9	75	42	2	7	47	1.46
3278619--3278679	28	2.3	26	83	13	79	40	3	6	49	1.45
3278774--3278805	15	2.1	16	94	5	57	40	9	0	50	1.35
3280568--3280593	13	2.0	13	100	0	52	30	15	15	38	1.88
3280547--3280611	32	2.0	32	87	6	94	29	10	15	44	1.80
3280663--3280718	20	2.8	20	89	5	78	28	17	16	37	1.91
3283142--3283179	13	2.9	13	96	0	67	31	15	18	34	1.92
3285254--3285291	15	2.5	15	91	0	58	13	21	15	50	1.78
3289333--3289385	19	2.7	20	88	8	81	28	11	15	45	1.80
3289436--3289491	20	2.8	20	89	5	78	28	17	16	37	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3289946--3289985	20	2.0	20	100	0	80	40	10	20	30	1.85
3290180--3290222	18	2.4	18	80	3	52	34	2	2	60	1.22
3290199--3290245	21	2.2	20	82	10	58	46	0	0	53	1.00
3298187--3298225	21	1.9	20	94	5	69	35	12	15	35	1.86
3306053--3306127	20	3.8	20	78	0	87	34	13	12	40	1.81
3306053--3306130	40	2.0	39	87	2	111	34	12	12	39	1.82
3307038--3307093	22	2.5	23	94	5	105	17	10	8	62	1.52
3307046--3307100	22	2.6	21	88	5	58	20	9	9	61	1.52
3314604--3315397	27	29.0	27	92	2	1266	23	35	14	27	1.93
3314604--3315397	82	9.7	81	92	2	1266	23	35	14	27	1.93
3315380--3316365	32	30.8	32	95	0	1650	31	35	18	14	1.91
3316848--3316922	20	3.8	20	78	0	87	34	13	12	40	1.81
3316848--3316925	40	2.0	39	87	2	111	34	12	12	39	1.82
3317833--3317889	22	2.5	24	88	11	100	17	10	8	63	1.51
3317842--3317896	22	2.6	21	88	5	58	20	9	9	61	1.52
3323855--3323881	10	2.7	10	100	0	54	0	0	22	77	0.76
3333575--3333692	1	118.0	1	80	0	110	88	8	1	1	0.66
3333574--3333692	33	3.5	33	83	10	141	87	9	1	1	0.69
3333575--3333692	37	3.2	36	86	7	157	88	8	1	1	0.66
3335160--3335574	33	12.9	33	82	11	458	21	32	12	33	1.91
3335136--3335574	89	4.6	92	80	14	409	21	32	13	32	1.92
3335160--3335594	70	6.7	68	79	14	419	21	33	12	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3335160--3335538	159	2.4	159	99	0	740	21	33	12	32	1.91
3335581--3335643	33	1.9	33	100	0	126	28	36	19	15	1.92
3335648--3336633	49	20.2	49	86	5	1324	24	25	17	32	1.97
3335648--3336637	242	4.1	238	90	5	1334	23	26	17	32	1.97
3335648--3336631	340	2.9	340	96	1	1782	23	26	17	32	1.97
3337351--3337417	33	2.0	33	88	0	98	34	11	13	40	1.81
3337371--3337395	13	1.9	13	100	0	50	36	16	16	32	1.90
3337460--3337484	13	1.9	13	100	0	50	32	16	16	36	1.90
3337493--3337613	52	2.3	52	94	0	215	35	17	18	28	1.93
3342618--3342642	13	1.9	13	100	0	50	32	16	20	32	1.94

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