genome.fa.s15.2.7.7.80.10.50.1000.21.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: Scaffold15
Parameters: 2 7 7 80 10 50 1000
Length:  4011073

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   

This is table  21  of  25  ( 2909 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)
3354534--3354564	15	2.1	15	93	0	53	12	22	16	48	1.80
3356368--3356412	21	2.1	21	84	8	56	22	20	4	53	1.63
3359557--3359608	19	2.8	18	85	8	68	19	5	17	57	1.59
3363364--3363396	16	2.1	16	94	0	57	9	15	9	66	1.43
3373200--3373234	2	17.5	2	100	0	70	48	0	0	51	1.00
3373493--3373614	62	2.0	62	100	0	244	32	6	8	52	1.57
3374411--3374436	13	2.0	13	100	0	52	38	15	15	30	1.88
3374895--3374961	37	1.9	35	88	11	102	32	11	25	29	1.92
3376488--3376652	84	2.0	84	82	7	201	51	3	19	25	1.63
3377782--3377806	13	1.9	13	100	0	50	36	16	16	32	1.90
3379499--3379524	13	2.0	13	100	0	52	38	15	15	30	1.88
3379983--3380049	37	1.9	35	88	11	102	32	11	25	29	1.92
3383859--3383935	35	2.2	35	95	0	136	41	22	3	32	1.72
3384542--3384574	17	2.0	17	88	5	50	45	9	0	45	1.35
3384983--3385041	5	11.6	5	85	8	75	33	0	3	62	1.12
3384966--3385041	19	3.6	21	82	12	84	34	0	5	60	1.19
3394935--3395049	53	2.2	53	96	1	214	42	20	19	17	1.89
3400207--3400505	150	2.0	150	98	0	580	32	22	21	23	1.98
3404360--3404404	22	2.0	23	91	4	74	22	24	0	53	1.46
3409017--3409074	28	2.1	28	100	0	116	18	17	10	53	1.71
3412601--3412642	18	2.3	18	88	8	59	40	0	0	59	0.97
3418212--3418246	3	12.0	3	93	6	63	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3418284--3418377	48	1.9	49	95	2	172	25	17	18	39	1.91
3419015--3419056	2	21.0	2	100	0	84	50	0	0	50	1.00
3425496--3425575	23	3.4	23	71	8	72	6	10	6	77	1.12
3425511--3425579	12	5.8	12	75	10	61	8	10	2	78	1.07
3425516--3425579	6	10.8	6	72	9	51	9	7	3	79	1.02
3425512--3425579	24	2.9	24	77	2	84	8	8	2	79	1.03
3425524--3425579	18	3.2	18	75	10	62	8	7	3	80	1.01
3426330--3426355	13	2.0	13	100	0	52	30	15	15	38	1.88
3426310--3426376	33	2.0	33	88	0	98	25	14	16	43	1.86
3428837--3428909	27	2.6	28	86	2	94	23	35	21	19	1.96
3428892--3429061	52	3.3	50	76	8	171	31	25	11	31	1.91
3428728--3429120	211	1.9	211	86	2	574	29	27	12	29	1.93
3430310--3430337	2	14.0	2	100	0	56	50	0	0	50	1.00
3430385--3430486	51	2.0	51	96	0	186	45	8	6	39	1.62
3436213--3436279	24	2.8	24	75	8	66	56	0	0	43	0.99
3437649--3437673	2	12.5	2	100	0	50	0	0	48	52	1.00
3438381--3438435	24	2.3	24	80	0	65	49	0	0	50	1.00
3438382--3438437	12	4.6	13	78	12	57	48	0	0	51	1.00
3439323--3439392	23	2.9	23	74	6	59	54	1	12	31	1.47
3440176--3440235	21	2.9	21	75	7	52	36	0	1	61	1.06
3442048--3442074	14	1.9	14	100	0	54	59	0	40	0	0.98
3442800--3442849	23	2.3	22	89	6	75	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3443135--3443171	11	3.4	11	84	0	56	37	0	0	62	0.96
3443711--3443773	33	1.9	32	87	12	92	36	15	15	31	1.90
3447100--3447206	52	2.1	52	89	0	160	35	12	20	31	1.89
3447184--3447224	10	4.1	10	90	0	64	39	7	31	21	1.81
3447253--3447277	13	1.9	13	100	0	50	36	16	16	32	1.90
3449187--3449233	23	2.0	24	84	12	62	61	19	4	14	1.49
3450108--3450167	21	2.9	21	79	20	72	20	25	1	53	1.55
3450131--3450174	21	2.1	21	83	8	54	20	27	0	52	1.47
3454809--3454933	52	2.4	52	95	0	223	28	17	18	36	1.94
3454809--3454953	52	2.8	51	89	4	211	29	17	18	34	1.94
3454942--3454966	13	1.9	13	100	0	50	36	16	16	32	1.90
3455032--3455056	13	1.9	13	100	0	50	32	16	16	36	1.90
3459955--3460004	21	2.4	22	83	9	61	32	20	0	48	1.50
3461742--3461784	21	2.0	23	86	9	63	37	4	18	39	1.72
3462358--3462382	13	1.9	13	100	0	50	36	16	16	32	1.90
3462337--3462401	33	2.0	32	88	8	96	30	15	15	38	1.88
3462367--3462425	20	3.0	20	82	7	77	37	13	15	33	1.86
3466320--3467420	95	12.1	90	81	6	1109	33	15	7	43	1.75
3467899--3468220	120	2.6	121	80	13	372	54	1	1	41	1.20
3468114--3468145	15	2.1	16	94	5	57	65	0	3	31	1.08
3467915--3468255	121	2.8	127	85	9	435	55	1	2	41	1.20
3468250--3468302	19	2.8	19	86	8	72	30	0	1	67	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3468243--3468295	21	2.5	21	73	14	54	35	0	0	64	0.94
3468575--3468767	106	1.8	106	83	7	257	43	2	2	51	1.27
3468876--3468908	9	3.7	9	88	11	50	42	0	0	57	0.98
3469012--3469060	15	3.3	15	77	11	57	57	4	0	38	1.18
3469360--3469398	15	2.7	15	84	11	55	38	0	0	61	0.96
3469366--3469407	15	2.9	15	86	10	52	35	0	0	64	0.94
3469754--3469805	20	2.6	19	85	11	61	59	0	0	40	0.97
3469721--3469807	27	3.0	27	79	17	72	56	1	0	42	1.07
3471236--3471269	3	11.3	3	100	0	68	0	67	0	32	0.91
3472756--3472825	20	3.4	21	79	13	67	41	0	0	58	0.98
3472813--3472864	14	3.6	14	76	2	59	34	0	1	63	1.06
3473216--3473299	34	2.5	34	78	5	82	32	1	0	66	0.99
3473241--3473291	17	3.0	17	83	11	68	29	0	0	70	0.87
3473243--3473301	17	3.6	16	78	13	57	32	0	0	67	0.91
3473249--3473301	17	3.1	18	83	8	65	32	0	0	67	0.91
3473263--3473295	14	2.3	15	89	5	50	36	0	0	63	0.95
3475486--3475545	24	2.6	22	81	5	75	56	1	0	41	1.09
3475486--3475552	22	2.9	23	82	4	82	56	1	0	41	1.08
3475570--3475612	13	3.3	13	80	6	52	60	2	4	32	1.30
3475548--3475590	22	2.0	22	85	0	59	58	0	6	34	1.25
3475570--3475635	26	2.5	26	79	13	73	54	1	3	40	1.25
3477025--3477066	20	2.2	19	83	12	50	42	0	0	57	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3480581--3480620	18	2.2	18	95	0	71	80	5	10	5	1.02
3481599--3481698	49	2.1	49	82	1	121	34	13	14	39	1.84
3481630--3481774	50	2.9	50	73	11	134	31	11	13	43	1.79
3491566--3491592	13	2.1	13	100	0	54	29	14	14	40	1.86
3493108--3493159	20	2.5	21	81	3	61	44	15	7	32	1.75
3493229--3493293	33	2.0	33	90	0	103	35	13	15	35	1.87
3499899--3500025	42	3.2	39	72	12	114	43	14	14	27	1.84
3499861--3500062	81	2.5	81	79	12	236	45	16	13	25	1.83
3499864--3499986	42	3.0	43	73	16	109	44	17	13	24	1.85
3502100--3502156	26	2.1	27	83	3	71	54	0	8	36	1.32
3503308--3503348	2	20.5	2	100	0	82	51	0	0	48	1.00
3504185--3504222	19	2.0	19	89	0	58	39	2	7	50	1.46
3504677--3504717	12	2.9	14	79	20	50	34	2	9	53	1.47
3504927--3505322	116	3.4	117	83	6	472	52	1	3	43	1.24
3505007--3505077	34	2.2	32	85	12	92	50	0	2	46	1.16
3505007--3505072	33	2.1	30	81	18	73	50	0	3	46	1.16
3504968--3505131	38	4.3	38	69	22	126	54	0	1	43	1.11
3505592--3505621	15	2.0	15	93	0	51	36	0	0	63	0.95
3505592--3505921	126	2.8	124	84	11	406	43	2	1	52	1.25
3506402--3506568	92	1.8	91	89	3	264	43	8	14	32	1.76
3506734--3506768	18	2.0	17	88	5	52	31	14	17	37	1.89
3506800--3507580	92	8.9	91	70	15	452	41	7	16	34	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3506800--3507151	90	3.9	92	81	3	426	41	8	15	34	1.77
3507085--3507235	74	2.0	75	88	3	225	38	9	19	33	1.83
3507216--3507368	78	2.0	78	85	2	209	45	7	17	28	1.76
3507300--3507577	88	3.1	87	78	8	290	42	6	16	34	1.74
3511054--3511697	298	2.2	291	89	4	970	46	7	9	36	1.65
3511854--3511951	36	2.9	32	73	17	92	42	0	0	57	0.99
3511972--3511996	13	1.9	13	100	0	50	24	0	0	76	0.80
3511941--3512172	116	2.0	114	93	3	394	41	0	3	54	1.19
3511923--3512125	42	5.0	41	67	21	110	44	0	1	53	1.15
3512286--3512349	28	2.2	29	78	13	69	51	6	1	40	1.36

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