genome.fa.s47.2.7.7.80.10.50.1000.10.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: Scaffold47
Parameters: 2 7 7 80 10 50 1000
Length:  2157611

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   

This is table  10  of  15  ( 1735 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)
1255350--1255379	3	10.0	3	100	0	60	66	0	33	0	0.92
1259079--1259123	20	2.2	20	80	0	54	40	0	0	60	0.97
1259124--1259225	46	2.1	48	87	5	145	53	0	0	45	1.06
1264097--1264155	8	6.6	9	80	7	59	55	3	1	38	1.26
1264819--1264850	17	1.9	16	93	6	55	40	21	6	31	1.78
1269427--1269483	23	2.5	24	80	13	66	42	0	0	57	0.98
1270367--1270425	17	3.4	17	79	11	66	67	1	0	30	1.00
1270749--1270778	16	1.9	15	93	6	51	46	3	0	50	1.18
1272080--1272116	15	2.3	17	90	9	60	43	2	5	48	1.40
1272079--1272119	16	2.5	17	84	15	59	41	2	7	48	1.44
1272721--1272775	16	3.4	17	72	25	55	41	0	0	58	0.98
1272967--1272996	12	2.6	12	94	5	53	30	0	0	70	0.88
1273540--1273612	29	2.6	27	81	14	85	65	5	2	26	1.27
1273923--1273950	2	14.0	2	100	0	56	0	0	50	50	1.00
1277238--1277334	29	3.2	29	73	17	74	42	3	1	53	1.23
1278649--1278681	2	16.5	2	100	0	66	51	0	0	48	1.00
1278887--1278940	25	2.2	24	83	9	65	62	0	3	33	1.12
1278935--1279021	16	5.3	16	72	13	70	55	0	2	42	1.12
1278916--1279024	32	3.3	32	82	6	130	55	0	1	42	1.10
1278925--1279039	16	6.8	17	67	20	64	57	0	1	40	1.15
1278935--1279037	32	3.2	32	82	8	102	56	0	1	40	1.17
1279008--1279080	23	3.3	24	72	18	68	64	2	0	32	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1279972--1280007	18	2.0	18	88	0	54	50	0	0	50	1.00
1280256--1280305	13	3.9	13	80	14	52	70	2	0	28	0.99
1280855--1280888	11	3.1	11	100	0	68	26	26	17	29	1.98
1281016--1281054	15	2.9	14	82	17	55	48	0	0	51	1.00
1281024--1281076	18	2.9	18	79	17	65	54	0	0	45	0.99
1281028--1281076	19	2.7	18	81	9	64	53	0	0	46	1.00
1281598--1281642	16	2.8	16	79	0	54	44	15	13	26	1.83
1282841--1282882	21	1.9	23	85	9	61	54	0	0	45	0.99
1282871--1282915	23	2.0	23	86	0	63	57	0	0	42	0.98
1283170--1283230	19	3.0	21	79	18	76	68	0	0	31	0.89
1283136--1283205	28	2.4	28	80	9	77	67	0	0	32	0.91
1283272--1283315	19	2.2	19	88	8	61	63	0	2	34	1.07
1283502--1283531	2	15.0	2	100	0	60	50	0	0	50	1.00
1284535--1284581	17	2.7	19	81	18	59	46	0	0	53	1.00
1284569--1284610	22	1.9	22	85	9	59	59	0	0	40	0.97
1296275--1296512	50	4.8	50	94	0	404	28	17	23	29	1.97
1304572--1304618	16	3.1	16	79	17	55	70	10	14	4	1.31
1305931--1306657	27	26.6	27	90	2	1033	24	32	14	29	1.94
1306677--1307041	28	12.3	28	84	8	322	30	30	17	21	1.96
1306683--1307068	86	4.3	88	81	10	347	30	29	17	22	1.97
1306653--1307041	114	3.3	114	82	9	381	29	30	18	21	1.97
1306730--1307132	32	13.2	32	81	6	310	30	29	17	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1308358--1308405	4	12.5	4	79	20	50	77	0	20	2	0.88
1308365--1308409	14	3.1	14	87	9	56	80	0	17	2	0.82
1308358--1308407	24	2.1	24	88	0	73	78	0	20	2	0.86
1311931--1311962	17	1.9	17	93	6	57	34	0	0	65	0.93
1312040--1312079	16	2.6	16	78	21	50	17	2	7	72	1.19
1312432--1312460	7	4.1	7	100	0	58	86	0	13	0	0.58
1314053--1314077	11	2.3	11	100	0	50	56	0	0	44	0.99
1314909--1314965	21	2.6	22	84	15	75	38	0	0	61	0.96
1314912--1314965	22	2.5	22	88	8	76	38	0	0	61	0.96
1315503--1315571	32	2.2	32	80	12	83	50	10	1	37	1.45
1319048--1319091	20	2.1	21	87	4	63	38	0	0	61	0.96
1319695--1319741	16	3.1	16	77	20	55	40	0	0	59	0.97
1321010--1321050	20	2.2	18	86	8	55	41	4	0	53	1.22
1321009--1321067	27	2.2	26	79	8	66	47	3	0	49	1.18
1326622--1326652	16	1.9	16	93	0	53	29	0	3	67	1.06
1328729--1328760	2	17.0	2	87	12	50	53	0	0	46	1.00
1328893--1328965	24	2.9	24	75	16	76	52	0	0	47	1.00
1332438--1332497	17	3.5	16	76	24	52	30	3	5	61	1.33
1333567--1333611	15	2.7	17	86	10	58	42	0	0	57	0.98
1333586--1333631	13	3.7	13	81	16	53	34	0	2	63	1.07
1333579--1333631	9	6.2	9	77	20	51	37	0	1	60	1.08
1334931--1334978	24	2.0	24	95	0	87	29	14	16	39	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1335690--1335747	21	2.6	22	81	13	66	39	0	0	60	0.97
1340230--1340280	11	4.9	11	76	13	54	35	0	1	62	1.06
1344568--1344600	13	2.5	13	95	0	57	42	0	0	57	0.98
1346190--1346246	29	2.0	29	82	6	71	45	7	3	43	1.48
1354422--1354464	23	2.0	21	86	9	59	60	9	2	27	1.40
1354664--1354702	2	19.5	2	89	0	60	48	5	0	46	1.24
1354656--1354702	12	3.9	12	88	0	58	46	6	0	46	1.28
1357149--1357217	23	3.0	23	73	14	70	59	0	0	40	0.97
1360299--1360365	32	2.1	32	85	2	89	46	13	7	32	1.71
1361373--1361403	10	3.0	10	95	4	53	41	0	0	58	0.98
1361554--1361619	20	3.2	20	73	14	55	9	6	10	74	1.22
1361553--1361619	21	3.2	21	75	10	66	8	5	10	74	1.21
1361574--1361648	35	2.2	34	81	11	82	13	5	6	74	1.19
1361597--1361644	25	1.9	25	83	8	62	16	4	4	75	1.12
1361820--1361858	13	3.0	13	85	11	53	30	0	0	69	0.89
1364751--1365015	87	3.0	90	84	5	333	30	15	13	40	1.86
1367400--1367459	21	2.9	21	71	0	57	50	10	3	36	1.53
1367439--1367517	41	2.1	36	81	13	88	49	6	3	40	1.46
1367524--1367572	17	2.9	17	81	3	64	85	8	0	6	0.73
1368232--1368278	18	2.6	18	86	3	67	68	6	0	25	1.13
1368554--1368629	35	2.2	36	86	11	106	65	7	9	17	1.44
1369868--1369921	20	2.7	20	94	5	92	37	16	12	33	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1369951--1370005	19	2.8	20	89	10	87	34	16	14	34	1.89
1370755--1370802	11	4.4	10	76	19	51	56	6	0	37	1.25
1371088--1371131	11	3.7	12	84	6	54	29	0	2	68	1.02
1371345--1371370	13	2.0	13	100	0	52	38	0	0	61	0.96
1371455--1371480	2	13.0	2	100	0	52	50	0	0	50	1.00
1373305--1373354	16	3.1	16	85	8	57	48	0	0	52	1.00
1373429--1373485	13	4.7	13	70	16	50	56	0	0	43	0.99
1374000--1374034	3	11.7	3	93	0	61	31	0	2	65	1.07
1374970--1375010	21	2.0	21	85	9	57	39	0	0	60	0.96
1375000--1375063	33	1.9	33	87	9	94	46	0	0	53	1.00
1375603--1375671	26	2.8	25	74	22	65	40	0	0	59	0.97
1375643--1375684	21	2.0	21	90	4	68	45	0	0	54	0.99
1377387--1377425	17	2.4	16	87	8	53	46	0	2	51	1.14
1377397--1377477	26	3.0	26	74	3	81	45	0	2	51	1.14
1377932--1377989	31	1.9	31	82	10	75	32	5	0	62	1.18
1382763--1382810	2	26.0	2	78	16	50	41	0	0	58	0.98
1382761--1382817	23	2.5	23	85	5	71	40	0	0	59	0.97
1382767--1382916	17	9.1	18	66	24	73	39	0	1	58	1.11
1382761--1382914	27	5.7	26	72	18	95	38	0	1	59	1.11
1382755--1382901	6	25.8	6	67	19	57	40	0	0	58	1.08
1384540--1384568	2	14.5	2	100	0	58	51	0	0	48	1.00
1385134--1385204	32	2.2	33	89	2	108	53	8	0	38	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1385740--1385813	13	5.4	14	69	23	50	39	1	0	59	1.06
1386227--1386269	22	2.0	22	81	9	52	46	2	2	48	1.27
1389109--1389190	8	9.8	8	72	15	58	28	2	0	69	1.01
1389109--1389150	15	2.7	16	88	3	59	26	0	0	73	0.83
1389130--1389167	18	2.2	18	90	4	60	18	2	0	78	0.86
1389115--1389178	25	2.6	25	82	4	87	26	3	0	70	1.02
1389559--1389596	17	2.2	17	90	0	58	52	2	2	42	1.29
1391544--1391586	22	2.0	21	82	13	52	48	4	2	44	1.36
1391678--1391714	14	2.6	14	95	0	65	51	8	0	40	1.32
1391677--1391714	16	2.4	16	95	0	67	50	7	0	42	1.31

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15