genome.fa.s21.2.7.7.80.10.50.1000.9.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: Scaffold21
Parameters: 2 7 7 80 10 50 1000
Length:  2821038

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

This is table  9  of  15  ( 1753 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)
1236059--1236113	27	2.0	27	92	0	92	32	5	9	52	1.56
1236049--1236077	2	14.5	2	100	0	58	48	0	0	51	1.00
1236318--1236383	20	3.2	20	70	27	57	39	1	0	59	1.07
1239393--1239445	15	3.3	16	73	19	56	37	0	3	58	1.16
1239457--1239525	11	6.1	11	75	18	61	30	0	2	66	1.06
1239468--1239537	19	3.6	18	71	19	59	32	0	1	65	1.01
1239482--1239536	17	3.4	17	80	9	71	32	0	0	67	0.91
1239451--1239531	41	2.0	42	85	7	112	32	0	2	65	1.06
1239489--1239531	12	3.6	12	90	9	70	32	0	0	67	0.91
1243123--1243175	8	7.2	8	80	16	62	33	0	0	66	0.92
1243123--1243175	14	4.1	14	75	20	62	33	0	0	66	0.92
1246615--1246712	20	5.1	20	68	19	64	50	0	1	48	1.07
1247505--1247553	22	2.5	20	81	18	66	61	0	0	38	0.96
1250317--1250355	21	1.9	20	89	5	60	46	0	7	46	1.31
1252473--1252517	15	3.0	16	84	12	60	51	0	2	46	1.13
1254034--1254073	13	2.9	14	81	7	55	35	0	0	65	0.93
1255255--1255284	2	15.0	2	100	0	60	50	0	0	50	1.00
1265070--1265189	6	20.7	6	68	19	51	34	0	1	63	1.10
1267139--1267194	23	2.4	23	80	17	62	60	1	0	37	1.07
1269534--1269560	2	13.5	2	100	0	54	48	0	0	51	1.00
1269557--1269584	6	4.7	6	100	0	56	35	0	14	50	1.43
1271786--1271820	2	17.5	2	100	0	70	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1273535--1273567	17	2.0	17	88	5	50	51	0	0	48	1.00
1273540--1273604	27	2.3	29	75	17	73	46	4	0	49	1.22
1274098--1274141	21	2.0	22	91	4	72	50	0	0	50	1.00
1274129--1274215	11	8.0	10	71	22	52	41	0	1	57	1.06
1274135--1274249	27	4.3	27	70	20	71	39	0	0	59	1.10
1274591--1274615	2	12.5	2	100	0	50	52	0	0	48	1.00
1280778--1280802	12	2.1	12	100	0	50	32	8	24	36	1.84
1283575--1283605	2	15.5	2	100	0	62	51	0	0	48	1.00
1283810--1283838	2	15.0	2	92	7	51	48	0	0	51	1.00
1285306--1285337	2	16.0	2	100	0	64	50	0	0	50	1.00
1289203--1289378	18	9.7	18	68	20	73	57	0	1	40	1.09
1289207--1289296	27	3.2	28	84	6	119	60	0	2	37	1.09
1289246--1289349	33	3.2	32	76	21	101	57	0	1	40	1.10
1289333--1289398	28	2.4	27	76	18	73	56	0	1	42	1.08
1289210--1289378	5	33.0	5	64	21	57	57	0	1	40	1.09
1289306--1289390	22	3.6	22	73	7	62	52	0	2	44	1.13
1290841--1290875	2	17.5	2	87	0	52	51	5	0	42	1.25
1295717--1295791	20	3.8	20	75	7	71	41	9	12	37	1.74
1303041--1303113	28	2.6	29	77	12	80	47	0	0	52	1.00
1303094--1303129	16	2.2	16	90	0	54	41	2	2	52	1.30
1303319--1303349	2	15.5	2	100	0	62	51	0	0	48	1.00
1305782--1305828	4	12.2	4	91	8	80	0	23	0	76	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1310365--1310448	45	1.9	41	81	13	96	48	2	1	47	1.22
1312013--1312072	17	3.6	17	76	19	63	41	1	0	56	1.09
1312019--1312085	33	2.1	32	88	8	100	41	1	1	55	1.18
1312287--1312352	26	2.4	29	74	20	70	51	0	0	48	1.00
1313665--1313709	15	2.9	15	83	3	54	40	2	6	51	1.41
1313908--1314164	50	5.1	50	81	4	230	30	13	17	38	1.88
1313978--1314162	101	1.8	100	83	3	246	30	14	19	35	1.91
1314966--1315037	35	2.1	35	92	2	119	55	0	23	20	1.43
1318296--1318501	50	4.1	50	84	5	236	30	16	18	33	1.94
1318315--1318501	100	1.9	100	86	4	270	31	17	19	31	1.95
1319359--1319392	13	2.8	12	86	8	50	67	0	0	32	0.91
1319353--1319396	18	2.4	18	85	11	54	63	0	0	36	0.95
1319353--1319393	12	3.3	12	83	6	55	65	0	0	34	0.93
1319463--1319510	18	2.6	19	77	12	55	39	2	0	58	1.10
1319612--1319642	15	2.1	15	100	0	62	45	0	0	54	0.99
1319616--1319648	17	1.9	17	93	0	57	45	0	0	54	0.99
1319612--1319656	17	2.8	16	80	12	56	48	0	0	51	1.00
1325144--1325187	20	2.1	22	84	16	58	31	0	0	68	0.90
1325132--1325197	11	6.5	10	80	15	57	33	0	0	66	0.92
1325132--1325190	19	2.9	20	78	19	68	33	0	0	66	0.92
1325638--1325722	44	2.0	42	81	11	100	38	0	5	55	1.24
1325717--1325762	16	2.9	16	82	17	60	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1327706--1327732	14	1.9	14	100	0	54	59	0	0	40	0.98
1329459--1329505	16	3.0	15	82	17	60	51	0	0	48	1.00
1329456--1329512	16	3.5	17	75	20	59	52	0	0	47	1.00
1330501--1330532	11	2.8	11	95	4	55	90	0	3	6	0.53
1331818--1331851	16	2.1	17	88	5	52	26	2	23	47	1.66
1334887--1334912	2	13.0	2	100	0	52	50	0	0	50	1.00
1336548--1336578	3	10.3	3	100	0	62	67	0	0	32	0.91
1339097--1339146	21	2.3	22	82	6	57	56	0	0	44	0.99
1339143--1339205	14	4.4	14	76	11	56	60	0	0	39	0.97
1339143--1339220	30	2.8	28	81	11	97	58	0	0	41	0.98
1339951--1340053	28	3.7	27	70	13	77	52	0	0	46	1.07
1340021--1340058	17	2.3	16	90	4	58	50	2	0	47	1.15
1343033--1343064	2	15.5	2	93	6	55	0	46	3	50	1.17
1349450--1349484	2	17.5	2	100	0	70	48	0	51	0	1.00
1350036--1350078	24	1.9	23	86	13	63	53	0	0	46	1.00
1353333--1353361	2	14.5	2	100	0	58	51	0	0	48	1.00
1353708--1353777	34	2.1	34	83	5	88	40	1	2	55	1.23
1353954--1353998	2	22.5	2	100	0	90	51	0	0	48	1.00
1355021--1355075	21	2.8	18	77	17	56	45	0	1	52	1.11
1355023--1355080	18	3.0	19	75	18	57	46	0	1	51	1.11
1358222--1358300	22	3.8	22	77	13	94	37	16	13	31	1.88
1359808--1359967	50	3.2	50	86	0	221	31	18	18	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1364358--1364467	50	2.2	50	85	0	157	32	20	20	27	1.97
1371273--1371341	25	2.9	24	74	8	61	43	2	0	53	1.15
1371500--1371564	2	32.5	2	85	11	89	47	3	0	49	1.17
1376565--1376616	23	2.3	23	79	0	59	50	3	0	46	1.20
1382181--1382210	15	2.0	15	93	0	51	50	0	0	50	1.00
1390997--1391031	18	1.9	18	88	11	54	37	0	2	60	1.12
1390997--1391069	28	2.6	28	73	18	71	36	0	1	61	1.05
1391675--1391716	2	21.5	2	90	4	68	50	0	2	47	1.14
1391789--1391818	8	3.8	8	90	0	51	86	0	0	13	0.57
1395229--1395311	10	8.2	10	69	24	50	33	2	2	61	1.22
1395269--1395309	12	3.6	12	77	12	50	31	0	0	68	0.90
1395298--1395328	15	2.1	15	93	0	53	35	6	0	58	1.24
1395266--1395320	23	2.4	22	84	6	65	34	1	0	63	1.05
1395532--1395600	26	2.7	23	74	22	59	34	0	1	63	1.03
1395562--1395611	18	2.8	18	72	19	50	32	0	0	68	0.90
1396560--1396612	4	13.2	4	84	7	63	79	1	18	0	0.83
1396566--1396617	25	2.1	24	89	3	77	82	1	15	0	0.75
1396562--1396614	21	2.6	21	82	11	65	81	1	16	0	0.79
1396560--1396616	12	4.8	12	87	6	71	80	1	17	0	0.79
1405944--1406012	21	3.0	21	74	19	59	40	2	0	56	1.14
1410453--1410551	10	9.5	11	66	21	52	41	0	0	58	0.98
1410455--1410485	10	3.0	10	90	9	53	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1410537--1410591	21	2.8	20	78	16	60	40	1	0	58	1.09
1410456--1410581	50	2.6	46	73	14	112	41	0	0	58	0.98
1414658--1414690	2	16.5	2	93	0	57	51	3	0	45	1.16
1414901--1414941	2	20.5	2	100	0	82	51	0	48	0	1.00
1416076--1416118	22	1.9	22	85	4	59	51	6	0	41	1.29
1417162--1417216	27	2.0	28	82	13	69	54	3	1	40	1.28
1417280--1417341	26	2.4	26	78	8	72	41	0	6	51	1.27
1417325--1417383	13	4.3	13	81	8	64	55	0	1	42	1.09
1417685--1417738	16	3.3	16	80	14	58	27	0	7	64	1.20
1418291--1418321	2	15.5	2	100	0	62	51	0	48	0	1.00

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