genome.fa.s189.2.7.7.80.10.50.1000.6.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: Scaffold189
Parameters: 2 7 7 80 10 50 1000
Length:  2243555

Tables:   1   2   3   4   5   6   7   8   9   

This is table  6  of  9  ( 1067 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)
1209441--1209484	22	2.0	23	86	13	65	45	0	0	54	0.99
1210039--1210074	2	18.0	2	94	0	63	50	2	0	47	1.15
1217291--1217344	23	2.5	21	80	13	65	57	0	1	40	1.09
1217312--1217362	25	2.0	25	85	7	68	60	0	0	39	0.97
1218214--1218283	31	2.2	32	82	10	81	40	0	5	54	1.24
1219339--1219387	22	2.1	24	85	7	66	46	0	0	53	1.00
1220348--1220378	2	15.5	2	100	0	62	51	48	0	0	1.00
1229119--1229172	20	2.7	20	81	13	58	81	1	12	3	0.91
1230685--1230731	21	2.4	18	83	16	58	53	0	0	46	1.00
1234276--1234311	7	5.1	7	89	0	54	33	30	13	22	1.93
1234726--1234750	2	12.5	2	100	0	50	52	0	0	48	1.00
1235225--1235347	43	2.8	45	74	13	121	56	2	0	39	1.18
1235312--1235370	20	3.0	19	76	11	57	52	3	0	44	1.17
1238563--1238633	2	37.5	2	71	10	51	52	2	2	42	1.31
1238576--1238607	14	2.2	15	94	5	57	56	0	0	43	0.99
1256650--1256734	21	4.0	21	76	15	93	41	1	2	55	1.20
1256708--1256765	26	2.3	26	81	3	73	41	0	3	55	1.17
1256759--1256817	21	2.8	21	70	10	57	37	6	5	50	1.51
1256652--1256774	12	10.8	11	67	23	60	43	0	2	53	1.19
1256885--1256976	21	4.3	21	76	13	89	32	2	6	58	1.36
1256902--1256985	43	2.0	41	81	9	98	35	1	5	57	1.31
1256902--1256976	31	2.3	32	76	15	75	34	1	5	58	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1257722--1257808	32	2.7	32	100	0	174	39	5	8	47	1.57
1257722--1257845	64	1.9	64	82	6	153	40	5	8	45	1.59
1258146--1258297	20	7.5	21	74	10	111	41	2	1	54	1.22
1258146--1258286	21	6.9	22	74	11	88	41	2	1	53	1.24
1258204--1258298	10	9.5	11	68	20	50	38	1	1	58	1.12
1258513--1258687	9	17.8	10	72	18	136	60	1	0	37	1.11
1258513--1258688	11	16.8	11	71	24	107	60	1	0	36	1.11
1258519--1258679	21	7.0	24	69	24	109	60	1	0	37	1.08
1258652--1258697	21	2.3	20	85	7	58	63	4	2	30	1.26
1264826--1264856	2	15.5	2	100	0	62	48	0	0	51	1.00
1267529--1267573	23	1.9	24	81	4	56	51	6	0	42	1.28
1268158--1268266	49	2.2	50	83	4	141	44	14	16	24	1.86
1277032--1277090	29	2.0	29	100	0	118	35	16	10	37	1.83
1281286--1281351	15	4.1	15	74	14	60	40	1	12	45	1.51
1282909--1282940	2	16.0	2	100	0	64	50	0	0	50	1.00
1283105--1283131	2	13.5	2	100	0	54	51	0	0	48	1.00
1287792--1287868	17	4.3	17	71	22	59	41	0	0	58	0.98
1290614--1290680	35	1.9	35	81	6	82	49	0	0	50	1.00
1290637--1290680	19	2.6	16	77	19	52	54	0	0	45	0.99
1290678--1290723	13	3.5	13	82	17	51	56	2	0	41	1.11
1295085--1295125	19	2.2	19	95	0	73	36	14	19	29	1.92
1299140--1299183	14	3.2	13	87	9	52	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1302323--1302358	19	2.0	18	89	10	56	50	0	0	50	1.00
1309953--1309978	4	6.5	4	100	0	52	76	0	0	23	0.78
1314596--1314624	3	9.7	3	100	0	58	0	31	0	68	0.89
1325348--1325397	17	3.0	17	79	2	57	62	0	0	38	0.96
1325349--1325418	28	2.6	27	82	8	79	61	0	2	35	1.11
1335345--1335401	14	3.9	14	80	14	62	24	0	0	75	0.80
1335345--1335397	27	2.0	27	89	7	83	24	0	0	75	0.80
1335345--1335397	26	2.1	24	86	10	70	24	0	0	75	0.80
1335346--1335403	10	5.9	9	77	16	53	24	0	0	75	0.80
1335346--1335403	20	3.0	21	83	16	72	24	0	0	75	0.80
1344986--1345029	13	3.2	14	84	12	56	56	2	2	38	1.24
1348858--1348923	32	2.0	31	88	8	96	46	0	0	53	1.00
1349877--1349913	13	2.6	15	83	12	51	43	0	5	51	1.24
1349983--1350033	15	3.3	15	81	8	50	56	5	0	37	1.23
1350262--1350353	5	19.6	5	71	16	56	36	4	0	58	1.18
1350262--1350374	14	8.4	13	71	20	72	36	4	0	59	1.18
1350264--1350353	19	4.6	19	75	16	94	36	4	0	58	1.18
1350284--1350374	12	6.9	12	75	23	69	35	4	0	60	1.17
1350264--1350351	9	10.0	9	67	16	51	36	4	0	59	1.18
1350351--1350411	30	2.0	30	87	6	88	32	16	0	50	1.45
1350829--1350868	17	2.6	16	85	14	50	15	5	2	77	1.04
1351201--1351230	2	15.0	2	100	0	60	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1351891--1351934	23	2.0	23	90	4	72	47	2	15	34	1.58
1360548--1360592	21	2.1	22	88	8	67	53	0	4	42	1.21
1360624--1360706	38	2.2	38	82	6	96	37	0	0	62	0.95
1360614--1360707	38	2.4	39	76	11	95	38	0	0	61	0.96
1361007--1361051	24	1.9	23	86	4	63	33	0	11	55	1.35
1361025--1361063	18	2.2	18	85	0	51	43	0	7	48	1.31
1363455--1363489	11	3.2	11	83	0	52	60	0	2	37	1.12
1363999--1364028	2	15.0	2	92	0	51	53	0	0	46	1.00
1371024--1371082	28	2.1	28	100	0	118	38	28	18	13	1.89
1386177--1386212	2	18.0	2	100	0	72	50	0	0	50	1.00
1386546--1386594	2	25.0	2	87	4	73	44	0	2	53	1.12
1387230--1387276	2	23.5	2	100	0	94	51	0	48	0	1.00
1388142--1388171	4	7.2	4	92	7	51	23	0	26	50	1.50
1390055--1390083	7	4.1	7	100	0	58	44	13	41	0	1.44
1393541--1393569	2	14.5	2	100	0	58	51	48	0	0	1.00
1393569--1393605	2	18.5	2	100	0	74	51	0	0	48	1.00
1393605--1393651	2	23.5	2	100	0	94	51	0	48	0	1.00
1398803--1398856	12	4.6	12	72	21	51	53	0	0	46	1.00
1398820--1398869	21	2.3	22	80	16	59	46	4	0	50	1.20
1399531--1399568	18	2.1	18	95	0	67	44	44	5	5	1.49
1399613--1399648	13	2.8	13	86	0	54	47	36	0	16	1.47
1410631--1410673	2	21.5	2	100	0	86	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1413393--1413419	2	13.5	2	100	0	54	48	0	0	51	1.00
1413685--1414386	123	5.6	122	79	7	671	22	26	27	24	2.00
1414018--1414268	132	1.9	132	90	0	403	21	28	27	22	1.99
1413685--1414336	246	2.6	245	81	6	756	22	26	27	23	1.99
1415616--1415653	19	2.0	19	85	10	51	55	0	0	44	0.99
1423733--1423775	16	2.8	16	85	3	61	41	0	0	58	0.98
1425820--1425853	2	17.0	2	100	0	68	50	0	0	50	1.00
1428030--1428060	2	15.5	2	100	0	62	48	0	0	51	1.00
1436929--1436966	12	3.0	13	85	14	53	63	0	5	31	1.17
1436942--1436987	19	2.4	19	85	7	58	56	0	4	39	1.19
1438415--1438452	2	19.0	2	100	0	76	50	0	0	50	1.00
1439379--1439445	21	3.2	20	79	12	64	32	0	7	59	1.25
1439378--1439459	10	7.7	10	69	18	51	31	0	6	62	1.20
1439431--1439498	22	3.0	22	75	14	59	25	1	2	70	1.09
1439442--1439499	23	2.7	21	74	10	55	24	1	3	70	1.12
1439726--1439762	12	3.2	12	82	17	51	24	0	5	70	1.08
1439712--1439836	21	5.8	21	67	12	56	36	5	2	55	1.37
1439708--1439783	21	3.3	23	69	9	57	36	3	2	56	1.32
1444223--1444250	4	7.0	4	100	0	56	25	0	0	75	0.81
1444558--1445331	259	3.0	259	96	0	1437	35	15	13	35	1.86
1447908--1447938	2	15.5	2	100	0	62	0	51	0	48	1.00
1450576--1450624	23	2.1	24	81	11	57	32	40	2	24	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1450816--1450849	5	6.8	5	86	0	50	0	38	2	58	1.13
1456338--1456537	96	2.1	96	99	0	391	38	17	14	30	1.88
1459462--1459522	25	2.5	26	82	10	67	40	4	0	54	1.22
1460613--1460687	26	2.9	26	78	7	73	57	0	0	42	0.98
1460608--1460671	32	2.0	31	88	8	94	57	0	0	42	0.98
1460622--1460685	31	2.0	32	82	8	78	60	0	0	39	0.97
1468443--1468485	18	2.4	17	77	11	50	48	2	0	48	1.14
1483357--1483407	21	2.5	20	81	9	57	52	0	0	47	1.00
1485183--1485219	18	2.0	19	89	5	58	37	24	13	24	1.91
1488297--1488329	2	17.0	2	93	6	59	48	0	0	51	1.00

Tables:   1   2   3   4   5   6   7   8   9