genome.fa.s54.2.7.7.80.10.50.1000.10.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: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  10  of  20  ( 2342 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)
1581369--1581488	23	4.6	26	73	18	81	51	0	0	47	1.06
1581428--1581499	29	2.4	29	86	6	101	63	0	0	36	0.94
1581419--1581501	23	3.3	24	75	18	80	59	0	0	40	0.98
1588141--1588182	2	21.5	2	90	4	68	50	2	0	47	1.14
1588446--1588487	18	2.5	17	82	14	52	30	0	4	64	1.14
1588883--1588962	5	15.2	5	75	14	72	66	0	0	33	0.92
1588885--1588975	11	9.1	11	75	17	65	67	0	1	31	0.98
1588880--1588977	10	9.6	10	77	16	103	67	0	1	31	0.98
1588880--1589001	21	6.1	20	76	18	103	64	0	0	34	0.99
1588955--1589039	17	5.1	16	73	17	57	52	0	1	45	1.08
1588975--1589026	16	3.3	15	75	19	52	50	0	0	50	1.00
1589868--1589912	17	2.6	17	85	0	63	48	2	2	46	1.26
1591203--1591242	18	2.2	18	86	8	55	70	0	0	30	0.88
1591456--1591506	15	3.4	15	81	5	50	45	0	3	50	1.20
1591625--1591679	17	3.1	18	75	15	51	63	3	1	30	1.22
1591642--1591670	11	2.5	12	88	11	51	68	0	0	31	0.89
1591968--1592011	20	2.2	20	87	0	61	63	2	0	34	1.07
1596775--1596825	22	2.3	22	100	0	102	35	0	0	64	0.94
1596775--1596826	11	4.7	11	82	0	68	36	0	0	63	0.95
1596899--1596967	10	7.2	9	71	22	52	34	1	1	62	1.13
1596897--1596983	19	4.3	19	75	21	72	36	1	1	60	1.11
1596889--1596969	8	8.9	8	72	24	54	34	1	1	62	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1597191--1597259	26	2.8	24	76	22	70	36	0	0	63	0.94
1597190--1597271	34	2.4	33	80	13	87	35	0	0	64	0.94
1597221--1597270	18	2.8	18	72	19	50	32	0	0	68	0.90
1597250--1597292	14	3.2	14	74	12	54	27	0	2	69	1.00
1597311--1597335	12	2.1	12	100	0	50	24	0	0	76	0.80
1597549--1597592	22	2.0	22	86	8	63	25	0	6	68	1.14
1598205--1598249	21	2.1	21	88	8	65	80	2	17	0	0.82
1598200--1598248	25	1.9	26	88	12	75	79	2	18	0	0.83
1600308--1600334	8	3.4	8	100	0	54	70	0	0	29	0.88
1601276--1601317	3	14.3	3	90	5	68	0	35	2	61	1.09
1601914--1602013	43	2.4	41	83	9	130	25	4	10	61	1.45
1601925--1602013	43	2.1	43	89	4	135	25	4	8	60	1.46
1602164--1602223	9	6.7	9	74	14	52	23	1	0	75	0.90
1609568--1609605	15	2.5	15	86	0	58	52	2	0	44	1.14
1610862--1610912	16	3.2	16	72	10	50	50	0	1	47	1.12
1610933--1611098	84	2.0	84	95	0	296	24	22	24	28	1.99
1616210--1616240	2	15.5	2	100	0	62	48	0	0	51	1.00
1620793--1620829	16	2.2	18	85	9	51	59	0	5	35	1.20
1623762--1623808	22	2.1	22	84	0	58	46	0	2	51	1.13
1623834--1623867	17	2.0	17	88	0	50	35	0	0	64	0.94
1626072--1626119	3	16.0	3	95	0	87	0	33	2	64	1.05
1627739--1627778	20	2.0	20	85	0	53	62	0	0	37	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1628462--1628532	31	2.3	31	95	0	124	39	1	0	59	1.06
1628992--1629037	21	2.1	22	84	11	60	43	2	6	47	1.41
1629027--1629060	17	2.1	16	88	5	50	55	0	0	44	0.99
1634646--1634685	20	2.0	20	100	0	80	40	25	20	15	1.90
1637124--1637164	20	2.1	20	86	4	57	41	2	0	56	1.13
1637250--1637286	19	2.0	19	94	5	67	43	0	0	56	0.99
1641802--1641834	2	16.5	2	93	0	57	48	0	0	51	1.00
1644199--1644254	18	3.4	16	72	18	53	42	0	1	55	1.10
1644391--1644438	8	5.9	8	78	11	53	72	0	0	27	0.84
1645490--1645563	32	2.2	33	83	9	89	54	1	1	43	1.17
1645506--1645568	32	2.0	32	87	6	92	52	0	0	47	1.00
1645549--1645619	28	2.6	28	80	13	85	61	1	0	36	1.05
1645519--1645633	27	4.3	26	75	16	76	57	1	0	40	1.09
1648214--1648241	3	9.3	3	100	0	56	0	32	35	32	1.58
1649088--1649112	3	8.3	3	100	0	50	36	32	32	0	1.58
1650228--1650259	2	16.0	2	100	0	64	50	0	0	50	1.00
1653609--1653662	24	2.2	24	84	12	67	38	0	0	61	0.96
1653610--1653660	19	2.7	19	81	3	68	39	0	0	60	0.97
1654277--1654335	13	4.6	13	77	12	68	42	0	0	57	0.98
1654277--1654335	26	2.3	26	85	11	86	42	0	0	57	0.98
1654800--1654826	7	3.9	7	100	0	54	14	0	0	85	0.61
1658281--1658319	2	19.5	2	100	0	78	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1663866--1663890	11	2.3	11	100	0	50	0	32	8	60	1.26
1667659--1667768	52	2.3	48	77	18	122	43	0	0	56	0.99
1667692--1667763	19	4.1	18	73	26	64	47	0	0	52	1.00
1667664--1667771	33	3.2	34	80	16	109	43	0	0	56	0.99
1667672--1667788	17	7.4	16	68	15	57	42	0	0	57	0.98
1668040--1668089	18	2.8	19	74	17	54	36	0	0	64	0.94
1669008--1669042	6	6.2	6	93	6	56	0	14	0	85	0.59
1669131--1669190	13	4.4	14	83	10	63	50	3	0	46	1.18
1673970--1674002	17	1.9	18	88	11	52	60	0	0	39	0.97
1674690--1674732	22	2.0	22	86	9	61	37	0	6	55	1.27
1675773--1675845	38	1.9	37	83	8	94	43	0	0	56	0.99
1675775--1675846	9	7.6	10	71	22	57	43	0	0	56	0.99
1676520--1676602	10	8.2	10	74	11	53	44	0	1	54	1.08
1676612--1676650	11	3.6	11	79	6	53	51	2	0	46	1.14
1676762--1676794	12	2.7	13	86	13	52	33	6	0	60	1.21
1677505--1677566	17	3.5	17	73	18	56	54	1	0	43	1.09
1677498--1677575	35	2.2	34	86	8	104	51	1	0	47	1.09
1677503--1677572	16	4.2	17	72	22	51	52	1	0	45	1.09
1679579--1679630	4	13.0	4	91	0	50	38	0	11	50	1.39
1687667--1687727	26	2.3	25	76	15	61	36	1	0	62	1.05
1688217--1688251	3	11.7	3	100	0	70	0	34	0	65	0.93
1700337--1700371	6	5.8	6	93	0	61	34	17	31	17	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1700627--1700683	18	3.1	18	76	14	53	57	1	0	40	1.09
1700658--1700695	17	2.2	18	85	4	51	55	0	0	44	0.99
1701952--1702126	87	2.0	88	96	1	325	37	18	12	32	1.88
1703414--1703568	76	2.0	76	98	0	301	36	21	10	30	1.88
1706733--1706870	73	1.9	73	98	0	267	21	15	17	45	1.85
1713453--1713486	16	2.1	16	89	10	52	50	0	0	50	1.00
1713469--1713533	34	1.9	33	82	14	80	49	0	0	50	1.00
1713506--1713558	20	2.7	19	80	13	63	43	1	0	54	1.11
1713498--1713564	19	3.7	18	77	14	59	41	1	0	56	1.08
1713506--1713569	19	3.4	19	77	12	60	39	1	0	59	1.07
1714080--1714128	22	2.2	21	83	16	64	55	4	2	38	1.31
1715878--1715907	12	2.5	12	94	0	51	46	10	33	10	1.71
1719680--1719711	2	16.0	2	93	0	55	46	0	3	50	1.17
1720538--1720587	19	2.6	19	72	15	50	52	4	2	42	1.31
1724641--1724666	12	2.2	12	100	0	52	53	0	0	46	1.00
1724638--1724666	12	2.3	13	88	11	51	55	0	0	44	0.99
1724911--1725009	52	1.9	52	95	0	180	19	34	26	20	1.96
1726747--1726796	20	2.5	20	83	3	64	54	4	2	40	1.31
1726985--1727165	21	8.7	21	72	10	66	53	8	4	33	1.52
1727071--1727127	9	5.9	9	76	15	60	57	3	1	36	1.26
1727059--1727157	40	2.4	42	86	3	130	56	6	2	35	1.35
1727012--1727157	42	3.5	42	75	8	129	52	8	4	34	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1727723--1727757	15	2.3	15	100	0	70	28	17	22	31	1.96
1727931--1727963	2	16.5	2	100	0	66	51	0	0	48	1.00
1731602--1731681	40	2.0	40	92	4	135	42	11	10	36	1.74
1731992--1732073	28	2.8	29	74	7	85	59	0	0	40	0.97
1732424--1732473	15	3.3	15	80	0	55	84	6	10	0	0.79
1732950--1733044	10	9.8	10	76	14	65	45	0	1	53	1.07
1732920--1733025	54	2.0	51	82	12	126	47	0	0	51	1.07
1733007--1733046	2	19.5	2	94	5	71	47	0	2	50	1.14
1735083--1735110	2	14.0	2	100	0	56	50	0	0	50	1.00
1741236--1741267	3	10.7	3	100	0	64	68	0	0	31	0.90

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20