genome.fa.s163.2.7.7.80.10.50.1000.12.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: Scaffold163
Parameters: 2 7 7 80 10 50 1000
Length:  1788591

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

This is table  12  of  13  ( 1505 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)
1522377--1522440	31	2.1	30	88	8	94	50	0	0	50	1.00
1522390--1522442	14	3.5	14	73	16	52	54	0	0	45	0.99
1523527--1523556	14	2.1	14	93	0	51	60	0	0	40	0.97
1523572--1523637	6	11.2	6	75	15	66	36	1	0	62	1.05
1523570--1523638	17	4.3	17	68	27	53	37	1	0	60	1.06
1523861--1523922	29	2.1	29	87	6	88	56	11	6	25	1.58
1524391--1524430	19	2.2	19	86	13	57	62	0	0	37	0.95
1524642--1524684	2	21.5	2	100	0	86	51	0	48	0	1.00
1525001--1525040	14	2.7	15	84	11	55	42	0	0	57	0.98
1525795--1525825	15	2.1	15	100	0	62	38	0	0	61	0.96
1526311--1526356	21	2.2	21	88	7	67	50	0	0	50	1.00
1527238--1527290	26	2.0	27	82	7	65	50	3	0	45	1.19
1534824--1534859	13	3.0	13	84	15	51	33	5	0	61	1.19
1535292--1535332	20	2.0	20	85	0	55	34	7	9	48	1.64
1535745--1535784	12	3.4	12	86	6	64	70	0	0	30	0.88
1535737--1535790	23	2.3	23	78	12	74	66	0	3	29	1.09
1536318--1536353	17	2.1	18	89	5	56	61	0	0	38	0.96
1536391--1536436	18	2.5	18	86	10	58	0	23	2	73	0.94
1537792--1537832	19	2.2	18	86	4	55	51	0	2	46	1.14
1537822--1537912	19	4.9	19	68	23	50	49	4	1	45	1.29
1537873--1537914	19	2.3	19	84	8	52	38	7	0	54	1.28
1538989--1539060	25	2.9	25	89	0	117	44	6	6	41	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1540920--1540958	3	13.0	3	100	0	78	33	0	0	66	0.92
1543294--1543327	16	2.0	18	88	11	54	61	5	0	32	1.20
1545135--1545164	7	4.3	7	95	0	51	36	0	0	63	0.95
1545563--1545623	25	2.5	24	81	7	61	62	4	4	27	1.37
1547544--1547655	1	112.0	1	78	0	98	0	6	6	87	0.67
1547544--1547655	31	3.6	32	88	9	160	0	6	6	87	0.67
1552773--1552931	86	1.8	85	79	12	182	40	5	3	49	1.44
1553063--1553121	31	2.0	29	83	12	75	49	1	0	49	1.11
1553707--1553750	12	3.8	12	81	6	54	27	0	2	70	0.99
1553701--1553750	23	2.2	23	88	0	73	26	0	2	72	0.96
1555197--1555250	22	2.4	22	81	9	65	53	1	1	42	1.22
1559120--1559222	22	4.7	22	64	26	58	46	0	0	53	1.00
1559120--1559220	33	3.0	32	71	25	84	46	0	0	53	1.00
1559120--1559177	17	3.6	16	75	20	59	48	0	0	51	1.00
1559127--1559252	67	1.9	66	82	8	157	48	0	0	50	1.06
1560078--1560102	3	8.3	3	100	0	50	68	0	0	32	0.90
1565831--1565931	34	3.0	34	85	0	121	26	0	32	39	1.63
1570606--1570685	34	2.3	34	78	2	88	22	2	36	38	1.68
1571020--1571047	7	4.0	7	100	0	56	57	0	0	42	0.99
1570977--1571057	41	2.0	41	82	4	101	45	0	0	54	0.99
1571117--1571169	15	3.5	15	82	10	63	41	0	0	58	0.98
1571208--1571250	18	2.5	17	75	10	52	37	0	0	62	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1571245--1571281	19	2.0	19	89	5	58	51	0	2	45	1.15
1571405--1571433	15	2.0	15	93	6	51	17	0	6	75	1.01
1573287--1573324	18	2.1	19	90	5	60	26	5	0	68	1.11
1578093--1578127	13	2.6	13	95	4	61	22	14	8	54	1.67
1578802--1578859	20	2.9	20	89	0	71	41	10	18	29	1.84
1579440--1579572	66	2.0	66	92	2	223	45	24	6	24	1.77
1581441--1581635	97	2.0	96	85	4	259	27	22	12	37	1.91
1582986--1583234	131	1.9	131	89	0	390	32	18	8	40	1.81
1584305--1584360	20	2.8	20	97	0	103	42	10	16	30	1.82
1584348--1584402	20	2.7	20	86	10	76	23	16	12	47	1.81
1586862--1586966	51	2.0	52	92	1	176	28	21	11	38	1.88
1586903--1587395	79	6.3	79	79	7	454	26	25	13	33	1.94
1586904--1587333	157	2.8	155	82	7	496	27	26	12	33	1.93
1586941--1587401	157	3.0	154	81	6	429	26	26	13	32	1.94
1591043--1591099	11	5.2	11	83	12	73	70	0	0	29	0.88
1593817--1593864	23	2.1	23	84	0	60	54	2	0	43	1.12
1594040--1594076	2	18.5	2	100	0	74	48	0	0	51	1.00
1600003--1600036	2	16.5	2	93	6	59	47	2	0	50	1.16
1600000--1600035	17	2.1	17	100	0	72	47	5	0	47	1.25
1600005--1600033	15	1.9	15	100	0	58	48	3	0	48	1.18
1600995--1601026	15	2.1	15	94	0	55	56	0	0	43	0.99
1608593--1608640	17	2.9	17	84	9	55	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1616425--1616475	17	3.1	16	76	21	52	27	0	3	68	1.07
1618337--1618387	16	3.0	17	76	18	52	52	1	0	45	1.12
1618425--1618462	13	3.1	13	85	7	53	44	0	0	55	0.99
1618427--1618499	12	6.1	12	76	13	53	45	2	0	52	1.15
1618427--1618508	24	3.4	24	78	10	78	46	2	0	51	1.14
1618427--1618529	24	4.3	23	76	13	77	46	2	0	50	1.16
1618495--1618543	10	5.1	10	72	18	50	48	2	0	48	1.12
1619166--1619280	27	4.1	30	76	13	88	59	0	1	39	1.08
1619172--1619275	26	4.0	26	74	16	83	61	0	0	37	1.03
1619210--1619246	7	5.1	7	96	3	65	70	0	0	29	0.88
1619203--1619250	14	3.8	12	81	13	51	68	0	0	31	0.90
1620167--1620211	20	2.2	21	88	4	65	26	0	2	71	0.98
1620595--1620624	14	2.2	13	94	5	51	43	6	0	50	1.28
1620754--1620842	9	10.0	9	76	11	69	74	0	22	3	0.97
1620752--1620802	14	3.7	14	76	10	52	68	0	29	1	1.00
1621630--1621693	28	2.2	29	78	8	69	26	3	1	68	1.13
1625945--1625973	2	14.5	2	100	0	58	48	0	0	51	1.00
1626076--1626113	20	1.9	20	88	0	58	21	15	5	57	1.57
1626950--1626976	8	3.4	8	100	0	54	77	0	0	22	0.76
1627405--1627485	29	2.9	29	87	5	114	48	0	8	43	1.34
1627524--1627609	29	3.0	28	72	17	77	62	0	2	34	1.08
1627533--1627609	29	2.6	31	80	16	99	61	0	1	37	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1628789--1628990	88	2.2	90	77	13	202	47	4	0	47	1.29
1629391--1629460	34	2.0	36	91	5	117	50	0	10	40	1.36
1630799--1630901	30	3.5	30	77	7	102	36	13	1	47	1.54
1631586--1631615	3	10.0	3	100	0	60	33	0	0	66	0.92
1635488--1635634	76	1.9	76	100	0	294	37	15	12	34	1.85
1639837--1639897	28	2.2	28	76	2	70	54	11	6	27	1.61
1640979--1641021	2	21.5	2	85	0	59	48	6	0	44	1.29
1640979--1641021	12	3.6	12	90	0	68	48	6	0	44	1.29
1642054--1642208	80	1.9	80	92	0	256	41	9	21	27	1.84
1646221--1646308	27	3.2	27	78	12	99	50	11	6	31	1.65
1661495--1661520	1	26.0	1	100	0	52	0	0	0	100	0.00
1662418--1662515	1	98.0	1	77	0	79	86	5	8	0	0.69
1662418--1662515	37	2.7	38	93	6	175	86	5	8	0	0.69
1666994--1667031	20	1.9	20	89	10	60	76	0	7	15	1.01
1666994--1667031	10	3.8	10	86	6	51	76	0	7	15	1.01
1668552--1668609	20	2.7	21	76	10	64	34	10	13	41	1.79
1673380--1673435	19	2.9	19	82	12	62	42	0	3	53	1.18
1677423--1677869	66	6.8	65	76	9	300	47	18	20	14	1.83
1677405--1677865	132	3.5	132	77	8	402	46	18	20	14	1.83
1677352--1677864	132	3.9	132	76	8	400	47	17	20	14	1.82
1677451--1677829	198	1.9	197	80	5	433	47	18	20	13	1.83
1677612--1677900	66	4.4	65	78	6	235	46	20	20	13	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1678831--1678986	60	2.7	60	79	3	174	49	16	15	19	1.80
1681779--1681829	20	2.5	20	87	0	66	39	13	11	35	1.82
1690278--1690373	19	5.8	18	73	26	104	33	12	17	36	1.88
1690280--1690381	32	3.2	32	98	1	197	33	12	18	35	1.89
1690299--1690381	13	5.5	13	72	27	67	33	13	18	34	1.89
1690425--1690449	13	1.9	13	100	0	50	32	16	16	36	1.90
1690458--1690586	52	2.5	52	90	0	213	37	17	16	28	1.92
1699042--1699109	11	5.9	11	78	14	59	63	0	0	36	0.95
1699141--1699196	18	3.3	18	73	19	66	53	0	0	46	1.00
1699149--1699197	16	3.1	15	73	21	55	55	0	0	44	0.99

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