genome.fa.s41.2.7.7.80.10.50.1000.14.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: Scaffold41
Parameters: 2 7 7 80 10 50 1000
Length:  2798036

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  14  of  21  ( 2447 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)
1528371--1528572	112	1.8	112	85	2	289	35	13	18	32	1.90
1529115--1529175	22	2.8	22	85	7	72	6	11	3	78	1.05
1529114--1529175	21	3.0	20	80	15	63	6	12	3	77	1.08
1531338--1531580	126	1.9	126	96	0	450	30	22	17	29	1.97
1535946--1535996	20	2.5	21	83	3	68	31	15	5	47	1.70
1536623--1537341	52	12.8	53	70	14	227	35	14	25	25	1.94
1536675--1537239	61	9.8	60	71	16	363	34	13	25	25	1.93
1536636--1537014	113	3.3	112	83	4	429	35	14	25	25	1.94
1536797--1537157	180	2.0	180	88	0	542	35	12	25	26	1.92
1536977--1537239	113	2.3	112	92	0	436	33	14	26	25	1.94
1537510--1538272	32	23.8	32	80	2	744	21	17	30	29	1.96
1537510--1538272	65	11.9	65	79	4	653	21	17	30	29	1.96
1537510--1538272	129	5.9	129	81	3	727	21	17	30	29	1.96
1542114--1542221	41	2.6	41	83	1	135	13	43	0	41	1.51
1545981--1546013	15	2.4	14	90	10	50	66	3	6	24	1.28
1546505--1546542	19	2.0	20	94	5	69	39	10	0	50	1.37
1546505--1546542	20	1.9	19	89	5	58	39	10	0	50	1.37
1546672--1546733	17	3.6	16	75	14	52	22	3	1	72	1.08
1550165--1550199	11	3.4	11	84	15	56	22	22	8	45	1.79
1550171--1550204	9	3.6	9	85	14	50	26	17	11	44	1.83
1550165--1550204	20	2.0	20	100	0	80	25	20	10	45	1.81
1551928--1552122	98	2.0	98	88	2	293	31	16	14	36	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1555618--1555649	3	10.7	3	93	0	55	68	0	3	28	1.04
1555618--1555652	12	2.9	12	95	0	61	68	0	5	25	1.11
1556167--1556218	23	2.3	23	86	6	70	40	1	0	57	1.10
1556184--1556232	17	3.0	17	88	8	75	44	0	0	55	0.99
1556189--1556260	15	4.7	15	77	16	58	50	4	0	45	1.21
1556208--1556264	30	1.9	30	92	0	96	52	7	0	40	1.28
1556347--1556401	19	2.7	20	83	11	67	47	3	1	47	1.30
1556654--1556702	15	3.1	15	79	8	53	55	0	0	44	0.99
1556633--1556742	39	2.8	40	74	13	93	51	0	0	47	1.06
1562453--1562491	21	1.9	20	84	5	51	51	0	0	48	1.00
1575194--1575236	2	21.5	2	95	0	77	51	0	2	46	1.13
1577833--1577905	26	3.1	23	75	23	71	52	0	1	46	1.09
1577864--1577905	13	3.2	13	75	24	52	54	0	0	45	0.99
1577852--1577910	26	2.3	26	91	2	93	52	1	0	45	1.10
1579072--1579097	2	13.0	2	100	0	52	50	0	0	50	1.00
1579549--1579592	23	1.9	23	85	0	61	38	2	4	54	1.33
1579662--1579763	30	3.5	30	75	15	90	45	0	10	43	1.45
1579823--1579863	19	2.2	19	86	0	55	24	4	2	68	1.22
1580246--1580292	20	2.3	21	88	3	69	59	4	0	36	1.17
1587947--1587972	6	4.3	6	100	0	52	65	0	34	0	0.93
1588077--1588107	16	1.9	16	100	0	62	54	0	0	45	0.99
1588398--1588428	2	15.0	2	93	6	53	48	3	0	48	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1588570--1588621	17	2.9	19	69	16	56	50	0	7	42	1.31
1588847--1588913	27	2.4	27	77	5	71	44	0	1	53	1.09
1588897--1588929	15	2.1	17	88	11	52	48	0	0	51	1.00
1589884--1589929	11	4.1	11	84	15	67	54	0	0	45	0.99
1607116--1607499	79	4.9	78	78	4	342	33	13	25	27	1.93
1607124--1607499	158	2.4	156	80	5	382	34	13	24	27	1.93
1610498--1611013	61	8.4	61	86	2	696	27	20	27	25	1.99
1610498--1611009	184	2.8	184	87	2	744	27	20	26	25	1.99
1610924--1611121	100	2.0	100	94	2	353	28	17	29	23	1.97
1612081--1612148	12	5.6	12	77	8	57	1	5	7	85	0.80
1612081--1612125	18	2.5	19	85	7	58	0	8	4	86	0.69
1612106--1612152	5	9.6	5	80	13	53	2	0	12	85	0.70
1612081--1612152	19	3.8	19	83	10	76	1	5	8	84	0.82
1612096--1612154	19	3.1	18	88	11	82	1	1	11	84	0.77
1612093--1612148	24	2.4	24	93	3	96	1	1	8	87	0.69
1619803--1620180	79	4.8	78	80	3	382	34	14	23	27	1.94
1622336--1622365	13	2.3	13	94	0	51	43	13	13	30	1.82
1622349--1622403	20	2.8	20	94	0	92	49	12	12	25	1.76
1623309--1623621	158	2.0	157	83	4	398	40	11	20	27	1.87
1623309--1623606	80	3.8	80	77	10	276	40	11	20	28	1.86
1623609--1623635	14	1.9	14	100	0	54	44	0	29	25	1.54
1623675--1623918	78	3.1	77	85	4	314	39	9	22	28	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1625769--1625834	32	2.1	32	85	5	89	42	12	13	31	1.81
1625802--1625857	20	2.8	20	88	0	85	44	7	14	33	1.72
1629099--1629160	7	8.3	7	79	13	70	82	1	16	0	0.75
1629102--1629160	8	7.6	8	76	12	61	83	1	15	0	0.74
1629266--1629353	42	2.1	42	95	0	158	42	11	20	26	1.86
1632049--1632096	21	2.3	20	86	6	69	43	4	22	29	1.72
1632056--1632096	21	2.0	21	95	0	73	41	4	21	31	1.74
1636939--1636980	20	2.1	20	100	0	84	30	19	14	35	1.91
1639796--1639855	28	2.1	29	82	14	72	30	13	8	48	1.71
1641785--1641828	18	2.5	18	77	3	54	59	0	0	40	0.98
1641821--1641874	10	5.0	11	77	16	51	53	0	0	46	1.00
1641821--1641873	22	2.4	23	81	15	67	52	0	0	47	1.00
1644288--1644337	21	2.5	20	72	18	50	56	0	0	44	0.99
1644788--1644853	28	2.4	28	75	10	64	50	3	0	46	1.16
1645236--1645283	20	2.3	20	86	13	62	29	0	0	70	0.87
1645245--1645280	11	3.2	11	88	4	54	30	0	0	69	0.89
1646524--1646585	32	1.9	32	90	0	97	30	14	12	41	1.83
1654141--1654243	45	2.2	45	79	6	107	30	21	30	18	1.97
1654278--1654718	64	7.0	64	86	4	549	20	17	30	31	1.96
1654268--1654764	96	5.3	96	87	3	597	20	17	30	31	1.96
1654705--1655406	28	25.5	28	92	2	1054	26	14	34	24	1.94
1654720--1655407	55	12.5	54	91	3	1070	26	14	35	24	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1660071--1660401	164	2.0	164	96	0	608	23	21	25	29	1.99
1663344--1663399	10	5.8	9	82	14	67	1	16	0	82	0.76
1663346--1663393	14	3.2	15	82	14	55	2	16	0	81	0.79
1663337--1663399	20	3.2	20	84	13	85	4	15	0	79	0.90
1663348--1663397	24	2.1	23	88	3	73	2	18	0	80	0.82
1663361--1663413	24	2.2	24	83	6	63	7	18	0	73	1.06
1666206--1666315	42	2.6	42	86	0	139	10	40	1	47	1.49
1670069--1670107	19	2.1	19	85	9	53	41	10	23	25	1.86
1673368--1673451	42	2.0	42	97	0	159	40	20	4	34	1.73
1681390--1681428	20	1.9	21	85	15	55	41	0	0	58	0.98
1682496--1682538	2	21.5	2	100	0	86	51	0	0	48	1.00
1683278--1683318	19	2.2	19	90	0	64	31	2	4	60	1.30
1688918--1688950	17	1.9	17	100	0	66	24	0	33	42	1.55
1702402--1702439	20	1.9	20	84	10	51	39	13	2	44	1.57
1703175--1703210	18	1.9	18	88	5	54	69	2	2	25	1.15
1703628--1703665	15	2.5	15	87	8	51	21	2	13	63	1.42
1703639--1703674	13	2.6	14	91	8	56	22	0	16	61	1.35
1703668--1703699	16	2.0	16	93	0	55	40	0	3	56	1.15
1703754--1703802	23	2.1	24	84	3	64	32	0	8	59	1.27
1703775--1703816	16	2.7	16	92	3	68	42	0	2	54	1.13
1703834--1703867	14	2.5	13	81	9	50	35	0	5	58	1.22
1704408--1704452	18	2.4	19	88	3	65	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1720544--1720616	20	3.7	19	87	7	85	28	15	17	38	1.90
1720645--1720710	20	3.7	20	69	26	74	34	16	18	30	1.93
1720646--1720743	33	3.0	33	91	5	155	34	15	18	31	1.92
1720699--1720723	13	1.9	13	100	0	50	36	16	16	32	1.90
1720712--1720765	20	2.7	20	97	0	99	31	11	16	40	1.84
1721124--1721163	16	2.4	17	87	8	64	20	12	15	52	1.74
1723234--1723285	6	8.7	6	85	8	70	36	13	1	48	1.54
1723276--1723310	5	6.8	5	96	3	61	57	0	0	42	0.99
1725105--1725139	18	1.9	18	100	0	70	34	0	5	60	1.21
1726175--1726228	12	5.2	12	68	32	52	35	11	18	35	1.86

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21