genome.fa.s174.2.7.7.80.10.50.1000.12.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: Scaffold174
Parameters: 2 7 7 80 10 50 1000
Length:  2085601

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

This is table  12  of  15  ( 1687 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)
1379815--1379908	27	3.4	26	70	20	73	37	0	2	60	1.09
1379889--1379933	25	1.9	24	86	13	67	46	0	0	53	1.00
1379923--1379983	25	2.5	24	82	15	72	26	3	3	67	1.22
1379939--1379975	11	3.3	11	88	3	56	27	0	2	70	1.01
1380095--1380149	6	9.5	6	72	7	51	30	0	1	67	1.01
1380149--1380195	16	2.9	16	69	12	51	42	10	8	38	1.70
1380681--1380716	2	18.0	2	100	0	72	50	0	0	50	1.00
1383871--1383940	24	3.0	22	81	10	68	44	0	0	55	0.99
1385481--1385514	17	2.0	18	88	11	54	38	0	0	61	0.96
1387829--1387866	18	2.1	18	100	0	76	28	13	26	31	1.93
1391093--1391136	22	1.9	24	86	9	65	54	0	2	43	1.12
1391893--1392045	78	1.9	79	86	4	218	16	35	11	37	1.84
1393006--1393057	8	6.1	8	76	10	50	55	0	3	40	1.18
1393012--1393057	25	1.9	24	82	8	58	56	0	2	41	1.11
1393450--1393488	20	2.0	20	89	0	60	43	0	2	53	1.14
1393696--1393729	17	2.0	17	88	0	50	64	0	0	35	0.94
1393699--1393742	21	2.0	22	91	4	72	56	0	0	43	0.99
1394072--1394153	27	2.9	27	81	15	87	40	2	1	56	1.20
1394177--1394237	22	2.8	22	82	5	79	57	0	0	42	0.98
1394681--1394731	26	2.0	26	84	7	68	45	1	0	52	1.12
1395648--1395743	30	3.2	29	77	4	93	41	7	4	46	1.51
1395648--1395728	29	2.7	29	82	3	90	43	6	3	46	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1402034--1402098	19	3.4	19	76	2	67	36	0	0	63	0.95
1403586--1403619	12	2.8	12	90	0	50	0	26	0	73	0.83
1411103--1411155	21	2.4	22	78	6	63	52	0	0	47	1.00
1411142--1411166	10	2.5	10	100	0	50	48	0	0	52	1.00
1418433--1418490	30	2.0	29	86	3	80	51	0	3	44	1.18
1418948--1418995	24	2.0	24	83	0	60	52	0	2	45	1.12
1419017--1419059	15	2.9	15	89	6	61	53	0	0	46	1.00
1419016--1419075	20	3.0	20	87	0	84	53	1	0	45	1.10
1421414--1421661	123	2.0	124	91	2	401	31	20	18	28	1.97
1425402--1425438	3	12.0	3	88	5	56	29	0	0	70	0.88
1425402--1425440	19	2.1	19	95	0	69	30	0	0	69	0.89
1425509--1425551	13	3.4	12	81	9	50	72	2	0	25	0.97
1425498--1425548	20	2.4	21	81	15	61	68	1	0	29	1.00
1425517--1425556	15	2.6	16	77	22	50	75	0	0	25	0.81
1425785--1425830	25	2.0	25	83	12	62	52	6	2	39	1.40
1426443--1426510	23	3.0	23	81	14	79	41	2	0	55	1.15
1426362--1426513	15	10.6	14	70	20	93	41	2	0	55	1.19
1427235--1427281	3	15.7	3	90	0	76	0	31	0	68	0.90
1427280--1427311	3	10.7	3	100	0	64	31	0	0	68	0.90
1428132--1428228	21	4.3	22	67	27	60	27	5	4	62	1.34
1428105--1428241	70	2.0	70	92	0	229	27	7	5	59	1.48
1429123--1429161	2	19.5	2	100	0	78	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)
1431267--1431308	21	2.0	21	85	0	57	40	0	4	54	1.21
1431268--1431308	16	2.6	15	84	7	55	41	0	2	56	1.13
1431607--1431663	30	1.9	30	85	7	80	61	0	0	38	0.96
1435779--1435840	29	2.1	29	100	0	124	40	17	12	29	1.87
1443971--1444013	2	21.5	2	100	0	86	48	0	51	0	1.00
1448818--1448881	29	2.2	29	81	8	76	54	0	0	45	0.99
1453599--1453626	14	2.0	14	100	0	56	42	7	14	35	1.73
1455201--1455227	2	13.5	2	100	0	54	48	0	0	51	1.00
1455722--1455763	19	2.2	19	87	8	59	78	0	4	16	0.91
1463417--1463491	30	2.5	30	93	0	123	37	33	12	17	1.86
1463417--1463512	30	3.2	30	89	2	122	36	34	11	17	1.86
1466601--1466640	20	2.0	20	95	0	71	30	7	15	47	1.72
1466603--1466651	20	2.6	19	81	12	66	32	8	14	44	1.74
1470997--1471078	41	2.0	41	97	0	155	25	20	9	43	1.82
1474821--1474902	40	2.0	40	100	0	164	34	12	9	43	1.75
1475368--1475394	2	13.5	2	100	0	54	48	0	0	51	1.00
1479542--1479596	26	2.1	26	83	6	67	45	0	1	52	1.11
1479576--1479637	17	3.9	16	78	12	58	56	1	1	40	1.19
1480998--1481049	27	2.0	27	85	11	72	46	5	9	38	1.61
1480998--1481049	26	2.0	26	85	11	70	46	5	9	38	1.61
1482502--1482526	2	12.5	2	100	0	50	52	0	0	48	1.00
1482883--1482946	20	3.0	22	75	13	71	46	1	0	51	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1489421--1489530	46	2.4	45	77	14	118	40	0	0	59	0.98
1489736--1489838	35	2.9	35	74	20	106	56	0	0	42	1.06
1489708--1489784	40	1.9	40	82	10	95	53	0	1	45	1.08
1490329--1490412	29	2.9	29	77	10	75	35	5	2	55	1.37
1490341--1490412	28	2.5	29	76	8	76	31	6	2	58	1.39
1497625--1497660	18	2.0	18	100	0	72	44	16	11	27	1.82
1501327--1501762	217	2.0	222	88	3	650	39	14	15	30	1.87
1513409--1513457	25	2.0	25	91	0	80	36	20	20	22	1.95
1513807--1513873	33	2.0	33	85	0	89	19	34	20	25	1.96
1518143--1518377	37	6.3	37	76	7	199	27	17	17	37	1.93
1518264--1518407	75	1.9	75	84	5	193	26	13	18	40	1.88
1518298--1518406	38	2.9	36	76	9	103	25	15	20	38	1.92
1520393--1520424	9	3.4	9	95	4	55	65	0	0	34	0.93
1520825--1520858	2	17.0	2	93	0	59	47	0	2	50	1.16
1525276--1525329	17	3.2	17	81	2	65	53	0	1	44	1.11
1525780--1525810	2	16.0	2	93	6	55	48	0	0	51	1.00
1526570--1526607	2	19.0	2	100	0	76	50	0	0	50	1.00
1535255--1535287	15	2.2	15	89	10	50	33	0	3	63	1.10
1537255--1537390	45	3.0	45	86	2	175	45	18	11	25	1.82
1537989--1538032	12	3.7	12	87	0	52	29	36	9	25	1.86
1538734--1538779	22	2.1	22	87	0	65	58	0	2	39	1.10
1538929--1538975	23	2.0	23	84	8	60	53	2	0	44	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1544541--1544583	18	2.4	18	85	11	54	41	0	2	55	1.12
1544571--1544615	22	2.0	22	86	4	63	57	0	0	42	0.98
1545112--1545152	21	2.0	21	85	0	55	41	0	0	58	0.98
1545235--1545279	20	2.2	20	84	7	56	66	2	0	31	1.04
1545218--1545282	27	2.3	29	79	15	73	60	3	0	36	1.13
1545873--1545940	23	3.0	22	70	18	59	58	2	1	36	1.22
1546246--1546299	20	2.6	22	77	14	60	37	0	5	57	1.22
1550817--1550860	14	3.1	15	78	21	51	50	0	0	50	1.00
1556699--1556802	50	2.1	50	82	13	126	50	0	0	48	1.07
1556756--1556797	22	1.9	22	90	9	68	61	2	0	35	1.09
1558524--1558548	2	12.5	2	100	0	50	48	0	0	52	1.00
1559360--1559386	13	2.1	13	100	0	54	51	0	0	48	1.00
1566051--1566076	2	13.0	2	100	0	52	50	0	0	50	1.00
1567376--1567402	2	13.5	2	100	0	54	0	48	0	51	1.00
1567402--1567432	2	15.5	2	93	0	53	48	0	3	48	1.17
1567760--1567802	15	2.9	14	83	13	50	39	2	2	55	1.25
1568970--1568995	9	2.9	9	100	0	52	76	0	0	23	0.78
1569367--1569403	2	18.5	2	94	0	65	48	0	2	48	1.15
1570219--1570245	2	13.5	2	100	0	54	48	0	0	51	1.00
1571248--1571277	15	2.0	15	93	0	51	50	3	6	40	1.45
1571261--1571317	19	2.9	20	81	5	71	43	1	8	45	1.45
1571957--1571985	4	7.2	4	100	0	58	51	24	0	24	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1573126--1573175	22	2.3	21	86	13	66	66	0	4	30	1.10
1573159--1573219	32	1.9	31	86	3	86	45	0	4	49	1.23
1574257--1574299	4	10.8	4	89	0	68	69	4	0	25	1.07
1575281--1575324	23	2.0	22	86	13	63	45	0	0	54	0.99
1575844--1575896	27	2.0	27	92	7	90	37	0	3	58	1.16
1576622--1576670	2	24.5	2	100	0	98	51	0	0	48	1.00
1580231--1580308	39	2.0	39	97	0	147	32	15	16	35	1.90
1580231--1580291	21	3.0	21	71	22	67	32	14	18	34	1.91
1580248--1580308	18	3.2	18	75	20	70	31	14	14	39	1.87
1588822--1588867	22	2.1	22	84	11	60	65	10	6	17	1.45

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