genome.fa.s78.2.7.7.80.10.50.1000.8.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: Scaffold78
Parameters: 2 7 7 80 10 50 1000
Length:  2238306

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

This is table  8  of  15  ( 1751 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)
1132463--1132552	2	45.5	2	79	2	101	42	1	7	48	1.39
1134682--1134749	34	2.0	34	85	5	93	30	2	1	64	1.17
1137408--1137651	121	2.0	120	98	0	470	44	17	13	25	1.84
1139086--1139112	2	13.5	2	100	0	54	0	51	0	48	1.00
1145849--1145887	16	2.6	14	81	14	51	53	0	0	46	1.00
1145851--1145885	16	2.1	17	89	5	54	57	0	0	42	0.99
1145883--1145914	8	3.8	9	88	12	50	43	0	0	56	0.99
1146051--1146080	7	4.1	7	95	4	51	30	0	0	70	0.88
1146424--1146465	15	2.8	15	96	0	75	35	4	0	59	1.19
1146818--1146874	29	1.9	30	82	10	73	35	1	3	59	1.25
1146903--1146962	20	2.8	22	79	16	63	50	1	0	48	1.11
1149159--1149207	21	2.3	21	89	6	73	44	2	0	53	1.12
1149317--1149365	11	4.7	11	73	21	52	36	2	0	61	1.08
1149328--1149375	19	2.5	19	83	10	53	39	2	2	56	1.23
1149647--1149694	18	2.4	21	80	16	57	45	0	0	54	0.99
1150792--1150865	14	4.8	15	74	21	64	41	0	2	55	1.14
1152238--1152337	27	3.8	27	73	24	81	56	1	0	43	1.06
1152654--1152774	29	4.2	30	73	22	91	46	0	0	53	1.00
1152662--1152750	10	9.2	10	72	16	55	44	0	0	55	0.99
1152658--1152756	27	3.6	27	79	17	89	43	0	0	56	0.99
1152690--1152776	20	4.3	20	65	26	51	49	0	0	50	1.00
1152681--1152784	31	3.4	29	73	24	90	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1153433--1153491	28	2.0	30	87	6	86	38	0	0	61	0.96
1154156--1154208	23	2.3	23	80	6	63	39	0	0	60	0.97
1154171--1154231	32	1.9	32	86	0	86	32	0	3	63	1.10
1154848--1154876	2	14.5	2	100	0	58	51	0	0	48	1.00
1156067--1156113	15	3.0	15	77	20	51	27	0	8	63	1.23
1158446--1158477	16	2.0	16	93	0	55	18	3	6	71	1.20
1160077--1160112	2	18.0	2	100	0	72	50	0	0	50	1.00
1161404--1161445	22	2.0	21	86	13	59	57	0	0	42	0.99
1162416--1162457	21	2.1	19	86	8	57	42	0	0	57	0.99
1162957--1163223	140	1.9	140	92	0	453	34	13	13	39	1.83
1163702--1163742	16	2.6	16	84	0	64	48	0	12	39	1.41
1164392--1164437	22	2.0	22	87	12	65	32	0	2	65	1.05
1178698--1178753	16	3.6	14	80	20	58	57	1	0	41	1.09
1179155--1179185	6	5.2	6	92	0	53	45	0	0	54	0.99
1179446--1179499	21	2.7	21	88	5	76	61	1	1	35	1.18
1180072--1180143	2	38.5	2	69	22	50	45	1	2	50	1.25
1180069--1180138	28	2.5	28	84	9	90	45	1	2	50	1.25
1180730--1180893	81	2.0	81	86	6	226	35	9	20	34	1.85
1182521--1182562	15	2.7	16	78	14	52	57	0	0	42	0.99
1182560--1182618	29	2.0	30	83	6	77	47	0	0	52	1.00
1183382--1183407	2	13.0	2	100	0	52	50	0	0	50	1.00
1184859--1184887	2	14.5	2	100	0	58	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)
1187362--1187422	15	3.8	15	74	16	50	63	0	0	36	0.94
1187364--1187422	24	2.4	25	86	11	86	62	0	0	37	0.95
1187349--1187410	5	12.6	5	79	16	60	61	0	1	37	1.06
1187445--1187488	20	2.2	20	87	0	61	54	0	0	45	0.99
1187732--1187776	21	2.1	21	84	8	56	22	4	4	68	1.25
1194907--1195065	5	32.8	5	71	12	82	35	0	0	64	0.94
1194908--1195053	10	14.4	10	73	13	111	34	0	0	65	0.93
1194909--1195065	21	7.3	21	70	12	88	35	0	0	64	0.93
1194934--1195018	27	3.2	27	73	18	81	37	0	0	62	0.96
1194979--1195053	26	2.9	26	79	13	68	28	0	0	72	0.86
1194909--1195057	31	4.9	30	76	11	117	34	0	0	65	0.93
1194980--1195063	16	5.7	15	77	18	63	28	0	0	71	0.86
1195067--1195100	17	2.0	17	94	0	59	44	0	5	50	1.26
1195094--1195130	13	2.8	13	83	0	56	43	0	0	56	0.99
1195218--1195420	105	1.9	105	89	0	316	45	3	4	46	1.41
1195562--1195618	12	5.0	11	77	14	53	33	1	0	64	1.04
1195551--1195710	24	6.8	24	69	21	83	37	1	1	59	1.16
1195558--1195738	20	8.7	20	71	21	92	37	1	1	60	1.14
1195592--1195639	18	2.8	17	78	12	53	39	4	0	56	1.19
1195558--1195678	47	2.7	45	78	16	112	36	1	1	60	1.17
1195651--1195746	7	12.6	8	69	26	59	38	0	1	60	1.04
1195660--1195747	6	14.0	6	71	15	54	37	0	1	61	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1195651--1195746	29	3.4	30	77	18	84	38	0	1	60	1.04
1195608--1195732	53	2.5	50	80	9	128	38	0	2	58	1.17
1195656--1195747	37	2.7	33	78	18	107	36	0	1	61	1.03
1195700--1195774	36	2.1	34	83	9	89	41	1	0	57	1.07
1196013--1196038	3	8.7	3	100	0	52	65	0	0	34	0.93
1197607--1197652	11	4.2	12	78	15	55	65	0	0	34	0.93
1197641--1197690	19	2.6	19	81	12	66	56	6	0	38	1.24
1197660--1197724	32	2.0	32	88	5	96	50	1	0	47	1.10
1198089--1198130	21	2.0	21	86	13	61	40	0	0	59	0.97
1198844--1198891	16	2.9	16	75	3	51	64	0	0	35	0.94
1199271--1199302	16	2.0	16	93	0	55	56	6	28	9	1.55
1199947--1199977	13	2.4	13	94	0	53	45	0	0	54	0.99
1200780--1200857	16	4.9	16	72	17	56	60	2	0	37	1.11
1200821--1200871	16	3.1	16	80	2	57	56	3	0	39	1.18
1205932--1205962	2	15.5	2	100	0	62	51	0	48	0	1.00
1206140--1206204	28	2.3	29	84	7	89	72	1	1	24	1.02
1206140--1206226	28	3.1	28	79	8	88	67	1	1	29	1.05
1206183--1206263	32	2.5	32	81	2	99	58	1	0	40	1.06
1206232--1206281	19	2.5	20	87	9	68	60	2	0	38	1.09
1206363--1206397	17	2.1	17	94	0	61	57	2	0	40	1.14
1206385--1206470	40	2.2	40	80	11	101	50	3	0	46	1.18
1209430--1209469	21	1.9	21	84	0	53	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1210354--1210410	29	2.0	29	85	0	78	45	1	0	52	1.11
1213534--1213569	16	2.2	17	95	5	65	63	5	5	25	1.38
1214043--1214085	23	1.9	22	86	13	61	37	2	0	60	1.10
1214413--1214483	30	2.3	30	92	2	115	53	0	2	43	1.15
1214563--1214598	16	2.2	16	95	0	63	33	2	11	52	1.51
1215473--1215503	3	10.3	3	100	0	62	35	0	0	64	0.94
1217332--1217399	21	3.0	24	75	14	63	39	2	0	57	1.14
1217313--1217387	27	2.6	29	79	10	73	41	5	0	53	1.24
1217503--1217542	20	2.0	20	100	0	80	55	0	10	35	1.34
1218566--1218628	26	2.4	28	80	17	73	46	0	1	52	1.10
1218638--1218699	20	3.1	20	79	9	81	38	0	0	61	0.96
1218643--1218708	18	3.3	19	71	23	55	37	0	1	60	1.06
1218639--1218727	40	2.3	40	82	5	103	41	0	1	57	1.06
1219530--1219569	20	1.9	22	90	10	66	70	0	0	30	0.88
1220001--1220039	20	1.9	21	89	5	62	66	0	0	33	0.92
1220001--1220050	19	2.5	20	83	3	57	60	0	0	40	0.97
1220727--1220772	24	2.0	22	87	8	65	23	6	4	65	1.35
1227215--1227246	14	2.4	14	94	5	57	12	0	0	87	0.54
1227362--1227409	20	2.4	19	80	13	51	60	0	4	35	1.16
1227486--1227522	19	2.0	18	89	5	56	32	5	0	62	1.18
1227992--1228037	13	3.4	14	73	11	51	50	0	0	50	1.00
1228739--1228781	22	2.0	22	90	9	70	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1232526--1232555	2	15.5	2	93	6	53	46	0	0	53	1.00
1234793--1234834	19	2.2	19	91	0	66	35	0	0	64	0.94
1235499--1235541	21	2.0	21	82	8	52	58	2	0	39	1.11
1235341--1235712	173	2.1	175	92	5	621	51	4	10	34	1.55
1235946--1236478	265	2.0	266	98	0	1023	39	6	6	47	1.57
1237252--1237298	21	2.3	21	85	10	62	42	0	0	57	0.98
1237452--1237496	21	2.1	21	84	8	56	40	0	0	60	0.97
1238240--1238286	21	2.2	22	77	11	53	48	10	0	40	1.38
1238534--1238580	22	2.1	22	88	7	69	42	0	0	57	0.98
1239080--1239110	4	7.8	4	100	0	62	77	0	0	22	0.77

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