genome.fa.s25.2.7.7.80.10.50.1000.21.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  21  of  56  ( 6609 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)
3721039--3721101	33	1.9	33	83	6	83	49	6	3	41	1.44
3721688--3721738	6	8.7	6	89	4	59	82	0	17	0	0.67
3725257--3725295	2	19.5	2	100	0	78	48	0	0	51	1.00
3725437--3725531	33	2.7	35	83	15	110	53	0	0	46	1.00
3726025--3726072	15	3.1	15	77	16	62	58	0	0	41	0.98
3726386--3726488	29	3.5	28	81	13	118	56	0	1	40	1.17
3726412--3726461	15	3.3	15	69	20	50	54	0	4	42	1.19
3726386--3726502	29	4.0	28	80	15	112	58	1	1	38	1.19
3726944--3727000	27	2.1	27	90	0	87	12	26	3	57	1.50
3727223--3727278	21	2.7	21	78	13	53	25	0	3	71	1.02
3727231--3727274	15	2.9	15	82	0	52	22	0	4	72	1.02
3737972--3738027	23	2.5	22	88	2	85	37	32	5	25	1.78
3746122--3746179	30	1.9	30	92	0	98	53	13	10	22	1.70
3746942--3746973	15	2.1	15	94	0	55	59	0	0	40	0.97
3746935--3746985	20	2.6	19	84	6	66	54	0	0	45	0.99
3747303--3747347	22	2.0	23	91	8	74	42	0	0	57	0.98
3747323--3747360	16	2.4	16	86	4	51	34	0	0	65	0.93
3747462--3747521	25	2.4	25	86	5	77	43	3	0	53	1.17
3752702--3752730	2	14.5	2	100	0	58	51	48	0	0	1.00
3752710--3752800	44	2.1	44	89	0	137	45	30	3	20	1.68
3755577--3755651	14	5.4	14	75	12	66	66	0	0	33	0.92
3755567--3755655	24	3.8	23	77	14	74	65	0	0	34	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3755584--3755638	22	2.7	19	76	15	56	69	0	0	30	0.89
3755567--3755648	33	2.5	33	81	13	98	64	0	0	35	0.94
3756443--3756477	16	2.1	17	89	5	54	68	5	0	25	1.11
3757007--3757040	10	3.3	10	87	4	50	47	0	0	52	1.00
3759684--3759804	50	2.7	43	73	21	129	59	0	0	39	1.03
3759736--3759802	18	3.6	18	70	18	57	59	0	0	40	0.97
3760746--3760792	22	2.2	22	84	3	60	36	0	4	59	1.17
3760850--3760989	30	4.7	29	69	19	83	49	0	2	47	1.18
3760897--3760931	18	1.9	18	88	11	54	54	0	0	45	0.99
3763134--3763189	27	2.1	27	96	0	103	44	14	21	19	1.86
3763961--3764028	17	4.1	17	75	16	61	60	0	0	39	0.97
3764014--3764053	18	2.2	18	91	8	64	47	0	0	52	1.00
3764416--3764459	23	1.9	23	86	9	63	38	0	2	59	1.10
3764555--3764585	2	15.5	2	100	0	62	48	0	0	51	1.00
3764601--3764639	19	2.0	21	90	10	64	56	5	5	33	1.43
3765625--3765662	18	2.1	19	85	14	53	21	10	0	68	1.19
3767685--3767795	45	2.5	45	82	2	125	22	21	20	35	1.96
3767554--3768329	180	4.3	180	80	4	681	19	25	20	34	1.96
3767857--3768389	45	11.8	45	74	7	263	18	25	20	34	1.96
3767554--3768389	90	9.3	90	68	7	368	19	25	20	33	1.97
3769438--3769488	16	3.2	16	77	5	50	23	3	11	60	1.47
3770148--3770196	15	2.9	18	77	22	70	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)
3770270--3770327	15	3.9	15	76	13	50	44	1	3	50	1.29
3770323--3770359	19	2.0	19	89	5	58	45	2	5	45	1.40
3770525--3770609	30	3.0	28	76	21	88	52	1	0	45	1.08
3770538--3770582	15	3.0	15	76	0	54	51	2	0	46	1.13
3773513--3773552	2	20.0	2	100	0	80	50	0	0	50	1.00
3774607--3774662	23	2.4	23	78	0	67	48	17	1	32	1.58
3775309--3775336	12	2.3	12	100	0	56	25	0	0	75	0.81
3776745--3776770	12	2.2	12	100	0	52	0	7	0	92	0.39
3780745--3780772	2	14.0	2	100	0	56	50	0	0	50	1.00
3780949--3780987	3	13.0	3	94	0	69	66	2	0	30	1.05
3781272--3781325	23	2.3	24	84	6	67	57	0	0	42	0.98
3781456--3781503	3	16.3	3	79	12	55	66	0	4	29	1.10
3786766--3786805	6	6.3	6	88	5	53	37	2	0	60	1.11
3786766--3786803	12	2.9	13	88	11	60	36	2	0	60	1.11
3793547--3793572	4	6.5	4	100	0	52	76	0	23	0	0.78
3797126--3797160	3	11.7	3	87	0	52	28	2	2	65	1.21
3798035--3798059	1	25.0	1	100	0	50	0	0	0	100	0.00
3801471--3801527	17	3.0	20	76	21	61	40	0	0	59	0.97
3801471--3801510	20	2.2	19	86	13	57	42	0	0	57	0.98
3802413--3802457	3	15.0	3	100	0	90	33	0	0	66	0.92
3803381--3803438	19	3.1	19	77	2	64	55	0	5	39	1.22
3809783--3809817	2	17.5	2	100	0	70	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)
3811854--3811908	1	55.0	1	77	0	56	89	9	1	0	0.57
3811855--3811901	7	6.6	7	95	4	69	89	10	0	0	0.49
3811854--3811906	22	2.3	23	87	6	81	88	9	1	0	0.58
3811854--3811898	8	5.9	8	94	5	76	88	11	0	0	0.50
3821741--3821798	24	2.4	24	85	0	71	34	3	0	62	1.12
3822773--3822818	16	2.8	17	80	12	51	45	6	0	47	1.28
3825253--3825305	15	3.7	15	72	7	56	54	0	0	45	0.99
3825751--3825844	28	3.2	29	68	15	70	57	3	2	37	1.27
3826383--3826424	22	1.9	22	90	0	66	57	2	2	38	1.25
3826380--3826437	28	2.1	28	87	6	82	58	3	1	36	1.25
3827421--3827484	29	2.2	29	80	2	76	56	1	0	42	1.09
3827421--3827494	28	2.7	29	79	6	73	58	1	0	40	1.07
3829063--3829101	14	2.7	14	84	4	51	41	0	0	58	0.98
3829328--3829394	29	2.3	26	75	20	62	50	2	1	44	1.26
3834398--3834423	4	6.5	4	100	0	52	23	23	53	0	1.46
3834700--3834788	47	2.0	44	82	10	108	55	0	0	44	0.99
3836295--3836335	16	2.5	17	81	18	52	68	2	0	29	1.03
3836290--3836334	13	3.2	13	77	17	54	71	2	0	26	0.98
3836977--3837002	2	13.0	2	100	0	52	50	0	0	50	1.00
3837956--3838001	25	1.9	24	86	8	67	52	0	0	47	1.00
3837995--3838050	26	2.1	26	83	12	69	51	1	0	46	1.11
3838125--3838153	2	15.0	2	92	7	51	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3839058--3839106	13	3.7	13	75	5	53	55	0	0	44	0.99
3846876--3846918	20	2.2	20	87	4	61	46	0	6	46	1.30
3847361--3847440	7	11.4	7	78	0	70	45	3	3	47	1.38
3847354--3847452	28	3.6	28	82	2	112	42	3	6	48	1.43
3847965--3848021	30	1.9	29	85	3	78	43	0	0	56	0.99
3848739--3848772	16	2.2	16	89	5	52	79	0	20	0	0.73
3853192--3853263	18	3.9	18	73	19	60	56	0	0	43	0.99
3853193--3853237	16	2.8	17	71	21	51	51	0	0	48	1.00
3853228--3853261	6	5.3	6	96	3	50	61	0	0	38	0.96
3853196--3853309	57	2.0	58	89	5	178	54	0	1	43	1.10
3853323--3853361	19	2.1	18	95	4	69	53	0	0	46	1.00
3853316--3853374	25	2.5	23	83	5	64	54	1	0	44	1.10
3857232--3857334	9	11.2	9	69	22	56	39	0	0	60	0.97
3857289--3857394	22	5.0	22	71	18	89	31	0	0	66	1.04
3857294--3857394	20	4.8	20	69	26	75	30	0	0	67	1.04
3857290--3857386	5	18.4	5	70	17	54	29	1	1	68	1.03
3857529--3857576	20	2.6	18	76	6	51	35	0	0	64	0.94
3858284--3858326	3	14.3	3	100	0	86	65	0	0	34	0.93
3859870--3859910	19	2.2	19	86	4	57	39	0	9	51	1.35
3868816--3868869	4	13.5	4	92	0	81	44	0	5	50	1.25
3868816--3868869	6	9.0	6	93	0	81	44	0	5	50	1.25
3868816--3868869	10	5.4	10	93	0	81	44	0	5	50	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3871792--3871835	21	2.0	23	87	12	67	27	0	20	52	1.47
3871792--3871843	21	2.5	21	81	12	63	30	0	23	46	1.53
3872432--3872468	2	18.5	2	100	0	74	51	0	0	48	1.00
3873423--3873469	2	23.5	2	100	0	94	51	0	48	0	1.00
3874168--3874203	18	1.9	19	88	5	56	36	36	8	19	1.82
3879702--3879743	23	1.9	21	85	9	57	38	0	2	59	1.10
3880194--3880272	24	3.2	25	71	20	67	60	1	1	36	1.13
3881935--3881963	2	14.5	2	100	0	58	51	0	48	0	1.00
3882964--3882990	1	27.0	1	100	0	54	0	0	0	100	0.00
3889663--3889702	3	13.3	3	94	0	71	35	0	0	65	0.93

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56