Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold963
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 40624
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3636 original size:20 final size:20
Alignment explanation
Indices: 3613--3698 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
3603 CACATCCAGA
3613 TGTATCGATACATTATACTT
1 TGTATCGATACATTATACTT
3633 TGTATCGATACATTATA--T
1 TGTATCGATACATTATACTT
** *
3651 TG-AT--AT--ATGCT-CAT
1 TGTATCGATACATTATACTT
*
3665 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATACTT
3685 TGTATCGATACATT
1 TGTATCGATACATT
3699 GTATTGATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 4 0.08
17 4 0.08
18 3 0.06
19 3 0.06
20 33 0.62
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATACTT
Found at i:3674 original size:19 final size:19
Alignment explanation
Indices: 3652--3746 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 19
3642 ACATTATATT
3652 GATATATGCTCATTGTATC
1 GATATATGCTCATTGTATC
3671 GATACATTATGCT--TTGTATC
1 GAT--A-TATGCTCATTGTATC
*
3691 G--ATA----CATTGTATT
1 GATATATGCTCATTGTATC
3704 GATATATGCTCATTGTATC
1 GATATATGCTCATTGTATC
* *
3723 GATACATACTCAATTGTATC
1 GATATATGCTC-ATTGTATC
3743 GATA
1 GATA
3747 CATGAACTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 23
0.69 0.05 0.26
Matches are distributed among these distances:
13 7 0.12
15 5 0.08
16 1 0.02
19 20 0.33
20 20 0.33
21 1 0.02
22 6 0.10
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (19 bp):
GATATATGCTCATTGTATC
Found at i:3691 original size:52 final size:52
Alignment explanation
Indices: 3613--3729 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
3603 CACATCCAGA
3613 TGTATCGATACATTATACTTTGTATCGATACATTATATTGATATATGCTCAT
1 TGTATCGATACATTATACTTTGTATCGATACATTATATTGATATATGCTCAT
* *
3665 TGTATCGATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCAT
1 TGTATCGATACATTATACTTTGTATCGATACATTATATTGATATATGCTCAT
3717 TGTATCGATACAT
1 TGTATCGATACAT
3730 ACTCAATTGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (52 bp):
TGTATCGATACATTATACTTTGTATCGATACATTATATTGATATATGCTCAT
Found at i:3740 original size:20 final size:19
Alignment explanation
Indices: 3695--3749 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3685 TGTATCGATA
* * *
3695 CATTGTATTGATATATGCT
1 CATTGTATCGATACATACT
3714 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
3733 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
3750 GAACTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:3740 original size:52 final size:52
Alignment explanation
Indices: 3613--3749 Score: 206
Period size: 52 Copynumber: 2.6 Consensus size: 52
3603 CACATCCAGA
* *
3613 TGTATCGATACATTATACTTTGTATCGATACATTATATTGATATATGCTCAT
1 TGTATCGATACATTATGCATTGTATCGATACATTATATTGATATATGCTCAT
* *
3665 TGTATCGATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCAT
1 TGTATCGATACATTATGCATTGTATCGATACATTATATTGATATATGCTCAT
3717 TGTATCGATACA-TACT-CAATTGTATCGATACAT
1 TGTATCGATACATTA-TGC-ATTGTATCGATACAT
3750 GAACTGGCAG
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
51 3 0.04
52 77 0.96
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (52 bp):
TGTATCGATACATTATGCATTGTATCGATACATTATATTGATATATGCTCAT
Found at i:3843 original size:165 final size:167
Alignment explanation
Indices: 3665--3988 Score: 571
Period size: 165 Copynumber: 2.0 Consensus size: 167
3655 ATATGCTCAT
*
3665 TGTATCGATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCATTGTATCGATACAT
1 TGTATCAATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCATTGTATCGATACAT
3730 ACTCAATTGTATCGATACATG-AACTGGCAGTAGCTACCCTAAGTAAAATGTATCAATACATGGG
66 ACTCAATTGTATCGATACATGAAACTGGCAGTAGCTACCCTAAGTAAAATGTATCAATACATGGG
*
3794 ATATTGTATCGATACA-AGTATCGATACACATCCAGA
131 ATATTATATCGATACATAGTATCGATACACATCCAGA
3830 TGTATCAATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCATTGTATCGATACAT
1 TGTATCAATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCATTGTATCGATACAT
* * * *
3895 ACTTAATTGTATCGATACATGAAATTGGCAGTAGCTACCCTAAGTGAAATGTATCGATACATGGG
66 ACTCAATTGTATCGATACATGAAACTGGCAGTAGCTACCCTAAGTAAAATGTATCAATACATGGG
*
3960 ATATTATATCGATACATTGTATCGATACA
131 ATATTATATCGATACATAGTATCGATACA
3989 TGGTAAAAAG
Statistics
Matches: 150, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
165 84 0.56
166 55 0.37
167 11 0.07
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (167 bp):
TGTATCAATACATTATGCTTTGTATCGATACATTGTATTGATATATGCTCATTGTATCGATACAT
ACTCAATTGTATCGATACATGAAACTGGCAGTAGCTACCCTAAGTAAAATGTATCAATACATGGG
ATATTATATCGATACATAGTATCGATACACATCCAGA
Found at i:4003 original size:33 final size:33
Alignment explanation
Indices: 3944--4008 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
3934 CTAAGTGAAA
**
3944 TGTATCGATACATGGGATATTATATCGATACAT
1 TGTATCGATACATGGGATAAAATATCGATACAT
*
3977 TGTATCGATACATGGTA-AAAAGTATCGATACA
1 TGTATCGATACATGGGATAAAA-TATCGATACA
4009 GCCCAACGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGGGATAAAATATCGATACAT
Found at i:7447 original size:17 final size:15
Alignment explanation
Indices: 7425--7468 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
7415 TTTTTGGTAC
7425 TATTTATTTATTATATA
1 TATTTATTTATTA-A-A
7442 TATTTAATTTGATTAAA
1 TATTT-ATTT-ATTAAA
7459 TATTTATTTA
1 TATTTATTTA
7469 GACAAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 4 0.16
17 11 0.44
18 5 0.20
19 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTTATTTATTAAA
Found at i:14490 original size:42 final size:42
Alignment explanation
Indices: 14435--14553 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
14425 TTTTTCTCTC
* *
14435 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
14477 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
14519 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
14554 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:14494 original size:12 final size:11
Alignment explanation
Indices: 14468--14543 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
14458 TCTATTATCT
*
14468 CTCCTGTCTCTC
1 CTCCTATCTC-C
14480 CTCCTATCATCC
1 CTCCTATC-TCC
14492 CTCCTATCT--
1 CTCCTATCTCC
*
14501 CTACTATCT--
1 CTCCTATCTCC
*
14510 CTCCTGTCTCTC
1 CTCCTATCTC-C
14522 CTCCTATCATCC
1 CTCCTATC-TCC
*
14534 CTCCTCTCTC
1 CTCCTATCTC
14544 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:14495 original size:24 final size:24
Alignment explanation
Indices: 14459--14544 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
14449 CCTCCTCTCT
* *
14459 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
14483 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
14504 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
14525 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
14545 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:14519 original size:18 final size:18
Alignment explanation
Indices: 14450--14520 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
14440 CCTGTCATCC
* *
14450 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
14468 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
14490 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
14510 CTCCTGTCTCT
1 CTCCTGTCTCT
14521 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:19960 original size:30 final size:30
Alignment explanation
Indices: 19926--20005 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
19916 TTCTCTCCTC
* *
19926 CTCCTGTCATC-CCTCCTCTCTCTATTATCT
1 CTCCTGTC-TCTCCTCCTATCTCTACTATCT
19956 CTCCTGTCTCTCCTCCTATCTCTACTATCT
1 CTCCTGTCTCTCCTCCTATCTCTACTATCT
19986 CTCCTGTCTCTCCTCCTATC
1 CTCCTGTCTCTCCTCCTATC
20006 ATCCCTCCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 2 0.04
30 45 0.96
ACGTcount: A:0.09, C:0.45, G:0.04, T:0.42
Consensus pattern (30 bp):
CTCCTGTCTCTCCTCCTATCTCTACTATCT
Found at i:19977 original size:21 final size:21
Alignment explanation
Indices: 19951--19990 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19941 CTCTCTCTAT
* *
19951 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTACTATCTCTCCTCC
19972 TATCTCTACTATCTCTCCT
1 TATCTCTACTATCTCTCCT
19991 GTCTCTCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (21 bp):
TATCTCTACTATCTCTCCTCC
Found at i:23873 original size:12 final size:11
Alignment explanation
Indices: 23851--23926 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
23841 AGAGAAAGAA
*
23851 GAGAGAGGAGG
1 GAGATAGGAGG
23862 GATGATAGGAGG
1 GA-GATAGGAGG
*
23874 AGAGACAGGA--
1 -GAGATAGGAGG
*
23884 GAGATAGTA--
1 GAGATAGGAGG
23893 GAGATAGGAGG
1 GAGATAGGAGG
23904 GATGATAGGAGG
1 GA-GATAGGAGG
*
23916 AGAGACAGGAG
1 -GAGATAGGAG
23927 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:23883 original size:24 final size:24
Alignment explanation
Indices: 23850--23935 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
23840 AAGAGAAAGA
*
23850 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
23874 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
23892 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
23916 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
23936 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:23902 original size:42 final size:42
Alignment explanation
Indices: 23841--23959 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
23831 TAGCCCTCAA
* *
23841 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
23883 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
23925 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
23960 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:29434 original size:9 final size:9
Alignment explanation
Indices: 29420--29480 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
29410 CTCTCTTTAT
29420 TATCTCTCC
1 TATCTCTCC
29429 TATCTCTCC
1 TATCTCTCC
* *
29438 T-CCTAT-C
1 TATCTCTCC
*
29445 -ATCCCTCC
1 TATCTCTCC
*
29453 TATCTCTAC
1 TATCTCTCC
29462 TATCTCTCC
1 TATCTCTCC
*
29471 TCTCTCTCC
1 TATCTCTCC
29480 T
1 T
29481 CCTATCATCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:29442 original size:12 final size:12
Alignment explanation
Indices: 29425--29501 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
29415 TTTATTATCT
29425 CTCCTATCTCTC
1 CTCCTATCTCTC
29437 CTCCTATCATC-C
1 CTCCTATC-TCTC
29449 CTCCTA--TCT-
1 CTCCTATCTCTC
*
29458 CTACTATCTCTC
1 CTCCTATCTCTC
29470 CT-C--TCTCTC
1 CTCCTATCTCTC
29479 CTCCTATCATC-C
1 CTCCTATC-TCTC
*
29491 CTCTTATCTCT
1 CTCCTATCTCT
29502 TCTTTCTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
9 15 0.28
10 1 0.02
11 6 0.11
12 27 0.51
13 4 0.08
ACGTcount: A:0.12, C:0.47, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:29451 original size:42 final size:42
Alignment explanation
Indices: 29396--29510 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 42
29386 TCTCTCCTCT
* * * *
29396 TCCTGTCATCCCTCCTCTCTTTATTATCTCTCCTATCTCTCC
1 TCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCC
*
29438 TCCTATCATCCCTCCTATCTCTACTATCTCTCCTCTCTCTCC
1 TCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCC
* * *
29480 TCCTATCATCCCTCTTATCTCTTCTTTCTCT
1 TCCTATCATCCCTCCTATCTCTACTATCTCT
29511 TTGGGGGCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.10, C:0.43, G:0.01, T:0.45
Consensus pattern (42 bp):
TCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCC
Found at i:29464 original size:21 final size:21
Alignment explanation
Indices: 29440--29501 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
29430 ATCTCTCCTC
29440 CTATCATCCCTCCTATCTCTA
1 CTATCATCCCTCCTATCTCTA
* *
29461 CTATC-TCTCCT-CTCTCTCCTC
1 CTATCATC-CCTCCTATCT-CTA
*
29482 CTATCATCCCTCTTATCTCT
1 CTATCATCCCTCCTATCTCT
29502 TCTTTCTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.42
Consensus pattern (21 bp):
CTATCATCCCTCCTATCTCTA
Found at i:31588 original size:17 final size:16
Alignment explanation
Indices: 31566--31613 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
31556 GGTTTTCCTC
31566 TCTTTTTTTGTATTTGT
1 TCTTTTTTTGTATTT-T
*
31583 TCTTTTTTTTTTATTTT
1 TC-TTTTTTTGTATTTT
* *
31600 TATTTTTTGGTATT
1 TCTTTTTTTGTATT
31614 CTTGAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.38
17 4 0.15
18 12 0.46
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTTTTGTATTTT
Found at i:31591 original size:18 final size:17
Alignment explanation
Indices: 31568--31607 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
31558 TTTTCCTCTC
*
31568 TTTTTTTGTATTTGTTCT
1 TTTTTTTGTATTT-TTAT
*
31586 TTTTTTTTTATTTTTAT
1 TTTTTTTGTATTTTTAT
31603 TTTTT
1 TTTTT
31608 GGTATTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.07, C:0.03, G:0.05, T:0.85
Consensus pattern (17 bp):
TTTTTTTGTATTTTTAT
Found at i:32745 original size:12 final size:12
Alignment explanation
Indices: 32725--32768 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
32715 AGAAAGAAGA
*
32725 GATAAGAGGGAT
1 GATAGGAGGGAT
32737 GATAGGAGGGAT
1 GATAGGAGGGAT
32749 GATAGGAGGAGA-
1 GATAGGAGG-GAT
32761 GATAGGAG
1 GATAGGAG
32769 AGATAATAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 28 0.93
13 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.48, T:0.14
Consensus pattern (12 bp):
GATAGGAGGGAT
Found at i:32777 original size:12 final size:12
Alignment explanation
Indices: 32734--32782 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
32724 AGATAAGAGG
*
32734 GATGATAGGAGG
1 GATGATAGGAGA
32746 GATGATAGGAGGA
1 GATGATAGGA-GA
32759 GA-GATAGGAGA
1 GATGATAGGAGA
*
32770 GATAATA-GAGA
1 GATGATAGGAGA
32781 GA
1 GA
32783 GGACGGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 10 0.30
12 20 0.61
13 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
GATGATAGGAGA
Found at i:35792 original size:16 final size:16
Alignment explanation
Indices: 35771--35804 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35761 AAGTAGGATG
*
35771 ATGGTTCTATGTGCCT
1 ATGGTTCTATGTGACT
*
35787 ATGGTTCTGTGTGACT
1 ATGGTTCTATGTGACT
35803 AT
1 AT
35805 AGAGAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (16 bp):
ATGGTTCTATGTGACT
Found at i:36139 original size:32 final size:32
Alignment explanation
Indices: 36055--36263 Score: 123
Period size: 32 Copynumber: 6.5 Consensus size: 32
36045 AACATCTTGT
* * **
36055 TCTTTAAGGACTAAGGTTAGTAATTGTCCTAC
1 TCTTTGAGGACTAAGGTTGGTAAGCGTCCTAC
* * *
36087 TTTTTGAGGATTAAGTTTGGTAAGCG-CCTTAC
1 TCTTTGAGGACTAAGGTTGGTAAGCGTCC-TAC
* * *
36119 TCTTTGAGGACTAAGGTTGGTAAGCATCTTGC
1 TCTTTGAGGACTAAGGTTGGTAAGCGTCCTAC
* * ** * *
36151 TCTTTAAGGATTGTGGTGGGTAAGCATCCTAC
1 TCTTTGAGGACTAAGGTTGGTAAGCGTCCTAC
* ** ** * * *
36183 TCTTTAAGGTTTGTGGTGGGTAAGCATCCAAC
1 TCTTTGAGGACTAAGGTTGGTAAGCGTCCTAC
* * * * *
36215 TCTTTAAGGACTGAGGTAGGCAAGCATCCTAC
1 TCTTTGAGGACTAAGGTTGGTAAGCGTCCTAC
* *
36247 TCTTTAAAGACTAAGGT
1 TCTTTGAGGACTAAGGT
36264 AAGTAAACAT
Statistics
Matches: 145, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
31 2 0.01
32 142 0.98
33 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (32 bp):
TCTTTGAGGACTAAGGTTGGTAAGCGTCCTAC
Found at i:36173 original size:64 final size:64
Alignment explanation
Indices: 36116--36290 Score: 188
Period size: 64 Copynumber: 2.7 Consensus size: 64
36106 GTAAGCGCCT
* * * *
36116 TACTCTTTGAGGACTAAGGTTGGTAAGCATCTTGCTCTTTAAGGATTGTGGTGGGTAAGCATCC
1 TACTCTTTAAGGACTAAGGTAGGTAAGCATCTTGCTCTTTAAGGATTGAGGTAGGTAAGCATCC
** ** * *** * *
36180 TACTCTTTAAGGTTTGTGGTGGGTAAGCATCCAACTCTTTAAGGACTGAGGTAGGCAAGCATCC
1 TACTCTTTAAGGACTAAGGTAGGTAAGCATCTTGCTCTTTAAGGATTGAGGTAGGTAAGCATCC
* * * *
36244 TACTCTTTAAAGACTAAGGTAAGTAAACATCTTGCTCTTTGAGGATT
1 TACTCTTTAAGGACTAAGGTAGGTAAGCATCTTGCTCTTTAAGGATT
36291 AAAAAGAAAA
Statistics
Matches: 85, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
64 85 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (64 bp):
TACTCTTTAAGGACTAAGGTAGGTAAGCATCTTGCTCTTTAAGGATTGAGGTAGGTAAGCATCC
Found at i:36264 original size:32 final size:32
Alignment explanation
Indices: 36116--36288 Score: 157
Period size: 32 Copynumber: 5.4 Consensus size: 32
36106 GTAAGCGCCT
* * * *
36116 TACTCTTTGAGGACTAAGGTTGGTAAGCATCT
1 TACTCTTTAAGGACTGAGGTAGGTAAGCATCC
* * * *
36148 TGCTCTTTAAGGATTGTGGTGGGTAAGCATCC
1 TACTCTTTAAGGACTGAGGTAGGTAAGCATCC
** * *
36180 TACTCTTTAAGGTTTGTGGTGGGTAAGCATCC
1 TACTCTTTAAGGACTGAGGTAGGTAAGCATCC
* *
36212 AACTCTTTAAGGACTGAGGTAGGCAAGCATCC
1 TACTCTTTAAGGACTGAGGTAGGTAAGCATCC
* * * * *
36244 TACTCTTTAAAGACTAAGGTAAGTAAACATCT
1 TACTCTTTAAGGACTGAGGTAGGTAAGCATCC
* *
36276 TGCTCTTTGAGGA
1 TACTCTTTAAGGA
36289 TTAAAAAGAA
Statistics
Matches: 116, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 116 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (32 bp):
TACTCTTTAAGGACTGAGGTAGGTAAGCATCC
Found at i:36372 original size:36 final size:36
Alignment explanation
Indices: 36314--36389 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
36304 GCATCCTGTA
* * *
36314 GACT-AAAAAGGAAATAAGGTGTCATGCTCTTTGAG
1 GACTAAAAAAGAAAAAAAAGTGTCATGCTCTTTGAG
*
36349 GACTAAAAAAGAAAAAAAAGTGTCCTGCTCTTTGAG
1 GACTAAAAAAGAAAAAAAAGTGTCATGCTCTTTGAG
36385 GACTA
1 GACTA
36390 GAAGGACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 4 0.11
36 32 0.89
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (36 bp):
GACTAAAAAAGAAAAAAAAGTGTCATGCTCTTTGAG
Found at i:36605 original size:20 final size:20
Alignment explanation
Indices: 36573--36614 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
36563 TTGTTGTATG
36573 AATGATGCATAAG-GATGCA
1 AATGATGCATAAGTGATGCA
*
36592 AATGCATGCTTAAGTGATGCA
1 AATG-ATGCATAAGTGATGCA
36613 AA
1 AA
36615 AGTGATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
AATGATGCATAAGTGATGCA
Done.