Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 19 of 19
Found at i:3912709 original size:21 final size:22
Alignment explanation
Indices: 3912685--3912731 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3912675 TGAAAATATG
3912685 ATTAAT-TATTATAATGATAAA
1 ATTAATATATTATAATGATAAA
* * *
3912706 ATT-ATATGTTATAGTGATTAA
1 ATTAATATATTATAATGATAAA
3912727 ATTAA
1 ATTAA
3912732 AATTAATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.10
21 18 0.86
22 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
ATTAATATATTATAATGATAAA
Found at i:3912836 original size:19 final size:20
Alignment explanation
Indices: 3912816--3912852 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3912806 TTAATAATTA
3912816 AAAATAT-TATAT-TAAAAT
1 AAAATATGTATATATAAAAT
3912834 AAAATATGTATATATAAAA
1 AAAATATGTATATATAAAA
3912853 ATATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAATATGTATATATAAAAT
Found at i:3912871 original size:34 final size:32
Alignment explanation
Indices: 3912796--3912878 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 32
3912786 GGTTGAGATA
3912796 AAAATAAAAATTA-ATAATTAAAAATATTATATT
1 AAAATAAAAATTATAT-A-TAAAAATATTATATT
3912829 AAAATAAAATATGTATATATAAAAATA-TA-ATT
1 AAAATAAAA-AT-TATATATAAAAATATTATATT
3912861 AATAATTAAAAATTATAT
1 AA-AA-TAAAAATTATAT
3912879 TTATATTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
32 10 0.22
33 15 0.33
34 15 0.33
35 3 0.07
36 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAATAAAAATTATATATAAAAATATTATATT
Found at i:3912872 original size:19 final size:19
Alignment explanation
Indices: 3912794--3912873 Score: 57
Period size: 20 Copynumber: 4.4 Consensus size: 19
3912784 GAGGTTGAGA
*
3912794 TAAAAATAAAAATTAATAAT
1 TAAAAAT-ATAATTAATAAT
3912814 TAAAAATATTATATTAA-AA-
1 TAAAAATA-TA-ATTAATAAT
*
3912833 T-AAAATAT--GT-AT-AT
1 TAAAAATATAATTAATAAT
3912847 ATAAAAATATAATTAATAAT
1 -TAAAAATATAATTAATAAT
3912867 TAAAAAT
1 TAAAAAT
3912874 TATATTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 21
0.66 0.04 0.30
Matches are distributed among these distances:
13 2 0.04
14 1 0.02
15 1 0.02
16 7 0.15
17 1 0.02
18 7 0.15
19 11 0.23
20 12 0.26
21 5 0.11
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATTAATAAT
Found at i:3912900 original size:53 final size:54
Alignment explanation
Indices: 3912793--3912906 Score: 140
Period size: 59 Copynumber: 2.0 Consensus size: 54
3912783 TGAGGTTGAG
**
3912793 ATAAAAATAAAAATTAATAATTAAAAATATTATATTAAAATAAAATATGTATAT
1 ATAAAAATAAAAATTAATAATTAAAAATATTATATTAAAATAAAATATAAATAT
*
3912847 ATAAAAAT-ATAATTAATAATTAAAAATTATATTTATATTAAATAATAAAATATAAATAT
1 ATAAAAATAAAAATTAATAATT-AAAA--ATA-TTATATT-AA-AATAAAATATAAATAT
3912906 A
1 A
3912907 AATTATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
53 12 0.24
54 12 0.24
56 3 0.06
57 7 0.14
58 2 0.04
59 15 0.29
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (54 bp):
ATAAAAATAAAAATTAATAATTAAAAATATTATATTAAAATAAAATATAAATAT
Found at i:3915226 original size:51 final size:51
Alignment explanation
Indices: 3915160--3915258 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
3915150 ATTAACTTAG
* *
3915160 GTTCGGTGCCTAATTTTCATAATTGCATGAGAAAATTTTAAAGCCATTTAT
1 GTTCGGTGCCAAATTTTCATAATTGCATGAGAAAATTTCAAAGCCATTTAT
*
3915211 GTTCGTTGCCAAATTTTCATAATTGCATGAGAAAATTTCAAAGCCATT
1 GTTCGGTGCCAAATTTTCATAATTGCATGAGAAAATTTCAAAGCCATT
3915259 CATGACAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (51 bp):
GTTCGGTGCCAAATTTTCATAATTGCATGAGAAAATTTCAAAGCCATTTAT
Found at i:3916620 original size:20 final size:21
Alignment explanation
Indices: 3916582--3916623 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3916572 TTATTTTTAA
*
3916582 TATATTATAAATTATATAAATT
1 TATATTAT-AATTAAATAAATT
3916604 TATATTAT-ATTAAATAAATT
1 TATATTATAATTAAATAAATT
3916624 ATAATATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATTATAATTAAATAAATT
Found at i:3919178 original size:19 final size:19
Alignment explanation
Indices: 3919156--3919195 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3919146 TAAAAATGAT
3919156 TACA-AAATTTAATTAATAA
1 TACATAAATTTAATTAA-AA
*
3919175 TACATAAATTTATTTAAAA
1 TACATAAATTTAATTAAAA
3919194 TA
1 TA
3919196 TTTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TACATAAATTTAATTAAAA
Found at i:3921603 original size:22 final size:22
Alignment explanation
Indices: 3921538--3921604 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
3921528 CCACGAAAAT
* *
3921538 AAAATATAAAAAATAATAATATA
1 AAAATATAATAAATTA-AATATA
* * *
3921561 TAAATATATTAAAATT-TATATA
1 AAAATATAAT-AAATTAAATATA
3921583 AAAATATAATAAATTAAATATA
1 AAAATATAATAAATTAAATATA
3921605 TTATATTAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 5 0.15
22 18 0.53
23 7 0.21
24 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATATAATAAATTAAATATA
Found at i:3922604 original size:14 final size:16
Alignment explanation
Indices: 3922587--3922626 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
3922577 TAAAAATAAA
3922587 TTATTAA-TATAA-TT
1 TTATTAATTATAATTT
3922601 TTA-TAATTATAATTT
1 TTATTAATTATAATTT
*
3922616 TTATTATTTAT
1 TTATTAATTAT
3922627 TTTGTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 8 0.36
15 5 0.23
16 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTAATTATAATTT
Found at i:3929361 original size:12 final size:13
Alignment explanation
Indices: 3929338--3929373 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3929328 TACAAAATAT
*
3929338 GAGCTAGGGCTAG
1 GAGCTAGTGCTAG
3929351 G-GCTAGTGCTAG
1 GAGCTAGTGCTAG
3929363 GAGCTAGTGCT
1 GAGCTAGTGCT
3929374 GTTTGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.19, C:0.17, G:0.42, T:0.22
Consensus pattern (13 bp):
GAGCTAGTGCTAG
Found at i:3944983 original size:15 final size:17
Alignment explanation
Indices: 3944963--3944999 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
3944953 TTTAGGAGCA
3944963 ACAAATTTT-AA-AATT
1 ACAAATTTTAAACAATT
3944978 ACAAATTTTAAACAATT
1 ACAAATTTTAAACAATT
3944995 ACAAA
1 ACAAA
3945000 AAAAATCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
16 2 0.10
17 9 0.45
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (17 bp):
ACAAATTTTAAACAATT
Found at i:3948741 original size:27 final size:28
Alignment explanation
Indices: 3948711--3948764 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
3948701 ATTCAATCAA
3948711 TTAAACTT-AATAATAAAATTT-TTTAAG
1 TTAAA-TTGAATAATAAAATTTATTTAAG
*
3948738 TTAAATTGAATAGTAAAATTTATTTAA
1 TTAAATTGAATAATAAAATTTATTTAA
3948765 AAATCTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 17 0.71
28 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (28 bp):
TTAAATTGAATAATAAAATTTATTTAAG
Found at i:3950435 original size:20 final size:21
Alignment explanation
Indices: 3950410--3950452 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3950400 GTTTCAATCA
*
3950410 CTTTTTTTAA-AGAAATTAAT
1 CTTTTTTAAATAGAAATTAAT
*
3950430 CTTTTTTAAATATAAATTAAT
1 CTTTTTTAAATAGAAATTAAT
3950451 CT
1 CT
3950453 CTCACTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
CTTTTTTAAATAGAAATTAAT
Found at i:3955347 original size:17 final size:17
Alignment explanation
Indices: 3955321--3955353 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
3955311 TAAAAAATAA
3955321 TTTTATATTAATATATAT
1 TTTTATATTAA-ATATAT
3955339 TTTTA-ATTAAATATA
1 TTTTATATTAAATATA
3955354 AATAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATATTAAATATAT
Found at i:3955827 original size:22 final size:22
Alignment explanation
Indices: 3955801--3955862 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
3955791 TTTATACAAG
*
3955801 ATATGTTCACCTAATACATCTA
1 ATATGTTTACCTAATACATCTA
*
3955823 ATATGTTTACCTAACACATCTA
1 ATATGTTTACCTAATACATCTA
*
3955845 AAATGTTTACCTAATACA
1 ATATGTTTACCTAATACA
3955863 CCACTTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (22 bp):
ATATGTTTACCTAATACATCTA
Found at i:3964188 original size:37 final size:34
Alignment explanation
Indices: 3964115--3964219 Score: 147
Period size: 34 Copynumber: 3.0 Consensus size: 34
3964105 AAGATATGTT
3964115 CACCTAACACACTTAATATGTTTACCTAACACAC
1 CACCTAACACACTTAATATGTTTACCTAACACAC
* *
3964149 CACCTAACACACTTAATATATTATTCACCTAACATAC
1 CACCTAACACACTTAATAT-GT-TT-ACCTAACACAC
* *
3964186 CACCTAACACACCTAATATGTTTGCCTAACACAC
1 CACCTAACACACTTAATATGTTTACCTAACACAC
3964220 TTAATAAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
34 28 0.45
35 3 0.05
36 3 0.05
37 28 0.45
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.27
Consensus pattern (34 bp):
CACCTAACACACTTAATATGTTTACCTAACACAC
Found at i:3964703 original size:18 final size:18
Alignment explanation
Indices: 3964682--3964719 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3964672 ATTTTGTAAT
*
3964682 ATTTAT-TAACATATTAAA
1 ATTTATATAA-ATATAAAA
3964700 ATTTATATAAATATAAAA
1 ATTTATATAAATATAAAA
3964718 AT
1 AT
3964720 ATTTACCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTATATAAATATAAAA
Found at i:3964814 original size:18 final size:17
Alignment explanation
Indices: 3964769--3964821 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
3964759 ATATGTCTCG
3964769 AAATTTATATAAA-AT-
1 AAATTTATATAAATATA
3964784 AAA-TTAT-TAAAATATCA
1 AAATTTATAT-AAATAT-A
3964801 AAATTTATATAAATATA
1 AAATTTATATAAATATA
3964818 AAAT
1 AAAT
3964822 ACCTTAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 7 0.22
15 5 0.16
17 8 0.25
18 10 0.31
19 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:3964954 original size:21 final size:21
Alignment explanation
Indices: 3964892--3964954 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3964882 CAATTCAAAA
* * *
3964892 ATTTGATGTAATTTTGGTAAC
1 ATTTGATATAATTTTGATAAT
* *
3964913 ATTTAATATGATTTTGATAAT
1 ATTTGATATAATTTTGATAAT
3964934 ATTTGATATAATTTTGATAAT
1 ATTTGATATAATTTTGATAAT
3964955 TTATAATGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.51
Consensus pattern (21 bp):
ATTTGATATAATTTTGATAAT
Found at i:3965426 original size:21 final size:20
Alignment explanation
Indices: 3965359--3965555 Score: 137
Period size: 21 Copynumber: 9.5 Consensus size: 20
3965349 ATGGTTTTTA
* * *
3965359 ATATGATTTTAATAACCTTG
1 ATATAATTTTGATAACTTTG
* * *
3965379 ATATAATATTGTTAACTTTT
1 ATATAATTTTGATAACTTTG
3965399 ATATAATTTTGATAACATTTG
1 ATATAATTTTGATAAC-TTTG
* *
3965420 ATGTAA-TTTGGTAACTATTG
1 ATATAATTTTGATAACT-TTG
* * *
3965440 -TTTCTATTTCGAGTAACTTTG
1 ATAT-AATTTTGA-TAACTTTG
* *
3965461 ATATAATTTTAATAACTTTTA
1 ATATAATTTTGATAAC-TTTG
* *
3965482 ATATAATTTTGGTAATCTTTA
1 ATATAATTTTGATAA-CTTTG
*
3965503 ATATAATTTTGATAAGCTTCG
1 ATATAATTTTGATAA-CTTTG
*
3965524 ATATAAATTTTTATAACATTTG
1 ATAT-AATTTTGATAAC-TTTG
*
3965546 ATATTATTTT
1 ATATAATTTT
3965556 ATTAATTTTT
Statistics
Matches: 138, Mismatches: 29, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
19 3 0.02
20 44 0.32
21 66 0.48
22 25 0.18
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (20 bp):
ATATAATTTTGATAACTTTG
Found at i:3965570 original size:16 final size:16
Alignment explanation
Indices: 3965549--3965580 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3965539 ACATTTGATA
3965549 TTATTTTATTAATTTT
1 TTATTTTATTAATTTT
*
3965565 TTATTTTTTTAATTTT
1 TTATTTTATTAATTTT
3965581 AGTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTATTAATTTT
Found at i:3965662 original size:21 final size:21
Alignment explanation
Indices: 3965638--3965678 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3965628 TTTAATTGAA
*
3965638 TTTTGATAAAATTTTAATAAC
1 TTTTAATAAAATTTTAATAAC
* *
3965659 TTTTAATATAATTTTGATAA
1 TTTTAATAAAATTTTAATAA
3965679 TCTAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTAATAAAATTTTAATAAC
Found at i:3966232 original size:16 final size:17
Alignment explanation
Indices: 3966201--3966233 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3966191 TTTTAGTTTG
*
3966201 AATAATTAATTTTAATA
1 AATAATTAAATTTAATA
3966218 AATAA-TAAATTTAATA
1 AATAATTAAATTTAATA
3966234 TTTGTATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAATTAAATTTAATA
Found at i:3967442 original size:20 final size:20
Alignment explanation
Indices: 3967416--3967467 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3967406 TTTTTATGAA
3967416 AATGTATTTTTAGATGAAATG
1 AATGTATTTTTAGATGAAA-G
* *
3967437 -ATGTATTAGTTGGATGAAAG
1 AATGTATT-TTTAGATGAAAG
3967457 AATGTATTTTT
1 AATGTATTTTT
3967468 TTATTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (20 bp):
AATGTATTTTTAGATGAAAG
Found at i:3971802 original size:14 final size:14
Alignment explanation
Indices: 3971783--3971809 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3971773 AAGCTGTAAA
3971783 GAATTTTTTTTTTG
1 GAATTTTTTTTTTG
3971797 GAATTTTTTTTTT
1 GAATTTTTTTTTT
3971810 CAAAACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (14 bp):
GAATTTTTTTTTTG
Found at i:3979095 original size:2 final size:2
Alignment explanation
Indices: 3979090--3979125 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3979080 GAGAGTTGTC
3979090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3979126 TATTGGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3979436 original size:17 final size:19
Alignment explanation
Indices: 3979406--3979451 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
3979396 AATTTCATAA
*
3979406 ATTTTTATATTTTATTTAT
1 ATTTTTATATTTTAATTAT
3979425 ATTTTTA-A-TTTAATTATT
1 ATTTTTATATTTTAATTA-T
3979443 ATATTTTAT
1 AT-TTTTAT
3979452 GAATACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTTATATTTTAATTAT
Found at i:3980668 original size:2 final size:2
Alignment explanation
Indices: 3980661--3980686 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3980651 CCACTTCCGC
3980661 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3980687 CCAAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3983390 original size:18 final size:18
Alignment explanation
Indices: 3983367--3983417 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3983357 AATTATGATA
*
3983367 TAATTTTTTATTTTTATT
1 TAATTTTTTATTATTATT
3983385 TAATTTTTT-TATATTATT
1 TAATTTTTTAT-TATTATT
*
3983403 TATATTTATTATTAT
1 TA-ATTTTTTATTAT
3983418 AATTAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.04
18 17 0.61
19 9 0.32
20 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TAATTTTTTATTATTATT
Found at i:3983394 original size:19 final size:19
Alignment explanation
Indices: 3983365--3983409 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3983355 TGAATTATGA
* *
3983365 TATAATTTTTTATTTTTATT
1 TATATTTTTTTA-TATTATT
3983385 TA-ATTTTTTTATATTATT
1 TATATTTTTTTATATTATT
3983403 TATATTT
1 TATATTT
3983410 ATTATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 12 0.55
20 2 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATATTTTTTTATATTATT
Found at i:3984040 original size:3 final size:3
Alignment explanation
Indices: 3984018--3984060 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
3984008 TTATGAATGA
* * *
3984018 ATT ATC ATT ATC AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3984061 CATAAGTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:3984476 original size:12 final size:11
Alignment explanation
Indices: 3984448--3984472 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3984438 ATTTTTTATT
3984448 AAATTATTTAA
1 AAATTATTTAA
3984459 AAATTATTTAA
1 AAATTATTTAA
3984470 AAA
1 AAA
3984473 ATTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTATTTAA
Found at i:3984872 original size:3 final size:3
Alignment explanation
Indices: 3984862--3984896 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3984852 CTCTTTTTTT
*
3984862 TAA T-A TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3984897 AACATGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3985602 original size:15 final size:15
Alignment explanation
Indices: 3985582--3985611 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3985572 CAATGTAATG
3985582 TAAAAAGAAAAGAAA
1 TAAAAAGAAAAGAAA
*
3985597 TAAAAAGGAAAGAAA
1 TAAAAAGAAAAGAAA
3985612 CCCAGATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAAAGAAAAGAAA
Found at i:3993699 original size:20 final size:22
Alignment explanation
Indices: 3993674--3993713 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3993664 TTTTGCACCG
3993674 TTTG-TTTT-TTCTTTTTTTTT
1 TTTGTTTTTATTCTTTTTTTTT
3993694 TTTGTTTTTATTCTTTTTTT
1 TTTGTTTTTATTCTTTTTTT
3993714 CCCTTTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.88
Consensus pattern (22 bp):
TTTGTTTTTATTCTTTTTTTTT
Found at i:3993710 original size:19 final size:20
Alignment explanation
Indices: 3993674--3993713 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3993664 TTTTGCACCG
* *
3993674 TTTGTTTTTTCTTTTTTTTT
1 TTTGTTTTTTATTCTTTTTT
3993694 TTTG-TTTTTATTCTTTTTT
1 TTTGTTTTTTATTCTTTTTT
3993713 T
1 T
3993714 CCCTTTGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.88
Consensus pattern (20 bp):
TTTGTTTTTTATTCTTTTTT
Found at i:3993720 original size:23 final size:22
Alignment explanation
Indices: 3993654--3993720 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
3993644 TTCACGTTTC
*
3993654 TTTATCTCTTTTTTGCACCGTTTGT
1 TTTAT-TCTTTTTTTC-CC-TTTGT
**
3993679 TTT-TTCTTTTTTT-TTTTTGTT
1 TTTATTCTTTTTTTCCCTTTG-T
3993700 TTTATTCTTTTTTTCCCTTTG
1 TTTATTCTTTTTTTCCCTTTG
3993721 GTGCCGGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 10 0.29
23 12 0.35
24 1 0.03
25 3 0.09
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.73
Consensus pattern (22 bp):
TTTATTCTTTTTTTCCCTTTGT
Found at i:3993897 original size:2 final size:2
Alignment explanation
Indices: 3993890--3993919 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3993880 GCGTGTATGC
3993890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3993920 GTGGCATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3994638 original size:2 final size:2
Alignment explanation
Indices: 3994631--3994659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3994621 TTATATTTAA
3994631 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3994660 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3994664 original size:2 final size:2
Alignment explanation
Indices: 3994659--3994684 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3994649 TCTCTCTCTC
3994659 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3994685 CACACACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.