Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2111
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: 32467
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:2541 original size:22 final size:23
Alignment explanation
Indices: 2516--2567 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2506 AAATGAATAT
2516 AATATATTTAA-TAAATATAAAA
1 AATATATTTAATTAAATATAAAA
* **
2538 AATA-ATATAATTAAATATAATT
1 AATATATTTAATTAAATATAAAA
2560 AATATATT
1 AATATATT
2568 ATATATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.21
22 17 0.71
23 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATATTTAATTAAATATAAAA
Found at i:2573 original size:18 final size:19
Alignment explanation
Indices: 2516--2578 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
2506 AAATGAATAT
*
2516 AATATATTTAATA-AATATA
1 AATATAATTAATATAAT-TA
2535 AA-A-AA-TAATATAATTA
1 AATATAATTAATATAATTA
2551 AATATAATTAATAT-ATTA
1 AATATAATTAATATAATTA
* *
2569 TATATCATTA
1 AATATAATTA
2579 TATTCTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 9 0.24
17 5 0.14
18 15 0.41
19 8 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATAATTAATATAATTA
Found at i:2834 original size:16 final size:16
Alignment explanation
Indices: 2792--2861 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
2782 AAAATATAAT
*
2792 AATAATTAGAAATTG-
1 AATAATTAGAATTTGA
* *
2807 ATTAATTTGAATTTGA
1 AATAATTAGAATTTGA
*
2823 AATAATTAGAATTTAA
1 AATAATTAGAATTTGA
*
2839 AATAATTTA-AATCTGA
1 AATAA-TTAGAATTTGA
2855 AATAATT
1 AATAATT
2862 TGAACTCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.31
16 28 0.62
17 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (16 bp):
AATAATTAGAATTTGA
Found at i:2856 original size:32 final size:32
Alignment explanation
Indices: 2792--2875 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 32
2782 AAAATATAAT
* * * *
2792 AATAATTAGAAATT-GATTAATTTGAATTTGA
1 AATAATTAGAAATTAAAATAATTTAAATCTGA
*
2823 AATAATTAGAATTTAAAATAATTTAAATCTGA
1 AATAATTAGAAATTAAAATAATTTAAATCTGA
* * *
2855 AATAATTTGAACTCAAAATAA
1 AATAATTAGAAATTAAAATAA
2876 ATAAATTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 13 0.30
32 31 0.70
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (32 bp):
AATAATTAGAAATTAAAATAATTTAAATCTGA
Found at i:2972 original size:16 final size:16
Alignment explanation
Indices: 2951--3001 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2941 ATTCAAACTC
2951 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
*
2967 AAAATAATCTAAACTTT
1 AAAATAATTTAAA-TTT
*
2984 --ATTAATTTAAATATT
1 AAAATAATTTAAAT-TT
2999 AAA
1 AAA
3002 CACGATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.04
15 11 0.39
16 12 0.43
17 4 0.14
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:3546 original size:27 final size:30
Alignment explanation
Indices: 3502--3561 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 30
3492 TATTTAAAAA
3502 TTAAATTATTTATGAATAA-AAT-AT-ATT
1 TTAAATTATTTATGAATAATAATAATAATT
*
3529 TTAAATTA-TTATTTAATAATAATAATAATT
1 TTAAATTATTTA-TGAATAATAATAATAATT
3559 TTA
1 TTA
3562 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.11
27 14 0.50
28 3 0.11
29 2 0.07
30 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAAATTATTTATGAATAATAATAATAATT
Found at i:3647 original size:17 final size:18
Alignment explanation
Indices: 3625--3673 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
3615 TAATAAAAAA
3625 TAAAATTTTAAATTAA-T
1 TAAAATTTTAAATTAATT
**
3642 TAAAA-TTTAAAAAAATT
1 TAAAATTTTAAATTAATT
3659 TAAAATTTTTAAATT
1 TAAAA-TTTTAAATT
3674 GGGAACAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 8 0.32
17 11 0.44
19 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTTTAAATTAATT
Found at i:8022 original size:20 final size:19
Alignment explanation
Indices: 7993--8038 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
7983 ATTATAAATT
7993 AATATAAAATTTTAATAATA
1 AATATAAAA-TTTAATAATA
*
8013 AATATTAAATTTAATAA-A
1 AATATAAAATTTAATAATA
8031 ATATATAA
1 A-ATATAA
8039 CTAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.57
20 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAAAATTTAATAATA
Found at i:12950 original size:20 final size:20
Alignment explanation
Indices: 12925--12962 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12915 TGTTTAAGGG
12925 AAAAAAAAAAAACAAAAAAC
1 AAAAAAAAAAAACAAAAAAC
* *
12945 AAAAAAAGAAAAGAAAAA
1 AAAAAAAAAAAACAAAAA
12963 GTTCGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAACAAAAAAC
Found at i:13300 original size:27 final size:27
Alignment explanation
Indices: 13270--13322 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
13260 TATAATTTAT
*
13270 TTTTAAGATTTTTTATAATTATATATA
1 TTTTAAGATATTTTATAATTATATATA
* * *
13297 TTTTAATATATTTTATTATTTTATAT
1 TTTTAAGATATTTTATAATTATATAT
13323 GTTTAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTAAGATATTTTATAATTATATATA
Found at i:13356 original size:15 final size:16
Alignment explanation
Indices: 13335--13380 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
13325 TTAAATGTAA
13335 ATATAAATTTTAAAAT
1 ATATAAATTTTAAAAT
13351 -TATAAATATTTAAAAT
1 ATATAAAT-TTTAAAAT
* *
13367 ATTTAAATATTAAA
1 ATATAAATTTTAAA
13381 TAAATAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 7 0.27
16 13 0.50
17 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAAATTTTAAAAT
Found at i:13368 original size:9 final size:8
Alignment explanation
Indices: 13338--13382 Score: 51
Period size: 7 Copynumber: 5.8 Consensus size: 8
13328 AATGTAAATA
13338 TAAAT-TT
1 TAAATATT
13345 TAAA-ATT
1 TAAATATT
13352 ATAAATATT
1 -TAAATATT
13361 TAAAATATT
1 T-AAATATT
13370 TAAATA-T
1 TAAATATT
13377 TAAATA
1 TAAATA
13383 AATAAAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 13 0.38
8 10 0.29
9 11 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TAAATATT
Found at i:13373 original size:17 final size:16
Alignment explanation
Indices: 13336--13377 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
13326 TAAATGTAAA
13336 TATAAAT-TTTAAAAT
1 TATAAATATTTAAAAT
13351 TATAAATATTTAAAAT
1 TATAAATATTTAAAAT
*
13367 ATTTAAATATT
1 -TATAAATATT
13378 AAATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAATATTTAAAAT
Found at i:14064 original size:19 final size:19
Alignment explanation
Indices: 14027--14074 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
14017 AAAGTTTTAA
*
14027 ATATAATTTTTATATTAAT
1 ATATAATTTTTATAATAAT
* *
14046 ATATGATTTTTTTAATAAT
1 ATATAATTTTTATAATAAT
14065 -T-TAATTTTTA
1 ATATAATTTTTA
14075 AGTAAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATAATTTTTATAATAAT
Found at i:14386 original size:14 final size:14
Alignment explanation
Indices: 14367--14440 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
14357 AAATTATTAT
*
14367 AATAAATCATATAA
1 AATAAATAATATAA
* *
14381 AATAAAAAATATTA
1 AATAAATAATATAA
*
14395 CATAAAT-ATAATAAA
1 AATAAATAAT-AT-AA
14410 AATAAATAAT-TAA
1 AATAAATAATATAA
14423 AATAAAATAATA-AA
1 AAT-AAATAATATAA
14437 AATA
1 AATA
14441 TAATTTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
13 8 0.17
14 31 0.65
15 7 0.15
16 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAATAATATAA
Found at i:14423 original size:69 final size:69
Alignment explanation
Indices: 14297--14428 Score: 151
Period size: 69 Copynumber: 1.9 Consensus size: 69
14287 AATTAAATAT
* * * ** ** *
14297 TAATAAATTATATAAAATATAAAATTGATTGAAATATAATATGAATATAATTTTTAAATTAAATT
1 TAATAAATCATATAAAATAAAAAATTGAATGAAATATAATAAAAATATAATAATTAAAATAAATT
14362 ATTA
66 ATTA
*
14366 TAATAAATCATATAAAATAAAAAATATTACAT-AAATATAATAAAAATA-AATAATTAAAATAAA
1 TAATAAATCATATAAAATAAAAAAT-TGA-ATGAAATATAATAAAAATATAATAATTAAAATAAA
14429 ATAATAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
69 35 0.67
70 16 0.31
71 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (69 bp):
TAATAAATCATATAAAATAAAAAATTGAATGAAATATAATAAAAATATAATAATTAAAATAAATT
ATTA
Found at i:14469 original size:19 final size:19
Alignment explanation
Indices: 14364--14481 Score: 98
Period size: 19 Copynumber: 6.3 Consensus size: 19
14354 ATTAAATTAT
*
14364 TATAAT-AAATCATATAAA
1 TATAATAAAATTATATAAA
* *
14382 -ATAAAAAATATTACATAAA
1 TATAATAAA-ATTATATAAA
* * *
14401 TATAATAAAAATAAATAAT
1 TATAATAAAATTATATAAA
* * *
14420 TAAAATAAAATAATAAAAA
1 TATAATAAAATTATATAAA
**
14439 TATAATTTAATTATATAAA
1 TATAATAAAATTATATAAA
14458 TATAATAAAATTTATATAAA
1 TATAATAAAA-TTATATAAA
14478 -ATAA
1 TATAA
14482 ATTATTTAAT
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
17 4 0.05
18 2 0.03
19 54 0.71
20 16 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAATAAAATTATATAAA
Found at i:14486 original size:14 final size:14
Alignment explanation
Indices: 14351--14486 Score: 56
Period size: 14 Copynumber: 9.9 Consensus size: 14
14341 ATATAATTTT
*
14351 TAAATTAAATTAT-
1 TAAAATAAATTATA
* *
14364 TATAATAAATCATA
1 TAAAATAAATTATA
**
14378 TAAAATAAAAAATA
1 TAAAATAAATTATA
* *
14392 TTACATAAA-TATAA
1 TAAAATAAATTAT-A
*
14406 TAAAAATAAATAAT-
1 T-AAAATAAATTATA
*
14420 TAAAATAAAATA-A
1 TAAAATAAATTATA
14433 TAAAAATATAATT-TAA
1 T-AAAATA-AATTAT-A
* *
14449 TTATATAAA-TATAA
1 TAAAATAAATTAT-A
14463 TAAAAT---TTATA
1 TAAAATAAATTATA
14474 TAAAATAAATTAT
1 TAAAATAAATTAT
14487 TTAATTGTTA
Statistics
Matches: 90, Mismatches: 19, Indels: 27
0.66 0.14 0.20
Matches are distributed among these distances:
11 7 0.08
12 3 0.03
13 23 0.26
14 40 0.44
15 13 0.14
16 4 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATAAATTATA
Found at i:18228 original size:18 final size:20
Alignment explanation
Indices: 18187--18228 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
18177 TTACTTATAT
* *
18187 AATATGTATAAATGTAAAAT
1 AATATATATAAATGTAAAAA
18207 AATATATAT-AAT-TAAAAA
1 AATATATATAAATGTAAAAA
18225 AATA
1 AATA
18229 AATTGAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
20 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATATATATAAATGTAAAAA
Found at i:18588 original size:2 final size:2
Alignment explanation
Indices: 18581--18613 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18571 AGAAGCCATA
18581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18614 CAAAAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18926 original size:14 final size:14
Alignment explanation
Indices: 18909--18950 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18899 AAATATAATG
*
18909 ATTAAATTAAATAA
1 ATTAAATTATATAA
*
18923 ATTAAATCATATAA
1 ATTAAATTATATAA
18937 A--AAATTATATAA
1 ATTAAATTATATAA
18949 AT
1 AT
18951 ATATAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTAAATTATATAA
Found at i:19356 original size:19 final size:20
Alignment explanation
Indices: 19332--19372 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
19322 GTCAACTACC
*
19332 TTAAATCAC-TTTTATTTAA
1 TTAAATAACTTTTTATTTAA
19351 TTAAATAACTTTTTATTTAA
1 TTAAATAACTTTTTATTTAA
19371 TT
1 TT
19373 TTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATAACTTTTTATTTAA
Found at i:20650 original size:17 final size:17
Alignment explanation
Indices: 20624--20657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20614 TTTGTACATA
20624 ATTAAAAGTTAATTTAT
1 ATTAAAAGTTAATTTAT
* *
20641 ATTAAGAGTTTATTTAT
1 ATTAAAAGTTAATTTAT
20658 GTACGAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
ATTAAAAGTTAATTTAT
Found at i:20892 original size:17 final size:17
Alignment explanation
Indices: 20870--20937 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 17
20860 TAATTGTATA
20870 AATAATAAACATATAATATT
1 AATAAT-AA-ATA-AATATT
20890 AATAATAAATAAATATT
1 AATAATAAATAAATATT
*
20907 -A-AATATGATAAATATTT
1 AATAATA-AATAAATA-TT
20924 AATAA-AATATAAAT
1 AATAATAA-ATAAAT
20938 TTGATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
15 4 0.10
16 8 0.20
17 8 0.20
18 11 0.27
19 4 0.10
20 6 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
AATAATAAATAAATATT
Found at i:20920 original size:27 final size:28
Alignment explanation
Indices: 20890--20947 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
20880 ATATAATATT
20890 AATAATAAAT-AAATATTAAATATGA-TA
1 AATAATAAATAAAATA-TAAATATGATTA
* * *
20917 AATATTTAATAAAATATAAATTTGATTA
1 AATAATAAATAAAATATAAATATGATTA
20945 AAT
1 AAT
20948 TATATGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
AATAATAAATAAAATATAAATATGATTA
Found at i:20927 original size:31 final size:30
Alignment explanation
Indices: 20867--20929 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
20857 GTTTAATTGT
20867 ATAAATAATAAACATATAATATTAATAATAA
1 ATAAATAATAAACATATAATATT-ATAATAA
* *
20898 ATAAATATTAAATATGATAAATATT-TAATAA
1 ATAAATAATAAACAT-AT-AATATTATAATAA
20929 A
1 A
20930 ATATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 20 0.71
32 2 0.07
33 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (30 bp):
ATAAATAATAAACATATAATATTATAATAA
Found at i:20939 original size:16 final size:17
Alignment explanation
Indices: 20872--20937 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
20862 ATTGTATAAA
20872 TAATAAACATAT-AATAT
1 TAATAAA-ATATAAATAT
20889 TAATAATAA-ATAAATAT
1 TAATAA-AATATAAATAT
*
20906 T-A-AATATGATAAATATT
1 TAATAAAAT-ATAAATA-T
20923 TAATAAAATATAAAT
1 TAATAAAATATAAAT
20938 TTGATTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 1 0.03
15 2 0.05
16 10 0.25
17 15 0.38
18 8 0.20
19 4 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATAAAATATAAATAT
Found at i:21698 original size:25 final size:26
Alignment explanation
Indices: 21653--21709 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
21643 AATATTTTTA
21653 TATTTTATTATATTAAAATAAATAT-T
1 TATTTTATTATATTAAAATAAAT-TCT
* *
21679 TATTTT-TTATATTTATATAAATTCT
1 TATTTTATTATATTAAAATAAATTCT
21704 TATTTT
1 TATTTT
21710 GAATGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.75
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTTTATTATATTAAAATAAATTCT
Found at i:21813 original size:30 final size:29
Alignment explanation
Indices: 21761--21817 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
21751 TTAATTAAAA
*
21761 TTTTATTTAAATATAAATTAAAAATTAATG
1 TTTTATTTAAATATAAACT-AAAATTAATG
* *
21791 TTTTATTTAAATTTACACTAAAATTAA
1 TTTTATTTAAATATAAACTAAAATTAA
21818 AAACTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTATTTAAATATAAACTAAAATTAATG
Found at i:22030 original size:5 final size:6
Alignment explanation
Indices: 21991--22019 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
21981 GTAGTTTAAT
21991 AATTTA AATTTA AATTTA AATTTA AATTT
1 AATTTA AATTTA AATTTA AATTTA AATTT
22020 GATTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:22274 original size:2 final size:2
Alignment explanation
Indices: 22267--22292 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22257 CTTAAATTAC
22267 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
22293 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:22637 original size:2 final size:2
Alignment explanation
Indices: 22632--22664 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
22622 TCTCTCACTC
22632 TA TA TA TA T- 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 TA TA TA TA
22665 AATGAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23338 original size:19 final size:18
Alignment explanation
Indices: 23305--23350 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
23295 CAAAGATTCA
*
23305 TTTATTTTTCATAAATTT
1 TTTATTTTTCATAAAATT
*
23323 TTTATTTTTCTTTAAAATT
1 TTTATTTTTC-ATAAAATT
*
23342 TTCATTTTT
1 TTTATTTTT
23351 TGAAATACGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTTTCATAAAATT
Found at i:23564 original size:166 final size:165
Alignment explanation
Indices: 23363--23729 Score: 481
Period size: 166 Copynumber: 2.2 Consensus size: 165
23353 AAATACGGAG
* * *
23363 TTTTCTACTTCGT-AATTTTTTTGAA-GATATTTTTCTT-AGTTTTTAATTTTTAAAAGTCATCA
1 TTTTCTACTCCATAAATTTTTTTGAAGGA-ATTTTTCTTGA-TTTTTAATTTTTAAAAGTCATAA
*
23425 AATATTATTATTTATTTCATATTCATTCAATTTTTAAAAATTCATTCATTTCCATAAATTTTAAA
64 AATATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCATTTCCATAAATTTTAAA
* * * *
23490 TTTTTTCCTTAAAATTCTCCTTTTTTCGAAATA-CAAAA
129 TTTTTTCCTTAAAA-TATCCTTTCTCCGAAAAATC-AAA
* * *
23528 TTTTTTACTCTATAAATTTTTTTGAAGGGATTTTTCTTGATTTTTAATTTTTAAAAGTCATAAAA
1 TTTTCTACTCCATAAATTTTTTTGAAGGAATTTTTCTTGATTTTTAATTTTTAAAAGTCATAAAA
* * * * * *
23593 TATTATTATTTATTTCATTTTAATTCAGTTTTTAAAAATTCATTTATTTTCATGAATTTTGAATT
66 TATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCATTTCCATAAATTTTAAATT
* * *
23658 TTTTCCTTGAAATATCCTTTCTCCGAAAAATCGAG
131 TTTTCCTTAAAATATCCTTTCTCCGAAAAATCAAA
*
23693 TTTTCTACTCCATAAATTTTTTCGAAGGAATTTTTCT
1 TTTTCTACTCCATAAATTTTTTTGAAGGAATTTTTCT
23730 CAATTTAGCA
Statistics
Matches: 174, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
165 57 0.33
166 115 0.66
167 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (165 bp):
TTTTCTACTCCATAAATTTTTTTGAAGGAATTTTTCTTGATTTTTAATTTTTAAAAGTCATAAAA
TATTATTATTTATTTCATATTAATTCAATTTTTAAAAATTCATTCATTTCCATAAATTTTAAATT
TTTTCCTTAAAATATCCTTTCTCCGAAAAATCAAA
Found at i:23783 original size:165 final size:165
Alignment explanation
Indices: 23300--23825 Score: 411
Period size: 166 Copynumber: 3.2 Consensus size: 165
23290 TTTCTCAAAG
* * * * ** * ** *
23300 ATTCATTTATTTTTCATAAATTTT-TTATTTTTCTTTAAAATTTTCATTT-TTTGAAATACGGAG
1 ATTCATTTA-TTTTCATAAATTTTAAT-TTTTTCCTTAAAATTATCCTTTCTCCGAAAAACAAAA
* * * * * ** *
23363 TTTTCTACTTCGT-AATTTTTTTGAA-GATATTTTTCTTAGTTTTTAATTTTTAAAAGTCATCAA
64 TTTTCTACTCCATAAATTTTTTCGAAGGA-ATTTTTCTCAATTTAGAATTTTTAAAAGTCATAAA
* * * * * *
23426 ATATTATTATTTATTTCATATTCATTCAATTTTTAAAA
128 ATATTATCATTAACTCCATATTAATTCAGTTTTTAAAA
* * * * * *
23464 ATTCATTCATTTCCATAAATTTTAAATTTTTTCCTTAAAATTCTCCTTTTTTCGAAATACAAAAT
1 ATTCATTTATTTTCATAAATTTT-AATTTTTTCCTTAAAATTATCCTTTCTCCGAAAAACAAAAT
* * * * ** **
23529 TTTTTACTCTATAAATTTTTTTGAAGGGATTTTTCTTGATTTTTAATTTTTAAAAGTCATAAAAT
65 TTTCTACTCCATAAATTTTTTCGAAGGAATTTTTCTCAATTTAGAATTTTTAAAAGTCATAAAAT
* * * * *
23594 ATTATTATTTATTTCATTTTAATTCAGTTTTTAAAA
130 ATTATCATTAACTCCATATTAATTCAGTTTTTAAAA
* * * *
23630 ATTCATTTATTTTCATGAATTTTGAATTTTTTCCTTGAAA-TATCCTTTCTCCGAAAAATC-GAG
1 ATTCATTTATTTTCATAAATTTT-AATTTTTTCCTTAAAATTATCCTTTCTCCGAAAAA-CAAAA
* * * **
23693 TTTTCTACTCCATAAATTTTTTCGAAGGAATTTTTCTCAATTTAGCATTTTTAAAATTTATCTAA
64 TTTTCTACTCCATAAATTTTTTCGAAGGAATTTTTCTCAATTTAGAATTTTTAAAAGTCATAAAA
* *
23758 TATTGTCATTGAACTCCA-ATTAATTCAGTTTTGAAAA
129 TATTATCATT-AACTCCATATTAATTCAGTTTTTAAAA
* * *
23795 TTTTAATTTATTTT-ATTAATTTTAATTTTTT
1 -ATTCATTTATTTTCATAAATTTTAATTTTTT
23826 TGTATATATT
Statistics
Matches: 299, Mismatches: 55, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
163 13 0.04
164 35 0.12
165 120 0.40
166 130 0.43
167 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (165 bp):
ATTCATTTATTTTCATAAATTTTAATTTTTTCCTTAAAATTATCCTTTCTCCGAAAAACAAAATT
TTCTACTCCATAAATTTTTTCGAAGGAATTTTTCTCAATTTAGAATTTTTAAAAGTCATAAAATA
TTATCATTAACTCCATATTAATTCAGTTTTTAAAA
Found at i:25654 original size:158 final size:156
Alignment explanation
Indices: 25250--25851 Score: 776
Period size: 158 Copynumber: 3.9 Consensus size: 156
25240 ATGTTTAATT
* * * * **
25250 ATTTTTTCTAATCTTTTATATTTCTATGGGTAT-TCGTAGGGGTATAAAAGATTTCAAAAATGTT
1 ATTTTTCCTAATCTTTTATATTCCTATGAGCATCT-GTAGGGGTATAAAAGATTTCAAAAACATT
* * ** *
25314 TTCGTATCCTTTCAGGCTTCCATTAGGGTACGAAATAACATTTTTAAAAATAAATAAAATTAAAT
65 TTCGTATCTTTTC-GGCTTCCATTAAGGTACGAAATAGTATTTTCAAAAATAAATAAAATTAAAT
* *
25379 TGAATTAATAATTTTGGATTAAATTCTA
129 TGAATTAATACTTTCGGATTAAATTCTA
*
25407 ATTTTTCCTAATCTTTTATATTCCTATGAGCATC---A----TATAAAAGATTTC-AAAA-TTTT
1 ATTTTTCCTAATCTTTTATATTCCTATGAGCATCTGTAGGGGTATAAAAGATTTCAAAAACATTT
* * * * ** *
25463 TCATATGTTTTTAGGCTTCCAATAAGGTTTGAAATAGTATTTTCGAAAATAAATAAAATTAAATT
66 TCGTAT-CTTTTCGGCTTCCATTAAGGTACGAAATAGTATTTTCAAAAATAAATAAAATTAAATT
*
25528 GAATTCATACTTTCGGATTAAATTCTA
130 GAATTAATACTTTCGGATTAAATTCTA
25555 ATTTTTCCTAATCTTTTATATTCCTATGAGCATCTGTAGGGGTATAAAAGATTTCAAAAACATTT
1 ATTTTTCCTAATCTTTTATATTCCTATGAGCATCTGTAGGGGTATAAAAGATTTCAAAAACATTT
*
25620 TCGTATCTTTTCGTGCTTCCATTAAGGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAAAT
66 TCGTATCTTTTCG-GCTTCCATTAA-GGTACGAAATAGTATTTTCAAAAATAAATAAAATTAAAT
*
25685 TGAATTAATACTTTCGGATTAAATTTTA
129 TGAATTAATACTTTCGGATTAAATTCTA
** * * *
25713 ATTTTTTTTAATCTTTTATATTCCTAT-AGATATCCGTAGGGGTATAAAATATTTCAAAAACATT
1 ATTTTTCCTAATCTTTTATATTCCTATGAG-CATCTGTAGGGGTATAAAAGATTTCAAAAACATT
*
25777 TTCGTATCTTTTCGTGCTTTCATTAAGGTACGAAATAGTATTTTCAAAAATAAATAAAATTAAAT
65 TTCGTATCTTTTCG-GCTTCCATTAAGGTACGAAATAGTATTTTCAAAAATAAATAAAATTAAAT
**
25842 CAAATTAATA
129 TGAATTAATA
25852 TTCTCAAGAA
Statistics
Matches: 393, Mismatches: 38, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
148 110 0.28
149 7 0.02
150 13 0.03
151 1 0.00
154 1 0.00
155 13 0.03
156 9 0.02
157 95 0.24
158 144 0.37
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (156 bp):
ATTTTTCCTAATCTTTTATATTCCTATGAGCATCTGTAGGGGTATAAAAGATTTCAAAAACATTT
TCGTATCTTTTCGGCTTCCATTAAGGTACGAAATAGTATTTTCAAAAATAAATAAAATTAAATTG
AATTAATACTTTCGGATTAAATTCTA
Found at i:27218 original size:21 final size:24
Alignment explanation
Indices: 27194--27239 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
27184 TTTATTATTA
27194 TCATTT-TCATT-TTTTA-ATGAT
1 TCATTTCTCATTCTTTTATATGAT
27215 TCATTTCTCATTCTTTTATATGAT
1 TCATTTCTCATTCTTTTATATGAT
27239 T
1 T
27240 TATGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 5 0.23
24 6 0.27
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61
Consensus pattern (24 bp):
TCATTTCTCATTCTTTTATATGAT
Found at i:27505 original size:2 final size:2
Alignment explanation
Indices: 27498--27530 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27488 AAAGCTCTTT
27498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27531 GTGCTCCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27623 original size:20 final size:20
Alignment explanation
Indices: 27598--27636 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27588 TTAATATTAT
27598 AAATTGAATATTATAAAAAG
1 AAATTGAATATTATAAAAAG
27618 AAATTGAATATTATAAAAA
1 AAATTGAATATTATAAAAA
27637 TAACAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (20 bp):
AAATTGAATATTATAAAAAG
Found at i:28832 original size:20 final size:19
Alignment explanation
Indices: 28772--28855 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 19
28762 CTTTCGGTAA
28772 TTTATAT-ATTCATATTAAAT
1 TTTATATAATT-AT-TTAAAT
* * *
28792 TTT-TATTATTTTTTATAT
1 TTTATATAATTATTTAAAT
* *
28810 TATA-ATTA-TATTTAAAAT
1 TTTATATAATTATTT-AAAT
28828 TTTATATAATTATTTAAAT
1 TTTATATAATTATTTAAAT
28847 TTTAGTATA
1 TTTA-TATA
28856 TTAATAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.08
18 17 0.33
19 15 0.29
20 15 0.29
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTATATAATTATTTAAAT
Found at i:28858 original size:19 final size:20
Alignment explanation
Indices: 28818--28855 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28808 ATTATAATTA
28818 TATTTAAAATTTTATATAAT
1 TATTTAAAATTTTATATAAT
28838 TATTT-AAATTTTAGTATA
1 TATTTAAAATTTTA-TATA
28856 TTAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTTAAAATTTTATATAAT
Found at i:29988 original size:3 final size:3
Alignment explanation
Indices: 29973--30009 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
29963 ATATATTTAT
*
29973 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30010 ATAAATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:30797 original size:14 final size:14
Alignment explanation
Indices: 30751--30800 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
30741 TCAAGAATTT
30751 TTTATTAAATTTTA
1 TTTATTAAATTTTA
* *
30765 TATATTTAATTTT-
1 TTTATTAAATTTTA
*
30778 TATTATAAAATTTTA
1 T-TTATTAAATTTTA
30793 TTTATTAA
1 TTTATTAA
30801 GTATTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTAAATTTTA
Done.