Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2014
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: 30159
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:8608 original size:41 final size:41
Alignment explanation
Indices: 8563--8642 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
8553 TTCTAATTGA
* * *
8563 AAGCATTTTCA-AGTGATTTGTAGAAAAATGTTTCCAACTAG
1 AAGCATTTTCAGCGT-ATTGGTAGAAAAATGCTTCCAACTAG
8604 AAGCATTTTCAGCGTATTGGTAGAAAAATGCTTCCAACT
1 AAGCATTTTCAGCGTATTGGTAGAAAAATGCTTCCAACT
8643 GAAAACACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (41 bp):
AAGCATTTTCAGCGTATTGGTAGAAAAATGCTTCCAACTAG
Found at i:8906 original size:3 final size:3
Alignment explanation
Indices: 8898--8928 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8888 TTGGTTCCTT
8898 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8929 ACCATTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9061 original size:15 final size:14
Alignment explanation
Indices: 9026--9065 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
9016 AAATGATCTA
* *
9026 AACTATAATTTCAT
1 AACTATTATATCAT
9040 AACTATTATATCAT
1 AACTATTATATCAT
9054 ATACTATTATAT
1 A-ACTATTATAT
9066 TTGTTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (14 bp):
AACTATTATATCAT
Found at i:11517 original size:3 final size:3
Alignment explanation
Indices: 11509--11536 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11499 GCTATAGTGT
11509 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11537 CTCTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12013 original size:18 final size:18
Alignment explanation
Indices: 11990--12025 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11980 CCAAGAAAAT
*
11990 AAAATACAACCGGCCCAA
1 AAAATACAAACGGCCCAA
12008 AAAATACAAACGGCCCAA
1 AAAATACAAACGGCCCAA
12026 TTTTTAGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.31, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAATACAAACGGCCCAA
Found at i:13315 original size:24 final size:24
Alignment explanation
Indices: 13270--13333 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
13260 TATATATATA
13270 ATATTATTTATTTTAAAATTTTTT
1 ATATTATTTATTTTAAAATTTTTT
**
13294 ATATTCATTTATTTTAAGTTTTCTTGT
1 ATATT-ATTTATTTTAAAATTT-TT-T
*
13321 ATATTGTTTATTT
1 ATATTATTTATTT
13334 GAACCTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.15
25 14 0.41
26 9 0.26
27 6 0.18
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.66
Consensus pattern (24 bp):
ATATTATTTATTTTAAAATTTTTT
Found at i:13408 original size:2 final size:2
Alignment explanation
Indices: 13401--13439 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
13391 TAGATTGTTG
13401 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13440 TTTGTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13892 original size:108 final size:109
Alignment explanation
Indices: 13745--14012 Score: 457
Period size: 108 Copynumber: 2.5 Consensus size: 109
13735 AAAAGTTTTA
*
13745 AATTAAGGCAATATTTCGCGTTTGGAAAATTTGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 AATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
13810 TTCTCGTT-GACCAAATGGCCAAATACCCTTTCAAACTTTCAAT
66 TTCTCGTTCGACCAAATGGCCAAATACCCTTTCAAACTTTCAAT
*
13853 AATTAAGGTAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 AATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
13918 TTCTCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAAT
66 TTCTCGTTCGACCAAATGGCCAAATACCCTTTCAAACTTTCAAT
* ** *
13962 AATAAAGGCAATATTTCGTATTTAGAAAATTCGAGAAAATCGTGCCCTAAC
1 AATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAA-CGTGCCCTAAC
14013 TTATTGAGCT
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
108 71 0.47
109 68 0.45
110 11 0.07
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (109 bp):
AATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAATGGCCAAATACCCTTTCAAACTTTCAAT
Found at i:13991 original size:109 final size:108
Alignment explanation
Indices: 13749--14012 Score: 447
Period size: 109 Copynumber: 2.4 Consensus size: 108
13739 GTTTTAAATT
*
13749 AAGGCAATATTTCGCGTTTGGAAAATTTGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
1 AAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
*
13814 CGTTGACCAAATGGCCAAATACCCTTTCAAACTTTCAATAATT
66 CGTTGACCAAATGGCCAAATACCCTTTCAAACTTTCAATAATA
*
13857 AAGGTAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
1 AAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
*
13922 CGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAATAATA
66 CGTT-GACCAAATGGCCAAATACCCTTTCAAACTTTCAATAATA
** *
13966 AAGGCAATATTTCGTATTTAGAAAATTCGAGAAAATCGTGCCCTAAC
1 AAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAA-CGTGCCCTAAC
14013 TTATTGAGCT
Statistics
Matches: 146, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
108 67 0.46
109 68 0.47
110 11 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (108 bp):
AAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
CGTTGACCAAATGGCCAAATACCCTTTCAAACTTTCAATAATA
Found at i:19084 original size:7 final size:8
Alignment explanation
Indices: 19062--19087 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
19052 AAAAAAAGAG
19062 AGCAAAAA
1 AGCAAAAA
19070 AGCAAAAA
1 AGCAAAAA
19078 AGCAAAAA
1 AGCAAAAA
19086 AG
1 AG
19088 AAGCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (8 bp):
AGCAAAAA
Found at i:19093 original size:11 final size:10
Alignment explanation
Indices: 19065--19130 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
19055 AAAAGAGAGC
19065 AAAAAAGC--
1 AAAAAAGCAA
19073 AAAAAAGCAA
1 AAAAAAGCAA
19083 AAAAGAAGCAAA
1 AAAA-AAGC-AA
*
19095 AAAAATGAGAAA
1 AAAAA--AGCAA
19107 ATAAAAAGCAA
1 A-AAAAAGCAA
*
19118 AAAAAACCAA
1 AAAAAAGCAA
19128 AAA
1 AAA
19131 TAAAAGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
8 8 0.17
10 15 0.31
11 10 0.21
12 9 0.19
13 6 0.12
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAAGCAA
Found at i:19130 original size:23 final size:24
Alignment explanation
Indices: 19088--19135 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
19078 AGCAAAAAAG
**
19088 AAGCAAAAAAAATGAGAAAATAAA
1 AAGCAAAAAAAACCAGAAAATAAA
19112 AAGCAAAAAAAACCA-AAAATAAA
1 AAGCAAAAAAAACCAGAAAATAAA
19135 A
1 A
19136 GAAAAGACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.06
Consensus pattern (24 bp):
AAGCAAAAAAAACCAGAAAATAAA
Found at i:19530 original size:23 final size:26
Alignment explanation
Indices: 19496--19557 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 26
19486 ACTTCACTTG
*
19496 AAAAAAATGAAAAG-AAAAA-GAGA-
1 AAAAAAAAGAAAAGAAAAAAGGAGAT
19519 AAAAAAAAGAAAAGAAAAAAGGAGAT
1 AAAAAAAAGAAAAGAAAAAAGGAGAT
*
19545 GAAAAAAAGAAAA
1 AAAAAAAAGAAAA
19558 AGGAGAGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 13 0.38
24 5 0.15
25 4 0.12
26 12 0.35
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAAAAAAGAAAAGAAAAAAGGAGAT
Found at i:20691 original size:46 final size:46
Alignment explanation
Indices: 20634--20838 Score: 154
Period size: 46 Copynumber: 4.5 Consensus size: 46
20624 AGAGCTGGTT
* *
20634 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATC
1 GAAGATGGCAGATCTTGCCTCCCTGTATTTGGCAGCGAAGTAGATC
* * * * * * * *
20680 GAAGATGGCAGATTTTACCTCCCTG-A-CT-ACAGTGGAGTACATT
1 GAAGATGGCAGATCTTGCCTCCCTGTATTTGGCAGCGAAGTAGATC
** * * *
20723 GAAGCCGACA-ACTCTAT--CTCCCTGTATTTGGCAGTGGAA-TAGATT
1 GAAGATGGCAGA-TCT-TGCCTCCCTGTATTTGGCAG-CGAAGTAGATC
* *
20768 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGTAGATC
1 GAAGATGGCAGATCTTGCCTCCCTGTATTTGGCAGCGAAGTAGATC
* * *
20814 AAAGATGGCAGATTTTACCTCCCTG
1 GAAGATGGCAGATCTTGCCTCCCTG
20839 ACTATAGGGA
Statistics
Matches: 118, Mismatches: 31, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
42 8 0.07
43 20 0.17
44 4 0.03
45 21 0.18
46 65 0.55
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (46 bp):
GAAGATGGCAGATCTTGCCTCCCTGTATTTGGCAGCGAAGTAGATC
Found at i:20994 original size:84 final size:83
Alignment explanation
Indices: 20903--23916 Score: 2084
Period size: 84 Copynumber: 35.9 Consensus size: 83
20893 AGAGTGAAGA
20903 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
20968 GTAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
20987 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21052 ATAGTGGAGCAGACAAAAG
66 GTAGTGGAGCAGAC-AAAG
* *
21071 AAACGAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGTA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21136 ATAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
21155 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21220 ATAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
* * * *
21239 ACACCGGATCTCATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
21304 GTAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
* * *
21323 AAATCAGATCTTATCTCCCTAAGTAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
21388 -TAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
* * *
21406 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTATCTCCCAAAACA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21471 ATAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
21490 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21555 ATAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
* * *
21574 ACACCAGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21639 ATAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
* * * *
21658 ACACCAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGATCACATGAAGTCTTATCTCCCAAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
21723 GTAGTGGAGCAGACAAAAG
66 GTAGTGGAGCAGAC-AAAG
* * *
21742 AAACCAGATCTTATCTCCCTAAGTAGTAGTGAAGCATATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
* * *
21807 ATATTGGAGTAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
*
21826 AAACCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21891 ATAGTGGAGCAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
* * * *
21910 ACACCAGATCTCATCTCCCTAAGCAGTAGTGAAGCAGATCACATGAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
*
21975 GTAGTGGAACAGACGAAAG
66 GTAGTGGAGCAGAC-AAAG
*
21994 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAAGCA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
22059 GTAGTGGAGCAGATC--A-
66 GTAGTGGAGCAGA-CAAAG
* * * * * * *
22075 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CAAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
22138 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * *
22159 CATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
22222 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * *
22243 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGACACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACA-TCA--AG-TCTTATCTCCCT
* *
22306 AAGCAGTAGTAGAGCAGATCACATG
61 AAGCAGTAGTGGAGCAGA-CA-AAG
* * *
22331 --A--AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
*
22390 AAGCAGTAGTGGAGCATATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
22411 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
22474 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * * *
22495 CATCAAG-T-TTATCTCCCTCAGCAAG-AGTGAAGCAGA-CGAAAGAAACCAAATCTTATCTCCC
1 AAACCAGATCTTATCTCCCTAAGC-AGTAGTGGAGCAGATC-----ACATCAAGTCTTATCTCCC
* *
22556 GAAGCAGTAGTGGAGCAGA-ACA-
60 TAAGCAGTAGTGGAGCAGACAAAG
* * * * * *
22578 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGACACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACA-TCA--AG-TCTTATCTCCCT
22641 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
22662 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGACACCAGATCTCATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACA-TCA--AG-TCTTATCTCCCT
22725 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * ** * * *
22746 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGAAAAAGAAACCAGATCTTATCTCCCTAA
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG-ATCA-CATCAAG-TCTTATCTCCCTAA
* *
22810 GTAGTAGTGGAGCAGATCACATG
63 GCAGTAGTGGAGCAGA-CA-AAG
* * * *
22833 --A--AG-TCTTATCTCCCTAAGCAGTAGTAGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
22892 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
22913 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGACACCAGATCTCATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACA-TCA--AG-TCTTATCTCCCT
* *
22976 AAGCAGTAGTAGAGCAGATCACATG
61 AAGCAGTAGTGGAGCAGA-CA-AAG
* * * *
23001 --A--AG-TCTTATCTTCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
*
23060 AAGCAGTAGTGGAGCATATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * * *
23081 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGTAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
23144 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
23165 CATCAAG-TTTTATCTCCCTAAGCAAG-AGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCC
1 AAACCAGATCTTATCTCCCTAAGC-AGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCC
*
23227 TATGCAGTAGTGGAGCAGATC--A-
60 TAAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
23249 CATCAAG-TCTTATCTCCCTAAGCAATAGT-AAGCAGA-CGAAAGACACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACA-TCA--AG-TCTTATCTCCCT
23311 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * * * *
23332 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGTAGA-CGAAAGACAGCAGATGTCATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACA-TCA--AG-TCTTATCTCCCT
*
23395 AAGCAGTAGTGGCGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
23416 CATCAAG-TCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
*
23479 AAGCAGTAGTGGAGCATATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
23500 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
23563 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * * *
23584 CATCAAG-TCTTATCTCCCTAAGAAATAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
*
23647 AAGTAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * *
23668 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGACACCAAATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-----ACATCAAGTCTTATCTCCCT
23731 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * * *
23752 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCTT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
23815 AAGCAGTAGTGGAGCAGATC--A-
61 AAGCAGTAGTGGAGCAGA-CAAAG
* * * * * * *
23836 CATCAAG-TCTTATCTCCCTAAGCAATAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCT
1 AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCT
23899 AAGCAGTAGTGGAGCAGA
61 AAGCAGTAGTGGAGCAGA
23917 TTACATCAAG
Statistics
Matches: 2667, Mismatches: 188, Indels: 150
0.89 0.06 0.05
Matches are distributed among these distances:
79 1 0.00
80 34 0.01
81 13 0.00
82 11 0.00
83 282 0.11
84 2296 0.86
85 11 0.00
86 13 0.00
87 6 0.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (83 bp):
AAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCA
GTAGTGGAGCAGACAAAG
Found at i:22659 original size:503 final size:504
Alignment explanation
Indices: 22042--23938 Score: 3316
Period size: 503 Copynumber: 3.8 Consensus size: 504
22032 TCACATCAAG
22042 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22107 GCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
66 GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
*
22172 CTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
131 CTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
*
22237 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGACACCAGATCTTATCT
196 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCT
* * *
22302 CCCTAAGCAGTAGTAGAGCAGATCACATGAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGA
261 CCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGA
*
22367 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAA
326 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
22432 GCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACA
391 GCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACA
* * *
22497 TCAAGT-TTATCTCCCTCAGCAAGAGTGAAGCAGACGAAAGAAACCAAA
456 TCAAGTCTTATCTCCCTAAGCAAGAGTGGAGCAGACGAAAGAAACCAGA
* *
22545 TCTTATCTCCCGAAGCAGTAGTGGAGCAGAACACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22610 GCAGACGAAAGACACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
66 GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
* *
22675 CTCCCTAAGCAATAGTGGAGCAGACGAAAGACACCAGATCTCATCTCCCTAAGCAGTAGTGGAGC
131 CTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
*
22740 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGA-AAAAGAAACCAGATCTTATCT
196 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCT
* * * *
22804 CCCTAAGTAGTAGTGGAGCAGATCACATGAAGTCTTATCTCCCTAAGCAGTAGTAGAGCAGACGA
261 CCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGA
22869 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
326 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
* * *
22934 GCAATAGTGGAGCAGACGAAAGACACCAGATCTCATCTCCCTAAGCAGTAGTAGAGCAGATCACA
391 GCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACA
* *
22999 TGAAGTCTTATCTTCCTAAGC-AGTAGTGGAGCAGACGAAAGAAACCAGA
456 TCAAGTCTTATCTCCCTAAGCAAG-AGTGGAGCAGACGAAAGAAACCAGA
*
23048 TCTTATCTCCCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
* *
23113 GTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTAT
66 GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
* *
23178 CTCCCTAAGCAAGAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTATGCAGTAGTGGAGC
131 CTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
23243 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGT-AAGCAGACGAAAGACACCAGATCTTATCT
196 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCT
*
23307 CCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGTAGACGA
261 CCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGA
* * * * *
23372 AAGACAGCAGATGTCATCTCCCTAAGCAGTAGTGGCGCAGATCACATCAAGTCTTATCTCCCTAA
326 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
* * *
23437 GTAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCACA
391 GCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACA
*
23502 TCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGA
456 TCAAGTCTTATCTCCCTAAGCAAGAGTGGAGCAGACGAAAGAAACCAGA
*
23551 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGAAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
23616 GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACATCAAGTCTTAT
66 GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
* *
23681 CTCCCTAAGCAATAGTGGAGCAGACGAAAGACACCAAATCTTATCTCCCTAAGCAGTAGTGGAGC
131 CTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
23746 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCT
196 AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCT
*
23811 CCTTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGA
261 CCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGA
* *
23876 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTACATCAAGTCTTGTCTCCCT
326 AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCT
23939 GAAGTTACAG
Statistics
Matches: 1316, Mismatches: 73, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
502 220 0.17
503 949 0.72
504 147 0.11
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (504 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTAT
CTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
AGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCT
CCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGAGCAGACGA
AAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAA
GCAATAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACA
TCAAGTCTTATCTCCCTAAGCAAGAGTGGAGCAGACGAAAGAAACCAGA
Found at i:23917 original size:84 final size:84
Alignment explanation
Indices: 22042--23938 Score: 3323
Period size: 84 Copynumber: 22.6 Consensus size: 84
22032 TCACATCAAG
22042 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22107 GCAGACAAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
22126 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
22191 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
22210 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22275 GCAGACGAAAGACACCAGA
66 GCAGACGAAAGAAACCAGA
* * *
22294 TCTTATCTCCCTAAGCAGTAGTAGAGCAGATCACATGAAGTCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
22359 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
22378 TCTTATCTCCCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
22443 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
* * *
22462 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGT-TTATCTCCCTCAGCAAGAGTGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22526 GCAGACGAAAGAAACCAAA
66 GCAGACGAAAGAAACCAGA
* *
22545 TCTTATCTCCCGAAGCAGTAGTGGAGCAGAACACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22610 GCAGACGAAAGACACCAGA
66 GCAGACGAAAGAAACCAGA
22629 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22694 GCAGACGAAAGACACCAGA
66 GCAGACGAAAGAAACCAGA
*
22713 TCTCATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22778 GCAGA-AAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
* * * *
22796 TCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACATGAAGTCTTATCTCCCTAAGCAGTAGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
22861 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
22880 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
22945 GCAGACGAAAGACACCAGA
66 GCAGACGAAAGAAACCAGA
* * * * *
22964 TCTCATCTCCCTAAGCAGTAGTAGAGCAGATCACATGAAGTCTTATCTTCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23029 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
23048 TCTTATCTCCCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
23113 GTAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
* *
23132 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTATCTCCCTAAGCAAGAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23197 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
* *
23216 TCTTATCTCCCTATGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGT-AA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
*
23280 GCAGACGAAAGACACCAGA
66 GCAGACGAAAGAAACCAGA
23299 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
* * *
23364 GTAGACGAAAGACAGCAGA
66 GCAGACGAAAGAAACCAGA
* * * * *
23383 TGTCATCTCCCTAAGCAGTAGTGGCGCAGATCACATCAAGTCTTATCTCCCTAAGTAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23448 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
23467 TCTTATCTCCCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23532 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
23551 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGAAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23616 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
23635 TCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
* *
23700 GCAGACGAAAGACACCAAA
66 GCAGACGAAAGAAACCAGA
23719 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23784 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
*
23803 TCTTATCTCCTTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
23868 GCAGACGAAAGAAACCAGA
66 GCAGACGAAAGAAACCAGA
* *
23887 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTACATCAAGTCTTGTCTCCCT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCT
23939 GAAGTTACAG
Statistics
Matches: 1717, Mismatches: 93, Indels: 6
0.95 0.05 0.00
Matches are distributed among these distances:
83 233 0.14
84 1484 0.86
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (84 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAATAGTGGA
GCAGACGAAAGAAACCAGA
Found at i:24256 original size:19 final size:19
Alignment explanation
Indices: 24232--24268 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24222 CCAAGGAAAT
*
24232 AAAATACAATCGGCCCAAA
1 AAAATACAAACGGCCCAAA
24251 AAAATACAAACGGCCCAA
1 AAAATACAAACGGCCCAA
24269 TTTTTAGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.27, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAATACAAACGGCCCAAA
Found at i:25556 original size:24 final size:24
Alignment explanation
Indices: 25511--25574 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
25501 TATATATATA
25511 ATATTATTTATTTTAAAATTTTTT
1 ATATTATTTATTTTAAAATTTTTT
**
25535 ATATTCATTTATTTTAAGTTTTCTTGT
1 ATATT-ATTTATTTTAAAATTT-TT-T
*
25562 ATATTGTTTATTT
1 ATATTATTTATTT
25575 GAACCTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.15
25 14 0.41
26 9 0.26
27 6 0.18
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.66
Consensus pattern (24 bp):
ATATTATTTATTTTAAAATTTTTT
Found at i:25649 original size:2 final size:2
Alignment explanation
Indices: 25642--25674 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
25632 TAGATTGTTG
*
25642 TA TA TA TA TT 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
25675 TATTTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:26177 original size:109 final size:109
Alignment explanation
Indices: 25983--26250 Score: 448
Period size: 109 Copynumber: 2.5 Consensus size: 109
25973 AAAAGTTTTA
*
25983 AATTAAGGCAATATTTCACGTTTGGAAAATTTGAGAAAACGTG-CCTAACGTGCTGGGTTTCGAT
1 AATTAAGGCAATATTTCACGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
26047 TTCTCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAAT
66 TTCTCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAAT
*
26091 AATTAAGGTAATATTTCACGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 AATTAAGGCAATATTTCACGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
26156 TTCTCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAAT
66 TTCTCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAAT
* *** * *
26200 AATAAAGGCAATATTTCGTATTTAGAAAATTCGAGAAAATAGTGCCCTAAC
1 AATTAAGGCAATATTTCACGTTTGGAAAATTCGAGAAAA-CGTGCCCTAAC
26251 TTATTGAGCT
Statistics
Matches: 149, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
108 41 0.28
109 98 0.66
110 10 0.07
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (109 bp):
AATTAAGGCAATATTTCACGTTTGGAAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAATGGCCAAATACCCTTTTAAACTTTCAAT
Found at i:27741 original size:25 final size:25
Alignment explanation
Indices: 27713--27910 Score: 110
Period size: 25 Copynumber: 8.0 Consensus size: 25
27703 ATACACCGCA
*
27713 GCTCTTATGAGCGTCCCGATATATG
1 GCTCTTATGAGCTTCCCGATATATG
*
27738 GCTCTCCA-GAGCTTCCC-ATTATATG
1 GCTCT-TATGAGCTTCCCGA-TATATG
* * ** *
27763 GTTATTGCGAGCTTCTC-AT-TATG
1 GCTCTTATGAGCTTCCCGATATATG
* *
27786 GCTCTTATGAGCTTCTCGATA-ATTA
1 GCTCTTATGAGCTTCCCGATATA-TG
*
27811 GCTTTTCA-GAGCTTCCCGATA-ACTG
1 GCTCTT-ATGAGCTTCCCGATATA-TG
* *
27836 GCTCTTATGAGCTTCTCGTTATATG
1 GCTCTTATGAGCTTCCCGATATATG
* *
27861 GCTC-GATAGAGCTTCCCG-TTTATG
1 GCTCTTAT-GAGCTTCCCGATATATG
* *
27885 TGCTCGTATGAGCATTCCTGA-ATATG
1 -GCTCTTATGAGC-TTCCCGATATATG
27911 AATTGACGAA
Statistics
Matches: 134, Mismatches: 25, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
23 17 0.13
24 13 0.10
25 90 0.67
26 14 0.10
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATATATG
Found at i:27750 original size:105 final size:105
Alignment explanation
Indices: 27565--27753 Score: 263
Period size: 105 Copynumber: 1.8 Consensus size: 105
27555 GATACAGGGT
* * *
27565 TCCCGATTGGCTGTGATCCTGCATGTGTTGCAGACACACCATAACTCTTACGAGCGTCCCTATAT
1 TCCCGATTGGCTGTGATCCTACATGTGTTGCAGACACACCACAACTCTTACGAGCGTCCCGATAT
*
27630 TTGGCTCTCACGAGCTTCCTGTTACTAGCTCTTTGGAGCA
66 ATGGCTCTCACGAGCTTCCTGTTACTAGCTCTTTGGAGCA
* ** * * * *
27670 TCCCGATTGGTTGTGATCCTACATGTGTTGTGGATACACCGCAGCTCTTATGAGCGTCCCGATAT
1 TCCCGATTGGCTGTGATCCTACATGTGTTGCAGACACACCACAACTCTTACGAGCGTCCCGATAT
27735 ATGGCTCTC-CAGAGCTTCC
66 ATGGCTCTCAC-GAGCTTCC
27754 CATTATATGG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 1 0.01
105 71 0.99
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (105 bp):
TCCCGATTGGCTGTGATCCTACATGTGTTGCAGACACACCACAACTCTTACGAGCGTCCCGATAT
ATGGCTCTCACGAGCTTCCTGTTACTAGCTCTTTGGAGCA
Found at i:27872 original size:50 final size:50
Alignment explanation
Indices: 27784--27878 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
27774 CTTCTCATTA
**
27784 TGGCTCTTATGAGCTTCTCGATAATTAGCTTTTCAGAGCTTCCCGATAAC
1 TGGCTCTTATGAGCTTCTCGATAATTAGCTGATCAGAGCTTCCCGATAAC
* *
27834 TGGCTCTTATGAGCTTCTCG-TTATATGGCTCGAT-AGAGCTTCCCG
1 TGGCTCTTATGAGCTTCTCGATAAT-TAGCT-GATCAGAGCTTCCCG
27879 TTTATGTGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 3 0.08
50 35 0.90
51 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (50 bp):
TGGCTCTTATGAGCTTCTCGATAATTAGCTGATCAGAGCTTCCCGATAAC
Done.