Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1868
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: 49153
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3787 original size:42 final size:42
Alignment explanation
Indices: 3732--3850 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
3722 TTCTTCTCTC
* *
3732 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
3774 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCTTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
3816 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
3851 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:3792 original size:24 final size:24
Alignment explanation
Indices: 3756--3841 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
3746 CCTCCTCTCT
* *
3756 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
3780 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
*
3801 CTATC-T--CTCTTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
3822 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
3842 TCTTTCTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 3 0.06
20 5 0.11
21 14 0.30
22 5 0.11
24 20 0.43
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:6095 original size:88 final size:88
Alignment explanation
Indices: 6002--6168 Score: 253
Period size: 88 Copynumber: 1.9 Consensus size: 88
5992 AAAATGATGG
* * * *
6002 ATGCATGTGGAATGATGCAAATACTATTGTCATCTAAAATGCAGATACAGGTGAAACGATGCAAA
1 ATGCATATGGAATAATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAA
*
6067 TGTAAACATCAATAAAAAGGCAA
66 TGCAAACATCAATAAAAAGGCAA
* * *
6090 ATGCATATGGAATAATGCAAATACTAATGTTATCTAAAATGTAGATGCAGGTGAAACGACGCAAA
1 ATGCATATGGAATAATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAA
*
6155 TGCAAGCATCAATA
66 TGCAAACATCAATA
6169 GGAAGACAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (88 bp):
ATGCATATGGAATAATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAA
TGCAAACATCAATAAAAAGGCAA
Found at i:6184 original size:88 final size:88
Alignment explanation
Indices: 5976--6184 Score: 247
Period size: 88 Copynumber: 2.4 Consensus size: 88
5966 GAAATGATGT
* * *** * * * *
5976 AAATGCAAGCATCAATAAAATGATGGATGCATGTGGAATGATGCAAATACTATTGTCATCTAAAA
1 AAATGCAAACATCAATAAAAAGACAAAAGCATATGGAATAATGCAAATACTAATGTCATCTAAAA
*
6041 TGCAGATACAGGTGAAACGATGC
66 TGCAGATACAGGTGAAACGACGC
* * * *
6064 AAATGTAAACATCAATAAAAAGGCAAATGCATATGGAATAATGCAAATACTAATGTTATCTAAAA
1 AAATGCAAACATCAATAAAAAGACAAAAGCATATGGAATAATGCAAATACTAATGTCATCTAAAA
* *
6129 TGTAGATGCAGGTGAAACGACGC
66 TGCAGATACAGGTGAAACGACGC
* **
6152 AAATGCAAGCATCAATAGGAAGACAAAAGCATA
1 AAATGCAAACATCAATAAAAAGACAAAAGCATA
6185 CAAAAAGATG
Statistics
Matches: 101, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
88 101 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (88 bp):
AAATGCAAACATCAATAAAAAGACAAAAGCATATGGAATAATGCAAATACTAATGTCATCTAAAA
TGCAGATACAGGTGAAACGACGC
Found at i:6196 original size:88 final size:89
Alignment explanation
Indices: 6015--6207 Score: 237
Period size: 88 Copynumber: 2.2 Consensus size: 89
6005 CATGTGGAAT
* * *
6015 GATGCAAATACTATTGTCATCTAAAATGCAGATACAGGTGAAACGATGCAAATGTAAACATCAAT
1 GATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAATGCAAACATCAAT
* * ** *
6080 AAAAAGGCAAATGCATATGGAATA
66 AAAAAGACAAAAGCATATCAAAAA
* * * *
6104 -ATGCAAATACTAATGTTATCTAAAATGTAGATGCAGGTGAAACGACGCAAATGCAAGCATCAAT
1 GATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAATGCAAACATCAAT
**
6168 AGGAAGACAAAAGCATA-CAAAAA
66 AAAAAGACAAAAGCATATCAAAAA
*
6191 GATGCAAATACTGATGT
1 GATGCAAATACTAATGT
6208 GGTCTAATTC
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 3 0.03
88 85 0.97
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (89 bp):
GATGCAAATACTAATGTCATCTAAAATGCAGATACAGGTGAAACGACGCAAATGCAAACATCAAT
AAAAAGACAAAAGCATATCAAAAA
Found at i:9474 original size:8 final size:8
Alignment explanation
Indices: 9458--9493 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
9448 AACGAAATAC
9458 AAAAAAAT
1 AAAAAAAT
*
9466 AATAAAAT
1 AAAAAAAT
*
9474 AAAATAAT
1 AAAAAAAT
9482 AAAAAAAT
1 AAAAAAAT
9490 AAAA
1 AAAA
9494 GATAGGGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:9477 original size:13 final size:13
Alignment explanation
Indices: 9461--9485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9451 GAAATACAAA
9461 AAAATAATAAAAT
1 AAAATAATAAAAT
9474 AAAATAATAAAA
1 AAAATAATAAAA
9486 AAATAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:9929 original size:20 final size:20
Alignment explanation
Indices: 9904--9958 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
9894 TTTTACCTAG
* *
9904 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTATGA
*
9924 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATGA
9944 ATGTATCGATACATT
1 ATGTATCGATACATT
9959 CTACTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTATGA
Found at i:20142 original size:154 final size:149
Alignment explanation
Indices: 19763--20213 Score: 419
Period size: 150 Copynumber: 3.0 Consensus size: 149
19753 ATAAAAATAA
* * * * * * * ** *
19763 GATGAACCTATCCTACATGCTCACCTTTGGCACAAAAAC-AGACCTGGCGATAACTTAGGAA-TT
1 GATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGA-ACCTGGCGACAACCTAAAAAGTG
* * * *
19826 AGTTTTGAAAAATTACTAAAATGCCCTTAGAGGATACCTTTGACGTAGAAGTACATGATACCCCT
65 A-TTTTGAAAAATTACTAAAATACCCTTA-AGGATACCTTTGACGTAAAAGTACCTGATACCCTT
* *
19891 AAAGGACTTAAAAAGGATAAAG
128 AAGGGACTTAAAAAGCATAAAG
* * *
19913 GATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGAACCTGGCGACAACCTAAAAATTGG
1 GATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCTGGCGACAACCTAAAAAGTGA
* * *
19978 TTTTGAAAAATTACTCAAATACCCTT-AGGATCCACCTTTGACGTAAAAGTACCTAACACCCTTA
66 TTTTGAAAAATTACTAAAATACCCTTAAGGAT--ACCTTTGACGTAAAAGTACCTGATACCCTTA
20042 AGGGACTTAAAAAGATCATAAAAGG
129 AGGGACTTAAAAAG--CAT-AAA-G
* * * * * ** ** *
20067 GATGAACCTATCCTAAATATCTACCTTTGGCATAAAAGTGGA-CTCGGTGATGACCTAGGAGGTG
1 GATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCT-GGCGACAACCTAAAAAGTG
* * * *
20131 ATTTT-AGAAAATTACAAAAATACCTTTAAGGGATACCTTTGACATAAAAGTACCCGATACCCTT
65 ATTTTGA-AAAATTACTAAAATACCCTTAA-GGATACCTTTGACGTAAAAGTACCTGATACCCTT
*
20195 AAGGGATTTAAAAA-CATAA
128 AAGGGACTTAAAAAGCATAA
20214 GGGAATGTAT
Statistics
Matches: 249, Mismatches: 40, Indels: 24
0.80 0.13 0.08
Matches are distributed among these distances:
148 5 0.02
150 116 0.47
151 5 0.02
152 2 0.01
153 6 0.02
154 110 0.44
155 1 0.00
156 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (149 bp):
GATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCTGGCGACAACCTAAAAAGTGA
TTTTGAAAAATTACTAAAATACCCTTAAGGATACCTTTGACGTAAAAGTACCTGATACCCTTAAG
GGACTTAAAAAGCATAAAG
Found at i:22540 original size:167 final size:167
Alignment explanation
Indices: 22309--22841 Score: 665
Period size: 168 Copynumber: 3.2 Consensus size: 167
22299 AAAAAATAAG
* * * ** * *
22309 AAATAAATTGAATTTTACAAAACTGATTAAATGGGAATTAAATAACAATATTAGATAAATTTTAA
1 AAATGAATTAAATTTT-CAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAA
* * * * * * * *
22374 AATTTTTAAATC-AAGAAAAATCCCCCTCAAAATATTTACGGAGTAGAAAACTCGATTTTTTAGG
65 AAATTTTAGACCAAAG-AAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGG
* * * * ** *
22438 AAAATAGTCAATTCAAGGAAAAAAATAAAAAACTCAAGA
129 AAAAAAGTGATTTCAAAGAAAAAAATCCAAAACTCATGA
* * * *
22477 AAATGAATTAAATTTTCAAAACTAATTTAATGGGAATTCCATGATATTATTAAATACATTTTAAA
1 AAATGAATTAAATTTTCAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
* *
22542 AATTTTAGACCAAAGAAAATTCTCCTAAAAATATTTATGGAATAGGAAACTCGATTTTTTGGGAA
66 AATTTTAGACCAAAGAAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGGAA
*
22607 AAAAATGATTTCAAAGAAGAAAAATCCAAAACTCATGA
131 AAAAGTGATTTCAAAGAA-AAAAATCCAAAACTCATGA
* * * *
22645 ATATGAGTTAAATTTTTAAAACCGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
1 AAATGAATTAAATTTTCAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
* * * *
22710 AATTTTAGACCAAAGAAAATCCTCCTGAAAATATTTATTGAATAGAAAACTTGATTTTTCGGGAA
66 AATTTTAGACCAAAGAAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGGAA
** *
22775 AAGGGAGATTTCAAAG-AAAAAATCCAAAACTCATGA
131 AAAAGTGATTTCAAAGAAAAAAATCCAAAACTCATGA
22811 AAATGAATTAAATTTTCAAAACTGATTTAAT
1 AAATGAATTAAATTTTCAAAACTGATTTAAT
22842 ATGATTTAAA
Statistics
Matches: 312, Mismatches: 51, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
166 46 0.15
167 105 0.34
168 161 0.52
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.31
Consensus pattern (167 bp):
AAATGAATTAAATTTTCAAAACTGATTTAATGGGAATTCCATAATATTATTAGATAAATTTTAAA
AATTTTAGACCAAAGAAAATCCTCCTAAAAATATTTATGGAATAGAAAACTCGATTTTTTGGGAA
AAAAGTGATTTCAAAGAAAAAAATCCAAAACTCATGA
Found at i:24454 original size:81 final size:80
Alignment explanation
Indices: 24313--24473 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 80
24303 GTCCAAAGTA
*
24313 AGTCACAACCAATAGGGCCCTTTATTACAAATGATTAAATTAACTCAAGTCCTAATTCAATCCAT
1 AGTCACAACCAACAGGGCCCTTTATTACAAATGATTAAATTAACTCAAGTCCTAATTCAATCCAT
24378 TGGAGCCCATATCTT
66 TGGAGCCCATATCTT
24393 AGTCACAACCAACAGGGCCCTTTATTACAAAGTGATTAAATTAACTCAAGTCCTAATTCAATCCA
1 AGTCACAACCAACAGGGCCCTTTATTACAAA-TGATTAAATTAACTCAAGTCCTAATTCAATCCA
24458 TTGGAGCCCATATCTT
65 TTGGAGCCCATATCTT
24474 CTGAATATAT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 30 0.38
81 49 0.62
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (80 bp):
AGTCACAACCAACAGGGCCCTTTATTACAAATGATTAAATTAACTCAAGTCCTAATTCAATCCAT
TGGAGCCCATATCTT
Found at i:25667 original size:34 final size:33
Alignment explanation
Indices: 25589--25853 Score: 200
Period size: 34 Copynumber: 7.7 Consensus size: 33
25579 AAATCTTCTT
*
25589 AAGTCCACGCAAGTCGATGGCAACCAAACCTTTTCCA
1 AAGTCCACACAAGTCG-TGGC-A-CAAACCTTTT-CA
25626 AAGTCCACACAAGTTCGTGGCACAAA-CTTTCTCA
1 AAGTCCACACAAG-TCGTGGCACAAACCTTT-TCA
25660 AAGTCCACACAAGTCGGTGGCAACTAAACCTTTTCCA
1 AAGTCCACACAAGTC-GTGGC-AC-AAACCTTTT-CA
* * * * *
25697 AAGTCTACATAA--CCTGGCAGC-ATCCTTTCCA
1 AAGTCCACACAAGTCGTGGCA-CAAACCTTTTCA
* * * *
25728 AAGTCTACATAACTCGATGGCACAAACCTTTTTA
1 AAGTCCACACAAGTCG-TGGCACAAACCTTTTCA
* *
25762 AAGTCCACATAAGTCGATGGCAAAAACCTTTTCA
1 AAGTCCACACAAGTCG-TGGCACAAACCTTTTCA
*
25796 AAGTCCACACAAGTCGGTGGCAACCAAACCCTTTTAA
1 AAGTCCACACAAGTC-GTGGC-A-CAAA-CCTTTTCA
*
25833 AAG-CC-CATAAGTCGGTGGCAC
1 AAGTCCACACAAGTC-GTGGCAC
25854 CCAAAGCCCA
Statistics
Matches: 194, Mismatches: 18, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
31 14 0.07
32 6 0.03
33 6 0.03
34 90 0.46
35 23 0.12
36 10 0.05
37 42 0.22
38 3 0.02
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (33 bp):
AAGTCCACACAAGTCGTGGCACAAACCTTTTCA
Found at i:25921 original size:30 final size:29
Alignment explanation
Indices: 25828--25924 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 29
25818 ACCAAACCCT
* *
25828 TTTAAAAGCCCATAAGTCGGTGGCACC-C
1 TTTAAAAGCCCACAAGTCAGTGGCACCAC
* *
25856 ----AAAGCCCATAAGTCAGTGGCACCCC
1 TTTAAAAGCCCACAAGTCAGTGGCACCAC
* *
25881 TTTCAAAGCCCACAAGTCAGTGGCACCAT
1 TTTAAAAGCCCACAAGTCAGTGGCACCAC
25910 TTTAAAAAGCCCACA
1 TTT-AAAAGCCCACA
25925 CAAGCTGGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 22 0.38
25 1 0.02
29 25 0.43
30 10 0.17
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (29 bp):
TTTAAAAGCCCACAAGTCAGTGGCACCAC
Found at i:26351 original size:18 final size:21
Alignment explanation
Indices: 26306--26359 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 21
26296 TATAACAAAT
*
26306 CAATGTATCGATACATAAGTG
1 CAATGTATCGATACATAAGTA
26327 C-ATGTATCGATAC-T-AG-A
1 CAATGTATCGATACATAAGTA
*
26344 CAATGTATCAATACAT
1 CAATGTATCGATACAT
26360 TACTCATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.45
19 2 0.07
20 12 0.41
21 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
CAATGTATCGATACATAAGTA
Found at i:27572 original size:28 final size:28
Alignment explanation
Indices: 27519--27572 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
27509 CTTGATTCCT
*
27519 TTTCCTTTGCAATTTCTTGCTTATTTTG
1 TTTCCTTTGCAATTTCTTGATTATTTTG
27547 TTTCCTTT-CATATTTCTT-ATTGATTT
1 TTTCCTTTGCA-ATTTCTTGATT-ATTT
27573 CACTTCCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (28 bp):
TTTCCTTTGCAATTTCTTGATTATTTTG
Found at i:36311 original size:42 final size:42
Alignment explanation
Indices: 36256--36374 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
36246 TTCTTCTCTC
* *
36256 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
36298 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
36340 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
36375 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:36315 original size:12 final size:11
Alignment explanation
Indices: 36289--36364 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
36279 TCTATTATCT
*
36289 CTCCTGTCTCTC
1 CTCCTATCTC-C
36301 CTCCTATCATCC
1 CTCCTATC-TCC
36313 CTCCTATCT--
1 CTCCTATCTCC
*
36322 CTACTATCT--
1 CTCCTATCTCC
*
36331 CTCCTGTCTCTC
1 CTCCTATCTC-C
36343 CTCCTATCATCC
1 CTCCTATC-TCC
*
36355 CTCCTCTCTC
1 CTCCTATCTC
36365 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:36316 original size:24 final size:24
Alignment explanation
Indices: 36280--36365 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
36270 CCTCCTCTCT
* *
36280 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
36304 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
36325 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
36346 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
36366 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:36340 original size:18 final size:18
Alignment explanation
Indices: 36271--36341 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
36261 CCTGTCATCC
* *
36271 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
36289 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
36311 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
36331 CTCCTGTCTCT
1 CTCCTGTCTCT
36342 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:42594 original size:12 final size:12
Alignment explanation
Indices: 42577--42601 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42567 TATTTTTGGA
42577 ATATTAAGTCGG
1 ATATTAAGTCGG
42589 ATATTAAGTCGG
1 ATATTAAGTCGG
42601 A
1 A
42602 CCCCTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
ATATTAAGTCGG
Found at i:49046 original size:42 final size:41
Alignment explanation
Indices: 48968--49082 Score: 158
Period size: 42 Copynumber: 2.8 Consensus size: 41
48958 TCTCTACTCC
* *
48968 TCCTGTCATCCCTTCCTCTCTCTATTATCTCTCTGTCTCTCA
1 TCCTATCATCCC-TCCTCTCTCTACTATCTCTCTGTCTCTCA
* *
49010 TCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCTCTCC
1 TCCTATCATCCCTCCTCTCTCTACTATCTCT-CTGTCTCTCA
* *
49052 TCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 TCCTATCATCCCTCCTCTCTCTACTATCTCT
49083 TTGAGGGCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 17 0.26
42 48 0.74
ACGTcount: A:0.10, C:0.43, G:0.03, T:0.44
Consensus pattern (41 bp):
TCCTATCATCCCTCCTCTCTCTACTATCTCTCTGTCTCTCA
Done.