Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009880.1 Corchorus capsularis cultivar CVL-1 contig09901, whole genome shotgun sequence
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: 169613
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1363 original size:23 final size:23
Alignment explanation
Indices: 1333--1382 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1323 AGCCATCTTA
1333 GCTT-TATCCTTCTTACCACCAC
1 GCTTGTATCCTTCTTACCACCAC
1355 GCTTGTATCCTTCTTACCACCAC
1 GCTTGTATCCTTCTTACCACCAC
1378 GCTTG
1 GCTTG
1383 CCCCTATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.16, C:0.38, G:0.10, T:0.36
Consensus pattern (23 bp):
GCTTGTATCCTTCTTACCACCAC
Found at i:6928 original size:221 final size:221
Alignment explanation
Indices: 6319--7375 Score: 1447
Period size: 221 Copynumber: 4.8 Consensus size: 221
6309 AAAAATCTAC
* * * * *
6319 TATTAGATGGCACTAAATTCATATGGATGGGGTTTATTTAATTAATTAGGATGAAAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGAATG-AAAATATGGAT
* * *
6384 TAAAGTACTTTTCAAAGCCAATTTTGGATATATGAG-AAAAATGTCAATCTCTAAAGAATTTGGG
65 TAAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGG
* **
6448 GAT-GTAGCATATGATTATTTGGGGATGATGAGAAACGATTTGGGTATAAAGTATATCAAATTGG
130 GATGGT-GCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGG
* *
6512 GGATAGTAAATTTTGCATTTTGTTTAAT
194 GGATACTGAATTTTGCATTTTGTTTAAT
* ** * * *
6540 TATTAGATGGCACTGAAATCATATAGACGGGGTTTATTCAATTTGTCACAATATAAAAATATGGA
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTA-GA-ATGAAAATATGGA
*
6605 TTAAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTAG
64 TTAAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGG
* * ** * * *
6670 GGATAGTGCATATCATTATTTGGGGATGACCAGAAATGATTTAGGTATAAAGTATATTACTTTGG
129 GGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGG
6735 GGATACTGAATTTTGCATTTTGTTTAAT
194 GGATACTGAATTTTGCATTTTGTTTAAT
6763 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGAATGAAAATATGGATT
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGAATGAAAATATGGATT
*
6828 AAAGCACTTTTTAAAGTCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGGG
66 AAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGGG
*
6893 ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGAG
131 ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
6958 ATACTGAATTTTGCATTTTGTTTGAA-
196 ATACTGAATTTTGCATTTTGTTT-AAT
* *
6984 TATTAGATGGCACTAAAATCATATAGACGAGGTTTATTCAATTAATTA-AATG--GA-AT--A--
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGAATGAAAATATGGATT
* * * *
7041 AAA-CACTTTTCAAAGTCAAGTTTGGGTATATGAG---AAATGTCAATTTCTAAAGAATTTGGGG
66 AAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGGG
7102 ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
131 ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
7167 ATACTGAATTTTGCATTTTGTTTAAT
196 ATACTGAATTTTGCATTTTGTTTAAT
** *** * *
7193 TATTAGATAACACTAAAATCATATAGATATGGTTTATAT-GATTAATTAGGATGAAAAATATGGA
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTAT-TCAATTAATTAGAATG-AAAATATGGA
* * *
7257 TTAAAGCACTTTTTAAAGCCAATTTTGGGTTTAT-A-AAAAATTGTTAA--TC-AAAGCAAAATT
64 TTAAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAG---AATT
* *
7317 TGGGGATGGTGCTTATGATTATTT-GGGATGATGAGAAATTATTTGGGTATAAAGTATAT
126 TGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATAT
7376 AGCTTTGCAG
Statistics
Matches: 750, Mismatches: 63, Indels: 48
0.87 0.07 0.06
Matches are distributed among these distances:
208 2 0.00
209 153 0.20
210 4 0.01
212 29 0.04
213 4 0.01
214 2 0.00
215 1 0.00
216 1 0.00
217 6 0.01
218 7 0.01
219 58 0.08
220 38 0.05
221 244 0.33
222 47 0.06
223 152 0.20
224 2 0.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (221 bp):
TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGAATGAAAATATGGATT
AAAGCACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGGG
ATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGG
ATACTGAATTTTGCATTTTGTTTAAT
Found at i:10201 original size:39 final size:39
Alignment explanation
Indices: 10158--10304 Score: 190
Period size: 39 Copynumber: 3.8 Consensus size: 39
10148 TTCTCTCCCC
* * *
10158 AAAGTCCCCAAACACATATAACACAGGGGCAACTCT-CT
1 AAAGTCCCCAAACACATATAACACAGAGGCATCTATACT
*
10196 CAAAGTCCTCAAACACATATAACACAGAGGCATCTATACT
1 -AAAGTCCCCAAACACATATAACACAGAGGCATCTATACT
* * * *
10236 AAAGTCCTCAAAAAAATATAACACAGAGCCATCTATACT
1 AAAGTCCCCAAACACATATAACACAGAGGCATCTATACT
*
10275 AAAGTCCCTAAACACATATAACACA-AGGCA
1 AAAGTCCCCAAACACATATAACACAGAGGCA
10305 ATTTTCTTCT
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 4 0.04
39 89 0.94
40 2 0.02
ACGTcount: A:0.45, C:0.27, G:0.10, T:0.18
Consensus pattern (39 bp):
AAAGTCCCCAAACACATATAACACAGAGGCATCTATACT
Found at i:11357 original size:477 final size:477
Alignment explanation
Indices: 10463--11426 Score: 1883
Period size: 477 Copynumber: 2.0 Consensus size: 477
10453 AAGACGTTGA
*
10463 GGCCTTGTCAACTAATCACACAAACAAAGGCATGAAGACAAAAGGCACAAAACTCAATTCCCTGT
1 GGCCTTGTTAACTAATCACACAAACAAAGGCATGAAGACAAAAGGCACAAAACTCAATTCCCTGT
10528 TGCAGCATGTCGGACTTCCTACTGAGGAAAGCATCTAAGGGAAGGATTATACTTAAATTCAAATT
66 TGCAGCATGTCGGACTTCCTACTGAGGAAAGCATCTAAGGGAAGGATTATACTTAAATTCAAATT
10593 CCTTCATATTTAACCATTTATGGCAGGGATTAAGTGCTAATTAATCTTCATTGCAGGTCTAAGGG
131 CCTTCATATTTAACCATTTATGGCAGGGATTAAGTGCTAATTAATCTTCATTGCAGGTCTAAGGG
10658 CTACTGTGGACCAACCCACAGCGGGAAACTCATTGGGAGATGTGGCTTGGAAGGAAAAAGAGGAA
196 CTACTGTGGACCAACCCACAGCGGGAAACTCATTGGGAGATGTGGCTTGGAAGGAAAAAGAGGAA
10723 GGAAACTCCTCCGATTACCCTCATTGAAGGGAACAACTATGCTTGGAAGTTGTTCCTTAACACAA
261 GGAAACTCCTCCGATTACCCTCATTGAAGGGAACAACTATGCTTGGAAGTTGTTCCTTAACACAA
10788 ATGGGGTAATCAGTGGCCTGCAGAGGGTGGAATAAAAAACAAAGCCTATTTTGACTTTGGGAGGA
326 ATGGGGTAATCAGTGGCCTGCAGAGGGTGGAATAAAAAACAAAGCCTATTTTGACTTTGGGAGGA
10853 ACCTCAACAAACTCCAATTGAAGAGTAGTTATCGACGACGCGACACATGAACACAAGAGCAGGGG
391 ACCTCAACAAACTCCAATTGAAGAGTAGTTATCGACGACGCGACACATGAACACAAGAGCAGGGG
10918 ACTAATTTCAAGACTAAAAGAG
456 ACTAATTTCAAGACTAAAAGAG
*
10940 GGCCTTGTTAACTAATCACACAAACAAAGGCATGAAGACAAAAGGCACAAAACTCAATTCTCTGT
1 GGCCTTGTTAACTAATCACACAAACAAAGGCATGAAGACAAAAGGCACAAAACTCAATTCCCTGT
11005 TGCAGCATGTCGGACTTCCTACTGAGGAAAGCATCTAAGGGAAGGATTATACTTAAATTCAAATT
66 TGCAGCATGTCGGACTTCCTACTGAGGAAAGCATCTAAGGGAAGGATTATACTTAAATTCAAATT
11070 CCTTCATATTTAACCATTTATGGCAGGGATTAAGTGCTAATTAATCTTCATTGCAGGTCTAAGGG
131 CCTTCATATTTAACCATTTATGGCAGGGATTAAGTGCTAATTAATCTTCATTGCAGGTCTAAGGG
11135 CTACTGTGGACCAACCCACAGCGGGAAACTCATTGGGAGATGTGGCTTGGAAGGAAAAAGAGGAA
196 CTACTGTGGACCAACCCACAGCGGGAAACTCATTGGGAGATGTGGCTTGGAAGGAAAAAGAGGAA
*
11200 GGAAACTCCTCCGATTACCCTCCTTGAAGGGAACAACTATGCTTGGAAGTTGTTCCTTAACACAA
261 GGAAACTCCTCCGATTACCCTCATTGAAGGGAACAACTATGCTTGGAAGTTGTTCCTTAACACAA
* *
11265 ATGGGGTAATCAGTGGGCTGCAGAGGGTGGAATAAAAAACAAAGCCTTTTTTGACTTTGGGAGGA
326 ATGGGGTAATCAGTGGCCTGCAGAGGGTGGAATAAAAAACAAAGCCTATTTTGACTTTGGGAGGA
11330 ACCTCAACAAACTCCAATTGAAGAGTAGTTATCGACGACGCGACACATGAACACAAGAGCAGGGG
391 ACCTCAACAAACTCCAATTGAAGAGTAGTTATCGACGACGCGACACATGAACACAAGAGCAGGGG
11395 ACTAATTTCAAGACTAAAAGAG
456 ACTAATTTCAAGACTAAAAGAG
11417 GGCCTTGTTA
1 GGCCTTGTTA
11427 GCTTCCTCAA
Statistics
Matches: 482, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
477 482 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (477 bp):
GGCCTTGTTAACTAATCACACAAACAAAGGCATGAAGACAAAAGGCACAAAACTCAATTCCCTGT
TGCAGCATGTCGGACTTCCTACTGAGGAAAGCATCTAAGGGAAGGATTATACTTAAATTCAAATT
CCTTCATATTTAACCATTTATGGCAGGGATTAAGTGCTAATTAATCTTCATTGCAGGTCTAAGGG
CTACTGTGGACCAACCCACAGCGGGAAACTCATTGGGAGATGTGGCTTGGAAGGAAAAAGAGGAA
GGAAACTCCTCCGATTACCCTCATTGAAGGGAACAACTATGCTTGGAAGTTGTTCCTTAACACAA
ATGGGGTAATCAGTGGCCTGCAGAGGGTGGAATAAAAAACAAAGCCTATTTTGACTTTGGGAGGA
ACCTCAACAAACTCCAATTGAAGAGTAGTTATCGACGACGCGACACATGAACACAAGAGCAGGGG
ACTAATTTCAAGACTAAAAGAG
Found at i:13148 original size:101 final size:102
Alignment explanation
Indices: 12973--13173 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 102
12963 TTACTGGAAA
12973 TTTGTATCCACAACATGCTGCTAGAATTTCGAGCTGTCATAGAGAACTTGGGCATAAATTAGTTC
1 TTTGTATCCACAACATGCTGCTAGAATTTCGAGCTGTCATAGAGAACTTGGGCATAAATTAGTTC
13038 ACAAGACTCCTT-AATGCGGCGAGAAGGACAGGCCCG
66 ACAAGACTCCTTAAATGCGGCGAGAAGGACAGGCCCG
*
13074 TTTGTATCCACAACATGCTGCTAGAATTTCGAGCTGTCTTAGAGAACTTGGGCATAAATTAGTTC
1 TTTGTATCCACAACATGCTGCTAGAATTTCGAGCTGTCATAGAGAACTTGGGCATAAATTAGTTC
13139 ACAAGACTCCTTAAATGCGGCGAGAAGGACAGGCC
66 ACAAGACTCCTTAAATGCGGCGAGAAGGACAGGCC
13174 AGTCAGTCGA
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 76 0.78
102 22 0.22
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (102 bp):
TTTGTATCCACAACATGCTGCTAGAATTTCGAGCTGTCATAGAGAACTTGGGCATAAATTAGTTC
ACAAGACTCCTTAAATGCGGCGAGAAGGACAGGCCCG
Found at i:15026 original size:72 final size:71
Alignment explanation
Indices: 14935--15273 Score: 384
Period size: 71 Copynumber: 4.9 Consensus size: 71
14925 CCCATGGTCC
14935 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAG-CCTTTCGCACAATCCTTA
1 TCTTCCT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCC-TTCGCACAATCCTTA
*
14999 CATAATCA
64 CATGATCA
* * *
15007 TCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATATGGCAGTCCTTCGCACAA-CCTT-T
1 TCTTCC-TATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
15070 ATGCGATTA
65 AT--GATCA
* * * *
15079 TCTTCTTCATTGCGATTGT---------A-TTCCCACATTAGGTAGTCCTTCGCACAATCCTTCC
1 TCTTCCT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
15134 ATGATAA
65 ATGATCA
* *
15141 TCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGG-AGTCCTTCGCACAATCCTTAT
1 TCTTCC-TATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
15205 ATGATTA
65 ATGATCA
15212 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTT
1 TCTTCCT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
15274 GCTACTACTT
Statistics
Matches: 228, Mismatches: 19, Indels: 41
0.79 0.07 0.14
Matches are distributed among these distances:
62 44 0.19
63 6 0.03
64 2 0.01
70 7 0.03
71 85 0.37
72 81 0.36
73 3 0.01
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (71 bp):
TCTTCCTATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
TGATCA
Found at i:15153 original size:62 final size:61
Alignment explanation
Indices: 15037--15160 Score: 137
Period size: 62 Copynumber: 2.0 Consensus size: 61
15027 GCCGAGGCAG
* * *
15037 TTCCCACATATGGCAGTCCTTCGCACAACCTTTATGCGATTATCTTCTTCATTGCGATTGTA
1 TTCCCACATATGGCAGTCCTTCGCACAACCTTCAT-CGATAATCTTCATCATTGCGATTGTA
* *
15099 TTCCCACAT-TAGGTAGTCCTTCGCACAATCCTTCCAT-GATAATCTTCCAT-ATTGCGGTTGTA
1 TTCCCACATAT-GGCAGTCCTTCGCACAA-CCTT-CATCGATAATCTT-CATCATTGCGATTGTA
15161 GCCGAGGCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
61 1 0.02
62 44 0.83
63 6 0.11
64 2 0.04
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (61 bp):
TTCCCACATATGGCAGTCCTTCGCACAACCTTCATCGATAATCTTCATCATTGCGATTGTA
Found at i:15589 original size:38 final size:38
Alignment explanation
Indices: 15547--15666 Score: 104
Period size: 38 Copynumber: 3.2 Consensus size: 38
15537 CTCTTTACAT
15547 CCAATTTGGCTCACACATACTAGAGCCATCTTACACAC
1 CCAATTTGGCTCACACATACTAGAGCCATCTTACACAC
** * * * * * *
15585 CCAA-TTAACATCAAGACCAGACCT-CA-CCCTCTT-TACAT
1 CCAATTTGGC-TC-ACA-CATA-CTAGAGCCATCTTACACAC
15623 CCAATTTGGCTCACACATACTAGAGCCATCTTACACAC
1 CCAATTTGGCTCACACATACTAGAGCCATCTTACACAC
15661 CCAATT
1 CCAATT
15667 GACATCAAGA
Statistics
Matches: 58, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
35 2 0.03
36 4 0.07
37 11 0.19
38 24 0.41
39 11 0.19
40 4 0.07
41 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.08, T:0.24
Consensus pattern (38 bp):
CCAATTTGGCTCACACATACTAGAGCCATCTTACACAC
Found at i:15663 original size:76 final size:76
Alignment explanation
Indices: 15537--15685 Score: 289
Period size: 76 Copynumber: 2.0 Consensus size: 76
15527 CCTCGCACAG
15537 CTCTTTACATCCAATTTGGCTCACACATACTAGAGCCATCTTACACACCCAATTAACATCAAGAC
1 CTCTTTACATCCAATTTGGCTCACACATACTAGAGCCATCTTACACACCCAATTAACATCAAGAC
15602 CAGACCTCACC
66 CAGACCTCACC
*
15613 CTCTTTACATCCAATTTGGCTCACACATACTAGAGCCATCTTACACACCCAATTGACATCAAGAC
1 CTCTTTACATCCAATTTGGCTCACACATACTAGAGCCATCTTACACACCCAATTAACATCAAGAC
15678 CAGACCTC
66 CAGACCTC
15686 GCCCATCTCG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.32, C:0.35, G:0.09, T:0.24
Consensus pattern (76 bp):
CTCTTTACATCCAATTTGGCTCACACATACTAGAGCCATCTTACACACCCAATTAACATCAAGAC
CAGACCTCACC
Found at i:15693 original size:40 final size:40
Alignment explanation
Indices: 15572--15693 Score: 103
Period size: 38 Copynumber: 3.1 Consensus size: 40
15562 CATACTAGAG
* *
15572 CCATCTTACACACCCAATTAACATCAAGACCAGACCTCAC
1 CCATCTTACACACCCAATTGACATCAAGACCAGACCTCGC
* * * * * * *
15612 CC-TCTT-TACATCCAATTTGGC-TC-ACA-CATA-CTAGAG
1 CCATCTTACACACCCAA-TTGACATCAAGACCAGACCTCG-C
15648 CCATCTTACACACCCAATTGACATCAAGACCAGACCTCGC
1 CCATCTTACACACCCAATTGACATCAAGACCAGACCTCGC
15688 CCATCT
1 CCATCT
15694 CGGTCCCCTG
Statistics
Matches: 58, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
35 2 0.03
36 5 0.09
37 10 0.17
38 18 0.31
39 9 0.16
40 11 0.19
41 3 0.05
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.22
Consensus pattern (40 bp):
CCATCTTACACACCCAATTGACATCAAGACCAGACCTCGC
Found at i:16026 original size:16 final size:16
Alignment explanation
Indices: 16005--16035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15995 AACGGAAGGT
*
16005 TACCGTAGTAGAATGG
1 TACCGTAGCAGAATGG
16021 TACCGTAGCAGAATG
1 TACCGTAGCAGAATG
16036 TCGCCGCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (16 bp):
TACCGTAGCAGAATGG
Found at i:18407 original size:23 final size:23
Alignment explanation
Indices: 18376--18422 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18366 CAACCGGCCA
*
18376 CAACTGGCCATCGCATGGGGCAT
1 CAACCGGCCATCGCATGGGGCAT
18399 CAACCGGCCATCGCATGGGGCAT
1 CAACCGGCCATCGCATGGGGCAT
18422 C
1 C
18423 CGCGCACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.34, G:0.30, T:0.15
Consensus pattern (23 bp):
CAACCGGCCATCGCATGGGGCAT
Found at i:19481 original size:9 final size:9
Alignment explanation
Indices: 19469--19495 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19459 GAAAAATATC
19469 AAAAAAAAT
1 AAAAAAAAT
19478 AAAAAAAAT
1 AAAAAAAAT
19487 AAAAAAAAT
1 AAAAAAAAT
19496 TTTCGACCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:25447 original size:21 final size:23
Alignment explanation
Indices: 25423--25469 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
25413 CAATAGGTTC
25423 ATGAC-AAATTT-AAAGAGCCTA
1 ATGACAAAATTTCAAAGAGCCTA
25444 ATGACAAAAATTTCAAAGAGCCTA
1 ATGAC-AAAATTTCAAAGAGCCTA
25468 AT
1 AT
25470 ATTTTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
23 6 0.26
24 12 0.52
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (23 bp):
ATGACAAAATTTCAAAGAGCCTA
Found at i:25734 original size:6 final size:6
Alignment explanation
Indices: 25702--25731 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
25692 TCCAAATAGA
*
25702 ACAAAT ACAAAT ACAAAT ACAAAT GCAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
25732 GCATGCAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.63, C:0.17, G:0.03, T:0.17
Consensus pattern (6 bp):
ACAAAT
Found at i:26787 original size:2 final size:2
Alignment explanation
Indices: 26780--26841 Score: 65
Period size: 2 Copynumber: 31.0 Consensus size: 2
26770 ACCGACCTAT
* * *
26780 TA TA TA TA -A TA TA TA TA TA TA TA TA AA TCA TA TT TC TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA
26822 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
26842 AATTATAACC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:37457 original size:27 final size:27
Alignment explanation
Indices: 37427--37494 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
37417 GTCAGACTCT
*
37427 CATTCCAAGTTAGTCA-AGACAG-TTCTC
1 CATTCAAAGTTAGTCAGA-ACAGTTTC-C
*
37454 CATTCAAAGCTAGTCAGAACAGTTTCC
1 CATTCAAAGTTAGTCAGAACAGTTTCC
*
37481 CAGTCAAAGTTAGT
1 CATTCAAAGTTAGT
37495 TCCCTAGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (27 bp):
CATTCAAAGTTAGTCAGAACAGTTTCC
Found at i:41391 original size:12 final size:12
Alignment explanation
Indices: 41374--41405 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41364 GCCGCGCAAC
41374 ACCGGCCACATG
1 ACCGGCCACATG
*
41386 ACCGGCCACTTG
1 ACCGGCCACATG
41398 ACCGGCCA
1 ACCGGCCA
41406 TCGCATGCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.09
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:41479 original size:33 final size:33
Alignment explanation
Indices: 41429--41493 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
41419 CGCATGGAGC
41429 AACCGGCCACAACCGGCCATCACATGGGGCATG
1 AACCGGCCACAACCGGCCATCACATGGGGCATG
* *
41462 AACCGGCCA-ACCGCGGCCATCGCATGGGGCAT
1 AACCGGCCACAAC-CGGCCATCACATGGGGCAT
41494 CCGCGCACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.25, C:0.37, G:0.29, T:0.09
Consensus pattern (33 bp):
AACCGGCCACAACCGGCCATCACATGGGGCATG
Found at i:44523 original size:10 final size:10
Alignment explanation
Indices: 44508--44532 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44498 GTTCCTGCTC
44508 AATTCCAGAA
1 AATTCCAGAA
44518 AATTCCAGAA
1 AATTCCAGAA
44528 AATTC
1 AATTC
44533 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:45475 original size:6 final size:6
Alignment explanation
Indices: 45464--45496 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
45454 ATTAATTTGC
45464 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
45497 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:45854 original size:37 final size:36
Alignment explanation
Indices: 45783--45861 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
45773 AATTAGTTTT
45783 GTTTTTCCGTTTTTCAAAAAAAAAAAAAGTTTTTCC
1 GTTTTTCCGTTTTTCAAAAAAAAAAAAAGTTTTTCC
* * *
45819 TTTTTTCCGATTTTTC-TAAAAAAAAAAATTATTTTCC
1 GTTTTTCCG-TTTTTCAAAAAAAAAAAAAGT-TTTTCC
45856 GTTTTT
1 GTTTTT
45862 AAAATTAGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 20 0.54
37 17 0.46
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (36 bp):
GTTTTTCCGTTTTTCAAAAAAAAAAAAAGTTTTTCC
Found at i:60437 original size:712 final size:712
Alignment explanation
Indices: 59074--60481 Score: 2636
Period size: 712 Copynumber: 2.0 Consensus size: 712
59064 CCTTTTTTTT
59074 TTTGACACCATGACATGTTTTGACTTTTGATATACTAAGTATCTATATCCATTGCCCAATAATTA
1 TTTGACACCATGACATGTTTTGACTTTTGATATACTAAGTATCTATATCCATTGCCCAATAATTA
* *
59139 AAAGTGTAGGGATGGGTGATGAATGTTGAAATGGTTGCAAAACCCATCGAAGTTGGTTGAGTTGC
66 AAAGTGTACGGATGGGTGATGAATGTTGAAATGGTTGCAAAACCCATCGAAATTGGTTGAGTTGC
*
59204 TAAGGTTTTGGAATTTTGTTTGAAAGATTCGGAGTTCGAGTCTTGTCAATGGTACTCATTAGTGG
131 TAAGGTTTTGGAATTTTGTTTGAAAGATTCGAAGTTCGAGTCTTGTCAATGGTACTCATTAGTGG
59269 CTGATTTGTAAGTACCACTGTCAACCCTTCCTGAAACTGTGACATGCTTGATCTTGGACTAAGTC
196 CTGATTTGTAAGTACCACTGTCAACCCTTCCTGAAACTGTGACATGCTTGATCTTGGACTAAGTC
*
59334 AGCATTTAAAACTTTTTTTTATAAAAATAATCAAGATGGAAAATTAAAGAATTAATAAGAAAAGA
261 AGCATTTAAAACTTTTTCTTATAAAAATAATCAAGATGGAAAATTAAAGAATTAATAAGAAAAGA
* **
59399 TAAAATTGCGTTTTTAGCTTGGGTGTGTATAGCCAAAAGTTAAATGTTGGGATACAAGTGGTTAA
326 TAAAATTACGTTTTTAGCTTGGGTGTGTATAGCCAAAAGTTAAACATTGGGATACAAGTGGTTAA
* *
59464 AGTTTTGGAGTTCTTGTGAAAGGTCTTGAGTTCGAATTATGAGATGAATGGGACGTGATTATGGG
391 AGTTTTGGAGTTCTTGTGAAAGGTCTTGAGTTCGAATCATGAGATGAATGGAACGTGATTATGGG
*
59529 AGATAGGATGTTAGAATTTGACCATAATTATTTGGCGCAATATCAAATCTGTCAATTACATAATT
456 AGATAGGATGTTAGAATTTGACCATAATTATTTGGCCCAATATCAAATCTGTCAATTACATAATT
59594 TGAGTAATTATACGATTGACCAACATTAATGTGGGTTAAATCAAATCTACCTAATTATGTTAATT
521 TGAGTAATTATACGATTGACCAACATTAATGTGGGTTAAATCAAATCTACCTAATTATGTTAATT
59659 GAGAGATATTTAAATACATTTAATAGTCAAATAAATCTCAACCGTTCAACTGGCTATTTGATGGA
586 GAGAGATATTTAAATACATTTAATAGTCAAATAAATCTCAACCGTTCAACTGGCTATTTGATGGA
59724 TGTACCAGATTCATATATATAAATTTGACCTCCCTCTACTCATTAGCCCGTTGTGAATTACG
651 TGTACCAGATTCATATATATAAATTTGACCTCCCTCTACTCATTAGCCCGTTGTGAATTACG
59786 TTTGACACCATGACATGTTTTGACTTTTGATATACTAAGTATCTATATCCATTGCCCAATAATTA
1 TTTGACACCATGACATGTTTTGACTTTTGATATACTAAGTATCTATATCCATTGCCCAATAATTA
** *
59851 AAAGTGTACGGATGGGTGATGAATGTTGAAATGGTTGCAAAGTCCATCGAAATTGGTTGAGTTTC
66 AAAGTGTACGGATGGGTGATGAATGTTGAAATGGTTGCAAAACCCATCGAAATTGGTTGAGTTGC
59916 TAAGGTTTTGGAATTTTGTTTGAAAGATTCGAAGTTCGAGTCTTGTCAATGGTACTCATTAGTGG
131 TAAGGTTTTGGAATTTTGTTTGAAAGATTCGAAGTTCGAGTCTTGTCAATGGTACTCATTAGTGG
* *
59981 CTGATTTGTAAGTACCACTGTCAACCCTTCCTGAGACTGTGGCATGCTTGATCTTGGACTAAGTC
196 CTGATTTGTAAGTACCACTGTCAACCCTTCCTGAAACTGTGACATGCTTGATCTTGGACTAAGTC
60046 AGCATTTAAAACTTTTTCTTATAAAAATAATCAAGATGGAAAATTAAAGAATTAATAAGAAAAGA
261 AGCATTTAAAACTTTTTCTTATAAAAATAATCAAGATGGAAAATTAAAGAATTAATAAGAAAAGA
*
60111 TAAAGTTACGTTTTTAGCTTGGGTGTGTATAGCCAAAAGTTAAACATTGGGATACAAGTGGTTAA
326 TAAAATTACGTTTTTAGCTTGGGTGTGTATAGCCAAAAGTTAAACATTGGGATACAAGTGGTTAA
*
60176 AGTTTTGGAGTTCTTGTGAAAGGTCTTGAGTTCGAATCATGAGATGAATGGAATGTGATTATGGG
391 AGTTTTGGAGTTCTTGTGAAAGGTCTTGAGTTCGAATCATGAGATGAATGGAACGTGATTATGGG
60241 AGATAGGATGTTAGAATTTGACCATAATTATTTGGCCCAATATCAAATCTGTCAATTACATAATT
456 AGATAGGATGTTAGAATTTGACCATAATTATTTGGCCCAATATCAAATCTGTCAATTACATAATT
*
60306 TGAGTAATTATACGATTGACCAACATTAATGTGGGTTAAATCAAATCTGCCTAATTATGTTAATT
521 TGAGTAATTATACGATTGACCAACATTAATGTGGGTTAAATCAAATCTACCTAATTATGTTAATT
*
60371 GAGAGATATTTAAATACATTTGATAGTCAAATAAATCTCAACCGTTCAACTGGCTATTTGATGGA
586 GAGAGATATTTAAATACATTTAATAGTCAAATAAATCTCAACCGTTCAACTGGCTATTTGATGGA
*
60436 TGTACCAGATTCATATATATAAATTTGTCCTCCCTCTACTCATTAG
651 TGTACCAGATTCATATATATAAATTTGACCTCCCTCTACTCATTAG
60482 GGTTTACGAC
Statistics
Matches: 676, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
712 676 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (712 bp):
TTTGACACCATGACATGTTTTGACTTTTGATATACTAAGTATCTATATCCATTGCCCAATAATTA
AAAGTGTACGGATGGGTGATGAATGTTGAAATGGTTGCAAAACCCATCGAAATTGGTTGAGTTGC
TAAGGTTTTGGAATTTTGTTTGAAAGATTCGAAGTTCGAGTCTTGTCAATGGTACTCATTAGTGG
CTGATTTGTAAGTACCACTGTCAACCCTTCCTGAAACTGTGACATGCTTGATCTTGGACTAAGTC
AGCATTTAAAACTTTTTCTTATAAAAATAATCAAGATGGAAAATTAAAGAATTAATAAGAAAAGA
TAAAATTACGTTTTTAGCTTGGGTGTGTATAGCCAAAAGTTAAACATTGGGATACAAGTGGTTAA
AGTTTTGGAGTTCTTGTGAAAGGTCTTGAGTTCGAATCATGAGATGAATGGAACGTGATTATGGG
AGATAGGATGTTAGAATTTGACCATAATTATTTGGCCCAATATCAAATCTGTCAATTACATAATT
TGAGTAATTATACGATTGACCAACATTAATGTGGGTTAAATCAAATCTACCTAATTATGTTAATT
GAGAGATATTTAAATACATTTAATAGTCAAATAAATCTCAACCGTTCAACTGGCTATTTGATGGA
TGTACCAGATTCATATATATAAATTTGACCTCCCTCTACTCATTAGCCCGTTGTGAATTACG
Found at i:61894 original size:15 final size:15
Alignment explanation
Indices: 61874--61905 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
61864 ATGTGTTGCG
61874 CAATATGCAAGAACA
1 CAATATGCAAGAACA
*
61889 CAATATGCAAGAGCA
1 CAATATGCAAGAACA
61904 CA
1 CA
61906 TTATTGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (15 bp):
CAATATGCAAGAACA
Found at i:66811 original size:25 final size:27
Alignment explanation
Indices: 66781--66831 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
66771 AAAAATAATT
*
66781 ATAAAGAAAAG-CAATTAAA-CTAAAA
1 ATAAAGAAAAGTAAATTAAATCTAAAA
*
66806 ATAAAGCAAAGTAAATTAAATCTAAA
1 ATAAAGAAAAGTAAATTAAATCTAAA
66832 CTATGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.20
Consensus pattern (27 bp):
ATAAAGAAAAGTAAATTAAATCTAAAA
Found at i:68047 original size:30 final size:30
Alignment explanation
Indices: 67991--68050 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
67981 AATTCTTGCC
* *
67991 TCTTGAAATAATTCTTCATTAGTCTTCAAT
1 TCTTGAAATAATTCTTCATAAATCTTCAAT
*
68021 TCTTGAAATTATT-TTCAATAAATCTTCAAT
1 TCTTGAAATAATTCTTC-ATAAATCTTCAAT
68051 CATGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (30 bp):
TCTTGAAATAATTCTTCATAAATCTTCAAT
Found at i:72036 original size:20 final size:20
Alignment explanation
Indices: 72011--72048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
72001 TAAATATATT
*
72011 AATTAATTTATATATTTACG
1 AATTAATATATATATTTACG
*
72031 AATTAATATATATTTTTA
1 AATTAATATATATATTTA
72049 ATAATAAAAA
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:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
AATTAATATATATATTTACG
Found at i:76045 original size:19 final size:20
Alignment explanation
Indices: 76021--76058 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
76011 CCAAGTAAGC
76021 TTTGAA-GTTTGATCTTTTG
1 TTTGAAGGTTTGATCTTTTG
76040 TTTGAAGGTTTGATCTTTT
1 TTTGAAGGTTTGATCTTTT
76059 ATCTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (20 bp):
TTTGAAGGTTTGATCTTTTG
Found at i:77950 original size:22 final size:21
Alignment explanation
Indices: 77922--77976 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
77912 TTTTTCAGTG
* *
77922 AAATAAAAAAT-AATAAATAT
1 AAATAAAAAATAAAGAAATAA
77942 AAATATAAAAATAAAGAAATAA
1 AAATA-AAAAATAAAGAAATAA
77964 AAAT-AAAAATAAA
1 AAATAAAAAATAAA
77977 TTATTTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.45
21 6 0.19
22 11 0.35
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATAAAAAATAAAGAAATAA
Found at i:77951 original size:20 final size:19
Alignment explanation
Indices: 77922--77975 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
77912 TTTTTCAGTG
*
77922 AAATAAAAAATAATAAATATA
1 AAAT-AAAAATAAGAAATA-A
77943 AATATAAAAATAAAGAAATAA
1 AA-ATAAAAAT-AAGAAATAA
77964 AAATAAAAATAA
1 AAATAAAAATAA
77976 ATTATTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 8 0.27
21 11 0.37
22 9 0.30
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAAAAATAAGAAATAA
Found at i:77953 original size:14 final size:13
Alignment explanation
Indices: 77922--77976 Score: 67
Period size: 14 Copynumber: 4.1 Consensus size: 13
77912 TTTTTCAGTG
77922 AAATAAAAAATAA
1 AAATAAAAAATAA
*
77935 TAAATATAAATATAA
1 -AAATA-AAAAATAA
77950 AAATAAAGAAATAA
1 AAATAAA-AAATAA
77964 AAAT-AAAAATAA
1 AAATAAAAAATAA
77976 A
1 A
77977 TTATTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 7 0.19
13 4 0.11
14 19 0.51
15 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:77967 original size:6 final size:6
Alignment explanation
Indices: 77922--77976 Score: 56
Period size: 7 Copynumber: 8.2 Consensus size: 6
77912 TTTTTCAGTG
77922 AAATAAA AAATAA TAAATATA AATATAA AAATAAA GAAATAA AAATAA
1 AAAT-AA AAATAA -AAATA-A AA-ATAA AAAT-AA -AAATAA AAATAA
77970 AAATAA A
1 AAATAA A
77977 TTATTTCTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
6 17 0.40
7 18 0.42
8 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:79082 original size:1 final size:1
Alignment explanation
Indices: 79076--79103 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
79066 GTGAAGAAGG
79076 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
79104 GCTCGAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:81675 original size:29 final size:29
Alignment explanation
Indices: 81632--81707 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 29
81622 ACCCACAAAC
*
81632 GTTATATCCCAAATTGAGTCA-TCCAAAAG
1 GTTATATCCTAAATTGAGT-ATTCCAAAAG
* * *
81661 GTTATATCCTTAATTGCGTATTTTCCCAAAG
1 GTTATATCCTAAATTGAGTA--TTCCAAAAG
*
81692 GTTATATCCTGAATTG
1 GTTATATCCTAAATTG
81708 CATATTTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 16 0.41
31 22 0.56
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (29 bp):
GTTATATCCTAAATTGAGTATTCCAAAAG
Found at i:88070 original size:12 final size:12
Alignment explanation
Indices: 88050--88081 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
88040 ACGACCTCAG
*
88050 CACCGAACTGGT
1 CACCAAACTGGT
88062 CACCAAACTGGT
1 CACCAAACTGGT
88074 CACCAAAC
1 CACCAAAC
88082 AAATCACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.38, G:0.16, T:0.12
Consensus pattern (12 bp):
CACCAAACTGGT
Found at i:93440 original size:2 final size:2
Alignment explanation
Indices: 93433--93468 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
93423 GAGACTTTTG
*
93433 AT AT AT AT AT AT AT AT AT AT AT CT 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
93469 GTACTGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103078 original size:16 final size:16
Alignment explanation
Indices: 103057--103091 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
103047 ACAATTCAGA
103057 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
103073 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
103089 AAG
1 AAG
103092 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:104839 original size:3 final size:3
Alignment explanation
Indices: 104831--104855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
104821 TAGCAAAATC
104831 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
104856 ACCATTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:105519 original size:17 final size:18
Alignment explanation
Indices: 105497--105530 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
105487 TTACGATATC
*
105497 AAAAAATTAA-TAAAATA
1 AAAAAAGTAATTAAAATA
105514 AAAAAAGTAATTAAAAT
1 AAAAAAGTAATTAAAAT
105531 TTGCAGCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAAAGTAATTAAAATA
Found at i:109476 original size:21 final size:21
Alignment explanation
Indices: 109451--109497 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
109441 TACAATTTAT
109451 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
109472 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
109493 ATTAT
1 ATTAT
109498 AAATTGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:109967 original size:16 final size:16
Alignment explanation
Indices: 109933--110078 Score: 165
Period size: 16 Copynumber: 9.2 Consensus size: 16
109923 AACCCGCCCA
*
109933 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
* *
109949 ACCTGGGACCCGAATG
1 ACCCGAGACCCGAATG
* *
109965 ACCCGAAACCTGAATG
1 ACCCGAGACCCGAATG
109981 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* *
109997 ACCCGAAACCCGTATG
1 ACCCGAGACCCGAATG
110013 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
110029 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
110045 ACCCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
110060 ACCCGTA-ACCCGAATG
1 ACCCG-AGACCCGAATG
110076 ACC
1 ACC
110079 GAAAATACTG
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
14 1 0.01
15 11 0.10
16 97 0.87
17 2 0.02
ACGTcount: A:0.32, C:0.37, G:0.23, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:116435 original size:22 final size:22
Alignment explanation
Indices: 116407--116480 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
116397 AAGGATCGCA
*
116407 TGGCCGGGTCATTTGGCCGGTG
1 TGGCCGGGTCATGTGGCCGGTG
** **
116429 TGGCCGGG-CATGTGCGATTGGCA
1 TGGCCGGGTCATGTG-G-CCGGTG
*
116452 TGGCCGGGTCATGTAGCCGGTG
1 TGGCCGGGTCATGTGGCCGGTG
116474 TGGCCGG
1 TGGCCGG
116481 TCAAGTGCTT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
21 5 0.13
22 18 0.46
23 11 0.28
24 5 0.13
ACGTcount: A:0.08, C:0.23, G:0.46, T:0.23
Consensus pattern (22 bp):
TGGCCGGGTCATGTGGCCGGTG
Found at i:120439 original size:22 final size:22
Alignment explanation
Indices: 120414--120483 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
120404 TGGACATGGT
120414 CGGGTCATGTGGCCGGTGTGGC
1 CGGGTCATGTGGCCGGTGTGGC
** *
120436 CGGG-CATGTGCGATTGGTATGGC
1 CGGGTCATGTG-G-CCGGTGTGGC
*
120459 CGGGTCATGTAGCCGGTGTGGC
1 CGGGTCATGTGGCCGGTGTGGC
120481 CGG
1 CGG
120484 TCAAGTGCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
21 6 0.16
22 15 0.39
23 12 0.32
24 5 0.13
ACGTcount: A:0.09, C:0.21, G:0.47, T:0.23
Consensus pattern (22 bp):
CGGGTCATGTGGCCGGTGTGGC
Found at i:135178 original size:18 final size:19
Alignment explanation
Indices: 135145--135180 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
135135 AATTTCTCCA
*
135145 ATCATCAATTATTCACTGC
1 ATCATCAATTACTCACTGC
135164 ATCAT-AATTACTCACTG
1 ATCATCAATTACTCACTG
135181 TGCTTGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (19 bp):
ATCATCAATTACTCACTGC
Found at i:136117 original size:15 final size:16
Alignment explanation
Indices: 136082--136135 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
136072 GACAGTTTTC
136082 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
136098 TCGGGTCA-TCTGGG-T
1 TCGGGTCATTC-GGGTT
*
136113 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
136129 TCGGGTC
1 TCGGGTC
136136 CGGGTCTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.06, C:0.19, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:136977 original size:16 final size:16
Alignment explanation
Indices: 136956--137057 Score: 98
Period size: 16 Copynumber: 6.4 Consensus size: 16
136946 GGTTAACTTC
*
136956 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
136972 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
*
136988 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
* *
137004 ACGGCTCATTCGGGTT
1 TCGGGTCATTCGGGTT
137020 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* * * *
137036 GCAGGTCATCCGGGTC
1 TCGGGTCATTCGGGTT
137052 TCGGGT
1 TCGGGT
137058 TGGGCGGGTT
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
15 2 0.03
16 64 0.96
17 1 0.01
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.31
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:136992 original size:32 final size:31
Alignment explanation
Indices: 136954--137057 Score: 109
Period size: 32 Copynumber: 3.3 Consensus size: 31
136944 CGGGTTAACT
* *
136954 TCTCGGGTTATTCGGGTTTCGGGTCATACGGG
1 TCTCGGGTCA-TCGGGTTACGGGTCATACGGG
* *
136986 TCTCGGGTCACTCGGGTTACGGCTCATTCGGG
1 TCTCGGGTCA-TCGGGTTACGGGTCATACGGG
* * * *
137018 TTTCGGGTCATCTGGGTTGCAGGTCATCCGGG
1 TCTCGGGTCATC-GGGTTACGGGTCATACGGG
137050 TCTCGGGT
1 TCTCGGGT
137058 TGGGCGGGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 2 0.03
32 58 0.97
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.32
Consensus pattern (31 bp):
TCTCGGGTCATCGGGTTACGGGTCATACGGG
Found at i:137122 original size:16 final size:15
Alignment explanation
Indices: 137097--137126 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
137087 GGTCAATTCA
137097 GGTTGGGCGGGTTCG
1 GGTTGGGCGGGTTCG
137112 GGTTCGGGCGGGTTC
1 GGTT-GGGCGGGTTC
137127 TCTGGTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.27
Consensus pattern (15 bp):
GGTTGGGCGGGTTCG
Found at i:146077 original size:20 final size:20
Alignment explanation
Indices: 146031--146083 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
146021 AAACCAGGTG
*
146031 GGGCGCCAAGCTTGCCGCAT
1 GGGCGCTAAGCTTGCCGCAT
146051 GGGCGCTAAGCTTGCCGCAT
1 GGGCGCTAAGCTTGCCGCAT
146071 GGGCGCTAGAGCT
1 GGGCGCTA-AGCT
146084 GGCAAAAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.17
Consensus pattern (20 bp):
GGGCGCTAAGCTTGCCGCAT
Found at i:146277 original size:31 final size:32
Alignment explanation
Indices: 146239--146309 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
146229 TTGGGTACCA
* * *
146239 GAACCCGAAATTACCCGAATCC-AAACGACCC
1 GAACCCGAAATGACCCAAACCCAAAACGACCC
*
146270 GAACCCGAAATGACCCAAACCCAAAATGACCC
1 GAACCCGAAATGACCCAAACCCAAAACGACCC
*
146302 GAATCCGA
1 GAACCCGA
146310 TCAACCCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.41, C:0.37, G:0.14, T:0.08
Consensus pattern (32 bp):
GAACCCGAAATGACCCAAACCCAAAACGACCC
Found at i:146290 original size:16 final size:16
Alignment explanation
Indices: 146239--146309 Score: 81
Period size: 16 Copynumber: 4.5 Consensus size: 16
146229 TTGGGTACCA
*
146239 GAACCCGAAATTACCC
1 GAACCCGAAATGACCC
* *
146255 GAATCC-AAACGACCC
1 GAACCCGAAATGACCC
146270 GAACCCGAAATGACCC
1 GAACCCGAAATGACCC
* *
146286 AAACCCAAAATGACCC
1 GAACCCGAAATGACCC
*
146302 GAATCCGA
1 GAACCCGA
146310 TCAACCCGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
15 12 0.27
16 32 0.73
ACGTcount: A:0.41, C:0.37, G:0.14, T:0.08
Consensus pattern (16 bp):
GAACCCGAAATGACCC
Found at i:147587 original size:16 final size:16
Alignment explanation
Indices: 147562--147593 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
147552 GAATTGTAAC
*
147562 GACCCTAACCCGAAAA
1 GACCCGAACCCGAAAA
147578 GACCCGAACCCGAAAA
1 GACCCGAACCCGAAAA
147594 ACCGACGTTG
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:0.44, C:0.38, G:0.16, T:0.03
Consensus pattern (16 bp):
GACCCGAACCCGAAAA
Found at i:152774 original size:14 final size:12
Alignment explanation
Indices: 152751--152789 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
152741 CAATTCCTTC
152751 TTTTTTTGTTTT
1 TTTTTTTGTTTT
152763 GTTTTTTCTGTTTT
1 -TTTTTT-TGTTTT
152777 TTTTTTT-TTTT
1 TTTTTTTGTTTT
152788 TT
1 TT
152790 AGCAAACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.24
12 1 0.04
13 12 0.48
14 6 0.24
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.90
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:152776 original size:20 final size:18
Alignment explanation
Indices: 152748--152787 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
152738 CTCCAATTCC
*
152748 TTCTTTTTTTGTTTTGTTTT
1 TTCTGTTTTT-TTTT-TTTT
152768 TTCTGTTTTTTTTTTTTT
1 TTCTGTTTTTTTTTTTTT
152786 TT
1 TT
152788 TTAGCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (18 bp):
TTCTGTTTTTTTTTTTTT
Found at i:154165 original size:20 final size:21
Alignment explanation
Indices: 154140--154181 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
154130 GGTTTTTTAG
154140 GAAAA-TGGGGTCTTGGCTGA
1 GAAAATTGGGGTCTTGGCTGA
**
154160 GAAAATTGTTGTCTTGGCTGA
1 GAAAATTGGGGTCTTGGCTGA
154181 G
1 G
154182 CATTAGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.31
Consensus pattern (21 bp):
GAAAATTGGGGTCTTGGCTGA
Found at i:158944 original size:49 final size:49
Alignment explanation
Indices: 158478--158945 Score: 407
Period size: 49 Copynumber: 9.7 Consensus size: 49
158468 TAAGACTAAC
** ** *
158478 GCCTTCCGTCCGAAAAGGGCGTTTTAGGGAAA-AGCCA-GTAAAAATTAGT
1 GCCTTCCGTCCGGGAAGGGCACTTT-GGGAAATAG-CAGGTAAAAATAAGT
** * *
158527 GCCTTCCGTCCAAGAAGGGCACTTTGGGAAAAAGTAGGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
* * * * * *
158576 GTCTTCCGTCCGGGAAGAGCATTCTTGGAAAATAGCAAGT-AGAATAAGT
1 GCCTTCCGTCCGGGAAGGGCACT-TTGGGAAATAGCAGGTAAAAATAAGT
* * * *
158625 CCCTTCCGTCCGGGAAGGGCACTTTGGGAAA-AACAGGTAAAGATTAGT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
* ** * * *
158673 GCATTCCGTCCGGGAAGGGCTTTTTAGGAAA-AACAGGTAAAAATTAGT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
** *
158721 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-A-CAGGTAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
* * * * ** *
158768 GGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGCGAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
* * * *
158817 GGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT-AAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
* * * * * *
158865 GGC-TCCGTCTGGGAATGGCGCTTTGGGAAATAGTAGGTAAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGT-AAAAATAAGT
* *
158914 ACCTTCCGTCC-GGAAGGGCATTTTGGGAAATA
1 GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATA
158946 ACAAGTGAAA
Statistics
Matches: 355, Mismatches: 55, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
47 78 0.22
48 103 0.29
49 156 0.44
50 18 0.05
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.23
Consensus pattern (49 bp):
GCCTTCCGTCCGGGAAGGGCACTTTGGGAAATAGCAGGTAAAAATAAGT
Found at i:158951 original size:96 final size:97
Alignment explanation
Indices: 158492--158956 Score: 408
Period size: 96 Copynumber: 4.8 Consensus size: 97
158482 TCCGTCCGAA
* * * **
158492 AAGGGCGTTTTAGGGAAA-AGCCA-GTAAAAATTAGTGCCTTCCGTCCAAGAAGGGCACTTTGGG
1 AAGGGCGCTTT-GGGAAATAG-CAGGTAAAAATAAATGCCTTCCGTCCGGGAAGGGCACTTTGGG
* * * *
158555 AAAAAGTAGGTAAAAATAAGTGTCTTCCGTCCGGG
64 AAAAA-CAAGTAAAAATAAGTGGCTTCCGTCTGGG
* ** * * * * *
158590 AAGAGCATTCTTGGAAAATAGCAAGT-AGAATAAGTCCCTTCCGTCCGGGAAGGGCACTTTGGGA
1 AAGGGCGCT-TTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGGAAGGGCACTTTGGGA
* * * *
158654 AAAACAGGTAAAGATTAGT-GCATTCCGTCCGGG
65 AAAACAAGTAAAAATAAGTGGC-TTCCGTCTGGG
** * * * * **
158687 AAGGGCTTTTTAGGAAA-AACAGGTAAAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGG-A
1 AAGGGCGCTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGGAAGGGCACTTTGGGAA
* *
158750 AAACAGGTAAAAATAAATGGCTTCCGTCTGGG
66 AAACAAGTAAAAATAAGTGGCTTCCGTCTGGG
* ** * * *
158782 AAGGGCGCTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTGGGAA
1 AAGGGCGCTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGGAAGGGCACTTTGGGAA
*
158847 ATAGCAAGT-AAAATAAGTGGC-TCCGTCTGGG
66 A-AACAAGTAAAAATAAGTGGCTTCCGTCTGGG
* * * *
158878 AATGGCGCTTTGGGAAATAGTAGGTAAAAAATAAATACCTTCCGTCC-GGAAGGGCATTTTGGGA
1 AAGGGCGCTTTGGGAAATAGCAGGT-AAAAATAAATGCCTTCCGTCCGGGAAGGGCACTTTGGGA
*
158942 AATAACAAGTGAAAA
65 AA-AACAAGTAAAAA
158957 CTGAAAATTT
Statistics
Matches: 303, Mismatches: 53, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
95 45 0.15
96 132 0.44
97 64 0.21
98 56 0.18
99 6 0.02
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (97 bp):
AAGGGCGCTTTGGGAAATAGCAGGTAAAAATAAATGCCTTCCGTCCGGGAAGGGCACTTTGGGAA
AAACAAGTAAAAATAAGTGGCTTCCGTCTGGG
Found at i:160343 original size:24 final size:23
Alignment explanation
Indices: 160298--160343 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
160288 CTTTTTTTTT
* * *
160298 TTTTTGTCGATTCCCTTTCTTTG
1 TTTTTGTCCATTCCCCTCCTTTG
160321 TTTTTGATCCATTCCCCTCCTTT
1 TTTTTG-TCCATTCCCCTCCTTT
160344 TCTTTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.07, C:0.28, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTTTGTCCATTCCCCTCCTTTG
Found at i:161733 original size:23 final size:23
Alignment explanation
Indices: 161703--161751 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
161693 AAAGGAACGG
*
161703 ATTTACTTAAAAATAAACTATGA
1 ATTTACTTAAAAATAAACTACGA
*
161726 ATTTACTTAAAAATGAACTACGA
1 ATTTACTTAAAAATAAACTACGA
161749 ATT
1 ATT
161752 GACCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (23 bp):
ATTTACTTAAAAATAAACTACGA
Found at i:168628 original size:17 final size:19
Alignment explanation
Indices: 168606--168651 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
168596 AGTTCGTACT
168606 TTTATATATTT-TATT-TA
1 TTTATATATTTATATTATA
168623 TTTATATATTTATATTATA
1 TTTATATATTTATATTATA
*
168642 TATATATATT
1 TTTATATATT
168652 AAAAAGTACG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTTATATTATA
Found at i:168640 original size:13 final size:13
Alignment explanation
Indices: 168617--168652 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
168607 TTATATATTT
168617 TATTTAT-TTATA
1 TATTTATATTATA
168629 TATTTATATTATA
1 TATTTATATTATA
*
168642 TATATATATTA
1 TATTTATATTA
168653 AAAAGTACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTATATTATA
Done.