Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 70 of 135
Found at i:23159250 original size:89 final size:91
Alignment explanation
Indices: 23159034--23159288 Score: 302
Period size: 89 Copynumber: 2.8 Consensus size: 91
23159024 TATTCTGGGG
* * * * * ** * * *
23159034 ATGCCATGGTATCTTTCAACCAAGGTCTTACACAATTCCAAAACGATGCAATAATACCTTTCAAC
1 ATGCCATAGTATCTTTCAACTATGGTCTTACACATTTCCAAGATAATGCCATAGTATCTTTCAAC
* *
23159099 TATGGTCTT-CATCATTCCTGATATG
66 TATGGTCTTACATCATTCCAGATATA
*
23159124 ATGCCATAATATCTTTCAACTATGGTCTTACACATTTCCAAGATAATGCCATAGTATCTTTCAAC
1 ATGCCATAGTATCTTTCAACTATGGTCTTACACATTTCCAAGATAATGCCATAGTATCTTTCAAC
*
23159189 TATGGTCTTACA-CATGT-CAGTTA-A
66 TATGGTCTTACATCAT-TCCAGATATA
* ** *
23159213 ATGCCATAGTATCTTTCAACTATGGTCTTACAGATTTCCGGGATAATGCCATAGTATATTTCAAC
1 ATGCCATAGTATCTTTCAACTATGGTCTTACACATTTCCAAGATAATGCCATAGTATCTTTCAAC
*
23159278 TATGGTTTTAC
66 TATGGTCTTAC
23159289 TGATGCCGAT
Statistics
Matches: 143, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
89 70 0.49
90 70 0.49
91 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (91 bp):
ATGCCATAGTATCTTTCAACTATGGTCTTACACATTTCCAAGATAATGCCATAGTATCTTTCAAC
TATGGTCTTACATCATTCCAGATATA
Found at i:23162861 original size:9 final size:9
Alignment explanation
Indices: 23162847--23162873 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
23162837 ACCCACTTTT
23162847 TGAAGCATC
1 TGAAGCATC
23162856 TGAAGCATC
1 TGAAGCATC
23162865 TGAAGCATC
1 TGAAGCATC
23162874 ACTAGCTTCA
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:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (9 bp):
TGAAGCATC
Found at i:23163443 original size:13 final size:13
Alignment explanation
Indices: 23163425--23163465 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
23163415 ACTTGTGAAG
23163425 AGTATTAATCTAA
1 AGTATTAATCTAA
23163438 AGTATTAATCTAA
1 AGTATTAATCTAA
*
23163451 ACTAAATTAATCTAA
1 AGT--ATTAATCTAA
23163466 GTTAAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.60
15 10 0.40
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (13 bp):
AGTATTAATCTAA
Found at i:23178366 original size:25 final size:25
Alignment explanation
Indices: 23178313--23178377 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 25
23178303 TAAACCCAAA
*
23178313 TTATTATTGAA-AT-ATTTTATAAT
1 TTATTATTAAATATAATTTTATAAT
** *
23178336 AAATTATTAAATATAATTTTATATT
1 TTATTATTAAATATAATTTTATAAT
* *
23178361 TTATTATTTAATTTAAT
1 TTATTATTAAATATAAT
23178378 CATGCTTGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 8 0.25
24 2 0.06
25 22 0.69
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTATTATTAAATATAATTTTATAAT
Found at i:23180704 original size:26 final size:25
Alignment explanation
Indices: 23180668--23180736 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
23180658 TTAATTAGTA
23180668 TAAAATATTAACAATTTAAAATAAAT
1 TAAAA-ATTAACAATTTAAAATAAAT
* *
23180694 TAAAAAGTTAATAAATT-AAATAAAT
1 TAAAAA-TTAACAATTTAAAATAAAT
*
23180719 TAAAAATT-AGAATTTAAA
1 TAAAAATTAACAATTTAAA
23180737 TTCTTACCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
23 5 0.14
24 4 0.11
25 15 0.41
26 13 0.35
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (25 bp):
TAAAAATTAACAATTTAAAATAAAT
Found at i:23180706 original size:16 final size:17
Alignment explanation
Indices: 23180687--23180727 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
23180677 AACAATTTAA
*
23180687 AATAAATTAAA-AAGTT
1 AATAAATTAAATAAATT
23180703 AATAAATTAAATAAATT
1 AATAAATTAAATAAATT
23180720 AA-AAATTA
1 AATAAATTA
23180728 GAATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AATAAATTAAATAAATT
Found at i:23180717 original size:9 final size:9
Alignment explanation
Indices: 23180686--23180722 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
23180676 TAACAATTTA
23180686 AAATAAATT
1 AAATAAATT
*
23180695 AAA-AAGTT
1 AAATAAATT
23180703 -AATAAATT
1 AAATAAATT
23180711 AAATAAATT
1 AAATAAATT
23180720 AAA
1 AAA
23180723 AATTAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 2 0.08
8 8 0.33
9 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
AAATAAATT
Found at i:23184519 original size:92 final size:92
Alignment explanation
Indices: 23184362--23184545 Score: 332
Period size: 92 Copynumber: 2.0 Consensus size: 92
23184352 TAACCGCTTG
* * *
23184362 ATAATTTCTTTCTTGACTACATCTTTCATAATTGGGTTCCATCTCTGTTGCCCATCAATCGTCCC
1 ATAATTTCTTTCTTGACTACATCCTTCATAATTGGGTTCAATCTCCGTTGCCCATCAATCGTCCC
23184427 TTTCTTATCATCTTCAAGAATAATCTT
66 TTTCTTATCATCTTCAAGAATAATCTT
*
23184454 ATAATTTCTTTCTTGACTACATCCTTCATAATTGGGTTCAATCTCCGTTGTCCATCAATCGTCCC
1 ATAATTTCTTTCTTGACTACATCCTTCATAATTGGGTTCAATCTCCGTTGCCCATCAATCGTCCC
23184519 TTTCTTATCATCTTCAAGAATAATCTT
66 TTTCTTATCATCTTCAAGAATAATCTT
23184546 GTGCATGCAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (92 bp):
ATAATTTCTTTCTTGACTACATCCTTCATAATTGGGTTCAATCTCCGTTGCCCATCAATCGTCCC
TTTCTTATCATCTTCAAGAATAATCTT
Found at i:23187581 original size:13 final size:13
Alignment explanation
Indices: 23187565--23187591 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23187555 ATTTGTAAAG
23187565 AGTATTAATCTAA
1 AGTATTAATCTAA
23187578 AGTATTAATCTAA
1 AGTATTAATCTAA
23187591 A
1 A
23187592 CTAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AGTATTAATCTAA
Found at i:23193433 original size:30 final size:30
Alignment explanation
Indices: 23193397--23193453 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
23193387 CATAGGTATT
23193397 CACACATCATTAGATAGCCACAAAGGCTTC
1 CACACATCATTAGATAGCCACAAAGGCTTC
* *
23193427 CACACATCGTTAGATAGCCATAAAGGC
1 CACACATCATTAGATAGCCACAAAGGC
23193454 ATCTAGACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (30 bp):
CACACATCATTAGATAGCCACAAAGGCTTC
Found at i:23193650 original size:27 final size:27
Alignment explanation
Indices: 23193619--23193698 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
23193609 ACATGTAATA
*
23193619 AAGAACAGCCACAAAGGCTTCCATATC
1 AAGAACAACCACAAAGGCTTCCATATC
* ** *
23193646 AAGAACATCCTTAAAGACTTTCACATATC
1 AAGAACAACCACAAAGGC-TTC-CATATC
23193675 AGAGAACAACCACAAAGGCTTCCA
1 A-AGAACAACCACAAAGGCTTCCA
23193699 CATTTCTGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 14 0.33
28 5 0.12
29 10 0.24
30 13 0.31
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.17
Consensus pattern (27 bp):
AAGAACAACCACAAAGGCTTCCATATC
Found at i:23193701 original size:30 final size:28
Alignment explanation
Indices: 23193619--23193701 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 28
23193609 ACATGTAATA
*
23193619 AAGAACAGCCACAAAGGCTTC-CATATC
1 AAGAACAACCACAAAGGCTTCACATATC
* ** *
23193646 AAGAACATCCTTAAAGACTTTCACATATC
1 AAGAACAACCACAAAGGC-TTCACATATC
23193675 AGAGAACAACCACAAAGGCTTCCACAT
1 A-AGAACAACCACAAAGGCTT-CACAT
23193702 TTCTGTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
27 14 0.32
28 3 0.07
29 9 0.20
30 18 0.41
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (28 bp):
AAGAACAACCACAAAGGCTTCACATATC
Found at i:23195836 original size:11 final size:11
Alignment explanation
Indices: 23195820--23195846 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23195810 TGTTTTAGTT
23195820 TTATTAATTAG
1 TTATTAATTAG
23195831 TTATTAATTAG
1 TTATTAATTAG
23195842 TTATT
1 TTATT
23195847 TGATTATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
TTATTAATTAG
Found at i:23196862 original size:990 final size:990
Alignment explanation
Indices: 23194943--23197512 Score: 4415
Period size: 990 Copynumber: 2.6 Consensus size: 990
23194933 AGTTATCCTT
* *
23194943 AAGGCCAGAGAATCCCTTAACATGATCACCAATCTCTTCCAAGCACTTATACATGCATTAAGTAT
1 AAGGCCAGAGAATCCCTTAACACGATCACCAATCTCTTCCATGCACTTATACATGCATTAAGTAT
** *
23195008 TGAATAGCCTTCAAGTCCCACCTTACCCAATTTTTGTGCCCTACTGTCGTATCGAGGTGCCAATT
66 TGAATAGCCTTCAAGTCCCACCTTACCCCTTTTTTGTGCCCTGCTGTCGTATCGAGGTGCCAATT
* *
23195073 CGGCAAATAGGACTATGCCAACCTGATCTCCTTGACCTGTACGTCCAAGCTTAAAACATGCCAAG
131 TGGCAAATAGGACTATGCCAACCTGATCTCCTTGACCTGTACATCCAAGCTTAAAACATGCCAAG
* *
23195138 TCTGGGTTGTTACACATTTGGTGCAGTTCTTCATGATGCTGAGGGTGTTTCGTCGTTGGTTTGAT
196 TCTGGGGTGTTACACATTTGGTGCAGTTCTTCACGATGCTGAGGGTGTTTCGTCGTTGGTTTGAT
* * * * *
23195203 ATGCTTCTTCTTGGCACTATATGATCCACTAACAAATATAACGATTCTTATCCGAGAGGCTCTCT
261 ATGCTTCTTCTTGGCACTATATGATCCACTTATAGACATAACGATGCTTATCCGAGAGGCTCTCT
*
23195268 GATGTAAGCATCAAAGCTGGTAAGCTAACCTTACCGTAAGGCCCAATTACAAGGTCAATGGCAAG
326 GATGTAAGCATCAAAGCTGGTAAGCTGACCTTACCGTAAGGCCCAATTACAAGGTCAATGGCAAG
*
23195333 GAAGATGAAAGCAAGGTTAAACAGATTTGTGCAAGGCTTCATCACAAAGGCCTTGGACGT-ACAT
391 GAAGATGAAAGCAAGATTAAACAGATTTGTGCAAGGCTTCATCACAAAGGCCTTGGAC-TCACAT
*
23195397 ACGAGCCAAAAAGAAAACCAAGATTCATGTTCTTACTTTCAAGAAAATCAAGAAACCAAATCTTG
455 ACGAGCCAAAAAGAAAACCAAGATTCATGTTCTTGCTTTCAAGAAAATCAAGAAACCAAATCTTG
* *
23195462 GTCTAATTATGACGTTTGGGGAGATTTCAGAAATCAAGAAAACCAGGAATACAAATCTTGGAATT
520 GTCTAATTATGACGTTTGGGGAGATTTCAGAAATCAAGAAAACCAAGAATTCAAATCTTGGAATT
* * *
23195527 CATGGTCCAAGAAACCAAATCTTGAAACTAACATTCGATGGATAATGTGCTCGAGCGTAAGCGGG
585 CATGGTCCAAGAAACCAAATCTTGAAACTAACATCCGATGGATAATGTGCTCGAGCATAAGCAGG
*
23195592 TCGATCTTGGAAGGAAACAATGTGCAAGATCAAAATTGGCCCATTTACGCGTCTCTAAGCCCAAC
650 TCGATCTTGGAAGGAAACAATGTGCAAGATCAAAATTGGCCCATTTACGCGTCACTAAGCCCAAC
*
23195657 CTTGAGTTTTGGACACCATTTGGAAGCTGAGAAGAACCCGCATTACAAATCAGGCCCAAAAGAGC
715 CTAGAGTTTTGGACACCATTTGGAAGCTGAGAAGAACCCGCATTACAAATCAGGCCCAAAAGAGC
*
23195722 CCAAATCGAATTTATCTTAGTTTTCGAAGTAAAAATTCGGCCAAAGCACAAGCCATTAAGCCTTA
780 CCAAATCAAATTTATCTTAGTTTTCGAAGTAAAAATTCGGCCAAAGCACAAGCCATTAAGCCTTA
*
23195787 GTCGAAATTCCATATTAGATAATTGTTTTAGTTTTATTAATTAGTTATTAATTAGTTATTTGATT
845 GCCGAAATTCCATATTAGATAATTGTTTTAGTTTTATTAATTAGTTATTAATTAGTTATTTGATT
* *
23195852 ATTCTGCTAAGTTGTAATCAGTTAT-TTATTTGACTTTAAACTCTTAAGGTTGATTAGGAGTCTG
910 ATTCTGCGAAGTTGTAATCAGTTATATTATTTGACTTTAAACTCCTAAGGTTGATTAGGAGTCTG
23195916 ACTTTGGGGGTTATTTA
975 ACTTT-GGGGTTATTTA
* * *
23195933 AAGGCCAGAGAATCTCTTAACACGACCACCAATCTCTTCCATGCACTTATACATGCATTAAGCAT
1 AAGGCCAGAGAATCCCTTAACACGATCACCAATCTCTTCCATGCACTTATACATGCATTAAGTAT
* * *
23195998 TGAATAGCCTTCAAGTCCTACCTTACCCCTTTTTTGTGCGCTGCTGTCATATCGAGGTGCCAATT
66 TGAATAGCCTTCAAGTCCCACCTTACCCCTTTTTTGTGCCCTGCTGTCGTATCGAGGTGCCAATT
*
23196063 TGGCAAATAAGACTATGCCAACCTGATCTCCTTGACCTGTACATCCAAGCTTAAAACATGCCAAG
131 TGGCAAATAGGACTATGCCAACCTGATCTCCTTGACCTGTACATCCAAGCTTAAAACATGCCAAG
23196128 TCTGGGGTGTTACACATTTGGTGCAGTTCTTCACGATGCTGAGGGTGTTTCGTCGTTGGTTTGAT
196 TCTGGGGTGTTACACATTTGGTGCAGTTCTTCACGATGCTGAGGGTGTTTCGTCGTTGGTTTGAT
* * * * *
23196193 ATGCTTCTTATTGGCACTATATGATCCACTTATAGGCATAGCAATGCTTATCTGAGAGGCTCTCT
261 ATGCTTCTTCTTGGCACTATATGATCCACTTATAGACATAACGATGCTTATCCGAGAGGCTCTCT
* ** *
23196258 GATGTAAGCATTAAAGCTACTAAGCGGACCTTACCGTAAGGCCCAATTACAAGGTCAATGGCAAG
326 GATGTAAGCATCAAAGCTGGTAAGCTGACCTTACCGTAAGGCCCAATTACAAGGTCAATGGCAAG
*
23196323 GAAGATGAAAGCAAGATTAAACAGATTTGTGCAAGGCTTCATCACAAAAGCCTTGGACTCACATA
391 GAAGATGAAAGCAAGATTAAACAGATTTGTGCAAGGCTTCATCACAAAGGCCTTGGACTCACATA
* *
23196388 CGAGCAAAAAAGAAAACCAAGATTCATGTTCTTGCTTTCAAGAAAATTAAGAAACCAAATCTTGG
456 CGAGCCAAAAAGAAAACCAAGATTCATGTTCTTGCTTTCAAGAAAATCAAGAAACCAAATCTTGG
* *
23196453 TCTAATTATTACGTTTGGGGAGATTTCAGAAATCAAGAAAACCAAGAATTTAAATCTTGGAATTC
521 TCTAATTATGACGTTTGGGGAGATTTCAGAAATCAAGAAAACCAAGAATTCAAATCTTGGAATTC
*
23196518 ATGGTCCAAGAAACCAAATCTTGAAACTAACATCCGATGGATAATGTGTTCGAGCATAAGCAGGT
586 ATGGTCCAAGAAACCAAATCTTGAAACTAACATCCGATGGATAATGTGCTCGAGCATAAGCAGGT
23196583 CGATCTTGGAAGGAAACAATGTGCAAGATCAAAATTGGCCCATTTACGCGTCACTAAGCCCAACC
651 CGATCTTGGAAGGAAACAATGTGCAAGATCAAAATTGGCCCATTTACGCGTCACTAAGCCCAACC
* *
23196648 TAGAGTTTTGGACACCATTTGGAAGCTGAGAAGAACCCGCATTACAAATCAGGCCCTAAGGAGCC
716 TAGAGTTTTGGACACCATTTGGAAGCTGAGAAGAACCCGCATTACAAATCAGGCCCAAAAGAGCC
*
23196713 CAAATCAAATTTATCTTAGTTTTCGAAGTAAAAATTTGGCCAAAGCACAAGCCATTAAGCCTTAG
781 CAAATCAAATTTATCTTAGTTTTCGAAGTAAAAATTCGGCCAAAGCACAAGCCATTAAGCCTTAG
* * *
23196778 CCGAAATTCCTTATTAGATTATTGTTTTAGTTTTATTAATTAGTTGTTAATTAGTTATTTGATTA
846 CCGAAATTCCATATTAGATAATTGTTTTAGTTTTATTAATTAGTTATTAATTAGTTATTTGATTA
*
23196843 TTCTGCGAAGTTGTAATCAGTTATATTATTTGACTTTAAACTCCTAAGTTTGATTAGGAGTCTGA
911 TTCTGCGAAGTTGTAATCAGTTATATTATTTGACTTTAAACTCCTAAGGTTGATTAGGAGTCTGA
23196908 CTTTGGGGTTATTTA
976 CTTTGGGGTTATTTA
* *
23196923 AAGGCCAGAGAATCCCTTAACACGATCACCAATCTCTTTCATGCACTTCTACATGCATTAAGTAT
1 AAGGCCAGAGAATCCCTTAACACGATCACCAATCTCTTCCATGCACTTATACATGCATTAAGTAT
*
23196988 TGAATAGCCTTCAAGTCCCACCTTTCCCCTTTTTTGTGCCCTGCTGTCGTATCGAGGTGCCAATT
66 TGAATAGCCTTCAAGTCCCACCTTACCCCTTTTTTGTGCCCTGCTGTCGTATCGAGGTGCCAATT
* *
23197053 TGGCAAATAGGACTATGCCAACCTGATCTCCTTAACCTATACATCCAAGCTTAAAACATGCCAAG
131 TGGCAAATAGGACTATGCCAACCTGATCTCCTTGACCTGTACATCCAAGCTTAAAACATGCCAAG
* *
23197118 TCTGGGGTGTTACACAGTTGGTGCAGTTCTTCACGATGCTGAGGGTGTTTCGTTGTTGGTTTGAT
196 TCTGGGGTGTTACACATTTGGTGCAGTTCTTCACGATGCTGAGGGTGTTTCGTCGTTGGTTTGAT
* *
23197183 ATGCTTCTTCTTGGCACTATATGATCCACTTATAGACATAACGATGCTTATCCAAGAGGCTCTCC
261 ATGCTTCTTCTTGGCACTATATGATCCACTTATAGACATAACGATGCTTATCCGAGAGGCTCTCT
* *
23197248 GATGTAAGCATCAAAGCTGGTAAGCTGACCTTACCGTAAGGCCCAAGTACAAGGTCAAAGGCAAG
326 GATGTAAGCATCAAAGCTGGTAAGCTGACCTTACCGTAAGGCCCAATTACAAGGTCAATGGCAAG
* * *
23197313 GAAGATGAAAGCAAGATTAAACGGATTTGTGCAAGGCTTCATCACAAAGGCCTTGGACGCACGTA
391 GAAGATGAAAGCAAGATTAAACAGATTTGTGCAAGGCTTCATCACAAAGGCCTTGGACTCACATA
*
23197378 CAAGCCAAAAAGAAAACCAAGATTCATGTTCTTGCTTTCAAGAAAATCAAGAAACCAAATCTTGG
456 CGAGCCAAAAAGAAAACCAAGATTCATGTTCTTGCTTTCAAGAAAATCAAGAAACCAAATCTTGG
* * * * *
23197443 TCTAATTATGCCGTTTGGGAAGATTTCAAAAATCATGAAAACCAAGAATTCAAATCTTGGAATTA
521 TCTAATTATGACGTTTGGGGAGATTTCAGAAATCAAGAAAACCAAGAATTCAAATCTTGGAATTC
23197508 ATGGT
586 ATGGT
23197513 TAGGGTTTCT
Statistics
Matches: 1480, Mismatches: 98, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
989 1 0.00
990 1437 0.97
991 42 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (990 bp):
AAGGCCAGAGAATCCCTTAACACGATCACCAATCTCTTCCATGCACTTATACATGCATTAAGTAT
TGAATAGCCTTCAAGTCCCACCTTACCCCTTTTTTGTGCCCTGCTGTCGTATCGAGGTGCCAATT
TGGCAAATAGGACTATGCCAACCTGATCTCCTTGACCTGTACATCCAAGCTTAAAACATGCCAAG
TCTGGGGTGTTACACATTTGGTGCAGTTCTTCACGATGCTGAGGGTGTTTCGTCGTTGGTTTGAT
ATGCTTCTTCTTGGCACTATATGATCCACTTATAGACATAACGATGCTTATCCGAGAGGCTCTCT
GATGTAAGCATCAAAGCTGGTAAGCTGACCTTACCGTAAGGCCCAATTACAAGGTCAATGGCAAG
GAAGATGAAAGCAAGATTAAACAGATTTGTGCAAGGCTTCATCACAAAGGCCTTGGACTCACATA
CGAGCCAAAAAGAAAACCAAGATTCATGTTCTTGCTTTCAAGAAAATCAAGAAACCAAATCTTGG
TCTAATTATGACGTTTGGGGAGATTTCAGAAATCAAGAAAACCAAGAATTCAAATCTTGGAATTC
ATGGTCCAAGAAACCAAATCTTGAAACTAACATCCGATGGATAATGTGCTCGAGCATAAGCAGGT
CGATCTTGGAAGGAAACAATGTGCAAGATCAAAATTGGCCCATTTACGCGTCACTAAGCCCAACC
TAGAGTTTTGGACACCATTTGGAAGCTGAGAAGAACCCGCATTACAAATCAGGCCCAAAAGAGCC
CAAATCAAATTTATCTTAGTTTTCGAAGTAAAAATTCGGCCAAAGCACAAGCCATTAAGCCTTAG
CCGAAATTCCATATTAGATAATTGTTTTAGTTTTATTAATTAGTTATTAATTAGTTATTTGATTA
TTCTGCGAAGTTGTAATCAGTTATATTATTTGACTTTAAACTCCTAAGGTTGATTAGGAGTCTGA
CTTTGGGGTTATTTA
Found at i:23200353 original size:201 final size:201
Alignment explanation
Indices: 23200008--23200409 Score: 741
Period size: 201 Copynumber: 2.0 Consensus size: 201
23199998 CTCTAATACC
* * * *
23200008 GTTAACACTTAAAGAAGTTCATGATGAACAACTCAAAATACTAAGATTTTGTGAGGGGGTTAAGG
1 GTTAACACCTAAAGAAGTTCATGACGAACAACTCAAAATACTAAGATTTTGTAAGGGGGTTAAGA
23200073 GTAAGAATATTGAAAAGACTGAGAGTAAAGAGGCCAATAGTAACAAAAGTCAATCGAAAGGCCCA
66 GTAAGAATATTGAAAAGACTGAGAGTAAAGAGGCCAATAGTAACAAAAGTCAATCGAAAGGCCCA
* *
23200138 TTGGTGAGTGAATCCTCTTGTGGTAAAAAGAGCGCGCAAAATTTATATGCGAGTGTAAAAGATGT
131 TTGGTGAGTGAATCCTCTTGTGGTAAAAAGAGCGCACAAAATTTATATGCGAATGTAAAAGATGT
23200203 GAGGGG
196 GAGGGG
*
23200209 GTTAACACCTAAAGAAGTTCATGACGAACAACTCAAAATTCTAAGATTTTGTAAGGGGGTTAAGA
1 GTTAACACCTAAAGAAGTTCATGACGAACAACTCAAAATACTAAGATTTTGTAAGGGGGTTAAGA
23200274 GTAAGAATATTGAAAAGACTGAGAGTAAAGAGGCCAATAGTAACAAAAGTCAATCGAAAGGCCCA
66 GTAAGAATATTGAAAAGACTGAGAGTAAAGAGGCCAATAGTAACAAAAGTCAATCGAAAGGCCCA
23200339 TTGGTGAGTGAATCCTCTTGTGGTAAAAAGAGCGCACAAAATTTATATGCGAATGTAAAAGATGT
131 TTGGTGAGTGAATCCTCTTGTGGTAAAAAGAGCGCACAAAATTTATATGCGAATGTAAAAGATGT
23200404 GAGGGG
196 GAGGGG
23200410 AGCTCTTGTC
Statistics
Matches: 194, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
201 194 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (201 bp):
GTTAACACCTAAAGAAGTTCATGACGAACAACTCAAAATACTAAGATTTTGTAAGGGGGTTAAGA
GTAAGAATATTGAAAAGACTGAGAGTAAAGAGGCCAATAGTAACAAAAGTCAATCGAAAGGCCCA
TTGGTGAGTGAATCCTCTTGTGGTAAAAAGAGCGCACAAAATTTATATGCGAATGTAAAAGATGT
GAGGGG
Found at i:23207229 original size:274 final size:274
Alignment explanation
Indices: 23206567--23207386 Score: 1579
Period size: 273 Copynumber: 3.0 Consensus size: 274
23206557 TCATTAAAGA
23206567 ATAAAAGTGAAAAAACAGTAAAAAAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATC
1 ATAAAAGTGAAAAAACAGT---AAAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATC
*
23206632 TACCATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTTTATATCATGTTCA
63 TACCATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTCTATATCATGTTCA
23206697 TCTTTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGAT
128 TCTTTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGAT
23206762 TCTGTTAAATTTAGCTTTATTTTCTCATATAGTTTACAGTGGACAGTGTCACAAATAGTAATACA
193 TCTGTTAAATTTAGCTTTATTTTCTCATATAGTTTACAGTGGACAGTGTCACAAATAGTAATACA
23206827 ATTTATAGCGGTGTCAT
258 ATTTATAGCGGTGTCAT
23206844 ATAAAAGTGAAAAAACAGT-AAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATCTAC
1 ATAAAAGTGAAAAAACAGTAAAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATCTAC
23206908 CATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTCTATATCATGTTCATCT
66 CATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTCTATATCATGTTCATCT
23206973 TTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGATTCT
131 TTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGATTCT
*
23207038 GTTAAATTTAGCTTTATTTTCTCATATAGTTTACAGTGGACAGTGTCACAAATAATAATACAATT
196 GTTAAATTTAGCTTTATTTTCTCATATAGTTTACAGTGGACAGTGTCACAAATAGTAATACAATT
23207103 TATAGCGGTGTCAT
261 TATAGCGGTGTCAT
23207117 ATAAAAGTGAAAAAACAGTAAAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATCTAC
1 ATAAAAGTGAAAAAACAGTAAAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATCTAC
23207182 CATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTCTATATCATGTTCATCT
66 CATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTCTATATCATGTTCATCT
23207247 TTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGATTCT
131 TTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGATTCT
*
23207312 GTTAAATTTAGCTTTATTTTCTCATATAGTTTACAATGGACAGTGTCACAAATAGTAATACAATT
196 GTTAAATTTAGCTTTATTTTCTCATATAGTTTACAGTGGACAGTGTCACAAATAGTAATACAATT
23207377 TATAGCGGTG
261 TATAGCGGTG
23207387 AATGTGCTGA
Statistics
Matches: 538, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
273 271 0.50
274 248 0.46
277 19 0.04
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (274 bp):
ATAAAAGTGAAAAAACAGTAAAAAAAAAAAGACTTCATTCAATGGGAAAAAGAATATTTATCTAC
CATTTCTTGCATAGAATGGCAATATCAATAAAATTTTCAATCATTTTTCTATATCATGTTCATCT
TTACTGATGCATACACTAAACATTCTTACAATTTTTTCTCTTTTTTTTTTCATTGCCTTGATTCT
GTTAAATTTAGCTTTATTTTCTCATATAGTTTACAGTGGACAGTGTCACAAATAGTAATACAATT
TATAGCGGTGTCAT
Found at i:23212723 original size:11 final size:12
Alignment explanation
Indices: 23212706--23212735 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
23212696 TAAACTTCAC
23212706 CTCTTTTCTTTT
1 CTCTTTTCTTTT
23212718 -TCTTTTCTTTT
1 CTCTTTTCTTTT
23212729 CTCTTTT
1 CTCTTTT
23212736 TGTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTCTTTTCTTTT
Found at i:23213250 original size:4 final size:4
Alignment explanation
Indices: 23213241--23213268 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
23213231 GAGCAAGAGT
23213241 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
23213269 AATAGAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:23225190 original size:21 final size:20
Alignment explanation
Indices: 23225166--23225218 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
23225156 TGAGACAATA
*
23225166 CTACCGATACAAGT-GTGACTT
1 CTACCGATACAAGTCATG-C-T
* *
23225187 CTACCGAAACATGTCATGCT
1 CTACCGATACAAGTCATGCT
23225207 CTACCGATACAA
1 CTACCGATACAA
23225219 AAAACTCCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.42
21 13 0.50
22 2 0.08
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (20 bp):
CTACCGATACAAGTCATGCT
Found at i:23239825 original size:29 final size:30
Alignment explanation
Indices: 23239790--23239867 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 30
23239780 CCCCAAAAAA
*
23239790 TTTAAGTACCAACTTAAAAAAA-TGTCAAG
1 TTTAAGTACCAAATTAAAAAAAGTGTCAAG
23239819 TTTAAGTACCAAATTAAGAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAA-AAAAAGTGTCAAG
23239850 TTTGAA-TACCAAATTAAA
1 TTT-AAGTACCAAATTAAA
23239868 CCAAAAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 16 0.36
30 6 0.13
31 21 0.47
32 2 0.04
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (30 bp):
TTTAAGTACCAAATTAAAAAAAGTGTCAAG
Found at i:23244126 original size:17 final size:18
Alignment explanation
Indices: 23244099--23244138 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23244089 ATGGGCATTT
23244099 AAATTAATCTA-TTATTC
1 AAATTAATCTAGTTATTC
* *
23244116 GAATTATTCTAGTTATTC
1 AAATTAATCTAGTTATTC
23244134 AAATT
1 AAATT
23244139 TTGAAATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (18 bp):
AAATTAATCTAGTTATTC
Found at i:23256898 original size:30 final size:30
Alignment explanation
Indices: 23256804--23257055 Score: 198
Period size: 29 Copynumber: 8.5 Consensus size: 30
23256794 GTCAAAAATA
* ** *
23256804 GAATTTTTGGAATTTTAAGGG-TAAAAATG
1 GAATTTTTGGAAGTTTCGGGGTTAAAATTG
* * *
23256833 TAA-TTTTGGAAGTTTCGAGGTTGAAA-TG
1 GAATTTTTGGAAGTTTCGGGGTTAAAATTG
*
23256861 TAATTTTTGGAAGTTTCGGGGTTAAAATTG
1 GAATTTTTGGAAGTTTCGGGGTTAAAATTG
* *
23256891 GAATTTTTGGAAG-TTCGACGG-TAAAAATG
1 GAATTTTTGGAAGTTTCG-GGGTTAAAATTG
* * *
23256920 TAATTTTTGGAAGTTTCGAGGTCAAAATTG
1 GAATTTTTGGAAGTTTCGGGGTTAAAATTG
* * *
23256950 GAATTTTTGAAAGTTTGGGGGGTAAAATAT-
1 GAATTTTTGGAAGTTTCGGGGTTAAAAT-TG
** *
23256980 -AATTTTTGGAAGTTTCATGGTCAAAATTG
1 GAATTTTTGGAAGTTTCGGGGTTAAAATTG
* *
23257009 GAATTTTAGAGAAG-TTCGGGGGTTAAAA-TA
1 GAATTTTTG-GAAGTTTC-GGGGTTAAAATTG
*
23257039 CAATTTTTGGATAGTTT
1 GAATTTTTGGA-AGTTT
23257056 AGGGACTTTC
Statistics
Matches: 176, Mismatches: 34, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
28 19 0.11
29 75 0.43
30 68 0.39
31 14 0.08
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (30 bp):
GAATTTTTGGAAGTTTCGGGGTTAAAATTG
Found at i:23256919 original size:59 final size:58
Alignment explanation
Indices: 23256738--23257055 Score: 259
Period size: 59 Copynumber: 5.4 Consensus size: 58
23256728 TCTTAAGGGC
* * *** * *
23256738 AAAATGGTAATTTTTGAAAGTTTCGGGATCAAAAACAGAATCTTTGGACA-TCCGAGGTCA
1 AAAAT-GTAATTTTTGGAAGTTTCGGGGTCAAAATTGGAATTTTTGGA-AGTTCGAGGT-A
* ** * * *
23256798 AAAATAG-AATTTTTGGAATTTTAAGGGT-AAAAATGTAA-TTTTGGAAGTTTCGAGGTT
1 AAAAT-GTAATTTTTGGAAGTTTCGGGGTCAAAATTGGAATTTTTGGAAG-TTCGAGGTA
* *
23256855 GAAATGTAATTTTTGGAAGTTTCGGGGTTAAAATTGGAATTTTTGGAAGTTCGACGGTA
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCAAAATTGGAATTTTTGGAAGTTCGA-GGTA
* * * *
23256914 AAAATGTAATTTTTGGAAGTTTCGAGGTCAAAATTGGAATTTTTGAAAGTTTGGGGGGT-
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCAAAATTGGAATTTTTGGAAG-TT-CGAGGTA
* ** * * *
23256973 AAAATATAATTTTTGGAAGTTTCATGGTCAAAATTGGAATTTTAGAGAAGTTCGGGGGTT
1 AAAATGTAATTTTTGGAAGTTTCGGGGTCAAAATTGGAATTTTTG-GAAGTTC-GAGGTA
**
23257033 AAAATACAATTTTTGGATAGTTT
1 AAAATGTAATTTTTGGA-AGTTT
23257056 AGGGACTTTC
Statistics
Matches: 214, Mismatches: 32, Indels: 23
0.80 0.12 0.09
Matches are distributed among these distances:
56 2 0.01
57 28 0.13
58 27 0.13
59 121 0.57
60 30 0.14
61 6 0.03
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTTCGGGGTCAAAATTGGAATTTTTGGAAGTTCGAGGTA
Found at i:23258774 original size:34 final size:35
Alignment explanation
Indices: 23258723--23258788 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
23258713 GTATTCTATT
*
23258723 TTGGGTTATTTTGGGCCCGTGTAATTGGGCTTGTG
1 TTGGGTTATATTGGGCCCGTGTAATTGGGCTTGTG
*
23258758 TTGGGTTA-ATTGGGCCCTTGTAATTGGGCTT
1 TTGGGTTATATTGGGCCCGTGTAATTGGGCTT
23258789 TGGTGTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.11, C:0.12, G:0.35, T:0.42
Consensus pattern (35 bp):
TTGGGTTATATTGGGCCCGTGTAATTGGGCTTGTG
Found at i:23258855 original size:15 final size:16
Alignment explanation
Indices: 23258831--23258864 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
23258821 TAATTGTGCC
*
23258831 TTTGTAATTTTGGACT
1 TTTGTAATTTTGCACT
23258847 TTTGT-ATTTTGCACT
1 TTTGTAATTTTGCACT
23258862 TTT
1 TTT
23258865 AATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.62
Consensus pattern (16 bp):
TTTGTAATTTTGCACT
Found at i:23258891 original size:17 final size:17
Alignment explanation
Indices: 23258865--23258940 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
23258855 TTGCACTTTT
*
23258865 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
*
23258882 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
* * * *
23258899 AA-TTCAGTTTCCAAATG
1 AATTTAAATTT-AAAATA
* *
23258916 AATTTGAATTTAGAATA
1 AATTTAAATTTAAAATA
23258933 AATTTAAA
1 AATTTAAA
23258941 CTTATTTAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
16 6 0.14
17 32 0.73
18 6 0.14
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:23259684 original size:201 final size:201
Alignment explanation
Indices: 23259327--23259966 Score: 1021
Period size: 201 Copynumber: 3.2 Consensus size: 201
23259317 GTTAGGCCTT
* * * * * *
23259327 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTGAATCCGCTTCTCTGTATTTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
* * * * *
23259392 CAAGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGTTAACTATTTTATTGGTTCGA
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
*
23259457 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCGCATTGAGCGTCGAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTCGAGTT
23259522 GGTATA
196 GGTATA
* *
23259528 CTTCTCTGTATTTCATCAGGAAGATGACCACCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
*
23259593 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGTTTCGA
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
*
23259658 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTAAGCGTC-AGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTCGAG-T
* *
23259722 TGATTGTCTT
195 TG---GTATA
*
23259732 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
*
23259797 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
* * * *
23259862 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTAGCTCGCATCGAGTGTTGAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTCGAGTT
23259927 GGTATA
196 GGTATA
23259933 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
23259967 GTTATTTGTG
Statistics
Matches: 404, Mismatches: 30, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
200 2 0.00
201 214 0.53
204 186 0.46
205 2 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCAT
CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCGTCGAGTT
GGTATA
Found at i:23260493 original size:50 final size:50
Alignment explanation
Indices: 23260224--23260652 Score: 247
Period size: 50 Copynumber: 8.6 Consensus size: 50
23260214 GTTCGCCCTC
* *** * * *
23260224 GCGACTTAAACCTTTTCCCTTCAAATCTTC-GTGGTACTAGATTCACCGTT
1 GCGACTTAAATC-TTTCCCTTCTTGTCTTCTGAGGTACTAGATCCGCCGTT
* * ** * * **
23260274 GTGGCTTAAATCTTTCTTTTCCTGTCTTTTGAGGTAC-ACGATTTGCC-TT
1 GCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACTA-GATCCGCCGTT
* * * *
23260323 CGTGACTTAAACCTTTCCCTT-TTGTATCTT-TGTGGTACTGGATCCGCCGTT
1 -GCGACTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTAGATCCGCCGTT
* * * * * *
23260374 GTGGCCTTAGATCTTTCCCTTCATGTCTTCATGA--TACTGGATTTC-CCGTT
1 G-CGACTTAAATCTTTCCCTTCTTGTCTTC-TGAGGTACTAGA-TCCGCCGTT
* * *
23260424 GCGGCTGAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-ACAGTCCGCCGTT
1 GCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACTAGA-TCCGCCGTT
* * *
23260474 GCGACTTAAACCTTTCCCTT-TTGTATCTT-TGTGGTACTGGATCCGCCGTT
1 GCGACTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTAGATCCGCCGTT
* * * * * *
23260524 GCAGTCTTAGATCTTTCCCTTCATGTCTTC--ATGGTACTGGATTCGCCATT
1 GC-GACTTAAATCTTTCCCTTCTTGTCTTCTGA-GGTACTAGATCCGCCGTT
* *
23260574 GCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACATAG-TTCGCCGTT
1 GCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TAGATCCGCCGTT
* * * *
23260624 ACGACTTAGACCTTTCCCTTCATGTCTTC
1 GCGACTTAAATCTTTCCCTTCTTGTCTTC
23260653 CTGGTACTGA
Statistics
Matches: 294, Mismatches: 60, Indels: 50
0.73 0.15 0.12
Matches are distributed among these distances:
48 3 0.01
49 69 0.23
50 170 0.58
51 46 0.16
52 6 0.02
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (50 bp):
GCGACTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACTAGATCCGCCGTT
Found at i:23260508 original size:150 final size:150
Alignment explanation
Indices: 23260237--23260643 Score: 568
Period size: 150 Copynumber: 2.7 Consensus size: 150
23260227 ACTTAAACCT
** * * * ** *
23260237 TTTCCCTTCAAATCTTCGTGGTACTAGATTCACCGTTGTGGCTTAAATCTTTCTTTTCCTGTCTT
1 TTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTT
* * *
23260302 TTGAGGTACAC-GATTTGCC-TTCGTGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGA
66 CTGAGGTACACAG-TTCGCCGTT-GCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGA
**
23260365 TCCGCCGTTGTGGCCTTAGATC
129 TCCGCCGTTGCAGCCTTAGATC
* *
23260387 TTTCCCTTCATGTCTTCATGATACTGGATTTC-CCGTTGCGGCTGAAATCTTTCCCTTCTTGTCT
1 TTTCCCTTCATGTCTTCATGGTACTGGA-TTCACCGTTGCGGCTTAAATCTTTCCCTTCTTGTCT
*
23260451 TCTGAGGTACACAGTCCGCCGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGAT
65 TCTGAGGTACACAGTTCGCCGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGAT
*
23260516 CCGCCGTTGCAGTCTTAGATC
130 CCGCCGTTGCAGCCTTAGATC
* *
23260537 TTTCCCTTCATGTCTTCATGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCTTGTCTT
1 TTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTT
* * *
23260602 CTGAGGTACATAGTTCGCCGTTACGACTTAGACCTTTCCCTT
66 CTGAGGTACACAGTTCGCCGTTGCGACTTAAACCTTTCCCTT
23260644 CATGTCTTCC
Statistics
Matches: 229, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
149 3 0.01
150 220 0.96
151 6 0.03
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.40
Consensus pattern (150 bp):
TTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTT
CTGAGGTACACAGTTCGCCGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATC
CGCCGTTGCAGCCTTAGATC
Found at i:23260610 original size:100 final size:98
Alignment explanation
Indices: 23260237--23260661 Score: 301
Period size: 100 Copynumber: 4.3 Consensus size: 98
23260227 ACTTAAACCT
** * * * * ** *
23260237 TTTCCCTTCAAATCTTCGTGGTACTAGATTCACCGTTGTGGCTTAAATCTTTCTTTTCCTGTCTT
1 TTTCCCTTCATGTCTTC-TGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTT
* ** * * * *
23260302 TTGAGGTACACGATTTGCC-TTCGTGACTTAAACC
65 CTGAGGTACTGGATTCGCCGTT-GCGACTTAGATC
* * * * *
23260336 TTTCCCTT-TTGTATCTTTGTGGTACTGGATCCGCCGTTGTGGCCTTAGATCTTTCCCTTCATGT
1 TTTCCCTTCATG--TC-TTCTGGTACTGGATCCGCCGTTGCGG-CTTAAATCTTTCCCTTCTTGT
* * *
23260400 CTTCATGA--TACTGGATTTC-CCGTTGCGGCTGAAATC
62 CTTC-TGAGGTACTGGA-TTCGCCGTTGCGACTTAGATC
* ** * *
23260436 TTTCCCTTCTTGTCTTCTGAGGTAC-ACAGTCCGCCGTTGCGACTTAAACCTTTCCCTT-TTGTA
1 TTTCCCTTCATGTCTTCT--GGTACTGGA-TCCGCCGTTGCGGCTTAAATCTTTCCCTTCTTG--
* * *
23260499 TCTT-TGTGGTACTGGATCCGCCGTTGCAGTCTTAGATC
61 TCTTCTGAGGTACTGGATTCGCCGTTGC-GACTTAGATC
* *
23260537 TTTCCCTTCATGTCTTCATGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCTTGTCTT
1 TTTCCCTTCATGTCTTC-TGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTT
* * *
23260602 CTGAGGTACATAG-TTCGCCGTTACGACTTAGACC
65 CTGAGGTAC-TGGATTCGCCGTTGCGACTTAGATC
23260636 TTTCCCTTCATGTCTTCCTGGTACTG
1 TTTCCCTTCATGTCTT-CTGGTACTG
23260662 AGACCTGTAG
Statistics
Matches: 258, Mismatches: 45, Indels: 46
0.74 0.13 0.13
Matches are distributed among these distances:
98 7 0.03
99 63 0.24
100 126 0.49
101 58 0.22
102 4 0.02
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (98 bp):
TTTCCCTTCATGTCTTCTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTC
TGAGGTACTGGATTCGCCGTTGCGACTTAGATC
Found at i:23261940 original size:15 final size:16
Alignment explanation
Indices: 23261905--23261939 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
23261895 TTGTTTTTGC
23261905 TTTTCTTCTTTTTCTT
1 TTTTCTTCTTTTTCTT
23261921 TTTTCTCTCTTTTT-TT
1 TTTTCT-TCTTTTTCTT
23261937 TTT
1 TTT
23261940 CGTCATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTCTTTTTCTT
Found at i:23267530 original size:26 final size:26
Alignment explanation
Indices: 23267452--23267530 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
23267442 TTCTGAATGT
* * ** *
23267452 AATTCTGGACGTTCTCATGCAGCGAT
1 AATTCTGGACATGCTCATATAGCGAC
* * *
23267478 AATTCTGGACATGTTCATGTAGTGAC
1 AATTCTGGACATGCTCATATAGCGAC
*
23267504 AATTTTGGACATGCTCATATAGCGAC
1 AATTCTGGACATGCTCATATAGCGAC
23267530 A
1 A
23267531 TTAGTAGTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (26 bp):
AATTCTGGACATGCTCATATAGCGAC
Found at i:23269102 original size:14 final size:14
Alignment explanation
Indices: 23269083--23269110 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23269073 ACCTTATCGA
23269083 TGACTGAGGTACCG
1 TGACTGAGGTACCG
23269097 TGACTGAGGTACCG
1 TGACTGAGGTACCG
23269111 AATGTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (14 bp):
TGACTGAGGTACCG
Found at i:23271064 original size:20 final size:21
Alignment explanation
Indices: 23271041--23271079 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
23271031 GTCATGTGGT
*
23271041 TGAGATACATGG-CGTGTGAC
1 TGAGATACACGGCCGTGTGAC
*
23271061 TGAGGTACACGGCCGTGTG
1 TGAGATACACGGCCGTGTG
23271080 GGCAGACCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.23
Consensus pattern (21 bp):
TGAGATACACGGCCGTGTGAC
Found at i:23271362 original size:30 final size:30
Alignment explanation
Indices: 23271272--23271347 Score: 152
Period size: 30 Copynumber: 2.5 Consensus size: 30
23271262 CTTTTTATGT
23271272 GGCACACAACCATGTGAGCCACCCGTGTGC
1 GGCACACAACCATGTGAGCCACCCGTGTGC
23271302 GGCACACAACCATGTGAGCCACCCGTGTGC
1 GGCACACAACCATGTGAGCCACCCGTGTGC
23271332 GGCACACAACCATGTG
1 GGCACACAACCATGTG
23271348 GACTACTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.25, C:0.36, G:0.26, T:0.13
Consensus pattern (30 bp):
GGCACACAACCATGTGAGCCACCCGTGTGC
Found at i:23273471 original size:20 final size:21
Alignment explanation
Indices: 23273446--23273484 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
23273436 TTTAGGGTTT
23273446 AAGAAGAAAA-AAGAAAAAAA
1 AAGAAGAAAAGAAGAAAAAAA
23273466 AAGAAGAAAAGAAGAAAAA
1 AAGAAGAAAAGAAGAAAAA
23273485 GGAGAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAGAAGAAAAGAAGAAAAAAA
Found at i:23273483 original size:17 final size:17
Alignment explanation
Indices: 23273449--23273498 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
23273439 AGGGTTTAAG
23273449 AAGAA-AAAAGAAAAAAA
1 AAGAAGAAAAG-AAAAAA
*
23273466 AAGAAGAAAAGAAGAAA
1 AAGAAGAAAAGAAAAAA
* *
23273483 AAGGAGAAGAGAAAAA
1 AAGAAGAAAAGAAAAA
23273499 TGGAGATGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAGAAAAAA
Found at i:23274214 original size:51 final size:45
Alignment explanation
Indices: 23274148--23274302 Score: 179
Period size: 44 Copynumber: 3.4 Consensus size: 45
23274138 GCTCATATTT
* * *
23274148 AAAGTTTAGATAACCATATGGCTAAGTTTAGAATACAAAAGATGAAATACA
1 AAAGTTTAGACAACCATATGCCTAATTTTAGAAT--AAAAG-T---ATACA
* *
23274199 AAAGTTTAGACAACCATATGCCTAATTTTAG-ATAATAGTTTACA
1 AAAGTTTAGACAACCATATGCCTAATTTTAGAATAAAAGTATACA
* *
23274243 AAAGTTTAGACAACCATATGCCTAATTTTAG-ATAATAGTTTACA
1 AAAGTTTAGACAACCATATGCCTAATTTTAGAATAAAAGTATACA
23274287 AAAGTTTAGACAACCA
1 AAAGTTTAGACAACCA
23274303 AATTGCATTG
Statistics
Matches: 99, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
44 64 0.65
47 1 0.01
48 4 0.04
50 2 0.02
51 28 0.28
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (45 bp):
AAAGTTTAGACAACCATATGCCTAATTTTAGAATAAAAGTATACA
Found at i:23274250 original size:22 final size:22
Alignment explanation
Indices: 23274225--23274296 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
23274215 TATGCCTAAT
23274225 TTTAGATAATAGTTTACAAAAG
1 TTTAGATAATAGTTTACAAAAG
* * * * ** *
23274247 TTTAGACAACCA-TATGCCTAAT
1 TTTAGATAA-TAGTTTACAAAAG
23274269 TTTAGATAATAGTTTACAAAAG
1 TTTAGATAATAGTTTACAAAAG
23274291 TTTAGA
1 TTTAGA
23274297 CAACCAAATT
Statistics
Matches: 34, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTTAGATAATAGTTTACAAAAG
Found at i:23274258 original size:44 final size:44
Alignment explanation
Indices: 23274195--23274302 Score: 216
Period size: 44 Copynumber: 2.5 Consensus size: 44
23274185 AAAGATGAAA
23274195 TACAAAAGTTTAGACAACCATATGCCTAATTTTAGATAATAGTT
1 TACAAAAGTTTAGACAACCATATGCCTAATTTTAGATAATAGTT
23274239 TACAAAAGTTTAGACAACCATATGCCTAATTTTAGATAATAGTT
1 TACAAAAGTTTAGACAACCATATGCCTAATTTTAGATAATAGTT
23274283 TACAAAAGTTTAGACAACCA
1 TACAAAAGTTTAGACAACCA
23274303 AATTGCATTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (44 bp):
TACAAAAGTTTAGACAACCATATGCCTAATTTTAGATAATAGTT
Found at i:23274769 original size:21 final size:21
Alignment explanation
Indices: 23274745--23274818 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
23274735 CAGTTTGCAA
23274745 CTGAGTTGGGGTAGCCTCTTG
1 CTGAGTTGGGGTAGCCTCTTG
* *
23274766 CTGAGTTGGGAT-GCTCTCTTA
1 CTGAGTTGGGGTAGC-CTCTTG
* * * *
23274787 TTGATTTGGGGTAGCTTGTTG
1 CTGAGTTGGGGTAGCCTCTTG
23274808 CTGAGTTGGGG
1 CTGAGTTGGGG
23274819 CAACCACTTG
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.11, C:0.14, G:0.38, T:0.38
Consensus pattern (21 bp):
CTGAGTTGGGGTAGCCTCTTG
Found at i:23276803 original size:43 final size:42
Alignment explanation
Indices: 23276755--23276889 Score: 216
Period size: 43 Copynumber: 3.1 Consensus size: 42
23276745 AACAAGACCC
*
23276755 TAAACAATAAACATTAAACAACTATCTTTCATTCAATAAACAA
1 TAAACAATAAACATTAAACAACTAT-TGTCATTCAATAAACAA
*
23276798 TAAACAATAAACATTAAACATCTATATGTCATTCAATAAACAA
1 TAAACAATAAACATTAAACAACTAT-TGTCATTCAATAAACAA
*
23276841 TAAACAATAAACATTAAACAACTATTCGCCATTCAATAAACAA
1 TAAACAATAAACATTAAACAACTATT-GTCATTCAATAAACAA
23276884 TAAACA
1 TAAACA
23276890 TTGTCCCAGA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
42 1 0.01
43 85 0.99
ACGTcount: A:0.54, C:0.19, G:0.01, T:0.26
Consensus pattern (42 bp):
TAAACAATAAACATTAAACAACTATTGTCATTCAATAAACAA
Found at i:23276818 original size:7 final size:7
Alignment explanation
Indices: 23276788--23276817 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
23276778 ATCTTTCATT
23276788 CAATAAA
1 CAATAAA
23276795 CAATAAA
1 CAATAAA
23276802 CAATAAA
1 CAATAAA
*
23276809 CATTAAA
1 CAATAAA
23276816 CA
1 CA
23276818 TCTATATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (7 bp):
CAATAAA
Found at i:23276843 original size:7 final size:7
Alignment explanation
Indices: 23276831--23276861 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
23276821 ATATGTCATT
23276831 CAATAAA
1 CAATAAA
23276838 CAATAAA
1 CAATAAA
23276845 CAATAAA
1 CAATAAA
*
23276852 CATTAAA
1 CAATAAA
23276859 CAA
1 CAA
23276862 CTATTCGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (7 bp):
CAATAAA
Found at i:23276933 original size:51 final size:51
Alignment explanation
Indices: 23276874--23277041 Score: 291
Period size: 51 Copynumber: 3.3 Consensus size: 51
23276864 ATTCGCCATT
* *
23276874 CAATAAACAATAAACATTGTCCCAGACAATAAACTTCATTTTCATGGCATA
1 CAATAAACAATAAACATTGTCCCAGACAATAAACATCAGTTTCATGGCATA
*
23276925 CAATAAACAATAAACATTGTCCCAGAGAATAAACATCAGTTTCATGGCATA
1 CAATAAACAATAAACATTGTCCCAGACAATAAACATCAGTTTCATGGCATA
* *
23276976 CAATAAACAATAAACATTGTCCCGGACAATAATCATCAGTTTCATGGCATA
1 CAATAAACAATAAACATTGTCCCAGACAATAAACATCAGTTTCATGGCATA
23277027 CAATAAACAATAAAC
1 CAATAAACAATAAAC
23277042 CCTAAACAGT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 111 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (51 bp):
CAATAAACAATAAACATTGTCCCAGACAATAAACATCAGTTTCATGGCATA
Found at i:23276984 original size:25 final size:25
Alignment explanation
Indices: 23276952--23277035 Score: 68
Period size: 25 Copynumber: 3.3 Consensus size: 25
23276942 TGTCCCAGAG
23276952 AATAAACATCAGTTTCATGGCATAC
1 AATAAACATCAGTTTCATGGCATAC
**
23276977 AATAAACAATAAACA-TTGTCCCGG---AC
1 AATAAAC-AT---CAGTT-TCATGGCATAC
*
23277003 AATAATCATCAGTTTCATGGCATAC
1 AATAAACATCAGTTTCATGGCATAC
23277028 AATAAACA
1 AATAAACA
23277036 ATAAACCCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
22 6 0.14
23 2 0.05
25 18 0.41
26 10 0.23
28 2 0.05
29 6 0.14
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (25 bp):
AATAAACATCAGTTTCATGGCATAC
Found at i:23277255 original size:6 final size:6
Alignment explanation
Indices: 23277232--23277311 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
23277222 AAATAACTCT
* * * ** *
23277232 AAATCGA AAATCA CAATCC AAATCG AAATCA AAAT-- AACCCT AAATCAA
1 AAATC-A AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATC-A
* *
23277280 AAATCA CAATCA ATATCA AAATCA AAATCA AA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AA
23277312 TAAACCCAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
4 2 0.04
6 44 0.79
7 10 0.18
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:23277283 original size:41 final size:41
Alignment explanation
Indices: 23277222--23277307 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
23277212 ACCAAAGTCG
* * *
23277222 AAATAACTCTAAATCGAAAATCACAATCCAA-ATCGAAATCA
1 AAATAACCCTAAATCAAAAATCACAAT-CAATATCAAAATCA
23277263 AAATAACCCTAAATCAAAAATCACAATCAATATCAAAATCA
1 AAATAACCCTAAATCAAAAATCACAATCAATATCAAAATCA
23277304 AAAT
1 AAAT
23277308 CAAATAAACC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 3 0.07
41 38 0.93
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.20
Consensus pattern (41 bp):
AAATAACCCTAAATCAAAAATCACAATCAATATCAAAATCA
Found at i:23277322 original size:41 final size:40
Alignment explanation
Indices: 23277238--23277323 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 40
23277228 CTCTAAATCG
* * *
23277238 AAAATCACAATCCAAATCGAAATCAAAATAACCCTAAATCA
1 AAAATCACAATCCAAATCAAAATCAAAATAA-CATAAACCA
*
23277279 AAAATCACAAT-CAATATCAAAATCAAAATCAA-ATAAACCC
1 AAAATCACAATCCAA-ATCAAAATCAAAAT-AACATAAACCA
23277319 AAAAT
1 AAAAT
23277324 AACCCTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
40 13 0.33
41 24 0.62
42 2 0.05
ACGTcount: A:0.59, C:0.22, G:0.01, T:0.17
Consensus pattern (40 bp):
AAAATCACAATCCAAATCAAAATCAAAATAACATAAACCA
Found at i:23283629 original size:10 final size:10
Alignment explanation
Indices: 23283614--23283650 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
23283604 GTTATTTTTA
23283614 AAAAAAATTC
1 AAAAAAATTC
23283624 AAAAAAATTC
1 AAAAAAATTC
23283634 --AAAAATTC
1 AAAAAAATTC
23283642 AAAACAAAT
1 AAAA-AAAT
23283651 AGTACATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.33
10 12 0.50
11 4 0.17
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:23283690 original size:26 final size:27
Alignment explanation
Indices: 23283657--23283709 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
23283647 AAATAGTACA
*
23283657 TTTATTTTCATT-TTCATT-TTTTTATT
1 TTTATTTT-ATTATGCATTATTTTTATT
23283683 TTTATTTTATTATGCATTATTTTTATT
1 TTTATTTTATTATGCATTATTTTTATT
23283710 CCTATGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 13 0.54
27 8 0.33
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTATTTTATTATGCATTATTTTTATT
Found at i:23285678 original size:30 final size:30
Alignment explanation
Indices: 23285619--23285679 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23285609 TAGATTTTAG
* **
23285619 GAGCCACACGGGTTGGACACACGGTCATGT
1 GAGCCACACAGGTTGGACACACGACCATGT
*
23285649 GAGCCACACAGGTTGGGCACACGACCATGT
1 GAGCCACACAGGTTGGACACACGACCATGT
23285679 G
1 G
23285680 CTAGACCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.28, G:0.33, T:0.15
Consensus pattern (30 bp):
GAGCCACACAGGTTGGACACACGACCATGT
Found at i:23288422 original size:153 final size:151
Alignment explanation
Indices: 23287913--23288455 Score: 710
Period size: 150 Copynumber: 3.6 Consensus size: 151
23287903 AGAAAGGGGG
* ** * ** *
23287913 AAAGAGA-GTTAATTTTTTAATTGTTTTTAATTTATTTTAAAAATATTTTGTTTTTAATTTAATT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTG---TT-A-GTAATT
* * * * *
23287977 ATTATAAATT-TTAGTTTAGTTTAATGTT--TATAATTTG-TTTGTTATAAATTTTTTTTGTTTA
61 ATTATAAATTATTTGTTTAGTTTAATGTTGGT-TCATGTGATTTTTTATAAAATTTTTTTGTTTA
* **
23288038 GTAGAGTAGATTAAAGGGGAAAAAAGCC
125 GTAGAGTAGATTAAA-GGGAAGAAAGTA
* * * *
23288066 AAAGAGATGT--ATTTTTTTTTTGTTTTTAATTTAATTTAAAGTTATATTATTAGTAATTATTAT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
23288129 AAATTATTTGTTTAGTTTAATGTTGGTTCATGTGATTTTTTAT-AAATTTTTTTGTTTAGTAGAG
66 AAATTATTTGTTTAGTTTAATGTTGGTTCATGTGATTTTTTATAAAATTTTTTTGTTTAGTAGAG
23288193 TAGATTAAAGGGAAGAAAGTCA
131 TAGATTAAAGGGAAGAAAGT-A
*
23288215 AAAGAGAGG-AAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATCATTAT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
*
23288279 AAATTATTTGTTTAGTTTAATGTTGGTTCATGTGATTTTTTATAAAAAATTTTTTGTTTA-TCAG
66 AAATTATTTGTTTAGTTTAATGTTGGTTCATGTGATTTTTTAT-AAAATTTTTTTGTTTAGT-AG
23288343 AGTAGATTAAAGGGAAGAAAGATA
129 AGTAGATTAAAGGGAAGAAAG-TA
* *
23288367 AAAGAAAGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
23288432 AAATTATTTGTTTAGTTTAATGTT
66 AAATTATTTGTTTAGTTTAATGTT
23288456 TATTTGATTT
Statistics
Matches: 352, Mismatches: 25, Indels: 26
0.87 0.06 0.06
Matches are distributed among these distances:
147 15 0.04
148 27 0.08
149 44 0.12
150 100 0.28
151 1 0.00
152 78 0.22
153 85 0.24
154 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (151 bp):
AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
AAATTATTTGTTTAGTTTAATGTTGGTTCATGTGATTTTTTATAAAATTTTTTTGTTTAGTAGAG
TAGATTAAAGGGAAGAAAGTA
Found at i:23289548 original size:41 final size:41
Alignment explanation
Indices: 23289489--23289602 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
23289479 CTTGGATAAG
* * *
23289489 AATTCAAGCTTCGACTTAGCAGGCTATGAGTTGGTGATGAA
1 AATTCAAGCTTCGGCTTAGCAGGCTATGAGTCGATGATGAA
*
23289530 AATTCAAGCTTCGGCTTAGCAGGCTATGAGCCGATGATGAA
1 AATTCAAGCTTCGGCTTAGCAGGCTATGAGTCGATGATGAA
* *
23289571 AATTCAAGCTTTGGCTTAGCAGGCTAAGAGTC
1 AATTCAAGCTTCGGCTTAGCAGGCTATGAGTC
23289603 AGTAATAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (41 bp):
AATTCAAGCTTCGGCTTAGCAGGCTATGAGTCGATGATGAA
Found at i:23291594 original size:47 final size:47
Alignment explanation
Indices: 23291513--23291744 Score: 250
Period size: 47 Copynumber: 4.9 Consensus size: 47
23291503 TTTAGTCTGT
* * * *
23291513 CCTCTGTATTTGGGGTATAACATTGGATGGGATGGCTTCAATCTACC
1 CCTCTGGATTTGAGGTATAAGATTGGATGTGATGGCTTCAATCTACC
*** * * * *
23291560 CCTCCAAATTTGAGGTATAAGATTGGATATGATGGCTTAAATTTGCC
1 CCTCTGGATTTGAGGTATAAGATTGGATGTGATGGCTTCAATCTACC
* *
23291607 CCTCTGGATTTGAGGTATAAGACTAGATGTGATGGCTTCAATCTACC
1 CCTCTGGATTTGAGGTATAAGATTGGATGTGATGGCTTCAATCTACC
* * * * ** *
23291654 TCTTTGGATTTAAGGTATAAGATTGAAT-TGGATAACTTTAATCTACC
1 CCTCTGGATTTGAGGTATAAGATTGGATGT-GATGGCTTCAATCTACC
* *
23291701 CCTCTGGATTTGAGGTATAATATTGGATGTGACGGCTTCAATCT
1 CCTCTGGATTTGAGGTATAAGATTGGATGTGATGGCTTCAATCT
23291745 GTCCATTGAT
Statistics
Matches: 146, Mismatches: 37, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
46 1 0.01
47 144 0.99
48 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (47 bp):
CCTCTGGATTTGAGGTATAAGATTGGATGTGATGGCTTCAATCTACC
Found at i:23293594 original size:46 final size:46
Alignment explanation
Indices: 23293453--23293911 Score: 640
Period size: 46 Copynumber: 10.1 Consensus size: 46
23293443 GACGCGATCA
* * *
23293453 CCCCTCTAGA-TTAGGGGTAAAATATTGGATGGTGGTTTCAATCTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* *
23293498 CCCCT-TTAACTTAGGGGTAAAAGATTGGA---TGGCTTCAATCTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
*
23293540 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTA
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
23293586 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* *
23293632 CCTCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATTTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* *
23293678 CCCCTCTTGAGTTAGGGGTAAAAGATTGGATGGTGGCTTTAATCTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* * * *
23293724 CCCCTCTTGACTTAGGGGTAAAACATTAGATGGTGGCTTTAATCTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* * * * * *
23293770 CCTCTCTTGACTTAAGGGTATAAGATTGGATAGTGGCTTCAATCTT
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* * *
23293816 CCCCTCTTGATTTAGGGATAAAAGATTGGATAGTGGCTTTAATCTG
1 CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
* * *
23293862 CCTCTCTTGACTTAAGGGGTAAAAGATTGGATGGTGACTTCAATCTG
1 CCCCTCTTGA-TTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
23293909 CCC
1 CCC
23293912 TTATTAACTT
Statistics
Matches: 369, Mismatches: 39, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
42 17 0.05
43 22 0.06
44 2 0.01
45 23 0.06
46 272 0.74
47 33 0.09
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (46 bp):
CCCCTCTTGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
Found at i:23316167 original size:15 final size:14
Alignment explanation
Indices: 23316149--23316194 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
23316139 TCAAATTACA
23316149 AAACCCAATACCACT
1 AAACCCAA-ACCACT
*
23316164 AAACCCTAAAACACT
1 AAACCC-AAACCACT
23316179 AAACCCAAACC-CT
1 AAACCCAAACCACT
23316192 AAA
1 AAA
23316195 ACTAAACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 5 0.18
14 4 0.14
15 17 0.61
16 2 0.07
ACGTcount: A:0.52, C:0.37, G:0.00, T:0.11
Consensus pattern (14 bp):
AAACCCAAACCACT
Found at i:23316235 original size:47 final size:47
Alignment explanation
Indices: 23316179--23316303 Score: 198
Period size: 47 Copynumber: 2.7 Consensus size: 47
23316169 CTAAAACACT
*
23316179 AAACCCAAACCCTAAA-ACTAAACCTTAACCCAATTACTTTACCCAAC
1 AAACCCAAACCC-AAACACTAAACCTTAACCCAATTACTTGACCCAAC
* *
23316226 AGACCCAAACCCAAACACTAAACCCTAACCCAATTACTTGACCCAAC
1 AAACCCAAACCCAAACACTAAACCTTAACCCAATTACTTGACCCAAC
*
23316273 AAACCCAAACCCAAACACTAAACCTAAACCC
1 AAACCCAAACCCAAACACTAAACCTTAACCC
23316304 TAAAACTAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
46 3 0.04
47 68 0.96
ACGTcount: A:0.46, C:0.39, G:0.02, T:0.14
Consensus pattern (47 bp):
AAACCCAAACCCAAACACTAAACCTTAACCCAATTACTTGACCCAAC
Found at i:23316250 original size:13 final size:13
Alignment explanation
Indices: 23316149--23316250 Score: 53
Period size: 13 Copynumber: 7.5 Consensus size: 13
23316139 TCAAATTACA
23316149 AAACCCAATACCACT
1 AAACCCAA-A-CACT
23316164 AAACCCTAAAACACT
1 AAACCC--AAACACT
*
23316179 AAACCCAAACCCT
1 AAACCCAAACACT
* *
23316192 AAAACTAAAC-CT
1 AAACCCAAACACT
* **
23316204 TAACCCAATTACT
1 AAACCCAAACACT
** * *
23316217 TTACCCAACAGACCC
1 AAACCCAA-ACA-CT
23316232 AAACCCAAACACT
1 AAACCCAAACACT
23316245 AAACCC
1 AAACCC
23316251 TAACCCAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
12 7 0.11
13 30 0.45
14 3 0.05
15 23 0.35
16 1 0.02
17 2 0.03
ACGTcount: A:0.47, C:0.38, G:0.01, T:0.14
Consensus pattern (13 bp):
AAACCCAAACACT
Found at i:23316301 original size:13 final size:13
Alignment explanation
Indices: 23316273--23316319 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
23316263 TTGACCCAAC
*
23316273 AAACCC-AAACCC
1 AAACCCTAAACCT
*
23316285 AAACACTAAACCT
1 AAACCCTAAACCT
*
23316298 AAACCCTAAAACT
1 AAACCCTAAACCT
23316311 AAACCCTAA
1 AAACCCTAA
23316320 CCCAATTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 5 0.17
13 25 0.83
ACGTcount: A:0.53, C:0.36, G:0.00, T:0.11
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:23316301 original size:19 final size:18
Alignment explanation
Indices: 23316273--23316324 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
23316263 TTGACCCAAC
*
23316273 AAACCCAAACCCAAACACT
1 AAACCTAAACCCAAA-ACT
23316292 AAACCTAAACCCTAAAACT
1 AAACCTAAACCC-AAAACT
23316311 AAACCCT-AACCCAA
1 AAA-CCTAAACCCAA
23316325 TTACTTGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 22 0.73
20 6 0.20
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.10
Consensus pattern (18 bp):
AAACCTAAACCCAAAACT
Found at i:23316302 original size:66 final size:65
Alignment explanation
Indices: 23316232--23316365 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 65
23316222 CAACAGACCC
23316232 AAACCC-AAACACTAAACCCTAACCCAATTACTTGACCCAACAAACCCAAACCCAAACACTAAAC
1 AAACCCTAAA-ACTAAACCCTAACCCAATTACTTGACCCAACAAACCCAAACCCAAA-ACTAAAC
23316296 CT
64 CT
* *
23316298 AAACCCTAAAACTAAACCCTAACCCAATTACTTGACCCAACAGACCCAAACCCAAAATTAAACCT
1 AAACCCTAAAACTAAACCCTAACCCAATTACTTGACCCAACAAACCCAAACCCAAAACTAAACCT
23316363 AAA
1 AAA
23316366 GTCAAACCCT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
65 11 0.17
66 51 0.78
67 3 0.05
ACGTcount: A:0.48, C:0.37, G:0.02, T:0.13
Consensus pattern (65 bp):
AAACCCTAAAACTAAACCCTAACCCAATTACTTGACCCAACAAACCCAAACCCAAAACTAAACCT
Found at i:23317765 original size:30 final size:30
Alignment explanation
Indices: 23317729--23317975 Score: 270
Period size: 30 Copynumber: 8.3 Consensus size: 30
23317719 CCATAATTAT
23317729 ATTTTAACCCCTAAACTTTTCTAAAATCAC
1 ATTTTAACCCCTAAACTTTTCTAAAATCAC
* * *
23317759 ATTTTAA-CGCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCCTAAACTTTTCTAAAATCAC
*
23317788 ATTTTAA-CCCTCAAAC-TTTCTTAAAATTAC
1 ATTTTAACCCCT-AAACTTTTC-TAAAATCAC
* *
23317818 ATTTTAA-CCCTAAAATTTTCTAAAATCAT
1 ATTTTAACCCCTAAACTTTTCTAAAATCAC
* * *
23317847 ATTATAACCCCTAAACATTCCTAAAATCAC
1 ATTTTAACCCCTAAACTTTTCTAAAATCAC
* *
23317877 ATTTTAACCCCCAAGA-TTTTCTAAAATTAC
1 ATTTTAACCCCTAA-ACTTTTCTAAAATCAC
* * * *
23317907 ATTTTAACCCTTAAACTTCTCCAAAATTAC
1 ATTTTAACCCCTAAACTTTTCTAAAATCAC
* * *
23317937 ATTTTAACCCTTAAACTTTCCCAAAATCAC
1 ATTTTAACCCCTAAACTTTTCTAAAATCAC
23317967 ATTTTAACC
1 ATTTTAACC
23317976 TCGAAATTCT
Statistics
Matches: 186, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
29 50 0.27
30 135 0.73
31 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTTTCTAAAATCAC
Found at i:23317963 original size:60 final size:59
Alignment explanation
Indices: 23317712--23317975 Score: 284
Period size: 59 Copynumber: 4.4 Consensus size: 59
23317702 AGAGCCACTG
* * * * *
23317712 AACTCTTCCATAATTATATTTTAACCCCTAAACTTTTCTAAAATCACATTTTAACGCTA
1 AACTTTTCCAAAATTACATTTTAACCCCTAAACTTCTCTAAAATCACATTTTAACCCTA
*
23317771 AACTTTTCCAAAATTACATTTTAA-CCCTCAAACTT-TCTTAAAATTACATTTTAACCCTA
1 AACTTTTCCAAAATTACATTTTAACCCCT-AAACTTCTC-TAAAATCACATTTTAACCCTA
* * * * * *
23317830 AAATTTTCTAAAATCATATTATAACCCCTAAACATTC-CTAAAATCACATTTTAACCCCCA
1 AACTTTTCCAAAATTACATTTTAACCCCTAAAC-TTCTCTAAAATCACATTTTAA-CCCTA
* * * *
23317890 AGA-TTTTCTAAAATTACATTTTAACCCTTAAACTTCTCCAAAATTACATTTTAACCCTTA
1 A-ACTTTTCCAAAATTACATTTTAACCCCTAAACTTCTCTAAAATCACATTTTAACCC-TA
* *
23317950 AACTTTCCCAAAATCACATTTTAACC
1 AACTTTTCCAAAATTACATTTTAACC
23317976 TCGAAATTCT
Statistics
Matches: 173, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
58 6 0.03
59 91 0.53
60 75 0.43
61 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.37
Consensus pattern (59 bp):
AACTTTTCCAAAATTACATTTTAACCCCTAAACTTCTCTAAAATCACATTTTAACCCTA
Found at i:23330181 original size:74 final size:74
Alignment explanation
Indices: 23330060--23330230 Score: 279
Period size: 74 Copynumber: 2.3 Consensus size: 74
23330050 AGCGGTCATT
*
23330060 TTCCTGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACGAATGAGACTTTA
1 TTCCTGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACGAATGAGACTTCA
23330125 AACCCCATC
66 AACCCCATC
* *
23330134 TTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGCGACTTCA
1 TTCCTGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACGAATGAGACTTCA
23330199 AACCCCATC
66 AACCCCATC
** *
23330208 TTCCAAATGAGATATAGAGAAGT
1 TTCCTGATGAGA-ACAGAGAAGT
23330231 GAGTCAAAGC
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
74 81 0.90
75 9 0.10
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (74 bp):
TTCCTGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACGAATGAGACTTCA
AACCCCATC
Found at i:23330268 original size:196 final size:196
Alignment explanation
Indices: 23329934--23330352 Score: 676
Period size: 196 Copynumber: 2.1 Consensus size: 196
23329924 ATGAAGTGGT
*
23329934 CATCTTCCTGATGAGAATAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
1 CATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
** * * *
23329999 TTCAAACCCCATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATTTTCC
66 TTCAAACCCCATCTTCCAAATAAGATACAGAGAAGTGAGTCAAAGCAATAAAGCAGTCATCTTCC
* *
23330064 TGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACGAATGAGACTTTAAACC
131 TGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACAAATGAGACTTCAAACC
23330129 C
196 C
*
23330130 CATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGCGAC
1 CATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
* * *
23330195 TTCAAACCCCATCTTCCAAATGAGATATAGAGAAGTGAGTCAAAGCAATAAATCAGTCATCTTCC
66 TTCAAACCCCATCTTCCAAATAAGATACAGAGAAGTGAGTCAAAGCAATAAAGCAGTCATCTTCC
* * *
23330260 TGATGAGAACAGAGAAGTAGACCAAATCAATGAAATGAAGCTCAATATAAATGAGACTTCAAACC
131 TGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACAAATGAGACTTCAAACC
*
23330325 T
196 C
*
23330326 CATATTCCTGATGAGATACAGAGAAGT
1 CATCTTCCTGATGAGA-ACAGAGAAGT
23330353 GAATTAAAGC
Statistics
Matches: 205, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
196 195 0.95
197 10 0.05
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (196 bp):
CATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
TTCAAACCCCATCTTCCAAATAAGATACAGAGAAGTGAGTCAAAGCAATAAAGCAGTCATCTTCC
TGATGAGAACAGAGAAGTAGACCAAAACAATGAAACGAAGCTCAATACAAATGAGACTTCAAACC
C
Found at i:23330349 original size:122 final size:121
Alignment explanation
Indices: 23330130--23330526 Score: 553
Period size: 122 Copynumber: 3.2 Consensus size: 121
23330120 CTTTAAACCC
* *
23330130 CATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGCGAC
1 CATCTTCCTAATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
** *
23330195 TTCAAACCCCATCTTCCAAATGAGATATAGAGAAGTGAGTCAAAGCAATAAATCAGT
66 TTCAAA-CCCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAATCAGT
* * **
23330252 CATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAATGAAGCTCAATATAAATGAGAC
1 CATCTTCCTAATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
* * * *
23330317 TTCAAACCTCATATTCCTGATGAGATACAGAGAAGTGAATTAAAGCAATAAATCGGT
66 TTCAAACC-CATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAATCAGT
* * * *
23330374 CATCTTCCTAATAAGAACAGAGCAGTAAACCAAATTAATGAAACGAAGCTCAATACGAATGAGAC
1 CATCTTCCTAATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
* * * *
23330439 TTCAAACCCTATCTTCCTGATGAGGTACAGAGAAGTGGGTCAAAGAAATAAA-GAGGT
66 TTCAAACCC-ATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAATCA-GT
23330496 CATCTTCCTAATGAGATACAGAGAAGTAGAC
1 CATCTTCCTAATGAGA-ACAGAGAAGTAGAC
23330527 TAAGAAATGA
Statistics
Matches: 241, Mismatches: 30, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
121 3 0.01
122 226 0.94
123 12 0.05
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (121 bp):
CATCTTCCTAATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAGAC
TTCAAACCCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAATCAGT
Found at i:23330939 original size:17 final size:17
Alignment explanation
Indices: 23330917--23330985 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
23330907 CCGAAAAAAA
23330917 TTAAATTTAAATTTACT
1 TTAAATTTAAATTTACT
23330934 TTAAATTTTAAATGTCCAATACATT
1 TTAAA-TTTAAAT-T----TAC--T
23330959 TTAAATTTAAATTTA-T
1 TTAAATTTAAATTTACT
23330975 TTAAATTTAAA
1 TTAAATTTAAA
23330986 ATTCCAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
16 12 0.27
17 5 0.11
18 7 0.16
19 3 0.07
23 4 0.09
24 7 0.16
25 6 0.14
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (17 bp):
TTAAATTTAAATTTACT
Found at i:23331498 original size:15 final size:16
Alignment explanation
Indices: 23331474--23331503 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23331464 AACTACATAA
23331474 TAAATAAATATAATAT
1 TAAATAAATATAATAT
23331490 TAAAT-AATATAATA
1 TAAATAAATATAATA
23331504 AATAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATAAATATAATAT
Found at i:23332397 original size:29 final size:29
Alignment explanation
Indices: 23332351--23332554 Score: 216
Period size: 30 Copynumber: 6.9 Consensus size: 29
23332341 TCCATATTTT
*
23332351 CATTTTGAACTCTAAACTTCTCCAAAATCA
1 CATTTT-AACCCTAAACTTCTCCAAAATCA
*
23332381 CA-TTTAGACCCTAAACTT-TCCCAAAAACA
1 CATTTTA-ACCCTAAACTTCT-CCAAAATCA
* *
23332410 CATTTTAACCCCCAAACTTTTCCAAAATCA
1 CATTTTAA-CCCTAAACTTCTCCAAAATCA
* * *
23332440 CATTTTGACCCATAAACTTTTCCAAAATTA
1 CATTTTAACCC-TAAACTTCTCCAAAATCA
* *
23332470 TATTTTAACACCTAAACTTCTCCAAAATTA
1 CATTTTAAC-CCTAAACTTCTCCAAAATCA
23332500 CATTTTAACCCTTAAACTTC-CCAAAATCA
1 CATTTTAACCC-TAAACTTCTCCAAAATCA
* * *
23332529 CATTTTGACCCTAAAATTCTCAAAAA
1 CATTTTAACCCTAAACTTCTCCAAAA
23332555 CTTCATTTTT
Statistics
Matches: 150, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.06
29 52 0.35
30 86 0.57
31 3 0.02
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (29 bp):
CATTTTAACCCTAAACTTCTCCAAAATCA
Found at i:23332487 original size:60 final size:58
Alignment explanation
Indices: 23332351--23332554 Score: 239
Period size: 60 Copynumber: 3.4 Consensus size: 58
23332341 TCCATATTTT
* * *
23332351 CATTTTGAACTCTAAACTTCTCCAAAATCACATTTAGACCCTAAACTTTCCCAAAAACA
1 CATTTT-AACCCTAAACTTCTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAATCA
* * * *
23332410 CATTTTAACCCCCAAACTTTTCCAAAATCACATTTTGACCCATAAACTTTTCCAAAATTA
1 CATTTTAA-CCCTAAACTTCTCCAAAATCACATTTTGACCC-TAAACTTTCCCAAAATCA
* * *
23332470 TATTTTAACACCTAAACTTCTCCAAAATTACATTTTAACCCTTAAAC-TTCCCAAAATCA
1 CATTTTAAC-CCTAAACTTCTCCAAAATCACATTTTGACCC-TAAACTTTCCCAAAATCA
* * *
23332529 CATTTTGACCCTAAAATTCTCAAAAA
1 CATTTTAACCCTAAACTTCTCCAAAA
23332555 CTTCATTTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
58 17 0.14
59 52 0.42
60 54 0.44
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (58 bp):
CATTTTAACCCTAAACTTCTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAATCA
Found at i:23339240 original size:12 final size:12
Alignment explanation
Indices: 23339225--23339249 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23339215 ATTAAATAAT
23339225 TAATAGCATTCA
1 TAATAGCATTCA
23339237 TAATAGCATTCA
1 TAATAGCATTCA
23339249 T
1 T
23339250 CATGATAACA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:23341441 original size:17 final size:17
Alignment explanation
Indices: 23341421--23341458 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
23341411 TTGGAGATTG
*
23341421 AATTTACTTTAAATTTA
1 AATTTACTTTAAATTAA
*
23341438 AATTTATTTTAAATTAA
1 AATTTACTTTAAATTAA
23341455 AATT
1 AATT
23341459 AAAAGTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTACTTTAAATTAA
Found at i:23341479 original size:15 final size:16
Alignment explanation
Indices: 23341459--23341492 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
23341449 AATTAAAATT
23341459 AAAAGTCCAAAA-TAC
1 AAAAGTCCAAAATTAC
23341474 AAAAGTCCAAAATTAC
1 AAAAGTCCAAAATTAC
23341490 AAA
1 AAA
23341493 GGCACAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.62, C:0.18, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAAGTCCAAAATTAC
Found at i:23341493 original size:15 final size:15
Alignment explanation
Indices: 23341453--23341493 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
23341443 ATTTTAAATT
23341453 AAAATTA-AAAGTCC
1 AAAATTACAAAGTCC
23341467 AAAA-TACAAAAGTCC
1 AAAATTAC-AAAGTCC
23341482 AAAATTACAAAG
1 AAAATTACAAAG
23341494 GCACAATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.08
14 4 0.17
15 15 0.62
16 3 0.12
ACGTcount: A:0.61, C:0.15, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAATTACAAAGTCC
Found at i:23343307 original size:30 final size:29
Alignment explanation
Indices: 23343269--23343495 Score: 123
Period size: 29 Copynumber: 7.7 Consensus size: 29
23343259 CCCTGGAAGT
*
23343269 CCCT-AAACTATCCAAAAATTGTATTTTGA
1 CCCTCAAACT-TCCAAAAATTATATTTTGA
*
23343298 CCCTCAAACTTTTTCC-AAAATTCTACTTTTGA
1 CCCTCAAAC---TTCCAAAAATTATA-TTTTGA
** *
23343330 CCC-CAAAACTTAAAAAAATTATATTTTTA
1 CCCTC-AAACTTCCAAAAATTATATTTTGA
* *
23343359 CCCTCGAACTTCC-AAAATTCCA-ATTTTCA
1 CCCTCAAACTTCCAAAAATT--ATATTTTGA
23343388 -CCTCGAAACTTCCAAAAATTCCA-ATTTT-A
1 CCCTC-AAACTTCCAAAAATT--ATATTTTGA
* * *
23343417 ACCTCGAAACTTCCAAAAATTACA-TTTCA
1 CCCTC-AAACTTCCAAAAATTATATTTTGA
* * * *
23343446 ACGTCGAAACTTCCAAAAATTACATTTTTGC
1 CCCTC-AAACTTCCAAAAATTATA-TTTTGA
*
23343477 CCCT-AAAATTCCAAAAATT
1 CCCTCAAACTTCCAAAAATT
23343496 CCATTTTTAA
Statistics
Matches: 165, Mismatches: 16, Indels: 34
0.77 0.07 0.16
Matches are distributed among these distances:
28 14 0.08
29 72 0.44
30 48 0.29
31 14 0.08
32 16 0.10
33 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTATATTTTGA
Found at i:23343375 original size:29 final size:30
Alignment explanation
Indices: 23343343--23343510 Score: 182
Period size: 29 Copynumber: 5.7 Consensus size: 30
23343333 CAAAACTTAA
* *
23343343 AAAAATTATATTTTTACCCTCG-AACTTCC
1 AAAAATTACATTTTTAACCTCGAAACTTCC
* * *
23343372 -AAAATTCCAATTTTCACCTCGAAACTTCC
1 AAAAATTACATTTTTAACCTCGAAACTTCC
* *
23343401 AAAAATTCCAATTTTAACCTCGAAACTTCC
1 AAAAATTACATTTTTAACCTCGAAACTTCC
* *
23343431 AAAAATTACA-TTTCAACGTCGAAACTTCC
1 AAAAATTACATTTTTAACCTCGAAACTTCC
* * * *
23343460 AAAAATTACATTTTT-GCCCCTAAAATTCC
1 AAAAATTACATTTTTAACCTCGAAACTTCC
*
23343489 AAAAATTCCATTTTTAACCTCG
1 AAAAATTACATTTTTAACCTCG
23343511 GATGTCCAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
28 16 0.14
29 57 0.49
30 43 0.37
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAATTACATTTTTAACCTCGAAACTTCC
Found at i:23348892 original size:21 final size:21
Alignment explanation
Indices: 23348868--23348920 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
23348858 TGCTAAAGGG
*
23348868 GAAGAAACTAAAGTTGAAGAA
1 GAAGAAACTAAAGATGAAGAA
*
23348889 GAAG-AAGTGAAAGATGAAGAA
1 GAAGAAACT-AAAGATGAAGAA
* *
23348910 AAAGAAGCTAA
1 GAAGAAACTAA
23348921 GGAAGAATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGAAACTAAAGATGAAGAA
Found at i:23349405 original size:17 final size:18
Alignment explanation
Indices: 23349385--23349425 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
23349375 ACATCTTAAC
*
23349385 TGTCATTGCATTTGCA-T
1 TGTCATTGCATTTCCATT
23349402 TGTCATTGCATTTCCATT
1 TGTCATTGCATTTCCATT
23349420 TGTCAT
1 TGTCAT
23349426 GGTATTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.49
Consensus pattern (18 bp):
TGTCATTGCATTTCCATT
Found at i:23350477 original size:26 final size:26
Alignment explanation
Indices: 23350441--23350498 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
23350431 TTACTACTAA
*
23350441 TGTCGCTGTATGAGCATGTCCAGAAT
1 TGTCGCTGTATGAGCACGTCCAGAAT
*
23350467 TGTCGCTGTATGAGCACGTTCAGAAT
1 TGTCGCTGTATGAGCACGTCCAGAAT
23350493 TGTCGC
1 TGTCGC
23350499 CGCATCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (26 bp):
TGTCGCTGTATGAGCACGTCCAGAAT
Found at i:23351111 original size:20 final size:20
Alignment explanation
Indices: 23351086--23351141 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
23351076 TGTAGACTTT
23351086 TACCGATACAAAAAAGCTTC
1 TACCGATACAAAAAAGCTTC
* * *
23351106 TACCGAAACAAATCATGCTTC
1 TACCGATACAAA-AAAGCTTC
23351127 TACCGATACTAAAAA
1 TACCGATAC-AAAAA
23351142 CTCCAAAGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 11 0.38
21 15 0.52
22 3 0.10
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.21
Consensus pattern (20 bp):
TACCGATACAAAAAAGCTTC
Found at i:23351795 original size:28 final size:28
Alignment explanation
Indices: 23351763--23351854 Score: 85
Period size: 36 Copynumber: 3.0 Consensus size: 28
23351753 GATATCCGAT
*
23351763 TTACTCCCTGTTGATCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
**
23351791 TTACTCGTTGTTGACCCAAAGGTCATGATGCTC
1 TTACTCCCTGTTGACCCAAAGGTC---ATG--C
23351824 ATTTTACTCCCTGTTGACCCAAAGGTCATGC
1 ---TTACTCCCTGTTGACCCAAAGGTCATGC
23351855 CTGTTACCAG
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
28 21 0.41
31 4 0.08
33 4 0.08
36 22 0.43
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:23353744 original size:14 final size:15
Alignment explanation
Indices: 23353725--23353762 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
23353715 ACTAACTTTT
23353725 AATTCCATAATT-AA
1 AATTCCATAATTCAA
23353739 AATTCC-TCAATTCAA
1 AATTCCAT-AATTCAA
23353754 AATTCCATA
1 AATTCCATA
23353763 TAAAACTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 10 0.48
15 9 0.43
16 1 0.05
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCCATAATTCAA
Found at i:23356764 original size:27 final size:27
Alignment explanation
Indices: 23356726--23356779 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
23356716 GATATTCGAT
23356726 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
23356753 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
23356780 ATGCTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (27 bp):
TTACTCCCTGTTGACCCAAAGGTCATG
Found at i:23356803 original size:36 final size:36
Alignment explanation
Indices: 23356755--23356851 Score: 158
Period size: 36 Copynumber: 2.7 Consensus size: 36
23356745 AGGTCATGTT
* *
23356755 ACTCCCTGTTGACCCAAAGGTCATGATGCTCATTTC
1 ACTCCCTATTGACCTAAAGGTCATGATGCTCATTTC
* *
23356791 ACTCCCTATTGACCTAAAGGTCATGATTCTCATTTT
1 ACTCCCTATTGACCTAAAGGTCATGATGCTCATTTC
23356827 ACTCCCTATTGACCTAAAGGTCATG
1 ACTCCCTATTGACCTAAAGGTCATG
23356852 CCTATTACTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (36 bp):
ACTCCCTATTGACCTAAAGGTCATGATGCTCATTTC
Found at i:23360480 original size:28 final size:28
Alignment explanation
Indices: 23360444--23360498 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
23360434 TTAAGAACAA
23360444 GAAAAAAGTACAAGAAA-ATGTTTTAATT
1 GAAAAAAGTACAA-AAAGATGTTTTAATT
23360472 GAAAAAAGTACAAAAAGATGTTTTAAT
1 GAAAAAAGTACAAAAAGATGTTTTAAT
23360499 AATCCTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.55, C:0.04, G:0.15, T:0.27
Consensus pattern (28 bp):
GAAAAAAGTACAAAAAGATGTTTTAATT
Found at i:23366303 original size:14 final size:14
Alignment explanation
Indices: 23366284--23366310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23366274 CTTTTACGAT
23366284 AAAATTTATTAACC
1 AAAATTTATTAACC
23366298 AAAATTTATTAAC
1 AAAATTTATTAAC
23366311 TATCTAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATTTATTAACC
Found at i:23370823 original size:67 final size:67
Alignment explanation
Indices: 23370715--23370850 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
23370705 TAATAGTACT
* *
23370715 ATAAAAAACCATTGATTTCTCTCTACTTATTGTTTAAGTTGTTCCCATTTGGTTATCTTTAGCAT
1 ATAAAAAACCATTGATTTCTCCCTACTTATTGTTTAAGTTGTTCCCATTTGGTCATCTTTAGCAT
23370780 AC
66 AC
*
23370782 ATAAAAAACCATTGATTTCTCCCTACTTATTGTTTAAGTTGTTCCTATTTGGTCATCTTTAGCAT
1 ATAAAAAACCATTGATTTCTCCCTACTTATTGTTTAAGTTGTTCCCATTTGGTCATCTTTAGCAT
23370847 AC
66 AC
23370849 AT
1 AT
23370851 TTTTAGCATT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (67 bp):
ATAAAAAACCATTGATTTCTCCCTACTTATTGTTTAAGTTGTTCCCATTTGGTCATCTTTAGCAT
AC
Found at i:23372186 original size:22 final size:23
Alignment explanation
Indices: 23372154--23372197 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
23372144 TATTTTCTAA
23372154 TCTTTATTTGTT-ACTAACTTTTT
1 TCTTTATTTGTTGACT-ACTTTTT
23372177 TCTTT-TTTGTTGACTACTTTT
1 TCTTTATTTGTTGACTACTTTT
23372198 ACATTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (23 bp):
TCTTTATTTGTTGACTACTTTTT
Found at i:23375330 original size:21 final size:24
Alignment explanation
Indices: 23375280--23375336 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 24
23375270 CAAGCATGCA
*
23375280 AACTACCGATACTTCTATACATTC
1 AACTACCGATACTTCTATAAATTC
*
23375304 AACTACCGATAC-TC-A-AAATTT
1 AACTACCGATACTTCTATAAATTC
23375325 AACTACCGATAC
1 AACTACCGATAC
23375337 AACTCAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.39, C:0.28, G:0.05, T:0.28
Consensus pattern (24 bp):
AACTACCGATACTTCTATAAATTC
Found at i:23376034 original size:51 final size:51
Alignment explanation
Indices: 23375972--23376207 Score: 339
Period size: 51 Copynumber: 4.6 Consensus size: 51
23375962 GGAATTTATA
* * * *
23375972 TACTCACGATGACACTGAGTCATCGGACCTTTAATACGTCATGGATCCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGGATTCATT
* *
23376023 TACTCATGATGATACTTAGTCATCGGACCTTTAATCCGTAAAT-GATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGT-AATGGATTCATT
* *
23376074 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGGATTCATT
* * *
23376125 TACTCACAATGACACTTAGTCATTGGACCTTTAATCCGTCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGGATTCATT
* *
23376176 TACTCACGATGATACTTAGTTATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
23376208 TCGTTTATAG
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
50 2 0.01
51 162 0.98
52 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAATGGATTCATT
Found at i:23384407 original size:19 final size:20
Alignment explanation
Indices: 23384383--23384424 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
23384373 CATTCAAAGT
23384383 TTGAATCACTG-TCGCTTTC
1 TTGAATCACTGTTCGCTTTC
*
23384402 TTGAATCATTGTTCGCTTTC
1 TTGAATCACTGTTCGCTTTC
23384422 TTG
1 TTG
23384425 GTGGCATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (20 bp):
TTGAATCACTGTTCGCTTTC
Found at i:23384483 original size:14 final size:15
Alignment explanation
Indices: 23384452--23384484 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23384442 GAAAGAAAGA
*
23384452 TGAATAGTAACCAAT
1 TGAATAGTAACAAAT
23384467 TGAATAGTAA-AAAT
1 TGAATAGTAACAAAT
23384481 TGAA
1 TGAA
23384485 GAAAACACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (15 bp):
TGAATAGTAACAAAT
Found at i:23386198 original size:13 final size:13
Alignment explanation
Indices: 23386180--23386206 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23386170 TACTATTTCA
23386180 TTTAACCATATTT
1 TTTAACCATATTT
23386193 TTTAACCATATTT
1 TTTAACCATATTT
23386206 T
1 T
23386207 AATAGAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAACCATATTT
Found at i:23387148 original size:25 final size:25
Alignment explanation
Indices: 23387108--23387173 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
23387098 CTTCCAGAAT
* * *
23387108 TTAGCTCATACGAGCCAAGATAAGG
1 TTAGCTCTTACAAGCCAAGATAAAG
*
23387133 TTAGCTCTTACAAGCCCAGATAAAG
1 TTAGCTCTTACAAGCCAAGATAAAG
23387158 TTAGCTCTTACAAGCC
1 TTAGCTCTTACAAGCC
23387174 TAGACAGAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (25 bp):
TTAGCTCTTACAAGCCAAGATAAAG
Found at i:23387184 original size:25 final size:25
Alignment explanation
Indices: 23387108--23387184 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 25
23387098 CTTCCAGAAT
* * * * *
23387108 TTAGCTCATACGAGCCAAGATAAGG
1 TTAGCTCTTACAAGCCCAGACAAAG
*
23387133 TTAGCTCTTACAAGCCCAGATAAAG
1 TTAGCTCTTACAAGCCCAGACAAAG
* *
23387158 TTAGCTCTTACAAGCCTAGACAGAG
1 TTAGCTCTTACAAGCCCAGACAAAG
23387183 TT
1 TT
23387185 TAACCAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (25 bp):
TTAGCTCTTACAAGCCCAGACAAAG
Found at i:23391813 original size:34 final size:34
Alignment explanation
Indices: 23391770--23391835 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
23391760 CCAATGATAT
*
23391770 TGTGCCCAACACTAGTCGGATAAACTGACGAATG
1 TGTGCCCAACACTAGTCAGATAAACTGACGAATG
*
23391804 TGTGTCCAACACTAGTCAGATAAACTGACGAA
1 TGTGCCCAACACTAGTCAGATAAACTGACGAA
23391836 ATAAATAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (34 bp):
TGTGCCCAACACTAGTCAGATAAACTGACGAATG
Found at i:23393086 original size:43 final size:43
Alignment explanation
Indices: 23393001--23393241 Score: 256
Period size: 43 Copynumber: 5.6 Consensus size: 43
23392991 TTGACATTGG
*
23393001 GAGGAACATTATTTCCTAAATATT-ATAAGTATGTGA-CTGAATGA
1 GAGGAACATTGTTTCCT-AATATTGA-AAGTATGTGATC-GAATGA
*
23393045 GAGGAACATTGTTTCCTAATATTGAAATTATGTGATCGAATGA
1 GAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAATGA
* * *
23393088 GAGGAAAATTGTTTCCTAATATTGAAAGTATGTGATCGATTGT
1 GAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAATGA
* * * * *
23393131 GTA-GAACACTATTTCCTAATATTGAAAGTATGTGCTCGATTGT
1 G-AGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAATGA
* * * * *
23393174 GTGGAACAATGTTTCCAAATGTTGAAAGTATGTGATCGAAAGA
1 GAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAATGA
* *
23393217 -ATGGAACACTGTTTCCTCATATTGA
1 GA-GGAACATTGTTTCCTAATATTGA
23393242 TGTATTGATC
Statistics
Matches: 168, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
43 149 0.89
44 19 0.11
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (43 bp):
GAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAATGA
Found at i:23393211 original size:129 final size:130
Alignment explanation
Indices: 23393004--23393241 Score: 313
Period size: 129 Copynumber: 1.8 Consensus size: 130
23392994 ACATTGGGAG
* * *
23393004 GAACATTATTTCCTAAATATTATAAGTATGTGACTGAATGAGAGGAACATTGTTTCCTAATATTG
1 GAACACTATTTCCTAAATATTATAAGTATGTGACTGAATGAGAGGAACAATGTTTCCAAATATTG
* * *
23393069 AAATTATGTGATCGAATGAGA-GGAAAATTGTTTCCTAATATTGAAAGTATGTGATCGATTGTGT
66 AAAGTATGTGATCGAAAGA-ATGGAAAACTGTTTCCTAATATTGAAAGTATGTGATCGATTGTGT
23393133 A
130 A
* * * *
23393134 GAACACTATTTCCT-AATATTGA-AAGTATGTG-CTCGATTGTGTGGAACAATGTTTCCAAATGT
1 GAACACTATTTCCTAAATATT-ATAAGTATGTGACT-GAATGAGAGGAACAATGTTTCCAAATAT
* *
23393196 TGAAAGTATGTGATCGAAAGAATGGAACACTGTTTCCTCATATTGA
64 TGAAAGTATGTGATCGAAAGAATGGAAAACTGTTTCCTAATATTGA
23393242 TGTATTGATC
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
128 3 0.03
129 76 0.82
130 14 0.15
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (130 bp):
GAACACTATTTCCTAAATATTATAAGTATGTGACTGAATGAGAGGAACAATGTTTCCAAATATTG
AAAGTATGTGATCGAAAGAATGGAAAACTGTTTCCTAATATTGAAAGTATGTGATCGATTGTGTA
Found at i:23400892 original size:11 final size:11
Alignment explanation
Indices: 23400876--23400903 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
23400866 TGAAATCAAG
23400876 TATTTTCATAA
1 TATTTTCATAA
23400887 TATTTTCATAA
1 TATTTTCATAA
23400898 TATTTT
1 TATTTT
23400904 GTTGGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTTCATAA
Found at i:23405253 original size:13 final size:14
Alignment explanation
Indices: 23405223--23405253 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
23405213 TTTCAGTACA
23405223 TTGACATTTAACCT
1 TTGACATTTAACCT
23405237 TTGACATTTAA-CT
1 TTGACATTTAACCT
23405250 TTGA
1 TTGA
23405254 TTGCGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (14 bp):
TTGACATTTAACCT
Found at i:23407242 original size:17 final size:17
Alignment explanation
Indices: 23407218--23407264 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
23407208 GCATGATTAA
**
23407218 TGTCATTGCATTTTTAT
1 TGTCATTGCATTTACAT
* *
23407235 TGTTATTGCATCTACAT
1 TGTCATTGCATTTACAT
23407252 TGTCATTGCATTT
1 TGTCATTGCATTT
23407265 CCATATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (17 bp):
TGTCATTGCATTTACAT
Found at i:23407850 original size:16 final size:18
Alignment explanation
Indices: 23407821--23407854 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
23407811 CTTGAAAAAG
23407821 GAAAATGAGAAAAAGAAA
1 GAAAATGAGAAAAAGAAA
23407839 GAAAA-GAG-AAAAGAAA
1 GAAAATGAGAAAAAGAAA
23407855 AGAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (18 bp):
GAAAATGAGAAAAAGAAA
Found at i:23407853 original size:12 final size:12
Alignment explanation
Indices: 23407828--23407864 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
23407818 AAGGAAAATG
23407828 AGAAAA-AG-AA
1 AGAAAAGAGAAA
23407838 AGAAAAGAGAAA
1 AGAAAAGAGAAA
23407850 AGAAAAGAAGAAA
1 AGAAAAG-AGAAA
23407863 AG
1 AG
23407865 CATGTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.25
11 2 0.08
12 9 0.38
13 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAAGAGAAA
Found at i:23407856 original size:17 final size:17
Alignment explanation
Indices: 23407815--23407858 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
23407805 CAGTAACTTG
*
23407815 AAAAAGGAAAATGAGAA
1 AAAAAAGAAAATGAGAA
23407832 AAAGAAAGAAAA-GAGAA
1 AAA-AAAGAAAATGAGAA
23407849 AAGAAAAGAA
1 AA-AAAAGAA
23407859 GAAAAGCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAATGAGAA
Found at i:23407860 original size:24 final size:24
Alignment explanation
Indices: 23407816--23407862 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
23407806 AGTAACTTGA
23407816 AAAAGGAAAATGAGAAAAAGAAAG
1 AAAAGGAAAATGAGAAAAAGAAAG
23407840 AAAAGAGAAAA-GA-AAAGAAGAAA
1 AAAAG-GAAAATGAGAAA-AAGAAA
23407863 AGCATGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (24 bp):
AAAAGGAAAATGAGAAAAAGAAAG
Found at i:23410475 original size:16 final size:17
Alignment explanation
Indices: 23410454--23410490 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
23410444 AAGACTGTGG
23410454 TTTGGGA-CTATTTTGC
1 TTTGGGATCTATTTTGC
*
23410470 TTTGGGATTTATTTTGC
1 TTTGGGATCTATTTTGC
23410487 TTTG
1 TTTG
23410491 TGTTTTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.11, C:0.08, G:0.24, T:0.57
Consensus pattern (17 bp):
TTTGGGATCTATTTTGC
Found at i:23416690 original size:43 final size:43
Alignment explanation
Indices: 23416654--23416874 Score: 165
Period size: 43 Copynumber: 5.1 Consensus size: 43
23416644 TATTATAAGT
**
23416654 ATGTGACCGAATGAGAGGAATGTTATTTCCTAATATTGAAAGC
1 ATGTGACCGAATGAGAGGAACATTATTTCCTAATATTGAAAGC
* * * * *
23416697 ATGTGATCGAATGATAGGAACATTGTTTCCTAATATTGAATGT
1 ATGTGACCGAATGAGAGGAACATTATTTCCTAATATTGAAAGC
* * * * * * *
23416740 ATGTGATCGATTGTGTGAAACACTATTTCCTAATATTGAAAGT
1 ATGTGACCGAATGAGAGGAACATTATTTCCTAATATTGAAAGC
** * * * * * *
23416783 ATGTGATTGATTGTGTGGAACACTATTTCCTAATATTAAAAGT
1 ATGTGACCGAATGAGAGGAACATTATTTCCTAATATTGAAAGC
* * * * * * *
23416826 ATATGATCAAATGA-ATGGAACATTGTTTCCTCATATTGATAGT
1 ATGTGACCGAATGAGA-GGAACATTATTTCCTAATATTGAAAGC
23416869 ATGTGA
1 ATGTGA
23416875 TTGATTTAGA
Statistics
Matches: 147, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
43 147 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (43 bp):
ATGTGACCGAATGAGAGGAACATTATTTCCTAATATTGAAAGC
Found at i:23416855 original size:86 final size:86
Alignment explanation
Indices: 23416677--23416880 Score: 230
Period size: 86 Copynumber: 2.4 Consensus size: 86
23416667 AGAGGAATGT
* * * * * * *
23416677 TATTTCCTAATATTGAAAGCATGTGATCGAATGATAGGAACATTGTTTCCTAATATTGAATGTAT
1 TATTTCCTAATATTGAAAGTATGTGATTGATTGATAGGAACACTATTTCCTAATATTAAAAGTAT
* * * **
23416742 GTGATCGATTGTGTGAAACAC
66 ATGATCAAATGAATGAAACAC
*
23416763 TATTTCCTAATATTGAAAGTATGTGATTGATTG-TGTGGAACACTATTTCCTAATATTAAAAGTA
1 TATTTCCTAATATTGAAAGTATGTGATTGATTGAT-AGGAACACTATTTCCTAATATTAAAAGTA
* *
23416827 TATGATCAAATGAATGGAACAT
65 TATGATCAAATGAATGAAACAC
* * *
23416849 TGTTTCCTCATATTGATAGTATGTGATTGATT
1 TATTTCCTAATATTGAAAGTATGTGATTGATT
23416881 TAGAGCATGA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 1 0.01
86 98 0.99
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (86 bp):
TATTTCCTAATATTGAAAGTATGTGATTGATTGATAGGAACACTATTTCCTAATATTAAAAGTAT
ATGATCAAATGAATGAAACAC
Found at i:23433750 original size:46 final size:46
Alignment explanation
Indices: 23433697--23433794 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
23433687 TATATTTGAG
*
23433697 TTGACAGATTTAATTCTTTGATTTGTGAAGTTTTAACCAAATTGCA
1 TTGACAGATTTAATTCTTTGATTTGTGAAGTTTTAACCAAATTACA
* *
23433743 TTGACAGATTTAATTCTTTGATTTGTGCAGTTTTAACCAAATTACG
1 TTGACAGATTTAATTCTTTGATTTGTGAAGTTTTAACCAAATTACA
23433789 TTGACA
1 TTGACA
23433795 TTACTCTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (46 bp):
TTGACAGATTTAATTCTTTGATTTGTGAAGTTTTAACCAAATTACA
Found at i:23436291 original size:20 final size:20
Alignment explanation
Indices: 23436266--23436313 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
23436256 TAAATTTTTA
23436266 GCATTTT-TAATTTAGTTATT
1 GCATTTTCTAA-TTAGTTATT
23436286 GCATTTTCTAATTAGTTATT
1 GCATTTTCTAATTAGTTATT
23436306 GCATTTTC
1 GCATTTTC
23436314 CAACTTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
GCATTTTCTAATTAGTTATT
Found at i:23438379 original size:38 final size:38
Alignment explanation
Indices: 23438332--23438441 Score: 176
Period size: 38 Copynumber: 3.0 Consensus size: 38
23438322 TTTTGAAACC
23438332 ATTAACACTTTTTTCTTTTTGGTTACATGAACCAATTA
1 ATTAACACTTTTTTCTTTTTGGTTACATGAACCAATTA
23438370 ATTAACACTTTTTTCTTTTTGGTTACATGAACCAATTA
1 ATTAACACTTTTTTCTTTTTGGTTACATGAACCAATTA
*
23438408 ATT-A-AC-TCTTT-TTTTT-GTTACATGAACCAATTA
1 ATTAACACTTTTTTCTTTTTGGTTACATGAACCAATTA
23438441 A
1 A
23438442 CTTTGATACA
Statistics
Matches: 71, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
33 18 0.25
34 5 0.07
35 4 0.06
36 2 0.03
37 1 0.01
38 41 0.58
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (38 bp):
ATTAACACTTTTTTCTTTTTGGTTACATGAACCAATTA
Found at i:23438599 original size:27 final size:27
Alignment explanation
Indices: 23438551--23438614 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
23438541 GAATATTCTC
*
23438551 TAAATTAAT-ATATATTAATTTATCGA
1 TAAATTAATAAAATATTAATTTATCGA
*
23438577 TAAATTAATAAAATATTCATTTATCGA
1 TAAATTAATAAAATATTAATTTATCGA
*
23438604 TAAACTAATAA
1 TAAATTAATAA
23438615 CCTCGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCGA
Found at i:23446023 original size:16 final size:16
Alignment explanation
Indices: 23445993--23446040 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
23445983 ATCCATCAAA
*
23445993 ATTTTTGAAACAAAATC
1 ATTTTTTAAA-AAAATC
*
23446010 ATTTTTTAAAAAAATT
1 ATTTTTTAAAAAAATC
* *
23446026 ATTTTATATAAAAAT
1 ATTTTTTAAAAAAAT
23446041 AAATTAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTTTTTAAAAAAATC
Found at i:23452338 original size:31 final size:30
Alignment explanation
Indices: 23452303--23452389 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
23452293 TACTTAAAGC
*
23452303 TTTTTATTTAATTTAGTATTTAAATTTAATA
1 TTTTT-TTTAATTTAGTACTTAAATTTAATA
23452334 TTTTTTTCTAATTT-GTTACTTAAATTTAATA
1 TTTTTTT-TAATTTAG-TACTTAAATTTAATA
* *
23452365 -CTTTTTTAAGTTAGTACTTAAATTT
1 TTTTTTTTAATTTAGTACTTAAATTT
23452390 TTTGGGTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
29 16 0.32
30 9 0.18
31 25 0.50
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTTTTTTAATTTAGTACTTAAATTTAATA
Found at i:23452652 original size:30 final size:30
Alignment explanation
Indices: 23452603--23452689 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 30
23452593 TTTGAGTCTA
* *
23452603 AAAAAAGCTTAGATACCAAATTAGGAAAAC
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAC
* * **
23452633 TACAAAGTTTAGGTACCAAATT-GG-ATCC
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAC
*
23452661 AAAAAAGTTTAGGTACCAAATTAGAAAAA
1 AAAAAAGTTTAGGTACCAAATTAGGAAAA
23452690 AGTGTCAAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
28 22 0.50
29 3 0.07
30 19 0.43
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.22
Consensus pattern (30 bp):
AAAAAAGTTTAGGTACCAAATTAGGAAAAC
Found at i:23457533 original size:16 final size:15
Alignment explanation
Indices: 23457512--23457549 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
23457502 AAAAATATTT
23457512 TATTTATTAATTTATA
1 TATTTATTAATTT-TA
23457528 TATTTATTAATTTTA
1 TATTTATTAATTTTA
23457543 T-TTTATT
1 TATTTATT
23457550 TTATTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.27
15 3 0.14
16 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATTAATTTTA
Found at i:23459785 original size:3 final size:3
Alignment explanation
Indices: 23459777--23459821 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
23459767 AAAATATTCA
23459777 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
23459822 CATCATCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:23465176 original size:158 final size:158
Alignment explanation
Indices: 23464888--23465208 Score: 464
Period size: 158 Copynumber: 2.0 Consensus size: 158
23464878 CTCCATAGCA
* * * * *
23464888 TGTAATGCTCACACGAGCTGTGAAATGAGTCTACTCATACGAGCTGTGGGTCGAGATGTTGGGCT
1 TGTAATGCTCACACGAGCTGTGAAAGGAGCCTACTCACACGAGCTGTGAGTCGAGATGTTAGGCT
* *
23464953 ACACGATGCTGCTCACACGAGCTATGGAGAATCCACAATAAATGTCAGATCTCAGCCATTGGTAG
66 ACACGATGCTGCTCACACGAGCTATGGAGAATCCACAATAAATGCCAGATCTCAGCCATCGGTAG
* *
23465018 GACATCTAAGATCAGCACCCATATAACT
131 GACATCTAAGACCAGCACCCATATAACC
* *
23465046 TGTAATGCTCACACGAGCTGTG-AAGGAAGCCTACTCACACGAGCTGTGAGTCTAGTTGTTAGGC
1 TGTAATGCTCACACGAGCTGTGAAAGG-AGCCTACTCACACGAGCTGTGAGTCGAGATGTTAGGC
* ** * * *
23465110 TACACGATGCTGCTCACACGAGCTGTGGAGAATCTGCACTAAATGCCGGATCTCATCCATCGGTA
65 TACACGATGCTGCTCACACGAGCTATGGAGAATCCACAATAAATGCCAGATCTCAGCCATCGGTA
*
23465175 GGACATTTAAGACCAGCACCCATATAACC
130 GGACATCTAAGACCAGCACCCATATAACC
23465204 TGTAA
1 TGTAA
23465209 ATCGTGAAAT
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
157 3 0.02
158 141 0.98
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (158 bp):
TGTAATGCTCACACGAGCTGTGAAAGGAGCCTACTCACACGAGCTGTGAGTCGAGATGTTAGGCT
ACACGATGCTGCTCACACGAGCTATGGAGAATCCACAATAAATGCCAGATCTCAGCCATCGGTAG
GACATCTAAGACCAGCACCCATATAACC
Found at i:23468332 original size:20 final size:20
Alignment explanation
Indices: 23468307--23468356 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
23468297 TCATTAAGCT
*
23468307 TTAATTAACCCTTTTTA-ATC
1 TTAATTAACCCTATTTATA-C
*
23468327 TTAATTAAACCTATTTATAC
1 TTAATTAACCCTATTTATAC
23468347 TTAATATAAC
1 TTAAT-TAAC
23468357 TCATTATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTAACCCTATTTATAC
Done.