Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007703.1 Hibiscus syriacus cultivar Beakdansim tig00109916_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1017536
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:589677 original size:21 final size:21
Alignment explanation
Indices: 589651--589692 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
589641 CAGAATGGGG
*
589651 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
589672 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
589693 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:589904 original size:29 final size:31
Alignment explanation
Indices: 589872--589930 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
589862 AAATTTTGAA
*
589872 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
589901 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
589931 TCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:593635 original size:39 final size:38
Alignment explanation
Indices: 593578--593804 Score: 168
Period size: 39 Copynumber: 6.1 Consensus size: 38
593568 TCAAGAAATT
*
593578 AAAATCAATCCAATGATTTATTTTCTTTTACACAAA-AGG
1 AAAATAAATCCAATGATTTATTTTCTTTTACA-AAATA-G
* * * *
593617 AAAATAAATCCAACGATTT-GTTTC-----CTAAATAT
1 AAAATAAATCCAATGATTTATTTTCTTTTACAAAATAG
* *
593649 AAAA-AAATCCAATGAGTTATTTCCTTTTACAAAATA-
1 AAAATAAATCCAATGATTTATTTTCTTTTACAAAATAG
* * * *
593685 ATAATGAATCAAATGATTTA-TTTCTTTTTACAAAATATT
1 AAAATAAATCCAATGATTTATTTTC-TTTTACAAAATA-G
* * *
593724 AAAATAAATCCAACGATTTATTTTATTCTACAAAATATG
1 AAAATAAATCCAATGATTTATTTTCTTTTACAAAATA-G
* * * * *
593763 TAAATAAATCCAAAGATTTATTTTATGTTATAAAATAG
1 AAAATAAATCCAATGATTTATTTTCTTTTACAAAATAG
593801 AAAA
1 AAAA
593805 AAAAATTCTA
Statistics
Matches: 148, Mismatches: 28, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
31 12 0.08
32 10 0.07
33 2 0.01
36 6 0.04
37 30 0.20
38 8 0.05
39 77 0.52
40 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.37
Consensus pattern (38 bp):
AAAATAAATCCAATGATTTATTTTCTTTTACAAAATAG
Found at i:593684 original size:37 final size:38
Alignment explanation
Indices: 593643--593833 Score: 161
Period size: 39 Copynumber: 5.0 Consensus size: 38
593633 TTTGTTTCCT
* *
593643 AAATA-TAAAAAAATCCAATGAGTTATTTCCTTTTACA
1 AAATATTAAAAAAATCCAATGATTTATTTCATTTTACA
* ** * *
593680 AAATAAT-AATGAATCAAATGATTTATTTCTTTTTACA
1 AAATATTAAAAAAATCCAATGATTTATTTCATTTTACA
* * *
593717 AAATATTAAAATAAATCCAACGATTTATTTTATTCTACA
1 AAATATTAAAA-AAATCCAATGATTTATTTCATTTTACA
* * * * *
593756 AAATATGTAAATAAATCCAAAGATTTATTTTATGTTATA
1 AAATAT-TAAAAAAATCCAATGATTTATTTCATTTTACA
** * * *
593795 AAATAGAAAAAAAAATTCTACGATTTATTTCATTTTACA
1 AAATA-TTAAAAAAATCCAATGATTTATTTCATTTTACA
593834 GATTATAATC
Statistics
Matches: 122, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
37 36 0.30
38 3 0.02
39 79 0.65
40 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (38 bp):
AAATATTAAAAAAATCCAATGATTTATTTCATTTTACA
Found at i:593917 original size:39 final size:39
Alignment explanation
Indices: 593856--594017 Score: 164
Period size: 39 Copynumber: 4.1 Consensus size: 39
593846 ATAAGATTCT
* *
593856 TAGGAAAATAAATTCAACGATTTATTTTCTTTTACAAAA
1 TAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAAA
* * *
593895 TAGGAAAATAGATCCAATGATTTATTTCCTTTTA-TAAA
1 TAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAAA
* * * * *
593933 TCAGAAAAATAAATTCAACGATTTGTTTTCTTTTTTTAAAAAA
1 T-AGGAAAATAAATCCAACGATTT-ATTTC--CTTTTACAAAA
** *
593976 TATTAAAATAAATCCAACAATTTATTTCCTTTTACAAAA
1 TAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAAA
594015 TAG
1 TAG
594018 AATCAGATAA
Statistics
Matches: 98, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
38 4 0.04
39 59 0.60
40 4 0.04
41 4 0.04
42 23 0.23
43 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.40
Consensus pattern (39 bp):
TAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAAA
Found at i:593999 original size:81 final size:78
Alignment explanation
Indices: 593860--594009 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 78
593850 GATTCTTAGG
* * **
593860 AAAATAAATTCAACGATTTATTTTCTTTTACAAAATAGGAAAATAGATCCAATGATTTATTTCCT
1 AAAATAAATTCAACGATTTATTTTCTTTTAAAAAATAGGAAAATAAATCCAACAATTTATTTCCT
593925 TTTATAAATCAGA
66 TTTATAAATCAGA
* **
593938 AAAATAAATTCAACGATTTGTTTTCTTTTTTTAAAAAATATTAAAATAAATCCAACAATTTATTT
1 AAAATAAATTCAACGATTTATTTTC---TTTTAAAAAATAGGAAAATAAATCCAACAATTTATTT
594003 CCTTTTA
63 CCTTTTA
594010 CAAAATAGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
78 24 0.39
81 38 0.61
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.41
Consensus pattern (78 bp):
AAAATAAATTCAACGATTTATTTTCTTTTAAAAAATAGGAAAATAAATCCAACAATTTATTTCCT
TTTATAAATCAGA
Found at i:594338 original size:58 final size:58
Alignment explanation
Indices: 594275--594440 Score: 226
Period size: 58 Copynumber: 2.9 Consensus size: 58
594265 TAGACACAAT
* * * * *
594275 TCTCAAGAAAATAAATTCGACAATTTATTTTTATTACGAAGTTAGAATCATTTAAGAG
1 TCTCAAGAAAATAAATTCAACTATTTATTTTCATTACAAAATTAGAATCATTTAAGAG
* * *
594333 TCTCAAGAATATAAATTCAACTATTTATTTTCGTTACAAAATTAGAATCATTTAAGAT
1 TCTCAAGAAAATAAATTCAACTATTTATTTTCATTACAAAATTAGAATCATTTAAGAG
* *
594391 TCTCAA-AGAAACAAATTCAACTATTTATTTTCCTTACAAAATTAGAATCA
1 TCTCAAGA-AAATAAATTCAACTATTTATTTTCATTACAAAATTAGAATCA
594441 ACGCAAGATT
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 1 0.01
58 95 0.99
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (58 bp):
TCTCAAGAAAATAAATTCAACTATTTATTTTCATTACAAAATTAGAATCATTTAAGAG
Found at i:594728 original size:45 final size:44
Alignment explanation
Indices: 594679--594837 Score: 167
Period size: 45 Copynumber: 3.6 Consensus size: 44
594669 AAATTATAAG
* *
594679 GAACTAATCATTTGATTTTACTTTTAACAACTAAATAATCAAAA
1 GAACTAATCATTTGATTTTACTTTTGACAACTCAATAATCAAAA
* * * * *
594723 TGAACTATTCCTTTTATTTTACTTTTGGCATCTCAATAAT-AATAA
1 -GAACTAATCATTTGATTTTACTTTTGACAACTCAATAATCAA-AA
* * * * *
594768 AAACAAATCCTTTGATTTTACTTTTGATAATTCAATAATCAAAA
1 GAACTAATCATTTGATTTTACTTTTGACAACTCAATAATCAAAA
*
594812 GGAACTAATTATTTGATTTTACTTTT
1 -GAACTAATCATTTGATTTTACTTTT
594838 TGGTAACCCA
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
44 35 0.38
45 57 0.62
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (44 bp):
GAACTAATCATTTGATTTTACTTTTGACAACTCAATAATCAAAA
Found at i:595180 original size:16 final size:16
Alignment explanation
Indices: 595155--595186 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
595145 TAAGAATTAC
595155 ATTAACTCTTTATTTT
1 ATTAACTCTTTATTTT
*
595171 ATTAATTCTTTATTTT
1 ATTAACTCTTTATTTT
595187 CAAAAAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTAACTCTTTATTTT
Found at i:598011 original size:15 final size:16
Alignment explanation
Indices: 597993--598022 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
597983 ATTTGAAATT
597993 TTAAAAAT-ATTAAAA
1 TTAAAAATGATTAAAA
598008 TTAAAAATGATTAAA
1 TTAAAAATGATTAAA
598023 TTAGAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TTAAAAATGATTAAAA
Found at i:603217 original size:3 final size:3
Alignment explanation
Indices: 603209--603285 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
603199 ACGCAACTAT
603209 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
603257 ATA ATA ATA ATA ATA AAA ATA ATT ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
603286 TAAAAAATGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:604833 original size:2 final size:2
Alignment explanation
Indices: 604826--604856 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
604816 TTTAATGTTC
604826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
604857 ATTGAAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:607956 original size:19 final size:19
Alignment explanation
Indices: 607932--607983 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
607922 CAAAATCATT
607932 TTTCAAAATTAAATTTTTC
1 TTTCAAAATTAAATTTTTC
*
607951 TTTCAAAATTAATTTTTTC
1 TTTCAAAATTAAATTTTTC
*
607970 TTTCAAAATCAAAT
1 TTTCAAAATTAAAT
607984 CATTTTCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCAAAATTAAATTTTTC
Found at i:610902 original size:22 final size:24
Alignment explanation
Indices: 610877--610926 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
610867 TAGTAACTTA
*
610877 ATTTATATTTT-TG-AT-ATTTTGT
1 ATTTA-ATTTTATGAATAATTTTAT
610899 ATTTAATTTTATGAATAATTTTAT
1 ATTTAATTTTATGAATAATTTTAT
610923 ATTT
1 ATTT
610927 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 7 0.29
23 2 0.08
24 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATTTAATTTTATGAATAATTTTAT
Found at i:613263 original size:22 final size:22
Alignment explanation
Indices: 613238--613318 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
613228 CTACGGCGAC
*
613238 ATCCGTCCCCATATCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
613260 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
613282 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
*
613304 ATCCGTCTCCATCTC
1 ATCCGTCCCCATCTC
613319 TCAGAGCCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.22, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:613771 original size:53 final size:54
Alignment explanation
Indices: 613691--613793 Score: 190
Period size: 53 Copynumber: 1.9 Consensus size: 54
613681 GTCAAATTCG
613691 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-TTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTATCT
*
613744 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGTTGCGATT
1 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATT
613794 TTAAGTTTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 34 0.71
54 14 0.29
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (54 bp):
CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTATCT
Found at i:613793 original size:20 final size:20
Alignment explanation
Indices: 613687--613795 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
613677 GATAGTCAAA
* **
613687 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
613707 TTCGTGTTGCGATTTTCA-T
1 TTCGTGTTGCGATTTTCATT
*
613726 TTCGCGTTGCGA--TT-A-T
1 TTCGTGTTGCGATTTTCATT
* **
613742 CTC--GTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
613760 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
613780 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
613796 AAGTTTCAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
14 7 0.09
16 5 0.07
17 3 0.04
18 3 0.04
19 12 0.16
20 44 0.59
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:613802 original size:20 final size:20
Alignment explanation
Indices: 613759--613802 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
613749 CGATAGTCAT
* *
613759 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
613779 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
613799 TTTC
1 TTTC
613803 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:613814 original size:73 final size:73
Alignment explanation
Indices: 613676--613814 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 73
613666 AAAATTGCAA
* * ***
613676 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGCGTTGCGATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTCGAGAAACGATTA
613741 TCTCGTTG
66 TCTCGTTG
** * ** *
613749 CGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGTTGCGATTTTAAGTTTC-AGAAACTATT
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAA-TTTCGAGAAACGATT
613813 AT
65 AT
613815 TCTTCTGCAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 50 0.93
74 4 0.07
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.44
Consensus pattern (73 bp):
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTCGAGAAACGATTA
TCTCGTTG
Found at i:615674 original size:20 final size:21
Alignment explanation
Indices: 615649--615693 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
615639 AATAGTTTCT
615649 GAAACTT-AAAATCGCAACAC
1 GAAACTTAAAAATCGCAACAC
*
615669 GAAACTTAAAAATCGCAACGC
1 GAAACTTAAAAATCGCAACAC
615690 GAAA
1 GAAA
615694 ATGACTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.13
Consensus pattern (21 bp):
GAAACTTAAAAATCGCAACAC
Found at i:615708 original size:20 final size:20
Alignment explanation
Indices: 615680--615733 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
615670 AAACTTAAAA
615680 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
615700 ATTGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
615720 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
615734 CTAAATTCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:615797 original size:34 final size:37
Alignment explanation
Indices: 615759--615846 Score: 92
Period size: 40 Copynumber: 2.4 Consensus size: 37
615749 GATTTTTATT
615759 TTCGCATTGCGATT-A-TCC-CGTTGCGATAGTCAAA
1 TTCGCATTGCGATTCATTCCGCGTTGCGATAGTCAAA
* **
615793 TTCGCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATT
1 TTCGCATTGCGAT--TCA-TTCCGCGTTGCGATAGTCAAA
*
615833 TTCACATTGCGATT
1 TTCGCATTGCGATT
615847 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
34 12 0.28
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.07
40 25 0.58
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (37 bp):
TTCGCATTGCGATTCATTCCGCGTTGCGATAGTCAAA
Found at i:615842 original size:20 final size:20
Alignment explanation
Indices: 615777--615845 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
615767 GCGATTATCC
**
615777 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
615797 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
*
615817 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCG
*
615837 CATTGCGAT
1 CGTTGCGAT
615846 TTTTAAGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:616392 original size:21 final size:21
Alignment explanation
Indices: 616363--616402 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
616353 ACTCACCTGT
*
616363 TATCGTTCAAGAGGCCTCTCA
1 TATCATTCAAGAGGCCTCTCA
616384 TATCATTCAAGAGGCCTCT
1 TATCATTCAAGAGGCCTCT
616403 ATCATCCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (21 bp):
TATCATTCAAGAGGCCTCTCA
Found at i:616414 original size:21 final size:21
Alignment explanation
Indices: 616369--616417 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
616359 CTGTTATCGT
*
616369 TCAAGAGGCCTCTCATATCAT
1 TCAAGAGGCCTCTCATATCAC
*
616390 TCAAGAGGCCTCT-ATCATCCC
1 TCAAGAGGCCTCTCAT-ATCAC
616411 TCAAGAG
1 TCAAGAG
616418 TCCCCTCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (21 bp):
TCAAGAGGCCTCTCATATCAC
Found at i:616435 original size:21 final size:21
Alignment explanation
Indices: 616411--616480 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
616401 CTATCATCCC
616411 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* ** *
616432 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
616453 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
616474 TCAAGAG
1 TCAAGAG
616481 CCCGATTCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:616435 original size:42 final size:42
Alignment explanation
Indices: 616387--616480 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
616377 CCTCTCATAT
*
616387 CATTCAAGAGGCCTCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCAC
* * ** *
616429 CGTTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
616471 CATTCAAGAG
1 CATTCAAGAG
616481 CCCGATTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.21
Consensus pattern (42 bp):
CATTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:617888 original size:14 final size:14
Alignment explanation
Indices: 617869--617905 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
617859 GTTTGTTTAA
617869 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
617883 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
617897 TTGATTTGT
1 TTGATTTGT
617906 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:618064 original size:20 final size:20
Alignment explanation
Indices: 618039--618102 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
618029 AACGATAAAC
618039 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
*
618059 TCAAAATCGCAATGTGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
618079 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
618099 TCAA
1 TCAA
618103 TTCGCGTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:618169 original size:20 final size:20
Alignment explanation
Indices: 618141--618237 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
618131 GCGATTTTCT
*
618141 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* * *
618161 CGTTACGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
618181 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
618201 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
618221 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
618238 GAATGTGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:620488 original size:14 final size:14
Alignment explanation
Indices: 620469--620495 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
620459 TCCCGTGGCA
620469 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
620483 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
620496 TTTCTTATTC
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:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:620729 original size:24 final size:24
Alignment explanation
Indices: 620695--620748 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
620685 CTGAAACATC
*
620695 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* *
620719 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
620743 ATCAAA
1 ATCAAA
620749 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:626635 original size:3 final size:3
Alignment explanation
Indices: 626627--626719 Score: 116
Period size: 3 Copynumber: 31.3 Consensus size: 3
626617 ATTCTCATTT
* * *
626627 TTA TTA TTA TTA TTA CTA ATA TTA TTA TTA TTA TT- TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
626674 TTA TTG TTA TTA ATA TTA TTA TTA TTA ATA TAA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
626720 AGGCCCAAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:628335 original size:2 final size:2
Alignment explanation
Indices: 628328--628365 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
628318 AGTCACATTA
628328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
628366 GAAAAATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:634228 original size:6 final size:6
Alignment explanation
Indices: 634208--634292 Score: 82
Period size: 6 Copynumber: 13.2 Consensus size: 6
634198 CATTAGAGAG
634208 AAAA-A AAAAGAA AAAAGAA AAAAGAAA AAAAGA AAAAGA AAAAGA GAGAAAGA
1 AAAAGA AAAAG-A AAAAG-A AAAAG--A AAAAGA AAAAGA AAAAGA -A-AAAGA
* *
634261 AAAAGA AAAAGA AAAAGA GAGATGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA A
634293 GAAAAAAGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.06
6 35 0.50
7 19 0.27
8 12 0.17
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:634230 original size:14 final size:14
Alignment explanation
Indices: 634211--634303 Score: 79
Period size: 14 Copynumber: 6.7 Consensus size: 14
634201 TAGAGAGAAA
634211 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
634225 AAAAAAGAAAAAA-
1 AAAAAAGAAAAAAG
634238 AGAAAAAG-AAAAAG
1 A-AAAAAGAAAAAAG
*
634252 AGAGAAAG-AAAAAG
1 A-AAAAAGAAAAAAG
634266 -AAAAAGAAAAAGAG
1 AAAAAAGAAAAA-AG
** *
634280 AGATGAA-AAAGAAG
1 A-AAAAAGAAAAAAG
634294 AAAAAAGAAA
1 AAAAAAGAAA
634304 TTGAATCAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
12 5 0.08
13 13 0.20
14 40 0.62
15 4 0.06
16 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:634247 original size:28 final size:27
Alignment explanation
Indices: 634208--634303 Score: 99
Period size: 26 Copynumber: 3.5 Consensus size: 27
634198 CATTAGAGAG
634208 AAAA-AAAAAGAAAAAAGAAAAAAGAAA
1 AAAAGAAAAAG-AAAAAGAAAAAAGAAA
*
634235 AAAAGAAAAAGAAAAAGAGAGAAAG--A
1 AAAAGAAAAAGAAAAAGA-AAAAAGAAA
* * *
634261 AAAAGAAAAAGAAAAAGAGAGATGAAA
1 AAAAGAAAAAGAAAAAGAAAAAAGAAA
634288 AAGAAGAAAAAAGAAA
1 AA-AAG-AAAAAGAAA
634304 TTGAATCAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.03
26 19 0.33
27 14 0.24
28 14 0.24
29 9 0.16
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (27 bp):
AAAAGAAAAAGAAAAAGAAAAAAGAAA
Found at i:635876 original size:52 final size:51
Alignment explanation
Indices: 635796--635928 Score: 167
Period size: 52 Copynumber: 2.6 Consensus size: 51
635786 CCATGAGGGT
* * * *
635796 ATCTTGAAGGCTGATATCAACATTAAAAAGATAGAAGTAATCCATATGGGAC
1 ATCTTGAAGGCTCACATCAGCA-TAAAAAGAAAGAAGTAATCCATATGGGAC
* * * *
635848 ATTTTGAAGGCTCACATCAGCATGAAAAAGAAAGAAGTATTCCATGTGGGGC
1 ATCTTGAAGGCTCACATCAGCAT-AAAAAGAAAGAAGTAATCCATATGGGAC
*
635900 ATCTTGAAGGCTCACACCAGCATAAAAAG
1 ATCTTGAAGGCTCACATCAGCATAAAAAG
635929 TTTGGGATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 7 0.10
52 63 0.90
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (51 bp):
ATCTTGAAGGCTCACATCAGCATAAAAAGAAAGAAGTAATCCATATGGGAC
Found at i:637717 original size:177 final size:177
Alignment explanation
Indices: 637398--638319 Score: 1280
Period size: 177 Copynumber: 5.3 Consensus size: 177
637388 TCTCGAATTG
* * *
637398 GTAAGTCCTTCGGGCAATCCATAAGACCTTTAGTGTAGGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
*
637463 TAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGA
66 TAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAAAAAGA
* *
637528 GGTTCCTTGACAACTAAGAAACTAAGCATTCGGGGGTTTCTTGATTT
131 GGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
* *
637575 GTAAATCCTTTGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
637640 TAAGCCTTTGGGGGTTTTCTAATTATCTCAAAAGAGTTTTTAAAGGAAGCTAAGCCTAAAAAAGA
66 TAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAAAAAGA
637705 GGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
131 GGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
* * * * * * * *
637752 TTAAGTCCTTTGAGCCATCTATAAGATCTTTAGTGCAGGATGTTTTTAAATGAGATTTTAGAAAT
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* * *
637817 TAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGATTTATTAAAGGAAGTTAAGCCTAAAAAA-A
66 TAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAAAAAGA
* *
637881 TGGTTCATTGACAAGTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTC
131 -GGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
*
637929 GTAAGT-CTTACGGGCCATCCATAAGACCTTCAGTGTAGGATGTTTTCAAATGAGATTTTAGAAA
1 GTAAGTCCTT-CGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
* * * *
637993 CCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCT-----A-
65 CTAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAAAAAG
* * *
638052 A----CA--AACAACTAAGAAACTAAGCCTCCGGGGG-TTCTTTATTT
130 AGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
* **
638093 ATAAGTCCTTCGGGCCATCCATAAGAAATTCAGTGCAGGATGTTTTCAAATGAGATTTTTAGAAA
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGA-TTTTAGAAA
* * * * * *
638158 CTAAGCCTTTGGGGGTTTCCTAATTATCTAAAAATAGTTGTTAAAGGAAACTAAGCCTAACAAAG
65 CTAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAAAAAG
* * **
638223 GGGTTCCTTGACAACTAAGAAACTAAGCCTTTAGGGGTTTCTTGATTT
130 AGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
* * * *
638271 ATAAGTCATTTGGGCCATCCATAAGACCTTCAGTGCTGGATGTTTTCAA
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAA
638320 CTTTTCTGTT
Statistics
Matches: 661, Mismatches: 67, Indels: 33
0.87 0.09 0.04
Matches are distributed among these distances:
164 55 0.08
165 87 0.13
167 2 0.00
170 1 0.00
172 2 0.00
175 1 0.00
176 4 0.01
177 456 0.69
178 53 0.08
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (177 bp):
GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
TAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAAAAAGA
GGTTCATTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
Found at i:637740 original size:87 final size:87
Alignment explanation
Indices: 637457--637743 Score: 214
Period size: 87 Copynumber: 3.3 Consensus size: 87
637447 ATGAGATTTT
*
637457 AGAAACTAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
1 AGAAACTAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTTTTAAAGGAAGCTAAGCCTAA
* *
637522 CAAAGAGGTTCCTTGACAACTA
66 AAAAGAGGTTCATTGACAACTA
* * * * * **
637544 AGAAACTAAGCATTCGGGGG-TTTCTTGATT-TGT---AA-A-TCCTTT--GGGCCATCCATAAG
1 AGAAACTAAGCCTTCGGGGGTTTTC-TAATTATCTCAAAAGAGT-TTTTAAAGG--AAGC-TAAG
*** * * * * ** *
637600 ACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
61 -CC-T-A-AAAAAGA-G-GTTC-ATTGACAACTA
*
637634 AGAAACTAAGCCTTTGGGGGTTTTCTAATTATCTCAAAAGAGTTTTTAAAGGAAGCTAAGCCTAA
1 AGAAACTAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTTTTAAAGGAAGCTAAGCCTAA
637699 AAAAGAGGTTCATTGACAACTA
66 AAAAGAGGTTCATTGACAACTA
637721 AGAAACTAAGCCTTCGGGGGTTT
1 AGAAACTAAGCCTTCGGGGGTTT
637744 CTTGATTTTT
Statistics
Matches: 141, Mismatches: 38, Indels: 42
0.64 0.17 0.19
Matches are distributed among these distances:
80 2 0.01
81 1 0.01
82 5 0.04
83 6 0.04
84 2 0.01
85 1 0.01
86 7 0.05
87 54 0.38
88 4 0.03
89 4 0.03
90 30 0.21
91 7 0.05
92 1 0.01
93 2 0.01
94 6 0.04
95 6 0.04
96 1 0.01
97 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (87 bp):
AGAAACTAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTTTTAAAGGAAGCTAAGCCTAA
AAAAGAGGTTCATTGACAACTA
Found at i:638760 original size:23 final size:23
Alignment explanation
Indices: 638714--638760 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
638704 TTGTTGTTAT
* * * *
638714 TAATATTATTATTATTGTATTAA
1 TAATAATATTATTAATATAATAA
638737 TAATAATATTATTAATATAATAA
1 TAATAATATTATTAATATAATAA
638760 T
1 T
638761 TATTATTACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAATAATATTATTAATATAATAA
Found at i:640017 original size:24 final size:24
Alignment explanation
Indices: 639973--640019 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
639963 ATAAAGAACC
*
639973 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
639997 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
640020 CAACCAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:643303 original size:19 final size:20
Alignment explanation
Indices: 643281--643324 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
643271 GAGAAAAGGT
643281 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
643300 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
643320 AAAAG
1 AAAAG
643325 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:649699 original size:17 final size:16
Alignment explanation
Indices: 649677--649710 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
649667 TAAAAACAGT
649677 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
649694 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
649710 A
1 A
649711 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:658983 original size:16 final size:17
Alignment explanation
Indices: 658946--658983 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
658936 ACAACTAGAA
658946 ATATA-AACACTTGAAC
1 ATATATAACACTTGAAC
*
658962 AGATATAACACTT-AAC
1 ATATATAACACTTGAAC
658978 ATATAT
1 ATATAT
658984 GACTAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (17 bp):
ATATATAACACTTGAAC
Found at i:660529 original size:30 final size:30
Alignment explanation
Indices: 660495--660567 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
660485 TAGGGATTTA
*
660495 TTTCAAGAGAAACAGACTCAGAGATGATTG
1 TTTCAAGAGAAACAGACTCAGAGATAATTG
660525 TTTCAAGAGAAACAGACTCAGAGATAATTG
1 TTTCAAGAGAAACAGACTCAGAGATAATTG
660555 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
660568 TGTCTCAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (30 bp):
TTTCAAGAGAAACAGACTCAGAGATAATTG
Found at i:660577 original size:15 final size:15
Alignment explanation
Indices: 660527--660579 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
660517 GATGATTGTT
* *
660527 TCAAGAGAAACAGAC
1 TCAAGAGAAACTGTC
* *
660542 TC-AGAGATAATTGTT
1 TCAAGAGA-AACTGTC
660557 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
660572 TCAAGAGA
1 TCAAGAGA
660580 GACAAAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 5 0.17
15 20 0.67
16 5 0.17
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:661195 original size:16 final size:16
Alignment explanation
Indices: 661174--661213 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
661164 TTCATGTATC
661174 ATGTATGTATGTGTTG
1 ATGTATGTATGTGTTG
*
661190 ATGTATATATGTGTTG
1 ATGTATGTATGTGTTG
*
661206 ATATATGT
1 ATGTATGT
661214 TTTCTCGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (16 bp):
ATGTATGTATGTGTTG
Found at i:662036 original size:2 final size:2
Alignment explanation
Indices: 662029--662078 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
662019 GCTTTATTAT
662029 TA TA TA TA TA TA TA TA TA TA TA TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
662072 TA TA TA T
1 TA TA TA T
662079 CGCCTTTATC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:667601 original size:5 final size:5
Alignment explanation
Indices: 667591--667624 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
667581 CTTTTTTCAC
* *
667591 AAAAT AAAAT AAAAT AAAAT AATAC AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
667625 AAAGATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:667621 original size:20 final size:20
Alignment explanation
Indices: 667596--667634 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
667586 TTCACAAAAT
667596 AAAATAAAATAAA-ATAATAC
1 AAAATAAAA-AAAGATAATAC
667616 AAAATAAAAAAAGATAATA
1 AAAATAAAAAAAGATAATA
667635 GAATGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAAAAAAAGATAATAC
Found at i:667910 original size:2 final size:2
Alignment explanation
Indices: 667856--667890 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
667846 CTAATATTAA
667856 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
667891 CACTAACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:669093 original size:113 final size:114
Alignment explanation
Indices: 668947--669174 Score: 422
Period size: 113 Copynumber: 2.0 Consensus size: 114
668937 AGATGATGAG
* *
668947 GTCTAGTGAGTAGGAAAATAGATTTCTGATTTTTACTAATGAAATCCTGATTTTTTGGGATTTAT
1 GTCTAGTGAGTAGGAAAATAGATTTCTGATTTTTACTAATGAAATCCCGATTTTTCGGGATTTAT
669012 TTTG-TTTTTTTAATGGGTTTTCGATTTGGTTTGGATTTCTACTGATTT
66 TTTGTTTTTTTTAATGGGTTTTCGATTTGGTTTGGATTTCTACTGATTT
669060 GTCTAGTGAGTAGGAAAATAGATTTCTGATTTTTACTAATGAAATCCCGATTTTTCGGGATTTAT
1 GTCTAGTGAGTAGGAAAATAGATTTCTGATTTTTACTAATGAAATCCCGATTTTTCGGGATTTAT
*
669125 TTTGTTTTTTTTAATGGGTTTTTGATTTGGTTTGGATTTCTACTGATTT
66 TTTGTTTTTTTTAATGGGTTTTCGATTTGGTTTGGATTTCTACTGATTT
669174 G
1 G
669175 GGTTATTGTT
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
113 67 0.60
114 44 0.40
ACGTcount: A:0.22, C:0.07, G:0.21, T:0.50
Consensus pattern (114 bp):
GTCTAGTGAGTAGGAAAATAGATTTCTGATTTTTACTAATGAAATCCCGATTTTTCGGGATTTAT
TTTGTTTTTTTTAATGGGTTTTCGATTTGGTTTGGATTTCTACTGATTT
Found at i:669508 original size:3 final size:3
Alignment explanation
Indices: 669495--669536 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
669485 CTGTAAAATG
669495 TAA TAAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA -AA TAA TA
1 TAA T-AA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
669537 GAAGATGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:669520 original size:20 final size:18
Alignment explanation
Indices: 669495--669536 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
669485 CTGTAAAATG
669495 TAATAAATAATAATTAATAA
1 TAATAAATAATAA-TAA-AA
669515 TAAT-AATAATAATAAAA
1 TAATAAATAATAATAAAA
669532 TAATA
1 TAATA
669537 GAAGATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 8 0.38
20 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAAATAATAATAAAA
Found at i:673016 original size:15 final size:15
Alignment explanation
Indices: 672993--673063 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
672983 TTCTGACTCC
*
672993 TCGTTGTCGTCATCA
1 TCGTCGTCGTCATCA
*
673008 TCGTCGTCGTCGTCA
1 TCGTCGTCGTCATCA
* * *
673023 TCATCATCATCATCA
1 TCGTCGTCGTCATCA
** *
673038 TCGTTATCGTCATCG
1 TCGTCGTCGTCATCA
673053 TCGTCGTCGTC
1 TCGTCGTCGTC
673064 GTCCTGAGCA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.14, C:0.31, G:0.18, T:0.37
Consensus pattern (15 bp):
TCGTCGTCGTCATCA
Found at i:673017 original size:6 final size:6
Alignment explanation
Indices: 673005--673066 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
672995 GTTGTCGTCA
* * * * * *
673005 TCATCG TCGTCG TCGTCA TCATCA TCATCA TCATCG TTATCG TCATCG
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
* *
673053 TCGTCG TCGTCG TC
1 TCATCG TCATCG TC
673067 CTGAGCAGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (6 bp):
TCATCG
Found at i:673019 original size:18 final size:18
Alignment explanation
Indices: 672993--673027 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
672983 TTCTGACTCC
*
672993 TCGTTGTCGTCATCATCG
1 TCGTCGTCGTCATCATCG
673011 TCGTCGTCGTCATCATC
1 TCGTCGTCGTCATCATC
673028 ATCATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.20, T:0.37
Consensus pattern (18 bp):
TCGTCGTCGTCATCATCG
Found at i:673066 original size:9 final size:9
Alignment explanation
Indices: 672999--673057 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
672989 CTCCTCGTTG
672999 TCGTCATCA
1 TCGTCATCA
* *
673008 TCGTCGTCG
1 TCGTCATCA
673017 TCGTCATCA
1 TCGTCATCA
*
673026 TCATCATCA
1 TCGTCATCA
* * *
673035 TCATCGTTA
1 TCGTCATCA
*
673044 TCGTCATCG
1 TCGTCATCA
673053 TCGTC
1 TCGTC
673058 GTCGTCGTCC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.17, C:0.32, G:0.15, T:0.36
Consensus pattern (9 bp):
TCGTCATCA
Found at i:673439 original size:18 final size:18
Alignment explanation
Indices: 673416--673453 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
673406 AGGCGATGGT
*
673416 GGCATCATATATGGCTGC
1 GGCATCATAAATGGCTGC
673434 GGCATCATAAATGGCTGC
1 GGCATCATAAATGGCTGC
673452 GG
1 GG
673454 TGGCTGCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (18 bp):
GGCATCATAAATGGCTGC
Found at i:675151 original size:111 final size:110
Alignment explanation
Indices: 674961--675289 Score: 583
Period size: 111 Copynumber: 3.0 Consensus size: 110
674951 ATTACAAAAA
* *
674961 TTAATTCTTAATCTAATAATCATGCATTAAATAAA-GAA--ACTATTACTAATAATTTAAATTAA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATATTACTAATAATTTAAATTAA
675023 ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
675068 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTCATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACT-AATATTACTAATAATTTAAATTA
675133 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
65 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
675179 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACT-AATATTACTAATAATTTAAATTA
*
675244 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
65 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
675290 ATGATTTCTA
Statistics
Matches: 213, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
107 35 0.16
108 2 0.01
111 176 0.83
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (110 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATATTACTAATAATTTAAATTAA
ATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:675371 original size:17 final size:18
Alignment explanation
Indices: 675351--675386 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
675341 GAATTATATT
675351 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
675368 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
675386 A
1 A
675387 TTATATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:675945 original size:28 final size:28
Alignment explanation
Indices: 675913--675967 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
675903 ACACATAGGT
* *
675913 TTTACTTTTAAAATAAAAGTTGCTTTTA
1 TTTACATTTAAAATAAAAGTTACTTTTA
*
675941 TTTACATTTAAAATAAATGTTACTTTT
1 TTTACATTTAAAATAAAAGTTACTTTT
675968 GCTTTACTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (28 bp):
TTTACATTTAAAATAAAAGTTACTTTTA
Found at i:693161 original size:22 final size:22
Alignment explanation
Indices: 693135--693203 Score: 104
Period size: 22 Copynumber: 3.1 Consensus size: 22
693125 GGAGACATCA
693135 GTCCCCATCTCTGACGAAATCC
1 GTCCCCATCTCTGACGAAATCC
*
693157 GTCCCCATCTCTGACGTAATCC
1 GTCCCCATCTCTGACGAAATCC
*
693179 ATCCCCATCTCCT-ACGAAATCC
1 GTCCCCATCT-CTGACGAAATCC
693201 GTC
1 GTC
693204 TATCTCCATC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 40 0.95
23 2 0.05
ACGTcount: A:0.22, C:0.42, G:0.12, T:0.25
Consensus pattern (22 bp):
GTCCCCATCTCTGACGAAATCC
Found at i:695630 original size:12 final size:12
Alignment explanation
Indices: 695604--695645 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
695594 TTTTTTGGCA
695604 TTATTTATTTG-T
1 TTATTTA-TTGAT
695616 TTATTTATTGAT
1 TTATTTATTGAT
* *
695628 TTATGTATTAAT
1 TTATTTATTGAT
695640 TTATTT
1 TTATTT
695646 TTAGCGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:695840 original size:21 final size:21
Alignment explanation
Indices: 695814--695890 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
695804 CTCTCCTACA
695814 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTATCATCC
* **
695835 TTCAAGAGACCCCTCCCA-CC
1 TTCAAGAGGCCCCTATCATCC
* * *
695855 GTTCAAGAGGCCCTTGTCATCA
1 -TTCAAGAGGCCCCTATCATCC
*
695877 TTCAAGAGGTCCCT
1 TTCAAGAGGCCCCT
695891 TCTACCGTTC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTATCATCC
Found at i:697225 original size:13 final size:14
Alignment explanation
Indices: 697200--697232 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
697190 AAATTAATGT
697200 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
697214 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
697227 ATTTGT
1 ATTTGT
697233 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:697412 original size:20 final size:20
Alignment explanation
Indices: 697356--697440 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
697346 AAGGTACACT
* *
697356 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*** *
697376 TTCGCGTTGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
697396 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
697416 TTCGTAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
697436 TTCGC
1 TTCGC
697441 GTTGTGATTT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:697484 original size:20 final size:20
Alignment explanation
Indices: 697459--697497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
697449 TTTCGCGTTT
*
697459 CGAATTTAACTTTTGCAACG
1 CGAATTTAACTTTCGCAACG
*
697479 CGAATTTGACTTTCGCAAC
1 CGAATTTAACTTTCGCAAC
697498 AATCGCAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
CGAATTTAACTTTCGCAACG
Found at i:700168 original size:12 final size:12
Alignment explanation
Indices: 700147--700180 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
700137 GGTTGTGGGT
*
700147 TTTGAGATTGTG
1 TTTGATATTGTG
700159 TTTGATATTGTG
1 TTTGATATTGTG
*
700171 TTTGGTATTG
1 TTTGATATTG
700181 GAAATGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:700995 original size:20 final size:20
Alignment explanation
Indices: 700948--701099 Score: 82
Period size: 20 Copynumber: 7.6 Consensus size: 20
700938 AAAACATTTG
* *
700948 TGTTGCGAAACTAAAA--CC
1 TGTTGCGAAATTAAAATTCA
*
700966 TGTTGTGAAATTAAAATTCA
1 TGTTGCGAAATTAAAATTCA
** *
700986 TGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCA
*
701006 CGTTGCG-AATTCAGAAA-TCGA
1 TGTTGCGAAATT-A-AAATTC-A
* *
701027 -GTTGCGAATTTGAAATTCA
1 TGTTGCGAAATTAAAATTCA
* *
701046 GTGTTGCGAATTTGAAATTCA
1 -TGTTGCGAAATTAAAATTCA
* * *
701067 GTGTTGCGAATTTGAAAACTGA
1 -TGTTGCGAAATT-AAAATTCA
701089 -GTTGCGAAATT
1 TGTTGCGAAATT
701100 GGAGATCGCG
Statistics
Matches: 107, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
18 14 0.13
19 6 0.06
20 44 0.41
21 38 0.36
22 5 0.05
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCA
Found at i:701053 original size:21 final size:21
Alignment explanation
Indices: 701027--701083 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
701017 CAGAAATCGA
701027 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCAGT
701048 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCAGT
701069 GTTGCGAATTTGAAA
1 GTTGCGAATTTGAAA
701084 ACTGAGTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.37
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTCAGT
Found at i:701099 original size:21 final size:21
Alignment explanation
Indices: 700999--701096 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 21
700989 TGCGAAAACA
* *
700999 AAATTC-GCGTTGCGAATTCAG
1 AAATTCAGAGTTGCGAATT-TG
701020 AAA-TC-GAGTTGCGAATTTG
1 AAATTCAGAGTTGCGAATTTG
*
701039 AAATTCAGTGTTGCGAATTTG
1 AAATTCAGAGTTGCGAATTTG
*
701060 AAATTCAGTGTTGCGAATTTG
1 AAATTCAGAGTTGCGAATTTG
* *
701081 AAA-ACTGAGTTGCGAA
1 AAATTCAGAGTTGCGAA
701097 ATTGGAGATC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 4 0.06
20 25 0.36
21 40 0.58
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (21 bp):
AAATTCAGAGTTGCGAATTTG
Found at i:711662 original size:13 final size:13
Alignment explanation
Indices: 711644--711677 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
711634 TCAAGTGGTG
711644 CTGGGTTTCGAAT
1 CTGGGTTTCGAAT
711657 CTGGGTTTCGAAT
1 CTGGGTTTCGAAT
711670 CTGGGTTT
1 CTGGGTTT
711678 GTTTTCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.15, G:0.32, T:0.41
Consensus pattern (13 bp):
CTGGGTTTCGAAT
Found at i:716237 original size:10 final size:10
Alignment explanation
Indices: 716224--716258 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
716214 TGATTCTCTC
716224 TTGATTGTTG
1 TTGATTGTTG
716234 TTGATTGTTG
1 TTGATTGTTG
**
716244 TTTCTTGTTG
1 TTGATTGTTG
716254 TTGAT
1 TTGAT
716259 CAATGGCTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.03, G:0.26, T:0.63
Consensus pattern (10 bp):
TTGATTGTTG
Found at i:716506 original size:18 final size:17
Alignment explanation
Indices: 716452--716500 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
716442 TTGGACCCTT
* *
716452 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
716470 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
716488 AGTGCATTCGATG
1 AGTGCA-TCGATG
716501 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:717375 original size:23 final size:24
Alignment explanation
Indices: 717331--717376 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
717321 AATAAGTTCA
717331 AAACATCCAACAACCATCAAAATT
1 AAACATCCAACAACCATCAAAATT
717355 AAACATCCAGA-AA-CATCAAAAT
1 AAACATCCA-ACAACCATCAAAAT
717377 CAATCCAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 11 0.52
25 1 0.05
ACGTcount: A:0.57, C:0.26, G:0.02, T:0.15
Consensus pattern (24 bp):
AAACATCCAACAACCATCAAAATT
Found at i:720274 original size:23 final size:22
Alignment explanation
Indices: 720248--720323 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
720238 TGACCTTGTT
720248 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACATTCAAGG-GTG
* * *
720271 CATCGGTGCACCTTC-ATGGTG
1 CATCGATGCACATTCAAGGGTG
* *
720292 TATCGATGCACATTCAAGGATG
1 CATCGATGCACATTCAAGGGTG
720314 CATCGATGCA
1 CATCGATGCA
720324 TTAAGCACAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
21 15 0.35
22 15 0.35
23 13 0.30
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGGTG
Found at i:721325 original size:19 final size:19
Alignment explanation
Indices: 721301--721351 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
721291 GAAAATATTC
721301 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
721320 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
721339 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
721352 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:721327 original size:65 final size:63
Alignment explanation
Indices: 721196--721353 Score: 210
Period size: 65 Copynumber: 2.5 Consensus size: 63
721186 TGCACCAAGT
* ***
721196 GTGCATCGATGCATAAATGCATTCGATG-TTTGAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATAAATGCATTCGATGTTTTGAAAATAGCCAGATGCATCGATGCATGGAGA
**
721258 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTTGAAAATAGCCAGA-TGCATCGATGCATGGAGA
* *
721323 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCAT-AAATGCATTCGATGTT
721354 CAATTAATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
62 14 0.17
63 14 0.17
64 13 0.15
65 43 0.51
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTTGAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:727763 original size:22 final size:21
Alignment explanation
Indices: 727721--727760 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
727711 GAGTTTGTTT
*
727721 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
727742 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
727761 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:729756 original size:64 final size:63
Alignment explanation
Indices: 729688--729868 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
729678 TTGGAACACT
* ***
729688 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
729752 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
729816 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
729869 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:729840 original size:19 final size:19
Alignment explanation
Indices: 729816--729866 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
729806 GAAAATATTC
729816 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
729835 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
729854 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
729867 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:729842 original size:65 final size:65
Alignment explanation
Indices: 729709--729868 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
729699 TGCACCAAGT
* ***
729709 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
729773 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
729837 A
65 A
* *
729838 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
729869 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:729908 original size:65 final size:63
Alignment explanation
Indices: 729710--729917 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
729700 GCACCAAGTG
* * *
729710 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGAC-TGA
*
729774 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCAT-GACT
729836 GA
62 GA
* * * *
729838 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATG-ACT
729902 GA
62 GA
*
729904 TGCATCGGTGCATG
1 TGCATCGATGCATG
729918 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 11 0.09
64 44 0.36
65 63 0.51
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGACTGA
Found at i:737188 original size:2 final size:2
Alignment explanation
Indices: 737181--737221 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
737171 TCAATAAGCT
737181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
737222 TTCTATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:739864 original size:24 final size:25
Alignment explanation
Indices: 739807--739870 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
739797 AAACATTAGG
739807 AAAAACATAATAAAATAAATAAATA
1 AAAAACATAATAAAATAAATAAATA
* *
739832 AATAA-ATAATAATAA-GAATAAA-A
1 AAAAACATAATAA-AATAAATAAATA
739855 AAAAACATAA-AAAATA
1 AAAAACATAATAAAATA
739871 TGTATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 2 0.06
23 7 0.22
24 17 0.53
25 6 0.19
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.19
Consensus pattern (25 bp):
AAAAACATAATAAAATAAATAAATA
Found at i:741902 original size:85 final size:84
Alignment explanation
Indices: 741667--742074 Score: 480
Period size: 85 Copynumber: 4.8 Consensus size: 84
741657 ATGTGCCATC
* * * * * *
741667 GAGCTGAATGGAATCGAACTCGACA-ATTTTGTTGACAAATAACCCTTTTTGCCTTGAGCTATAC
1 GAGCTGAATGTAATCGAACTCGA-AGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
741731 TGTAAATTTGACATGCCTCT
65 TGTAAATTTGATATGCCTTT
* * * * * * *
741751 AAGGTGAATAG-AATCGATCTCAAAGG-TTTGTTGACAGATAACCCTTTTCACCTTGAGTTATGC
1 GAGCTGAAT-GTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
741814 TGTAAATTTGATGTTCCTTT
65 TGTAAATTTGATATGCCTTT
* * * *
741834 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGCTGACAGATAACTCTTCTCTCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
741899 TGTAAGTTTGATATGCCTTT
65 TGTAAATTTGATATGCCTTT
* * *
741919 GAGCTAAATGTAATCTAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGG--TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
741984 CCGTAAATTTGATATGCCTTT
64 CTGTAAATTTGATATGCCTTT
* * *
742005 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTCGATAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
742070 TGTAA
65 TGTAA
742075 TTGGCTGGGA
Statistics
Matches: 277, Mismatches: 39, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
82 1 0.00
83 69 0.25
84 21 0.08
85 111 0.40
86 74 0.27
87 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (84 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCT
GTAAATTTGATATGCCTTT
Found at i:742276 original size:50 final size:50
Alignment explanation
Indices: 742201--742349 Score: 199
Period size: 57 Copynumber: 2.8 Consensus size: 50
742191 ATGAAGTTGA
*
742201 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATATTGTTTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATATTGTTTG
* *
742251 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAATATTTTTTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAAT-C---C---AATATTGTTTG
*
742308 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAAT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
742350 CATGTATAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
50 38 0.44
51 1 0.01
53 1 0.01
54 1 0.01
56 1 0.01
57 45 0.52
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (50 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATATTGTTTG
Found at i:742399 original size:122 final size:122
Alignment explanation
Indices: 742248--742667 Score: 716
Period size: 122 Copynumber: 3.4 Consensus size: 122
742238 CCAATATTGT
* *
742248 TTGGCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAATATTTTTTGGCTTT
1 TTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTT
* * *
742313 GAGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCATGTATAAATTTCACCGAT
66 GGGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCTTGTATAAATTTCACCGAA
*
742370 TTGGTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTT
1 TTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTT
742435 GGGTTGGATATCCTTCGTTGTGAAGTTGAAAA-CCAATCTTGTATAAATTTCACCGAA
66 GGGTTGGATATCCTTCGTTGTGAAGTT-AAAATCCAATCTTGTATAAATTTCACCGAA
* *
742492 TTGGCTTTGAGTTGGATATACTTCGTTGTGAAGTTGAAAACCAATCTTGAATATTATTTGGCTTT
1 TTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTT
* * *
742557 GGGTTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGCATAAATTTCACCGAA
66 GGGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCTTGTATAAATTTCACCGAA
*
742614 TTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAT
1 TTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAT
742668 GTTGCGTTAT
Statistics
Matches: 281, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
121 3 0.01
122 274 0.98
123 4 0.01
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (122 bp):
TTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTATTTGGCTTT
GGGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCTTGTATAAATTTCACCGAA
Found at i:742410 original size:65 final size:64
Alignment explanation
Indices: 742304--742663 Score: 469
Period size: 65 Copynumber: 5.8 Consensus size: 64
742294 TTGAATATTT
* *
742304 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCATGTATAAATTTCACCGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG-ATAAATTTCACCGA
* *
742369 TTTGGTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGA-ATA-TT-----A
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGATAAATTTCACCGA
* *
742426 TTTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAAACCAATCTTGTATAAATTTCACCGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG-ATAAATTTCACCGA
* * * *
742491 ATTGGCTTTGAGTTGGATATACTTCGTTGTGAAGTTGAAAACCAATCTTGA-ATA-TT-----A
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGATAAATTTCACCGA
* *
742548 TTTGGCTTTGGGTTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGCATAAATTTCACCGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG-ATAAATTTCACCGA
* *
742613 ATTGGCTTTGGGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGA
1 TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGA
742664 ATATGTTGCG
Statistics
Matches: 259, Mismatches: 20, Indels: 33
0.83 0.06 0.11
Matches are distributed among these distances:
57 94 0.36
58 2 0.01
59 4 0.02
60 4 0.02
62 4 0.02
63 4 0.02
64 3 0.01
65 144 0.56
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (64 bp):
TTTGGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGATAAATTTCACCGA
Found at i:743826 original size:20 final size:21
Alignment explanation
Indices: 743789--743827 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
743779 CTAAATCTTG
* *
743789 CATAGGGGTATCGGTACCCCT
1 CATAGGGGTACCGATACCCCT
743810 CATA-GGGTACCGATACCC
1 CATAGGGGTACCGATACCC
743828 TCTGGGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (21 bp):
CATAGGGGTACCGATACCCCT
Found at i:745908 original size:19 final size:18
Alignment explanation
Indices: 745886--745924 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
745876 AACAATATAA
745886 TTAAATAAAAAAAACAATT
1 TTAAA-AAAAAAAACAATT
**
745905 TTAAAATCAAAAACAATT
1 TTAAAAAAAAAAACAATT
745923 TT
1 TT
745925 TTATTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAAAAAAACAATT
Found at i:746345 original size:20 final size:22
Alignment explanation
Indices: 746318--746377 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 22
746308 CCAAAACTCG
746318 AAGGGGGTATCGATACCC-TC-
1 AAGGGGGTATCGATACCCATCA
* *
746338 ATGGGGGTATCGGTACCCATTCA
1 AAGGGGGTATCGATACCCA-TCA
746361 AAGGGGGTATCGATACC
1 AAGGGGGTATCGATACC
746378 TAGCGTACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.48
22 2 0.06
23 15 0.45
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (22 bp):
AAGGGGGTATCGATACCCATCA
Found at i:749202 original size:74 final size:73
Alignment explanation
Indices: 749114--749258 Score: 195
Period size: 74 Copynumber: 2.0 Consensus size: 73
749104 AAACTCAAAT
*
749114 TTAGGATAATA-TTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGTTCTTTAGTA
1 TTAGGATAATATTTTTAAA-ATTATATCTTTATCTTTGTA-TTTAGTTTAAATAGAT-TTTAGTA
749177 TTTTAATTAAG
63 TTTTAATTAAG
* ** * *
749188 TTAGGATATTATTTTTTTATTTTTATCTTTATCTTTGTATTTAGTTTAAATAGATTTTAGTATTT
1 TTAGGATAATATTTTTAAAATTATATCTTTATCTTTGTATTTAGTTTAAATAGATTTTAGTATTT
749253 TAATTA
66 TAATTA
749259 GGTTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
73 16 0.25
74 30 0.48
75 17 0.27
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (73 bp):
TTAGGATAATATTTTTAAAATTATATCTTTATCTTTGTATTTAGTTTAAATAGATTTTAGTATTT
TAATTAAG
Found at i:749282 original size:75 final size:75
Alignment explanation
Indices: 749140--749285 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
749130 AACATTATAT
* ** *
749140 TTTATCTTTGTATTTTAGTTTAAATAGTTCTTTAGTATTTTAATTAAGTTAGGATATTATTTTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGATCTTTAGTATTTTAATTAAGTTAAAATATTATTTATT
749205 TATTTTTATC
66 TATTTTTATC
*
749215 TTTATCTTTGTA-TTTAGTTTAAATAGAT-TTTAGTATTTTAATTAGGTTTTAAAATA-TATTAT
1 TTTATCTTTGTATTTTAGTTTAAATAGATCTTTAGTATTTTAATTAAG--TTAAAATATTATT-T
749277 ATTTATTTT
63 ATTTATTTT
749286 AGTTTAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
73 17 0.27
74 19 0.30
75 27 0.43
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.60
Consensus pattern (75 bp):
TTTATCTTTGTATTTTAGTTTAAATAGATCTTTAGTATTTTAATTAAGTTAAAATATTATTTATT
TATTTTTATC
Found at i:749909 original size:16 final size:16
Alignment explanation
Indices: 749888--749919 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
749878 AATCTCTTTA
749888 ATTTGTTTATTTAATT
1 ATTTGTTTATTTAATT
749904 ATTTGTTTATTTAATT
1 ATTTGTTTATTTAATT
749920 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTTGTTTATTTAATT
Found at i:757349 original size:77 final size:76
Alignment explanation
Indices: 757221--757371 Score: 232
Period size: 77 Copynumber: 2.0 Consensus size: 76
757211 TAAACTCAAA
*
757221 TTTAGGATAATATTTTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGTTCTTTAGT
1 TTTAGGATAATATTTTTT-AACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGT-TTTAGT
757286 ATTTTAATTAAGT
64 ATTTTAATTAAGT
* * *
757299 TTTAGGATATTATTTTTT-ATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
1 TTTAGGATAATATTTTTTAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
757363 TTTTAATTA
65 TTTTAATTA
757372 GGATTTAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
76 23 0.34
77 28 0.41
78 17 0.25
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.59
Consensus pattern (76 bp):
TTTAGGATAATATTTTTTAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAGT
Found at i:758053 original size:16 final size:16
Alignment explanation
Indices: 758032--758063 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
758022 AATCTCTTTA
758032 ATTTGTTTATTTAATT
1 ATTTGTTTATTTAATT
758048 ATTTGTTTATTTAATT
1 ATTTGTTTATTTAATT
758064 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTTGTTTATTTAATT
Found at i:763029 original size:99 final size:99
Alignment explanation
Indices: 762858--763066 Score: 303
Period size: 99 Copynumber: 2.1 Consensus size: 99
762848 GGACAACTCA
* * * **
762858 ATATTATAATCACCTTTATTAGGTTAGCTGAATCTTATCCATAGATACGGGGCTTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAATACGGGGCGGTTAACCAATT
* * *
762923 GCTCTAGAGGGATAGCTCAAGCTTTATTGTATAG
66 ACTCTAGAGGGACAACTCAAGCTTTATTGTATAG
*
762957 ATATTATAATCGCCTTTATCAGGCTAGCTGAATCTTATCCATAAAGT-CGGGGCGGTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAA-TACGGGGCGGTTAACCAAT
*
763021 TACTCTAGAGGGACAACTCAAGCTTTATTGTATAT
65 TACTCTAGAGGGACAACTCAAGCTTTATTGTATAG
*
763056 ATAATATAATC
1 ATATTATAATC
763067 TGGGAATACG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 97 0.99
100 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAATACGGGGCGGTTAACCAATT
ACTCTAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:767081 original size:9 final size:9
Alignment explanation
Indices: 767058--767124 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 9
767048 TTATGGAAAC
767058 AAATAAAATA
1 AAATAAAA-A
*
767068 AAATAAAGA
1 AAATAAAAA
767077 AAATAAAAA
1 AAATAAAAA
767086 GAAATAAAAA
1 -AAATAAAAA
*
767096 ACGATAAATAA
1 A-AATAAA-AA
*
767107 AAACAAAAA
1 AAATAAAAA
767116 CAAA-AAAAA
1 -AAATAAAAA
767125 GAAAAAAGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 17 0.35
10 28 0.58
11 3 0.06
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.10
Consensus pattern (9 bp):
AAATAAAAA
Found at i:767091 original size:24 final size:24
Alignment explanation
Indices: 767063--767109 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
767053 GAAACAAATA
767063 AAATAAAATAAAGA-AAATAAAAAG
1 AAATAAAA-AAAGATAAATAAAAAG
*
767087 AAATAAAAAACGATAAATAAAAA
1 AAATAAAAAAAGATAAATAAAAA
767110 CAAAAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (24 bp):
AAATAAAAAAAGATAAATAAAAAG
Found at i:767418 original size:28 final size:26
Alignment explanation
Indices: 767387--767439 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
767377 ATATAGTATT
767387 TAATAAAATA-AGTAAATAATAATAATAA
1 TAATAAAATATA-TAAAT-ATAA-AATAA
767415 TAATAAAATATATAAATATAAAATA
1 TAATAAAATATATAAATATAAAATA
767440 TTAGGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.17
27 4 0.17
28 15 0.62
29 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
TAATAAAATATATAAATATAAAATAA
Found at i:767429 original size:15 final size:15
Alignment explanation
Indices: 767356--767440 Score: 54
Period size: 15 Copynumber: 5.5 Consensus size: 15
767346 AAATGTTAGG
767356 TAAAATATATAAATATA
1 TAAAATATAT-AATA-A
* *
767373 TATAATATAGTATTTAA
1 TAAAATATA-TA-ATAA
767390 TAAAATA-AGT-A-AA
1 TAAAATATA-TAATAA
767403 TAATAATA-ATAATAA
1 TAA-AATATATAATAA
767418 TAAAATATATAA-ATA
1 TAAAATATATAATA-A
767433 TAAAATAT
1 TAAAATAT
767441 TAGGTAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 6 0.11
14 11 0.19
15 18 0.32
16 3 0.05
17 16 0.28
18 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
TAAAATATATAATAA
Found at i:767504 original size:76 final size:76
Alignment explanation
Indices: 767388--767576 Score: 205
Period size: 76 Copynumber: 2.5 Consensus size: 76
767378 TATAGTATTT
767388 AATAAAAT-AAGTAAATAATAATAATAATAATAAAATATATAAA-TAT-AAAATATTAGGTAAAA
1 AATAAAATAAAGTAAATAATAATAATAATAATAAAATATATAAACTATAAAAATATTAGG-AAAA
767450 ACAAAAAAAAATA
65 AC-AAAAAAAATA
*
767463 AA-AAAATAAAGTAAAGTAAT-AT-ATATATATATAAGATATATAAACGTATAAACAAAATATTA
1 AATAAAATAAAGTAAA-TAATAATAATA-ATA-ATAAAATATATAAAC-TAT--A-AAAATATTA
*
767525 GGAAAAACAAAATAAATA
59 GGAAAAACAAAAAAAATA
*
767543 AATAAAATAAA-T-AATAAATAATAATAATAGTAAA
1 AATAAAATAAAGTAAAT-AATAATAATAATAATAAA
767577 TAATAGTAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 24
0.77 0.03 0.19
Matches are distributed among these distances:
74 8 0.08
75 14 0.15
76 17 0.18
78 4 0.04
79 8 0.08
80 17 0.18
81 17 0.18
82 11 0.11
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (76 bp):
AATAAAATAAAGTAAATAATAATAATAATAATAAAATATATAAACTATAAAAATATTAGGAAAAA
CAAAAAAAATA
Found at i:767551 original size:13 final size:12
Alignment explanation
Indices: 767533--767635 Score: 63
Period size: 13 Copynumber: 8.5 Consensus size: 12
767523 TAGGAAAAAC
767533 AAAATAAATAAAT
1 AAAATAAAT-AAT
767546 AAAATAAATAAT
1 AAAATAAATAAT
767558 -AAAT-AATAAT
1 AAAATAAATAAT
*
767568 AATAGTAAATAAT
1 AA-AATAAATAAT
*
767581 AGTAAA-AAATAGT
1 A--AAATAAATAAT
* *
767594 AAAAAATAATAAA
1 AAAATA-AATAAT
767607 AATAATAAA-AAT
1 AA-AATAAATAAT
* *
767619 AAAA-ACATAAA
1 AAAATAAATAAT
767630 AAAATA
1 AAAATA
767636 TGTATAATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
10 8 0.11
11 16 0.23
12 11 0.15
13 31 0.44
14 4 0.06
15 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:767560 original size:20 final size:20
Alignment explanation
Indices: 767535--767635 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 20
767525 GGAAAAACAA
767535 AATAAATAAATAAAATAAAT
1 AATAAATAAATAAAATAAAT
*
767555 AATAAATAATAATAATAGTAAAT
1 AATAAAT-A-AATAA-AATAAAT
* *
767578 AAT-AGTAAA-AAATAGTAAAA
1 AATAAATAAATAAA-A-TAAAT
767598 AAT-AATAAA-AATAATAAA-
1 AATAAATAAATAA-AATAAAT
767616 AATAAA-AACATAAAA-AAAT
1 AATAAATAA-ATAAAATAAAT
767635 A
1 A
767636 TGTATAATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
18 9 0.14
19 12 0.18
20 26 0.39
21 3 0.05
22 7 0.11
23 9 0.14
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (20 bp):
AATAAATAAATAAAATAAAT
Found at i:767567 original size:10 final size:10
Alignment explanation
Indices: 767539--767620 Score: 71
Period size: 10 Copynumber: 8.2 Consensus size: 10
767529 AAACAAAATA
767539 AATAAATAA-
1 AATAAATAAT
767548 AATAAATAAT
1 AATAAATAAT
767558 AAATAATAATAAT
1 -AAT-A-AATAAT
*
767571 AGTAAATAAT
1 AATAAATAAT
* *
767581 AGTAAAAAAT
1 AATAAATAAT
* *
767591 AGTAAAAAAT
1 AATAAATAAT
767601 AATAAA-AAT
1 AATAAATAAT
767610 AATAAA-AAT
1 AATAAATAAT
767619 AA
1 AA
767621 AAACATAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
9 23 0.35
10 30 0.45
11 4 0.06
12 3 0.05
13 6 0.09
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (10 bp):
AATAAATAAT
Found at i:767631 original size:9 final size:8
Alignment explanation
Indices: 767533--767635 Score: 64
Period size: 9 Copynumber: 11.8 Consensus size: 8
767523 TAGGAAAAAC
767533 AAAATAAA
1 AAAATAAA
*
767541 TAAATAAA
1 AAAATAAA
767549 ATAAAT-AA
1 A-AAATAAA
*
767557 TAAATAATA
1 AAAATAA-A
*
767566 ATAATAGTAA
1 AAAATA--AA
*
767576 ATAATAGTAA
1 AAAATA--AA
767586 AAAATAGTAA
1 AAAATA--AA
767596 AAAATAATA
1 AAAATAA-A
767605 AAAATAATA
1 AAAATAA-A
767614 AAAATAAA
1 AAAATAAA
*
767622 AACATAAA
1 AAAATAAA
767630 AAAATA
1 AAAATA
767636 TGTATAATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
7 4 0.05
8 24 0.30
9 26 0.32
10 26 0.32
11 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (8 bp):
AAAATAAA
Found at i:767631 original size:15 final size:16
Alignment explanation
Indices: 767533--767635 Score: 63
Period size: 16 Copynumber: 6.4 Consensus size: 16
767523 TAGGAAAAAC
767533 AAAATAAATAAATAA-A
1 AAAATAAA-AAATAATA
*
767549 ATAAATAATAAATAATA
1 A-AAATAAAAAATAATA
* **
767566 ATAATAGTAAATAAT-
1 AAAATAAAAAATAATA
* *
767581 --AGTAAAAAATAGTAA
1 AAAATAAAAAATAAT-A
767596 AAAATAATAAAAATAATA
1 AAAAT-A-AAAAATAATA
767614 AAAATAAAAACATAA-A
1 AAAATAAAAA-ATAATA
767630 AAAATA
1 AAAATA
767636 TGTATAATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
13 9 0.13
16 30 0.43
17 15 0.22
18 7 0.10
19 8 0.12
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAATAAAAAATAATA
Found at i:773594 original size:22 final size:22
Alignment explanation
Indices: 773568--773613 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
773558 TTATCAGTTG
773568 CGATTTTGCTCTATCCGATAGC
1 CGATTTTGCTCTATCCGATAGC
773590 CGATTTTGCTCTATCCGATAGC
1 CGATTTTGCTCTATCCGATAGC
773612 CG
1 CG
773614 TCTTCCGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (22 bp):
CGATTTTGCTCTATCCGATAGC
Found at i:779679 original size:17 final size:17
Alignment explanation
Indices: 779649--779720 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
779639 AATTAATAGT
* *
779649 TAGTCTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
779666 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
779683 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
779700 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
779718 TAG
1 TAG
779721 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:791335 original size:13 final size:13
Alignment explanation
Indices: 791303--791349 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
791293 TGCGTGTTGC
*
791303 GCGTCATAAATAA
1 GCGTCATAAATGA
*
791316 GCATCATAAATGA
1 GCGTCATAAATGA
* *
791329 GTGTCATAAATGC
1 GCGTCATAAATGA
791342 GCGTCATA
1 GCGTCATA
791350 GATTTATGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (13 bp):
GCGTCATAAATGA
Found at i:792718 original size:65 final size:64
Alignment explanation
Indices: 792641--792790 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 64
792631 TTACACTAGG
* *** * *
792641 TTGTGCATCGGTGCACAAATTTGCTTCGATGTTTCAA-AAATAGCCGGGGTGCATCGATGCATGA
1 TTGTGCATCGGTGCATAAATTCAATTCGATGTTTCAATAAA-AGCCAGAGTGCATCGATGCATG-
792705 C
64 C
* * * *
792706 TTGTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAAAATCCAGAGTGCATCGATGCATGG
1 TTGTGCATCGGTGCATAAATTCAATTCGATGTTTCAATAAAAGCCAGAGTGCATCGATGCATGC
* *
792770 TTGTTCATTGGTGCATAAATT
1 TTGTGCATCGGTGCATAAATT
792791 GTATTCGAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 18 0.25
65 50 0.70
66 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (64 bp):
TTGTGCATCGGTGCATAAATTCAATTCGATGTTTCAATAAAAGCCAGAGTGCATCGATGCATGC
Found at i:795346 original size:21 final size:22
Alignment explanation
Indices: 795288--795349 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
795278 AGTAGAGTGC
*
795288 ATCGATGCACATTCAAGGCATGC
1 ATCGATGCACATTCAAGG-ATGA
* * * *
795311 ACCGGTGCACCTTCATGG-TGA
1 ATCGATGCACATTCAAGGATGA
795332 ATCGATGCACATTCAAGG
1 ATCGATGCACATTCAAGG
795350 GAAGCATCAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 16 0.53
23 14 0.47
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGATGA
Found at i:801003 original size:21 final size:21
Alignment explanation
Indices: 800955--801004 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
800945 GGAGCGTATG
*
800955 GTGCATCGATGCATAGACTTT
1 GTGCATTGATGCATAGACTTT
* *
800976 GTGCATTGTTGCATAGGCTTT
1 GTGCATTGATGCATAGACTTT
800997 GTGCATTG
1 GTGCATTG
801005 GTACACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (21 bp):
GTGCATTGATGCATAGACTTT
Found at i:808457 original size:7 final size:7
Alignment explanation
Indices: 808445--808486 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
808435 TAAACCAAAA
808445 AATATTT
1 AATATTT
808452 AATATTT
1 AATATTT
808459 AATATTT
1 AATATTT
*
808466 AATATAT
1 AATATTT
*
808473 ATTATTT
1 AATATTT
808480 ATATATT
1 A-ATATT
808487 ATTTATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 26 0.87
8 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:808482 original size:11 final size:11
Alignment explanation
Indices: 808468--808493 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
808458 TAATATTTAA
808468 TATATATTATT
1 TATATATTATT
808479 TATATATTATT
1 TATATATTATT
808490 TATA
1 TATA
808494 AATTTGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:811297 original size:5 final size:5
Alignment explanation
Indices: 811287--811561 Score: 392
Period size: 5 Copynumber: 54.6 Consensus size: 5
811277 TTATTAAACG
* * * * * * * *
811287 GATAT GATAT GATAG GATAG GATAG GATAG GATAG GATAG GATAG GATAG
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
* * * *
811337 GATAG GATAG GATAG GATAG GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
811387 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
811437 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT G--ATAT GATAT
811489 GATAT GATAT GATATAT GATAT GATAT G--AT GATAT GATAT GATAT GATAT
1 GATAT GATAT G--ATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
811539 GATAT GATAT GATAT GATAT GAT
1 GATAT GATAT GATAT GATAT GAT
811562 TGTATGTTGT
Statistics
Matches: 262, Mismatches: 2, Indels: 12
0.95 0.01 0.04
Matches are distributed among these distances:
3 3 0.01
5 249 0.95
7 10 0.04
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (5 bp):
GATAT
Found at i:811855 original size:18 final size:18
Alignment explanation
Indices: 811822--811894 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
811812 AAAATTTAAA
* *
811822 ATAAGTATGTAAGTTATG
1 ATAAATATGAAAGTTATG
* * *
811840 GTAAATACGAAAGTTATA
1 ATAAATATGAAAGTTATG
*
811858 ATAAGTATGAAAGTTATG
1 ATAAATATGAAAGTTATG
*
811876 ATACATATGAAAGTTATG
1 ATAAATATGAAAGTTATG
811894 A
1 A
811895 AATATGTACG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (18 bp):
ATAAATATGAAAGTTATG
Done.