Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 54
Found at i:3553469 original size:24 final size:21
Alignment explanation
Indices: 3553427--3553485 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
3553417 TGATTTATTA
*
3553427 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
**
3553448 TTATGGATTTCAAGAATGTTG
1 TTATGGATTTCAAGTTTGTTG
*
3553469 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
3553486 AATGGATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:3553721 original size:45 final size:44
Alignment explanation
Indices: 3553667--3553782 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
3553657 TTATACAAAA
* * *
3553667 AAATGCCACTATATGTCCTG-ACATTTAACGACGT-TTTTTTGGAAC
1 AAATGCCACTAAATGT-CAGAACATTTAACGA--TATTTTTGGGAAC
* *
3553712 AAATGCCACTAAAAGTCAGAACATTTAGCGATATTTTTGGGAAC
1 AAATGCCACTAAATGTCAGAACATTTAACGATATTTTTGGGAAC
* *
3553756 AAATGCCACTAAATGTAAGAATATTTA
1 AAATGCCACTAAATGTCAGAACATTTA
3553783 GCAGCATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.02
44 36 0.59
45 24 0.39
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (44 bp):
AAATGCCACTAAATGTCAGAACATTTAACGATATTTTTGGGAAC
Found at i:3553792 original size:44 final size:44
Alignment explanation
Indices: 3553687--3553793 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
3553677 ATATGTCCTG
* * * *
3553687 ACATTTAACGACGTTTTTTTGGAACAAATGCCACTAAAAGTCAGA
1 ACATTTAGCGAC-ATTTTTGGGAACAAATGCCACTAAAAGTAAGA
* *
3553732 ACATTTAGCGATATTTTTGGGAACAAATGCCACTAAATGTAAGA
1 ACATTTAGCGACATTTTTGGGAACAAATGCCACTAAAAGTAAGA
*
3553776 ATATTTAGC-AGCATTTTT
1 ACATTTAGCGA-CATTTTT
3553794 TTGAAACAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.02
44 42 0.79
45 10 0.19
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (44 bp):
ACATTTAGCGACATTTTTGGGAACAAATGCCACTAAAAGTAAGA
Found at i:3553809 original size:45 final size:43
Alignment explanation
Indices: 3553700--3553814 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 43
3553690 TTTAACGACG
* *
3553700 TTTTTTTGGAACAAATGCCACTAAAAGTCAGAACATTTAGCGA
1 TTTTTTTGGAACAAATGCCACTAAATGTAAGAACATTTAGCGA
* *
3553743 TATTTTTGGGAACAAATGCCACTAAATGTAAGAATATTTAGCAGCA
1 T-TTTTTTGGAACAAATGCCACTAAATGTAAGAACATTTAGC-G-A
* * *
3553789 TTTTTTTGAAACAAACGCCACAAAAT
1 TTTTTTTGGAACAAATGCCACTAAAT
3553815 AAAAGATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.02
44 36 0.59
45 22 0.36
46 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (43 bp):
TTTTTTTGGAACAAATGCCACTAAATGTAAGAACATTTAGCGA
Found at i:3557888 original size:21 final size:21
Alignment explanation
Indices: 3557863--3558005 Score: 177
Period size: 21 Copynumber: 6.8 Consensus size: 21
3557853 ATTTTGGACT
3557863 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
3557884 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
*
3557903 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
3557924 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
3557945 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
3557966 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
3557987 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
3558006 CTATCGCAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
19 27 0.25
21 60 0.57
23 19 0.18
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:3557984 original size:63 final size:61
Alignment explanation
Indices: 3557863--3558005 Score: 223
Period size: 63 Copynumber: 2.3 Consensus size: 61
3557853 ATTTTGGACT
* *
3557863 ATCGCAACGAACTTGGAATAAATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGACTATCGCAACGAACTTGGAATAA
*
3557924 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTCGACTATCGCAACGAACTTGGAATAA
3557987 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
3558006 CTATCGCAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
61 27 0.36
63 38 0.51
65 9 0.12
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (61 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:3558854 original size:2 final size:2
Alignment explanation
Indices: 3558847--3558881 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3558837 TTTAATACAC
3558847 AT AT 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 AT AT A
3558882 AACTTTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3560808 original size:14 final size:14
Alignment explanation
Indices: 3560791--3560847 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
3560781 CACCCACACA
*
3560791 CACGCACTCGCACG
1 CACGCACACGCACG
*
3560805 CACGCACAAGCACG
1 CACGCACACGCACG
3560819 CACGCACACGCACG
1 CACGCACACGCACG
* *
3560833 CGCGCACACACACG
1 CACGCACACGCACG
3560847 C
1 C
3560848 GCACACACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.28, C:0.49, G:0.21, T:0.02
Consensus pattern (14 bp):
CACGCACACGCACG
Found at i:3560848 original size:14 final size:14
Alignment explanation
Indices: 3560785--3560856 Score: 69
Period size: 14 Copynumber: 5.3 Consensus size: 14
3560775 CACTTTCACC
* *
3560785 CACACACACGCACT
1 CACACGCACGCACA
*
3560799 CGCACGCACGCACA
1 CACACGCACGCACA
3560813 -AGCACGCACGCACA
1 CA-CACGCACGCACA
* *
3560827 CGCACGCGCGCACA
1 CACACGCACGCACA
3560841 CACACG--CGCACA
1 CACACGCACGCACA
3560853 CACA
1 CACA
3560857 TATTTTTTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
12 10 0.20
14 39 0.80
ACGTcount: A:0.32, C:0.49, G:0.18, T:0.01
Consensus pattern (14 bp):
CACACGCACGCACA
Found at i:3561463 original size:19 final size:19
Alignment explanation
Indices: 3561435--3561477 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3561425 AAAAAAACTT
3561435 AAAATGAAGGATAAA-ATGA
1 AAAATGAAGGA-AAATATGA
3561454 AGAAAT-AAGGAAAATATGA
1 A-AAATGAAGGAAAATATGA
3561473 AAAAT
1 AAAAT
3561478 TGAGGACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.32
19 11 0.50
20 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAATGAAGGAAAATATGA
Found at i:3570062 original size:18 final size:18
Alignment explanation
Indices: 3570041--3570085 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
3570031 TAATTATTAT
*
3570041 TTTTAATAAAAAATATAA
1 TTTTAATAAAAAATAAAA
* *
3570059 TTTT-ATTAAAATTAAAA
1 TTTTAATAAAAAATAAAA
3570076 TTTTAATAAA
1 TTTTAATAAA
3570086 TGTTTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAATAAAAAATAAAA
Found at i:3570815 original size:16 final size:17
Alignment explanation
Indices: 3570788--3570823 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3570778 GTCTTTTCAA
3570788 ATTTTATTTTATTTTTT
1 ATTTTATTTTATTTTTT
3570805 ATTTT-TTTTATTTTTT
1 ATTTTATTTTATTTTTT
3570821 ATT
1 ATT
3570824 CAGTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
ATTTTATTTTATTTTTT
Found at i:3572169 original size:17 final size:18
Alignment explanation
Indices: 3572147--3572193 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3572137 TATGGAATTG
*
3572147 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
3572164 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
3572182 GATTCTAATTCC
1 GATTCCAATTCC
3572194 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:3572752 original size:3 final size:3
Alignment explanation
Indices: 3572744--3572849 Score: 126
Period size: 3 Copynumber: 35.0 Consensus size: 3
3572734 TTTGTCCAAG
* *
3572744 TTA TTA TTA TAA ATA TTA TTA TT- TTA TTA TTTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA
*
3572790 TTA TTA TTTA TTA AT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
3572835 TTC TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA
3572850 CATGTTTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
2 3 0.03
3 76 0.86
4 9 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3574371 original size:2 final size:2
Alignment explanation
Indices: 3574351--3574413 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
3574341 TTAGCATCAT
*
3574351 TA TA T- TA TG TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3574391 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3574414 TTGTGTGTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3576886 original size:159 final size:159
Alignment explanation
Indices: 3576598--3576916 Score: 622
Period size: 159 Copynumber: 2.0 Consensus size: 159
3576588 CACTTTGTTA
3576598 TCTTATTTGTACTAACTTGTTTTTTATGTTATTTTTCTTTTTTGCTTGCATCGCATGATCATGAC
1 TCTTATTTGTACTAACTTGTTTTTTATGTTATTTTTCTTTTTTGCTTGCATCGCATGATCATGAC
3576663 ATAATCATAAGGTGTTGATTTGTGAGTGGTCATCAGAGTAAAAGGTTTTTATGATAGAAAAAGGG
66 ATAATCATAAGGTGTTGATTTGTGAGTGGTCATCAGAGTAAAAGGTTTTTATGATAGAAAAAGGG
3576728 TTTCATGGTCAAGTAGAC-ATAACACAGC
131 TTTCATGGTCAAGTAGACAATAACACAGC
3576756 TCTTATTTGTACTAACTTGTTTTTTTATGTTATTTTTCTTTTTTGCTTGCATCGCATGATCATGA
1 TCTTATTTGTACTAACTTG-TTTTTTATGTTATTTTTCTTTTTTGCTTGCATCGCATGATCATGA
3576821 CATAATCATAAGGTGTTGATTTGTGAGTGGTCATCAGAGTAAAAGGTTTTTATGATAGAAAAAGG
65 CATAATCATAAGGTGTTGATTTGTGAGTGGTCATCAGAGTAAAAGGTTTTTATGATAGAAAAAGG
3576886 GTTTCATGGTCAAGTAGACAATAACACAGC
130 GTTTCATGGTCAAGTAGACAATAACACAGC
3576916 T
1 T
3576917 AGGGAACTTC
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
158 19 0.12
159 129 0.81
160 11 0.07
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (159 bp):
TCTTATTTGTACTAACTTGTTTTTTATGTTATTTTTCTTTTTTGCTTGCATCGCATGATCATGAC
ATAATCATAAGGTGTTGATTTGTGAGTGGTCATCAGAGTAAAAGGTTTTTATGATAGAAAAAGGG
TTTCATGGTCAAGTAGACAATAACACAGC
Found at i:3582636 original size:257 final size:257
Alignment explanation
Indices: 3582169--3583392 Score: 1422
Period size: 257 Copynumber: 4.7 Consensus size: 257
3582159 TTTTATATAA
* * * *
3582169 TTTGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTAAAAAAATGAAATTTTTG
1 TTTGAAAAATGAAAAAGTAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTG
* * * * *
3582234 AAAAGTAATAAAGTGATTTCCAGAGTTTCTTATCCATTAGACTATTTCCAAAATTGGTAAGTCCT
66 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCT
* * * * * * * *
3582299 TCAGGCCATCATTAAGTCTTTCAAGCACGATGATTAAATCTTTTGGGTCATCTGTCAATCTTTCG
131 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTATCAGTCTTTCG
* * * ** *
3582364 AGCGAGATAATAAGTCCTTCGGGCCGTCCCTAAGGCCTTTAGGCAGAAT-TTTTCACATGATT
196 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTAGGCAG-ATGTTTTCACATGATT
* * * * *
3582426 TTTGAAAAATGAAAAAGTGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAGTTTTTC
1 TTTGAAAAATGAAAAAGTAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTG
** * *
3582491 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACAAAGTAGACTATTTCCAAACTTGGTAAGTCCT
66 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCT
* * * *
3582556 TCGGGCCATTAGTAAGCCTTTCAAGCATGATGATTTAATCATTCGGGTCATCTATCAGTCTTTCG
131 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTATCAGTCTTTCG
* *** * * * *
3582621 AGCAAGATGATAAGTCTTTAATGCCATCTAAAAGACTTTTGGGCAAGATGTTTTCATATGATGT
196 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTAGGC-AGATGTTTTCACATGAT-T
* * * * *
3582685 TTGTGAAAAATAAGAAAAGTAATTTTTAAA----CTCATTTAACGT-TTTT-AGGAAATCAAAAT
1 TT-TGAAAAATGA-AAAAGTAATTTTCAAAGTTTCTCATTT-A-GTATTTTCAGAAAATGAAATT
* * *
3582744 TTTGAAAAGTAGGAAAGTGATTTCTAAAGTTTCTTACCCAGTTAACTATTTCCAAAATTGGTAAG
62 TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAG
* * * * *
3582809 TCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTAAATAATTTGGGTCATCTATTAGTCT
127 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTATCAGTCT
* ** * * *
3582874 TTCAAATAAGATGATAAGTCCGTT-GGGCCATCTATAAGACCTTTGGGCTAGATGTTCTCATATG
192 TTCGAGCAAGATGATAAGTCC-TTCGGGCCATCTATAAGACCTTTAGGC-AGATGTTTTCACATG
3582938 ATGTT
255 A--TT
* * *
3582943 TTTGAAAATTGAGAAAAATAATTTTCAAAGTTTCTCATTTAGTATTTTCAGTAAATGAAATTTTT
1 TTTGAAAAATGA-AAAAGTAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTT
* * * * *
3583008 GAAAAGTAAGAAAGCGATTTCCAGAGTTTCCTACCTAGTAAACTATTTCCAAAATTGGTAAGTCT
65 GAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCC
* * * *
3583073 TTCGGGCCATCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTC
130 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTATCAGTCTTTC
* * *
3583138 GAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGACATGATAG-TTTCACATGGTT
195 GAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTAGGCA-GAT-GTTTTCACATGATT
** * * * * *
3583202 TTCAAAAAATGAGAAAGCAATTTTCAAATTTTCTCATTTAGTAATTTCAAAAAATGAAATTTTTG
1 TTTGAAAAATGAAAAAGTAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTG
** * *
3583267 AAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTACT
66 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCT
* * * *
3583332 TCGGGCCATCAGTAAGTCTTTCGAGCATGTTGATTAAATCTTTCTGGTTATCTATCAGTCT
131 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTATCAGTCT
3583393 CACTTGAGAC
Statistics
Matches: 820, Mismatches: 128, Indels: 37
0.83 0.13 0.04
Matches are distributed among these distances:
257 406 0.50
258 183 0.22
259 18 0.02
260 17 0.02
261 195 0.24
262 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (257 bp):
TTTGAAAAATGAAAAAGTAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTG
AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCT
TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCTATCAGTCTTTCG
AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTAGGCAGATGTTTTCACATGATT
Found at i:3583120 original size:42 final size:41
Alignment explanation
Indices: 3583073--3583166 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 41
3583063 TGGTAAGTCT
3583073 TTCGGGCCATCAGTAAGTCTTTCGAGCATA-ATGATTAAATCC
1 TTCGGGCCATCAGTAAGTCTTTCGAGCA-AGATGA-TAAATCC
* * *
3583115 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAATCC
3583156 TTCGGGCCATC
1 TTCGGGCCATC
3583167 TATAAGACCT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 17 0.36
42 30 0.64
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (41 bp):
TTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAATCC
Found at i:3583264 original size:518 final size:514
Alignment explanation
Indices: 3582173--3583370 Score: 1455
Period size: 518 Copynumber: 2.3 Consensus size: 514
3582163 ATATAATTTG
3582173 AAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAGTATTTTAAAAAAATGAAATTTTTGAAAA
1 AAAAATGAGAAAGCAATTTTCAAA-TTTCTCATTTAGTA-TTTAAAAAAATGAAATTTTTGAAAA
* * * * *
3582238 GTAATAAAGTGATTTCCAGAGTTTCTTATCCA-TTAGACTATTTCCAAAATTGGTAAGTCCTTCA
64 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTTA-ACTATTTCCAAAATTGGTAAGTCATTCG
* * * ** * * *
3582302 GGCCATCATTAAGTCTTTCAAGCACGATGATTAAATCTTTTGGGTCATCTGTCAATCTTTCGAGC
128 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATAATTTGGGTCATCTATCAATCTTTCAAAC
* * * * *
3582367 GAGATAATAAGTCCTTCGGGCCGTCCCTAAGGCCTTTAGGCAGAATTTTTCACATGATTTTTGAA
193 AAGATAATAAGTCCTTCGGGCCATCCATAAGACCTTTAGGCAGAATTTCTCACATGATTTTTGAA
* * * *
3582432 AAATGAAAAAGTGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAGTTTTTCAAAAGT
258 AAATGAAAAAATAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTCAAAAGT
* * * *
3582497 AAGAAAGTGATTTCCAAAGTTTCTTACAAAGTAGACTATTTCCAAACTTGGTAAGTCCTTCGGGC
323 AAGAAAGCGATTTCCAAAGTTTCCTACAAAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGC
* * * *
3582562 CATTAGTAAGCCTTTCAAGCATGATGATTTAATCATTCGGGTCATCTATCAGTCTTTCGAGCAAG
388 CATCAGTAAGCCTTTCAAGCATAATGATTAAATCATTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * * ** * * *
3582627 ATGATAAGTCTTTAATGCCATCTAAAAGACTTTTGGGCAAGATGTTTTCATATGATGTTTGTG
453 ATGATAAGTCCTTAAGGCCATCTAAAAGACCTTCAGACAAGATGTTTTCACATGA-GTTTGTA
* * * * ** * *
3582690 AAAAATAAGAAAAGTAATTTTTAAA---CTCATTTAACGT-TTTTAGGAAATCAAAATTTTGAAA
1 AAAAATGAG-AAAGCAATTTTCAAATTTCTCATTT-A-GTATTTAAAAAAATGAAATTTTTGAAA
* *
3582751 AGTAGGAAAGTGATTTCTAAAGTTTCTTACCCAGTTAACTATTTCCAAAATTGGTAAGTCATTCG
63 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTTAACTATTTCCAAAATTGGTAAGTCATTCG
* * * *
3582816 GGCCATCAGTAAGTCTTTCGAGCATGATAATTAAATAATTTGGGTCATCTATTAGTCTTTCAAAT
128 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATAATTTGGGTCATCTATCAATCTTTCAAAC
* * * *
3582881 AAGATGATAAGTCCGTT-GGGCCATCTATAAGACCTTTGGGCTAG-ATGTTCTCATATGATGTTT
193 AAGATAATAAGTCC-TTCGGGCCATCCATAAGACCTTTAGGC-AGAAT-TTCTCACATGA--TTT
* * * *
3582944 TTGAAAATTGAGAAAAATAATTTTCAAAGTTTCTCATTTAGTATTTTCAGTAAATGAAATTTTTG
253 TTGAAAAATGA-AAAAATAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTC
* ** *
3583009 AAAAGTAAGAAAGCGATTTCCAGAGTTTCCTACCTAGTAAACTATTTCCAAAATTGGTAAGTCTT
317 AAAAGTAAGAAAGCGATTTCCAAAGTTTCCTACAAAGTAAACTATTTCCAAAATTGGTAAGTCCT
* * * *
3583074 TCGGGCCATCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
382 TCGGGCCATCAGTAAGCCTTTCAAGCATAATGATTAAATCATTCGGGTCATCTATAAGTCTTTCG
** * *
3583139 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGACATGATAG-TTTCACATG-GTT
447 AGCAAGATGATAAGTCCTTAAGGCCATCTAAAAGACCTTCAGACAAGAT-GTTTTCACATGAGTT
3583202 T-TCA
511 TGT-A
*
3583206 AAAAATGAGAAAGCAATTTTCAAATTTTCTCATTTAGTAATTTCAAAAAATGAAATTTTTGAAAA
1 AAAAATGAGAAAGCAATTTTCAAA-TTTCTCATTTAGT-ATTTAAAAAAATGAAATTTTTGAAAA
** * *
3583271 GTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGT-ACTTCG
64 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTTAACTATTTCCAAAATTGGTAAGTCA-TTCG
*
3583335 GGCCATCAGTAAGTCTTTCGAGCATGTTGATTAAAT
128 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT
3583371 CTTTCTGGTT
Statistics
Matches: 574, Mismatches: 88, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
514 166 0.29
515 31 0.05
516 14 0.02
517 23 0.04
518 222 0.39
519 118 0.21
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (514 bp):
AAAAATGAGAAAGCAATTTTCAAATTTCTCATTTAGTATTTAAAAAAATGAAATTTTTGAAAAGT
AAGAAAGTGATTTCCAAAGTTTCTTACCCAGTTAACTATTTCCAAAATTGGTAAGTCATTCGGGC
CATCAGTAAGTCTTTCGAGCATGATGATTAAATAATTTGGGTCATCTATCAATCTTTCAAACAAG
ATAATAAGTCCTTCGGGCCATCCATAAGACCTTTAGGCAGAATTTCTCACATGATTTTTGAAAAA
TGAAAAAATAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTCAAAAGTAAG
AAAGCGATTTCCAAAGTTTCCTACAAAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCAT
CAGTAAGCCTTTCAAGCATAATGATTAAATCATTCGGGTCATCTATAAGTCTTTCGAGCAAGATG
ATAAGTCCTTAAGGCCATCTAAAAGACCTTCAGACAAGATGTTTTCACATGAGTTTGTA
Found at i:3583518 original size:3 final size:3
Alignment explanation
Indices: 3583512--3583556 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3583502 TTTTTTCGGC
* * *
3583512 TTA TTA TTA TTA TTA TAA ATA TTA TTA ATA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
3583557 CATATTATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3583562 original size:9 final size:9
Alignment explanation
Indices: 3583513--3583564 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
3583503 TTTTTCGGCT
*
3583513 TATTATTAT
1 TATTATTAA
*
3583522 TATTATAAA
1 TATTATTAA
3583531 TATTATTAA
1 TATTATTAA
*
3583540 TATTATTTAT
1 TATTA-TTAA
*
3583550 TATTATTCA
1 TATTATTAA
3583559 TATTAT
1 TATTAT
3583565 AGGCCCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
9 28 0.78
10 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATTAA
Found at i:3592946 original size:17 final size:17
Alignment explanation
Indices: 3592924--3592958 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3592914 TGTTAAAATG
3592924 TTTTGGATTGATATGTT
1 TTTTGGATTGATATGTT
*
3592941 TTTTGGATTGTTATGTT
1 TTTTGGATTGATATGTT
3592958 T
1 T
3592959 GAATTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (17 bp):
TTTTGGATTGATATGTT
Found at i:3595727 original size:20 final size:19
Alignment explanation
Indices: 3595698--3595739 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
3595688 ACATATACAC
3595698 ATATATACAAAATA-TATAT
1 ATATATAC-AAATACTATAT
3595717 ATATAATACAAATACTATAT
1 ATAT-ATACAAATACTATAT
3595737 ATA
1 ATA
3595740 ATGTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATATACAAATACTATAT
Found at i:3595729 original size:19 final size:19
Alignment explanation
Indices: 3595681--3595739 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
3595671 AAAAATTGGG
* *
3595681 ATATAATAC--ATATACAC
1 ATATAATACAAATATATAT
3595698 ATAT-ATACAAAATATATAT
1 ATATAATAC-AAATATATAT
3595717 ATATAATACAAATACTATAT
1 ATATAATACAAATA-TATAT
3595737 ATA
1 ATA
3595740 ATGTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
19 15 0.43
20 12 0.34
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (19 bp):
ATATAATACAAATATATAT
Found at i:3599901 original size:19 final size:19
Alignment explanation
Indices: 3599879--3599928 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3599869 GTTGTGGTTA
*
3599879 AAATAAAAAAATAAGAATT
1 AAATAAAAAAATAAAAATT
3599898 AAATAAAAGAAA-AAAAATT
1 AAATAAAA-AAATAAAAATT
*
3599917 AAATAAACAAAT
1 AAATAAAAAAAT
3599929 TAAAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (19 bp):
AAATAAAAAAATAAAAATT
Found at i:3600405 original size:12 final size:12
Alignment explanation
Indices: 3600390--3600419 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3600380 AAAAGTATGC
3600390 GAAAAATAGAGA
1 GAAAAATAGAGA
*
3600402 GAAAGATAGAGA
1 GAAAAATAGAGA
3600414 GAAAAA
1 GAAAAA
3600420 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:3600519 original size:21 final size:20
Alignment explanation
Indices: 3600495--3600549 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
3600485 TTCAAAATCC
3600495 TAAAAAC-AAGTTAAAACATCT
1 TAAAAACTAA-TTAAAACA-CT
**
3600516 TAAATCCTAATTAAAACACT
1 TAAAAACTAATTAAAACACT
*
3600536 T-AAAACTATTTAAA
1 TAAAAACTAATTAAA
3600550 CTAAAATACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 13 0.46
22 2 0.07
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAAACTAATTAAAACACT
Found at i:3600640 original size:75 final size:76
Alignment explanation
Indices: 3600559--3600735 Score: 225
Period size: 76 Copynumber: 2.3 Consensus size: 76
3600549 ACTAAAATAC
* * *
3600559 TAAAA-ATAATAATATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAAT
1 TAAAATATAA-AA-ATAATATCCTAAAACCTAATTAAAATACTAAAAACATATTTAAACTAAAAT
3600622 ACAAAGATAAAGA
64 ACAAAGATAAAGA
* *
3600635 TAAAATATAAAAATAATATCCTAAAACTTAATTAAATTACTAAAAACATATTTAAACTAAAATAC
1 TAAAATATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACATATTTAAACTAAAATAC
3600700 AAAGATAAA-A
66 AAAGATAAAGA
* * * *
3600710 TATAATGTTTAAAATATTATCCTAAA
1 TAAAAT-ATAAAAATAATATCCTAAA
3600736 TTTGAGTTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
75 31 0.35
76 54 0.61
77 4 0.04
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (76 bp):
TAAAATATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACATATTTAAACTAAAATAC
AAAGATAAAGA
Found at i:3602618 original size:21 final size:21
Alignment explanation
Indices: 3602591--3602639 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3602581 AGTTCGATAA
3602591 AAAAATAAAAATAAAT-AAAAC
1 AAAAATAAAAA-AAATAAAAAC
*
3602612 GAAAATAAAAAAAATAAAAAC
1 AAAAATAAAAAAAATAAAAAC
3602633 AAAAATA
1 AAAAATA
3602640 TAACGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (21 bp):
AAAAATAAAAAAAATAAAAAC
Found at i:3602631 original size:15 final size:15
Alignment explanation
Indices: 3602589--3602637 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
3602579 AAAGTTCGAT
3602589 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
* **
3602604 AATAAAACGAAAATA
1 AAAAAAATAAAAATA
*
3602619 AAAAAAATAAAAACA
1 AAAAAAATAAAAATA
3602634 AAAA
1 AAAA
3602638 TATAACGAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:3606419 original size:15 final size:15
Alignment explanation
Indices: 3606395--3606428 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3606385 TTCCTCTTGT
3606395 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
* *
3606410 TCTTCTTGATGTGTG
1 TCTTCCTGATGTGCG
3606425 TCTT
1 TCTT
3606429 TTTCTGCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.50
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:3608108 original size:23 final size:25
Alignment explanation
Indices: 3608073--3608121 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3608063 GATGAAGTTG
*
3608073 AAAAGATATATTAAAATAA-AATAA
1 AAAAGATAAATTAAAATAATAATAA
*
3608097 AAAAGA-AAATTAATATAATAATAA
1 AAAAGATAAATTAAAATAATAATAA
3608121 A
1 A
3608122 TATTAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAAGATAAATTAAAATAATAATAA
Found at i:3608210 original size:21 final size:22
Alignment explanation
Indices: 3608177--3608217 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3608167 GGTTAAAATA
3608177 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
3608199 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
3608218 CAAACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:3608935 original size:75 final size:76
Alignment explanation
Indices: 3608868--3609031 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 76
3608858 AAAAAATAAT
* * *
3608868 ATAATATTCTAAATCCTAATAAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACATAATAAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
3608932 AAAATATAAAA
66 AAAATATAAAA
*
3608943 ATAATATCCTAAAACATAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACATAATAAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
3609007 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
3609019 ATATTATCCTAAA
1 ATAATATCCTAAA
3609032 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 31 0.39
76 48 0.61
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (76 bp):
ATAATATCCTAAAACATAATAAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:3612197 original size:24 final size:22
Alignment explanation
Indices: 3612162--3612206 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
3612152 ATTCATGTGA
3612162 TTTAAATAACTACAT-GATCATT
1 TTTAAATAACTAC-TGGATCATT
3612184 TTTACAATATACTACTGGATCAT
1 TTTA-AATA-ACTACTGGATCAT
3612207 GATTTTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAAATAACTACTGGATCATT
Found at i:3632592 original size:76 final size:76
Alignment explanation
Indices: 3632407--3632592 Score: 318
Period size: 76 Copynumber: 2.4 Consensus size: 76
3632397 ATTTTAAATA
* * * *
3632407 TTATATTTTATCTTTGTTTTAGGTAGTTTAGTTCAAATATGTTTTAGTATTTCAATAAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATAAAGGTTTA
3632472 GGATATTATTT
66 GGATATTATTT
* *
3632483 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGGTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATAAAGGTTTA
3632548 GGATATTATTT
66 GGATATTATTT
3632559 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTT
3632593 TAAGTGTTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 104 1.00
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATAAAGGTTTA
GGATATTATTT
Found at i:3633258 original size:18 final size:18
Alignment explanation
Indices: 3633235--3633274 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3633225 TAATTTGCCT
*
3633235 ATTTAATTATTTTCTTTA
1 ATTTAATTATTATCTTTA
* *
3633253 ATTTAATTCTTATCTTTT
1 ATTTAATTATTATCTTTA
3633271 ATTT
1 ATTT
3633275 TAAAAACAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTAATTATTATCTTTA
Found at i:3641344 original size:24 final size:24
Alignment explanation
Indices: 3641317--3641399 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
3641307 ATTTCTGACT
*
3641317 TGAATTCTGTTCTGATACATGATC
1 TGAATTCTGTTCTGATATATGATC
* *
3641341 TGAATTCTGTTCTGATTTATGATT
1 TGAATTCTGTTCTGATATATGATC
* * *
3641365 TGTATTTTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATATATGATC
3641389 TGAATTCTGTT
1 TGAATTCTGTT
3641400 TTGTTTTCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:3641354 original size:12 final size:12
Alignment explanation
Indices: 3641317--3641399 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
3641307 ATTTCTGACT
3641317 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
3641329 TG-ATACATGATC
1 TGAATTC-TGTTC
3641341 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
3641353 TGATTTATGATT-
1 TGAATTCTG-TTC
* *
3641365 TGTATTTTGTTC
1 TGAATTCTGTTC
*
3641377 TG-ATATATGTTC
1 TGAAT-TCTGTTC
3641389 TGAATTCTGTT
1 TGAATTCTGTT
3641400 TTGTTTTCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
11 7 0.13
12 40 0.74
13 7 0.13
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:3641377 original size:48 final size:48
Alignment explanation
Indices: 3641303--3641399 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
3641293 AAATATTTTA
*
3641303 TCTGATTTCTGACTTGAATTCTGTTCTGATACATGATCTGAATTCTGT
1 TCTGATTTATGACTTGAATTCTGTTCTGATACATGATCTGAATTCTGT
* * * * *
3641351 TCTGATTTATGATTTGTATTTTGTTCTGATATATGTTCTGAATTCTGT
1 TCTGATTTATGACTTGAATTCTGTTCTGATACATGATCTGAATTCTGT
3641399 T
1 T
3641400 TTGTTTTCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (48 bp):
TCTGATTTATGACTTGAATTCTGTTCTGATACATGATCTGAATTCTGT
Found at i:3641581 original size:2 final size:2
Alignment explanation
Indices: 3641574--3641633 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
3641564 TGGGATGGGG
3641574 AT AT 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 AT AT
3641616 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3641634 GTTTTAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3643221 original size:11 final size:12
Alignment explanation
Indices: 3643207--3643249 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
3643197 TTTGTTCTAG
3643207 TTTT-TTTTTCA
1 TTTTATTTTTCA
*
3643218 TTTTA-TCTTCA
1 TTTTATTTTTCA
3643229 TTTTATTTTT-A
1 TTTTATTTTTCA
3643240 TTTTATTTTT
1 TTTTATTTTT
3643250 TAGCAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 25 0.89
12 3 0.11
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:3643283 original size:20 final size:20
Alignment explanation
Indices: 3643258--3643300 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3643248 TTTAGCAAAC
*
3643258 TTTATTTTCATTCTA-TTTAT
1 TTTATTTTAATT-TATTTTAT
3643278 TTTATTTTAATTTATTTTAT
1 TTTATTTTAATTTATTTTAT
3643298 TTT
1 TTT
3643301 TCTCTGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTTTAATTTATTTTAT
Found at i:3643299 original size:15 final size:14
Alignment explanation
Indices: 3643258--3643300 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
3643248 TTTAGCAAAC
*
3643258 TTTATTTTCATTCTA
1 TTTATTTT-ATTTTA
3643273 TTTATTTTATTTTAA
1 TTTATTTTATTTT-A
3643288 TTTATTTTATTTT
1 TTTATTTTATTTT
3643301 TCTCTGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:3643301 original size:6 final size:5
Alignment explanation
Indices: 3643258--3643300 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
3643248 TTTAGCAAAC
* *
3643258 TTTAT TTTCAT TCTA- TTTAT TTTAT TTTAA TTTAT TTTAT TTT
1 TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3643301 TCTCTGAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 25 0.78
6 4 0.12
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:3645258 original size:44 final size:42
Alignment explanation
Indices: 3645204--3645335 Score: 106
Period size: 44 Copynumber: 3.3 Consensus size: 42
3645194 TAGGATAATA
3645204 TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATG
1 TTTTATATTTTATCTTTGTTTTAGGTATTTTAG-TTAAATATG
**
3645247 TTTTAGTATTTTAAT-TAAGTTTTAGG-A---TA--T---TAT-
1 TTTTA-TATTTT-ATCTTTGTTTTAGGTATTTTAGTTAAATATG
* *
3645280 TTTTATATTTTATCATTGTTTTAGGTATTTTAGCTTAAATAGG
1 TTTTATATTTTATCTTTGTTTTAGGTATTTTAG-TTAAATATG
3645323 TTTTAGTATTTTA
1 TTTTA-TATTTTA
3645336 ATTAACTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 29
0.66 0.06 0.28
Matches are distributed among these distances:
31 2 0.03
32 14 0.21
33 6 0.09
34 3 0.04
36 2 0.03
37 1 0.01
39 1 0.01
40 2 0.03
42 2 0.03
43 11 0.16
44 22 0.32
45 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (42 bp):
TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTAAATATG
Found at i:3645443 original size:76 final size:76
Alignment explanation
Indices: 3645188--3645415 Score: 379
Period size: 76 Copynumber: 3.0 Consensus size: 76
3645178 AATTAAACTC
* *
3645188 AAGTTTTAGGATAATA-TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTA
1 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
3645252 GTATTTTAATT
66 GTATTTTAATT
* *
3645263 AAGTTTTAGGATATTATTTTTATATTTTATCATTGTTTTAGGTATTTTAGCTTAAATAGGTTTTA
1 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
3645328 GTATTTTAATT
66 GTATTTTAATT
*
3645339 AACTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTA
1 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-
*
3645403 AGTGTTTTAATT
65 AGTATTTTAATT
3645415 A
1 A
3645416 GGATTTAAGA
Statistics
Matches: 143, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
75 20 0.14
76 123 0.86
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (76 bp):
AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
GTATTTTAATT
Found at i:3646055 original size:18 final size:18
Alignment explanation
Indices: 3646013--3646059 Score: 78
Period size: 17 Copynumber: 2.6 Consensus size: 18
3646003 AATCTCTTTA
3646013 ATCTGTTTATTTAATTATT
1 ATCT-TTTATTTAATTATT
3646032 -TCTTTTATTTAATTATT
1 ATCTTTTATTTAATTATT
3646049 ATCTTTTATTT
1 ATCTTTTATTT
3646060 TAAAAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (18 bp):
ATCTTTTATTTAATTATT
Found at i:3646951 original size:15 final size:15
Alignment explanation
Indices: 3646931--3646962 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3646921 TCAGCTAGCC
3646931 TCTTTCTTAGCAACT
1 TCTTTCTTAGCAACT
*
3646946 TCTTTCTTATCAACT
1 TCTTTCTTAGCAACT
3646961 TC
1 TC
3646963 GTTCCCTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (15 bp):
TCTTTCTTAGCAACT
Found at i:3653734 original size:76 final size:76
Alignment explanation
Indices: 3653608--3653777 Score: 322
Period size: 76 Copynumber: 2.2 Consensus size: 76
3653598 TTAAACTCAA
*
3653608 TTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATA
1 TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATA
3653673 TTTTATCATTG
66 TTTTATCATTG
3653684 TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATA
1 TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATA
*
3653749 TTTTATCTTTG
66 TTTTATCATTG
3653760 TTTTAGGTATTTTAGTTT
1 TTTTAGGTATTTTAGTTT
3653778 TAAGTGTTTT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 92 1.00
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.60
Consensus pattern (76 bp):
TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATA
TTTTATCATTG
Found at i:3654430 original size:18 final size:18
Alignment explanation
Indices: 3654388--3654434 Score: 78
Period size: 17 Copynumber: 2.6 Consensus size: 18
3654378 AATCTCTTTA
3654388 ATCTGTTTATTTAATTATT
1 ATCT-TTTATTTAATTATT
3654407 -TCTTTTATTTAATTATT
1 ATCTTTTATTTAATTATT
3654424 ATCTTTTATTT
1 ATCTTTTATTT
3654435 TAAAAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (18 bp):
ATCTTTTATTTAATTATT
Found at i:3655323 original size:15 final size:15
Alignment explanation
Indices: 3655303--3655334 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3655293 TCAGCTAGCC
3655303 TCTTTCTTAGCAACT
1 TCTTTCTTAGCAACT
*
3655318 TCTTTCTTATCAACT
1 TCTTTCTTAGCAACT
3655333 TC
1 TC
3655335 GTTCCCTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (15 bp):
TCTTTCTTAGCAACT
Found at i:3669463 original size:17 final size:18
Alignment explanation
Indices: 3669441--3669477 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3669431 TCTTATGCAC
3669441 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
3669458 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
3669476 AT
1 AT
3669478 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:3675117 original size:17 final size:18
Alignment explanation
Indices: 3675095--3675131 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3675085 TCTTATGCAC
3675095 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTT-TCAG
3675112 ATCAATATGTCTTTTCAG
1 ATCAATATGTCTTTTCAG
3675130 AT
1 AT
3675132 TTATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATCAATATGTCTTTTCAG
Found at i:3681939 original size:20 final size:20
Alignment explanation
Indices: 3681914--3681958 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3681904 TTATCCGGAA
*
3681914 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
3681934 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
3681954 AAAAA
1 AAAAA
3681959 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:3684918 original size:14 final size:14
Alignment explanation
Indices: 3684899--3684949 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
3684889 CTGTCTATAT
3684899 GCAGAGATTTTTTC
1 GCAGAGATTTTTTC
3684913 GCAGAGATTTTTTC
1 GCAGAGATTTTTTC
*
3684927 GCAGGGATTTATTT-
1 GCAGAGATTT-TTTC
*
3684941 GCAGGGATT
1 GCAGAGATT
3684950 ACTTCCCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 32 0.91
15 3 0.09
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (14 bp):
GCAGAGATTTTTTC
Found at i:3689802 original size:39 final size:39
Alignment explanation
Indices: 3689753--3690396 Score: 819
Period size: 39 Copynumber: 16.6 Consensus size: 39
3689743 TTCGTAAAAT
* * *
3689753 AAGA-TTTATCTCGCTTAAGATAGTTTCACTGGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3689791 AAGATTTTATCTCACTTGAGATAGTTTCACTGGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
3689830 AAGATTTTATCTCACTTGAGATAGTATCACTCAAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3689869 AAGATTTTATCTCGCTTGATATAGTTTCACTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
3689908 AAGATTTCATCTCGCTTGATACAG-TTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3689946 AATATTTTCTCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3689985 AAGATTTTAGCTCGCTTGAGATAGTTTCACTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
3690024 AAGATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
3690063 AAGATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
3690102 AAGATTTTATCTCGCTTGAGATAGTTTTATTCAAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
3690141 AAGATTTTATCGCGCTTGAGATAGATTT-ACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAG-TTTCACTCGAAACAG
* * *
3690180 AAGATTTTATCTCGCTTGAGATAGATTCAATCAAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
** * *
3690219 AAGATTTTATCTCGCTTGAGATAGTTTCACTTAAAAATAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCAC-TCGAAACAG
* * *
3690259 AAGATTTTATCTCGCTTGAGATAGTTTTACTCAAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
3690298 AAGATTTTATCTTGCTTAAGATAGTTTCACTAGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
3690337 AAGATTTTATCTTGCTTGAGATAGATTCACTCAAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
3690376 AAGA-TTTATCTCACTTGAGAT
1 AAGATTTTATCTCGCTTGAGAT
3690397 TATTTTTCTT
Statistics
Matches: 537, Mismatches: 64, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
38 52 0.10
39 447 0.83
40 38 0.07
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
Found at i:3689978 original size:19 final size:19
Alignment explanation
Indices: 3689951--3690055 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 19
3689941 AACAGAATAT
*
3689951 TTTCTCTCGCTTGAGATAG
1 TTTCACTCGCTTGAGATAG
****
3689970 TTTCACTCGAAACAGA-AG
1 TTTCACTCGCTTGAGATAG
*
3689988 ATTTTAGCTCGCTTGAGATAG
1 -TTTCA-CTCGCTTGAGATAG
* *
3690009 TTTCACTCGAAACATAAGAT--
1 TTTCACTCG---CTTGAGATAG
3690029 TTT-ATCTCGCTTGAGATAG
1 TTTCA-CTCGCTTGAGATAG
3690048 TTTCACTC
1 TTTCACTC
3690056 AAAACAGAAG
Statistics
Matches: 61, Mismatches: 15, Indels: 20
0.64 0.16 0.21
Matches are distributed among these distances:
17 6 0.10
18 2 0.03
19 26 0.43
20 19 0.31
21 2 0.03
22 6 0.10
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (19 bp):
TTTCACTCGCTTGAGATAG
Found at i:3690168 original size:21 final size:21
Alignment explanation
Indices: 3690142--3690206 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
3690132 TCAAAACATA
*
3690142 AGATTTTATCGCGCTTGAGAT
1 AGATTTTATCTCGCTTGAGAT
****
3690163 AGA-TTTA-CTCGAAACAGA-
1 AGATTTTATCTCGCTTGAGAT
3690181 AGATTTTATCTCGCTTGAGAT
1 AGATTTTATCTCGCTTGAGAT
3690202 AGATT
1 AGATT
3690207 CAATCAAAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 3 0.09
19 10 0.31
20 11 0.34
21 8 0.25
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (21 bp):
AGATTTTATCTCGCTTGAGAT
Found at i:3693192 original size:13 final size:13
Alignment explanation
Indices: 3693174--3693198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3693164 ATAACTTATG
3693174 AAATAAAGAAAAT
1 AAATAAAGAAAAT
3693187 AAATAAAGAAAA
1 AAATAAAGAAAA
3693199 AAAGGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAATAAAGAAAAT
Found at i:3693575 original size:24 final size:25
Alignment explanation
Indices: 3693532--3693580 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3693522 CCTTAAAATA
3693532 TTTAAAATTTAAAAATATATATATT
1 TTTAAAATTTAAAAATATATATATT
* *
3693557 TTTAATATTT-AAAATATATTTATT
1 TTTAAAATTTAAAAATATATATATT
3693581 AACGATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTAAAATTTAAAAATATATATATT
Found at i:3694510 original size:21 final size:21
Alignment explanation
Indices: 3694486--3694535 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3694476 AGTAATAATT
*
3694486 TTGTTTTCCTGCTCGTTTTGA
1 TTGTTTTCCTGCTCGTTTCGA
*
3694507 TTGTTTTCCTGCTTGTTTCGA
1 TTGTTTTCCTGCTCGTTTCGA
3694528 TTGTTTTC
1 TTGTTTTC
3694536 TTTCTAGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.18, G:0.18, T:0.60
Consensus pattern (21 bp):
TTGTTTTCCTGCTCGTTTCGA
Found at i:3698141 original size:6 final size:6
Alignment explanation
Indices: 3698130--3698155 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3698120 AATCCTTTCA
3698130 TTGCAT TTGCAT TTGCAT TTGCAT TT
1 TTGCAT TTGCAT TTGCAT TTGCAT TT
3698156 ACCTTTACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTGCAT
Found at i:3703591 original size:55 final size:56
Alignment explanation
Indices: 3703493--3703650 Score: 191
Period size: 54 Copynumber: 2.9 Consensus size: 56
3703483 GTGATGTCTT
* * *
3703493 CAAATGAATTTTGAAAGAAACTAAGCCTGATTTTCATGG-GTTTCTTGATTGTATC
1 CAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTATGGAGTTTCTTGATTGTATC
* * * * * *
3703548 CAAATGAGTTTTT-AAGAAGCTATGCCTAATTTTT-TAGGAGTTTCTT-AATGTTTT
1 CAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAT-GGAGTTTCTTGATTGTATC
3703602 CAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTATGGA-TTTCTTGAT
1 CAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTATGGAGTTTCTTGAT
3703651 GATAATTGTA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
53 1 0.01
54 42 0.49
55 41 0.48
56 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (56 bp):
CAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTATGGAGTTTCTTGATTGTATC
Found at i:3704263 original size:237 final size:230
Alignment explanation
Indices: 3703713--3704292 Score: 840
Period size: 230 Copynumber: 2.5 Consensus size: 230
3703703 TTTCTTGATG
* ** * *
3703713 AGTAAGTCTTTCAGGCCATCAGTAAGTATTTCGAGCATGATGCTTAAATCCTTCAGGACATCTAT
1 AGTAAGTCCTTCAGGCCATCAGTAAGGCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
* * *
3703778 AAGTCTTTTGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAGATCTTCGGGTAGGATGTTTTC
66 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTC
* *
3703843 ACATGATTTTAAAAAAACGATTTCCAAAATTTCTCATTTAAATCTTTTCTGAAAGTTGATTTTTT
131 ACATGATTTTAAAAAAACGATTTCCAAAATTTCTCATTTAAATATTTTCTGAAAGTTGATTTTTG
* **
3703908 AATAGTAAGAAAATGATTTCCAAAGTTTCTTACTT
196 AAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTT
* *
3703943 AGTAAGTCCTTCAGGCCATCAGTAAGGCTTTCAAGCATGATGCTTAAATCCTTCGGGTCGTCTAT
1 AGTAAGTCCTTCAGGCCATCAGTAAGGCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
* *
3704008 AAGTATTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTC
66 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTC
* *
3704073 ACATGATTTTCAAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAGTT
131 ACATGATTTT----AAA--A-AAA-CGATTTCCAAAATTTCTCATTTAAATATTTTCTGAAAGTT
3704138 GATTTTTGAAAAGTAAGAAAACAATTTCCAAAG-TTCTTACTT
188 GATTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTT
* ** * *
3704180 AGTAATTCCTTTGGGCTATCAGTAAGGCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
1 AGTAAGTCCTTCAGGCCATCAGTAAGGCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
* *
3704245 AAGTCTTTCGAACAAGATGATAAGTCCTTCGGGCCATTCATAAG-CCTT
66 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTT
3704293 TCGAGCAAGA
Statistics
Matches: 312, Mismatches: 30, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
230 128 0.41
234 3 0.01
236 5 0.02
237 110 0.35
238 66 0.21
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (230 bp):
AGTAAGTCCTTCAGGCCATCAGTAAGGCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTC
ACATGATTTTAAAAAAACGATTTCCAAAATTTCTCATTTAAATATTTTCTGAAAGTTGATTTTTG
AAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTT
Found at i:3704267 original size:21 final size:21
Alignment explanation
Indices: 3704243--3704316 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
3704233 CGGGTCATCT
*
3704243 ATAAGTCTTTCGAACAAGATG
1 ATAAGTCTTTCGAGCAAGATG
* * * * *
3704264 ATAAGTCCTTCGGGCCA-TTC
1 ATAAGTCTTTCGAGCAAGATG
*
3704284 ATAAGCCTTTCGAGCAAGATG
1 ATAAGTCTTTCGAGCAAGATG
3704305 ATAAGTCTTTCG
1 ATAAGTCTTTCG
3704317 GATCATCCAT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
ATAAGTCTTTCGAGCAAGATG
Found at i:3704273 original size:41 final size:41
Alignment explanation
Indices: 3704228--3704334 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
3704218 GATGCTTAAA
*
3704228 TCCTTCGGGTCATCTATAAGTCTTTCGAACAAGATGATAAG
1 TCCTTCGGGTCATCTATAAGACTTTCGAACAAGATGATAAG
* * *
3704269 TCCTTCGGGCCAT-TCATAAGCCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGTCATCT-ATAAGACTTTCGAACAAGATGATAAG
* * *
3704310 TCTTTCGGATCATCCATAAGACTTT
1 TCCTTCGGGTCATCTATAAGACTTT
3704335 TGGACATGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 55 0.98
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGTCATCTATAAGACTTTCGAACAAGATGATAAG
Found at i:3705092 original size:207 final size:207
Alignment explanation
Indices: 3704737--3705146 Score: 820
Period size: 207 Copynumber: 2.0 Consensus size: 207
3704727 AGAGACCACA
3704737 TTGAATAATGGTGTTTTGTGTCTTTGCTCTATTCTCATTTCACTATAACGAGCAAAGAGGGGCAT
1 TTGAATAATGGTGTTTTGTGTCTTTGCTCTATTCTCATTTCACTATAACGAGCAAAGAGGGGCAT
3704802 CTATGATCACTATTTTTCAACCGGCCTCAATCCAGACTCAACCCAGATCTAATCTAACCCTAACC
66 CTATGATCACTATTTTTCAACCGGCCTCAATCCAGACTCAACCCAGATCTAATCTAACCCTAACC
3704867 CTAGGGTAGCCACCCTAAACTCCCAATCAATTATCGTCACTCTTTGCACCCAAATAGTGAAATAC
131 CTAGGGTAGCCACCCTAAACTCCCAATCAATTATCGTCACTCTTTGCACCCAAATAGTGAAATAC
3704932 CTCCCCAATCAC
196 CTCCCCAATCAC
3704944 TTGAATAATGGTGTTTTGTGTCTTTGCTCTATTCTCATTTCACTATAACGAGCAAAGAGGGGCAT
1 TTGAATAATGGTGTTTTGTGTCTTTGCTCTATTCTCATTTCACTATAACGAGCAAAGAGGGGCAT
3705009 CTATGATCACTATTTTTCAACCGGCCTCAATCCAGACTCAACCCAGATCTAATCTAACCCTAACC
66 CTATGATCACTATTTTTCAACCGGCCTCAATCCAGACTCAACCCAGATCTAATCTAACCCTAACC
3705074 CTAGGGTAGCCACCCTAAACTCCCAATCAATTATCGTCACTCTTTGCACCCAAATAGTGAAATAC
131 CTAGGGTAGCCACCCTAAACTCCCAATCAATTATCGTCACTCTTTGCACCCAAATAGTGAAATAC
3705139 CTCCCCAA
196 CTCCCCAA
3705147 CACGCCATCA
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 203 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (207 bp):
TTGAATAATGGTGTTTTGTGTCTTTGCTCTATTCTCATTTCACTATAACGAGCAAAGAGGGGCAT
CTATGATCACTATTTTTCAACCGGCCTCAATCCAGACTCAACCCAGATCTAATCTAACCCTAACC
CTAGGGTAGCCACCCTAAACTCCCAATCAATTATCGTCACTCTTTGCACCCAAATAGTGAAATAC
CTCCCCAATCAC
Found at i:3705528 original size:39 final size:38
Alignment explanation
Indices: 3705468--3705545 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 38
3705458 TCTTCAAGAA
*
3705468 AAACATCAATAACGCACAAAAAA-CTCTCCTTTAGTTTCG
1 AAACAACAATAACGCACAAAAAATC-CT-CTTTAGTTTCG
* *
3705507 AAACAACAATAA-TCACTAAAAAATCCTCTTTTGTTTCG
1 AAACAACAATAACGCAC-AAAAAATCCTCTTTAGTTTCG
3705545 A
1 A
3705546 GTAACAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
38 14 0.41
39 19 0.56
40 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.28
Consensus pattern (38 bp):
AAACAACAATAACGCACAAAAAATCCTCTTTAGTTTCG
Found at i:3708676 original size:31 final size:31
Alignment explanation
Indices: 3708640--3708703 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
3708630 ACCGGTCATA
3708640 ACCCGACCCGACCCGTTAACCCAACCCGTTG
1 ACCCGACCCGACCCGTTAACCCAACCCGTTG
* * * *
3708671 ACCCGACCCGATCTGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTAACCCAACCCGTTG
3708702 AC
1 AC
3708704 TGTTGACTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.45, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTAACCCAACCCGTTG
Found at i:3708679 original size:18 final size:18
Alignment explanation
Indices: 3708658--3708697 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3708648 CGACCCGTTA
3708658 ACCCAACCCGTTGACCCG
1 ACCCAACCCGTTGACCCG
* * *
3708676 ACCCGATCTGTTGACCCG
1 ACCCAACCCGTTGACCCG
3708694 ACCC
1 ACCC
3708698 GTTGACTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.47, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCAACCCGTTGACCCG
Found at i:3708701 original size:13 final size:13
Alignment explanation
Indices: 3708644--3708703 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
3708634 GTCATAACCC
3708644 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
3708657 AACCCAACCCGTT
1 GACCCGACCCGTT
3708670 GACCCGACCCGATCTGTT
1 GACCCGA-CC---C-GTT
3708688 GACCCGACCCGTT
1 GACCCGACCCGTT
3708701 GAC
1 GAC
3708704 TGTTGACTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 22 0.58
14 3 0.08
17 3 0.08
18 10 0.26
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3708728 original size:10 final size:10
Alignment explanation
Indices: 3708715--3708742 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3708705 GTTGACTGGC
3708715 GTTGACCACT
1 GTTGACCACT
3708725 GTTGACCACT
1 GTTGACCACT
3708735 GTTGACCA
1 GTTGACCA
3708743 AAACTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (10 bp):
GTTGACCACT
Found at i:3709974 original size:29 final size:25
Alignment explanation
Indices: 3709928--3710015 Score: 119
Period size: 24 Copynumber: 3.6 Consensus size: 25
3709918 ATCATAACAT
*
3709928 AATCCAAGTCAAGTATCAGATCA-A
1 AATCCAAGTCAAGTATCCGATCAGA
3709952 AATCCAAGTCAAGTATCCGATCAG-
1 AATCCAAGTCAAGTATCCGATCAGA
*
3709976 AATCCAGGTCAAGTATCCGATCAG-
1 AATCCAAGTCAAGTATCCGATCAGA
* *
3710000 AATCCAGGTCAGGTAT
1 AATCCAAGTCAAGTAT
3710016 TATAATAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (25 bp):
AATCCAAGTCAAGTATCCGATCAGA
Found at i:3712528 original size:18 final size:18
Alignment explanation
Indices: 3712505--3712550 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
3712495 CAACGGTCAA
3712505 CGGGTCGGGTCAACAGAT
1 CGGGTCGGGTCAACAGAT
* * *
3712523 CGGGTCGGATCAACGGGT
1 CGGGTCGGGTCAACAGAT
3712541 CGGGTCGGGT
1 CGGGTCGGGT
3712551 TGTGACCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGAT
Found at i:3722712 original size:12 final size:12
Alignment explanation
Indices: 3722674--3722765 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
3722664 ATTTCCGAAT
3722674 TGAATTCTGTTC
1 TGAATTCTGTTC
*
3722686 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
3722698 TGAATTCTGTTC
1 TGAATTCTGTTC
*
3722710 TG-ATTCTGATC
1 TGAATTCTGTTC
*
3722721 TGGATTCTGTTC
1 TGAATTCTGTTC
* *
3722733 TG-ATATCTGATA
1 TGAAT-TCTGTTC
*
3722745 TGAATTCTGTTT
1 TGAATTCTGTTC
*
3722757 TGATTTCTG
1 TGAATTCTG
3722766 ATATCTCCGT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
10 3 0.05
11 15 0.23
12 38 0.59
13 5 0.08
14 3 0.05
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:3722728 original size:47 final size:48
Alignment explanation
Indices: 3722660--3722767 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
3722650 AAATATTTTA
* * *
3722660 TCTGATTTCCGAAT-TGAATTCTGTTCTGATA-C-GTTACCTGAATTCTGT
1 TCTGATTTCTG-ATCTGGATTCTGTTCTGATATCTGATA--TGAATTCTGT
3722708 TCTGA-TTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
*
3722755 TTTGATTTCTGAT
1 TCTGATTTCTGAT
3722768 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
46 2 0.04
47 34 0.65
48 13 0.25
49 3 0.06
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
Found at i:3722765 original size:24 final size:24
Alignment explanation
Indices: 3722660--3722769 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
3722650 AAATATTTTA
*
3722660 TCTGATTTCCGA-ATTGAATTCTGT
1 TCTGATTTCTGATA-TGAATTCTGT
* *
3722684 TCTGA-TAC-GTTACCTGAATTCTGT
1 TCTGATTTCTGATA--TGAATTCTGT
* *
3722708 TCTGA-TTCTGATCTGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
3722731 TCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
3722755 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
3722770 CTCCGTTTAC
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 17 0.24
24 50 0.71
25 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:3728083 original size:1 final size:1
Alignment explanation
Indices: 3728046--3728070 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3728036 TTTTCCTACC
3728046 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3728071 GAAGAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3729197 original size:30 final size:31
Alignment explanation
Indices: 3729157--3729215 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
3729147 CCCTTTCATT
* **
3729157 TTCTGCTCTTTCCTTCTTTCTTCTTCCCATC
1 TTCTGCTCTTTACTTCCCTCTTCTTCCCATC
*
3729188 TTCT-CTCTTTATTTCCCTCTTCTTCCCA
1 TTCTGCTCTTTACTTCCCTCTTCTTCCCA
3729216 GATTCCGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.05, C:0.39, G:0.02, T:0.54
Consensus pattern (31 bp):
TTCTGCTCTTTACTTCCCTCTTCTTCCCATC
Found at i:3730313 original size:2 final size:2
Alignment explanation
Indices: 3730308--3730344 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3730298 TTTTTTAATT
3730308 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 T
3730345 CTATGTACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3730316 original size:28 final size:28
Alignment explanation
Indices: 3730258--3730314 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
3730248 TTAAAATAAG
*
3730258 TATTTAAAATATATTATTTTTATTTAAA
1 TATTTAAAATATATTATTTTAATTTAAA
*
3730286 TATTTAAAATAT-TT-TTTTAATTTATA
1 TATTTAAAATATATTATTTTAATTTAAA
3730312 TAT
1 TAT
3730315 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 2 0.07
28 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTTAAAATATATTATTTTAATTTAAA
Found at i:3730578 original size:56 final size:57
Alignment explanation
Indices: 3730465--3730582 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
3730455 GAACATGGAT
* *
3730465 TAAAAATAATATAGTTTAAATATCTATTTTGATAAAGAAATAGTTTAGGTAACTATA
1 TAAAAATAATATAGTTTAAATATCTATTTTGATAAAGAAATACTTTAAGTAACTATA
* * *
3730522 TGAAAAATAATA-ATTTTAGATATTTATTTTGACT-AA-AAATACTTTAAGT-ACTTATA
1 T-AAAAATAATATAGTTTAAATATCTATTTTGA-TAAAGAAATACTTTAAGTAAC-TATA
3730578 TAAAA
1 TAAAA
3730583 GAAGATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
55 6 0.11
56 16 0.30
57 20 0.38
58 11 0.21
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.40
Consensus pattern (57 bp):
TAAAAATAATATAGTTTAAATATCTATTTTGATAAAGAAATACTTTAAGTAACTATA
Found at i:3731428 original size:14 final size:14
Alignment explanation
Indices: 3731409--3731448 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
3731399 AGCTATAGTA
3731409 TATTATCATAAATT
1 TATTATCATAAATT
*
3731423 TATTATCATAACTT
1 TATTATCATAAATT
3731437 TATT-TCA-AAATT
1 TATTATCATAAATT
3731449 ATTTCTGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 3 0.12
14 17 0.71
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:3749413 original size:23 final size:22
Alignment explanation
Indices: 3749371--3749428 Score: 89
Period size: 23 Copynumber: 2.6 Consensus size: 22
3749361 TTGGTGCAGA
* *
3749371 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
3749393 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
3749416 GGGAACCGATTCC
1 GGGAACCGATTCC
3749429 GCATGTAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:3750906 original size:18 final size:18
Alignment explanation
Indices: 3750874--3750908 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3750864 GCAGCGCGAG
*
3750874 GAACAAGCTCCACCAGAC
1 GAACAAGCACCACCAGAC
*
3750892 GAACAAGCACGACCAGA
1 GAACAAGCACCACCAGA
3750909 AGATCAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.34, G:0.20, T:0.03
Consensus pattern (18 bp):
GAACAAGCACCACCAGAC
Found at i:3751577 original size:17 final size:16
Alignment explanation
Indices: 3751544--3751575 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3751534 GAGAAATGTT
3751544 AAAGTATTTTTAAGGG
1 AAAGTATTTTTAAGGG
3751560 AAAGTATTTTTAAGGG
1 AAAGTATTTTTAAGGG
3751576 GAGAAGTGTT
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:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (16 bp):
AAAGTATTTTTAAGGG
Found at i:3752137 original size:17 final size:17
Alignment explanation
Indices: 3752115--3752156 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3752105 ATTGATCAAC
*
3752115 AACAAGAAAAAATAATA
1 AACAAGAAAAAACAATA
*
3752132 AACAAGAAAAAACAATC
1 AACAAGAAAAAACAATA
3752149 AACAAGAA
1 AACAAGAA
3752157 TCAAGAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.74, C:0.12, G:0.07, T:0.07
Consensus pattern (17 bp):
AACAAGAAAAAACAATA
Found at i:3754527 original size:8 final size:8
Alignment explanation
Indices: 3754509--3754555 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
3754499 GCAACATGCA
3754509 AAAATAAAT
1 AAAA-AAAT
3754518 AAAAAAAT
1 AAAAAAAT
3754526 AAAAAAAAT
1 -AAAAAAAT
3754535 ATAAAAAA-
1 A-AAAAAAT
*
3754543 ATAAAAAT
1 AAAAAAAT
3754551 AAAAA
1 AAAAA
3754556 TAAAAGTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 5 0.15
8 10 0.30
9 18 0.55
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3754530 original size:9 final size:9
Alignment explanation
Indices: 3754508--3754549 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
3754498 AGCAACATGC
3754508 AAAAATAAAT
1 AAAAA-AAAT
3754518 -AAAAAAAT
1 AAAAAAAAT
3754526 AAAAAAAAT
1 AAAAAAAAT
3754535 ATAAAAAAAT
1 A-AAAAAAAT
3754545 AAAAA
1 AAAAA
3754550 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.13
9 17 0.57
10 9 0.30
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:3754538 original size:19 final size:20
Alignment explanation
Indices: 3754514--3754560 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
3754504 ATGCAAAAAT
3754514 AAATAAAAAAATAAAAA-AA
1 AAATAAAAAAATAAAAATAA
*
3754533 ATATAAAAAAATAAAAATAA
1 AAATAAAAAAATAAAAATAA
3754553 AAATAAAA
1 AAATAAAA
3754561 GTAGGACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (20 bp):
AAATAAAAAAATAAAAATAA
Found at i:3754556 original size:12 final size:11
Alignment explanation
Indices: 3754508--3754560 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 11
3754498 AGCAACATGC
3754508 AAAAATAAATAA
1 AAAAATAAA-AA
3754520 AAAAAT--AAA
1 AAAAATAAAAA
*
3754529 AAAAAT-ATAA
1 AAAAATAAAAA
3754539 AAAAATAAAAA
1 AAAAATAAAAA
3754550 TAAAAATAAAA
1 -AAAAATAAAA
3754561 GTAGGACTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 8 0.22
10 9 0.25
11 3 0.08
12 16 0.44
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:3755232 original size:2 final size:2
Alignment explanation
Indices: 3755225--3755280 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3755215 AAAATAAGAA
3755225 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3755267 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
3755281 TCTATCATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3756072 original size:15 final size:15
Alignment explanation
Indices: 3756052--3756081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3756042 ATTAATTAAT
3756052 TAATAATAATAAAAA
1 TAATAATAATAAAAA
*
3756067 TAATAATAGTAAAAA
1 TAATAATAATAAAAA
3756082 AGGGACGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
TAATAATAATAAAAA
Found at i:3756502 original size:134 final size:133
Alignment explanation
Indices: 3756254--3756909 Score: 719
Period size: 134 Copynumber: 4.9 Consensus size: 133
3756244 GGAAGAATTA
* *
3756254 TTCCACTGTTACTTAGGGAAAATCAAATCCTGAAAGAGAGGGA-CATGTTCTGCTTCTTCTTGAG
1 TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGATC-TGTTCTGCTTCTTCTTGAG
* * *
3756318 GGAAAATC-TAATTTAGGGATGTTGATTCATTCCACTGTTCCTTA-AGGAAGATTGAATCAAGGC
65 GGAAAATCAT-ATAT-GGGATGTTGATTCATTCCACTGTTGCTCAGA-GAAGATTGAATCAAGGC
3756381 AGACTTG
127 AGACTTG
* ** *
3756388 TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGATGGATCTGTTCCACTTCTTCTTAAGG
1 TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCTGCTTCTTCTTGAGG
* * * * **
3756453 GAAAATCATATATGGAGACGTTGATTCATTCTACTGTTGCTTAGAGAAGATTGAATCGAGATAGA
66 GAAAATCATATATGG-GATGTTGATTCATTCCACTGTTGCTCAGAGAAGATTGAATCAAGGCAGA
3756518 CTTG
130 CTTG
* * * ** * * *
3756522 TTACACTGTCACTCATAGAATATCAAATCTTGAAAGAGAGAGATTTGTTCCGCTTCTTCTTGAGG
1 TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCTGCTTCTTCTTGAGG
* * * * * * *
3756587 GAAAATCAGATCTGAGGACGTTGATTCATTCCACTATTGGTCAGGGAAGATTGAATCGAGGCAGA
66 GAAAATCATATATG-GGATGTTGATTCATTCCACTGTTGCTCAGAGAAGATTGAATCAAGGCAGA
3756652 CTTG
130 CTTG
* * * * ** * * *
3756656 TTTCACTGTCACTTAAGGAATATCAAATATTGAAAGAGAGGGAAATCTTCTGTTTCTTATTGAGG
1 TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCTGCTTCTTCTTGAGG
* * * *
3756721 GAAGATCTTATATGGGGATGTTGATTCATTCCACTATTGCTCA-AGGAAGATTAAATCAAGGCAG
66 GAAAATCATATAT-GGGATGTTGATTCATTCCACTGTTGCTCAGA-GAAGATTGAATCAAGGCAG
3756785 ACTTG
129 ACTTG
* ** * * *
3756790 TTTCGTTGTTACTTAGGGAATATCAAATCTTGAAAGAGA-TGATTTGTTCTACTTCTTCTTGAGG
1 TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCTGCTTCTTCTTGAGG
* ** * *
3756854 GAAAATCAGATATGGGATAATGATTCATTCCACTGTTCCTCAGGGAAGATTGAATC
66 GAAAATCATATATGGGATGTTGATTCATTCCACTGTTGCTCAGAGAAGATTGAATC
3756910 GTGTTCGATT
Statistics
Matches: 440, Mismatches: 74, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
132 36 0.08
133 30 0.07
134 369 0.84
135 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (133 bp):
TTCCACTGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCTGCTTCTTCTTGAGG
GAAAATCATATATGGGATGTTGATTCATTCCACTGTTGCTCAGAGAAGATTGAATCAAGGCAGAC
TTG
Found at i:3766883 original size:3 final size:3
Alignment explanation
Indices: 3766875--3766928 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
3766865 TAAAAAGTAT
3766875 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3766923 TAA TAA
1 TAA TAA
3766929 CAACAACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3767400 original size:9 final size:10
Alignment explanation
Indices: 3767383--3767446 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 10
3767373 TGAGATTAAA
3767383 ATATA-TATT
1 ATATATTATT
3767392 ATAT-TTATT
1 ATATATTATT
*
3767401 AT-TATATACT
1 ATATAT-TATT
3767411 ATAGTATTATT
1 ATA-TATTATT
3767422 AT-TATTATT
1 ATATATTATT
3767431 AT-TATTATT
1 ATATATTATT
3767440 AT-TATTA
1 ATATATTA
3767447 CTAATATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
8 1 0.02
9 34 0.71
10 5 0.10
11 5 0.10
12 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (10 bp):
ATATATTATT
Found at i:3767404 original size:3 final size:3
Alignment explanation
Indices: 3767396--3767446 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
3767386 TATATTATAT
* *
3767396 TTA TTA TTA TATA CTA -TA GTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3767441 TTA TTA
1 TTA TTA
3767447 CTAATATCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3767407 original size:21 final size:22
Alignment explanation
Indices: 3767383--3767446 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
3767373 TGAGATTAAA
3767383 ATATA-TATTATATTTATTATT
1 ATATACTATTATATTTATTATT
3767404 ATATACTA-TAGTA-TTATTATT
1 ATATACTATTA-TATTTATTATT
*
3767425 AT-TATTATTAT-TATTATTATT
1 ATATACTATTATAT-TTATTATT
3767446 A
1 A
3767447 CTAATATCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.14
21 28 0.76
22 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATACTATTATATTTATTATT
Found at i:3770390 original size:20 final size:20
Alignment explanation
Indices: 3770365--3770404 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3770355 GTAGAGAAGA
3770365 GTCATTGACCGTTAACTGTC
1 GTCATTGACCGTTAACTGTC
* *
3770385 GTCATTGATCGTTGACTGTC
1 GTCATTGACCGTTAACTGTC
3770405 ATCGTTGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
GTCATTGACCGTTAACTGTC
Found at i:3774225 original size:15 final size:15
Alignment explanation
Indices: 3774192--3774225 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3774182 AGTCGCACAC
**
3774192 AGTCGAGCCATGCTT
1 AGTCGAGCCATGCCG
3774207 AGTCGAGCCATGCCG
1 AGTCGAGCCATGCCG
3774222 AGTC
1 AGTC
3774226 TTTGACTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (15 bp):
AGTCGAGCCATGCCG
Found at i:3779336 original size:19 final size:19
Alignment explanation
Indices: 3779312--3779349 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3779302 AGATACCCAA
3779312 GGGTATATAGGGTGAAATC
1 GGGTATATAGGGTGAAATC
3779331 GGGTATATAGGGTGAAATC
1 GGGTATATAGGGTGAAATC
3779350 TAGAACTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.37, T:0.26
Consensus pattern (19 bp):
GGGTATATAGGGTGAAATC
Found at i:3781890 original size:11 final size:11
Alignment explanation
Indices: 3781874--3781902 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3781864 TCCTCTCTAG
3781874 AAAAAAAAACA
1 AAAAAAAAACA
3781885 AAAAAAAAACA
1 AAAAAAAAACA
3781896 AAAAAAA
1 AAAAAAA
3781903 TGAGAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:3782261 original size:51 final size:51
Alignment explanation
Indices: 3782187--3782399 Score: 205
Period size: 51 Copynumber: 4.1 Consensus size: 51
3782177 TTTATTTTAA
* * *
3782187 TTTAGTCACTGTTTATTTATGATTTTGAC-ACTATTCTTTTATTTTATGCAC
1 TTTAGTCACTGTTTATTTCTGA-TTTGGCTACTATTCTTTTATTTTATGCAT
* * *
3782238 TTTAGTCATTGTTTAATTCTGATTTGGCTACTATTCTTTTATTTTATACAT
1 TTTAGTCACTGTTTATTTCTGATTTGGCTACTATTCTTTTATTTTATGCAT
* * * * ** *
3782289 TTTAATCACCGTTTATTTCTGATTTGGCTATTGTTCTTTCGTTTCATGCAT
1 TTTAGTCACTGTTTATTTCTGATTTGGCTACTATTCTTTTATTTTATGCAT
* * * * *
3782340 TTTAGTCATTGTTTTTTATTTCTGAGTTGGTTTCTACT-TTTTATTTTATGGCAT
1 TTTAGTCACTG---TTTATTTCTGATTTGGCTACTATTCTTTTATTTTAT-GCAT
3782394 TTTAGT
1 TTTAGT
3782400 TTTTATTATT
Statistics
Matches: 129, Mismatches: 28, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
50 5 0.04
51 88 0.68
53 8 0.06
54 28 0.22
ACGTcount: A:0.18, C:0.13, G:0.12, T:0.57
Consensus pattern (51 bp):
TTTAGTCACTGTTTATTTCTGATTTGGCTACTATTCTTTTATTTTATGCAT
Found at i:3786611 original size:26 final size:23
Alignment explanation
Indices: 3786549--3786648 Score: 80
Period size: 23 Copynumber: 4.2 Consensus size: 23
3786539 TTGATGAGAC
* * *
3786549 AGAAAAAAGAAGATATAACAAAA
1 AGAAAAAAGAAAAAATAAGAAAA
*
3786572 AGAAAAAAGAAAAATTAAGAAAA
1 AGAAAAAAGAAAAAATAAGAAAA
3786595 AGATAGAAAAGAAAAAAATAAGAGAGATA
1 AGA-A-AAAAG-AAAAAATAAGA-A-A-A
*
3786624 A-AAGAAAG-AAAAA-AAGAAAA
1 AGAAAAAAGAAAAAATAAGAAAA
3786644 AGAAA
1 AGAAA
3786649 GAAATAGGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.03
21 3 0.05
22 1 0.02
23 26 0.41
24 6 0.10
25 5 0.08
26 14 0.22
27 2 0.03
28 2 0.03
29 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (23 bp):
AGAAAAAAGAAAAAATAAGAAAA
Found at i:3786612 original size:40 final size:39
Alignment explanation
Indices: 3786568--3786666 Score: 92
Period size: 40 Copynumber: 2.4 Consensus size: 39
3786558 AAGATATAAC
**
3786568 AAAAAGAAAAAAGAAAAATTAAGAAAAAGATAG-AAAAGAA
1 AAAAAGAAAAAAGAAAAAGAAAGAAAAA-A-AGAAAAAGAA
* * *
3786608 AAAAATAAGAGAGATAAAAGAAAGAAAAAAAGAAAAAGAA
1 AAAAAGAAAAAAGA-AAAAGAAAGAAAAAAAGAAAAAGAA
*
3786648 AGAAATAGGAAAAAGAAAA
1 A-AAA-AGAAAAAAGAAAA
3786667 GATAAAAGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
39 2 0.04
40 20 0.43
41 18 0.39
42 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (39 bp):
AAAAAGAAAAAAGAAAAAGAAAGAAAAAAAGAAAAAGAA
Found at i:3786629 original size:22 final size:19
Alignment explanation
Indices: 3786601--3786682 Score: 73
Period size: 18 Copynumber: 4.3 Consensus size: 19
3786591 AAAAAGATAG
*
3786601 AAAAGAAAAAAATAAGAGAGA
1 AAAAGAAAGAAATAA-A-AGA
3786622 TAAAAGAAAGAAA-AAAAGA
1 -AAAAGAAAGAAATAAAAGA
*
3786641 AAAAGAAAGAAAT--AGGA
1 AAAAGAAAGAAATAAAAGA
*
3786658 AAAAGAAA-AGATAAAAGA
1 AAAAGAAAGAAATAAAAGA
3786676 AAGAAGA
1 AA-AAGA
3786683 GATATAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 3 0.06
17 11 0.21
18 17 0.33
19 7 0.13
20 1 0.02
21 2 0.04
22 11 0.21
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAGAAAGAAATAAAAGA
Found at i:3786640 original size:66 final size:67
Alignment explanation
Indices: 3786568--3786710 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 67
3786558 AAGATATAAC
* *
3786568 AAAAAGAAAAAAGAAA-AATTAAGAAAAAGATAGAAAAGAAAA-AAATAAGAGAGATAAAAGAAA
1 AAAAAGAAAAAAGAAAGAAATAAGAAAAAGA-A-AAAAGAAAAGAAAGAAGAGAGATAAAAGAAA
3786631 G-AA
64 GCAA
* * * * *
3786634 AAAAAG-AAAAAGAAAGAAATAGGAAAAAGAAAAGATAAAAGAAAGAAGAGATATAAAATAAAGC
1 AAAAAGAAAAAAGAAAGAAATAAGAAAAAGAAAAAAGAAAAGAAAGAAGAGAGATAAAAGAAAGC
3786698 AA
66 AA
*
3786700 AAAAATAAAAA
1 AAAAAGAAAAA
3786711 GATGAATGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
64 7 0.11
65 29 0.45
66 25 0.38
67 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (67 bp):
AAAAAGAAAAAAGAAAGAAATAAGAAAAAGAAAAAAGAAAAGAAAGAAGAGAGATAAAAGAAAGC
AA
Found at i:3786644 original size:65 final size:66
Alignment explanation
Indices: 3786568--3786712 Score: 170
Period size: 66 Copynumber: 2.2 Consensus size: 66
3786558 AAGATATAAC
* *
3786568 AAAAAGAAAAAAGAAA-AATTAAGAAAAAGATAGAAAAGAAAA-AAATAAGAGAGATAAAAGAAA
1 AAAAAG-AAAAAGAAAGAAATAAGAAAAAGA-A-AAAAGAAAAGAAAGAAGAGAGATAAAAGAAA
3786631 G-AA
63 GCAA
* * * * *
3786634 AAAAAGAAAAAGAAAGAAATAGGAAAAAGAAAAGATAAAAGAAAGAAGAGATATAAAATAAAGCA
1 AAAAAGAAAAAGAAAGAAATAAGAAAAAGAAAAAAGAAAAGAAAGAAGAGAGATAAAAGAAAGCA
3786699 A
66 A
*
3786700 AAAAATAAAAAGA
1 AAAAAGAAAAAGA
3786713 TGAATGAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 7 0.10
65 29 0.43
66 32 0.47
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.08
Consensus pattern (66 bp):
AAAAAGAAAAAGAAAGAAATAAGAAAAAGAAAAAAGAAAAGAAAGAAGAGAGATAAAAGAAAGCA
A
Found at i:3786659 original size:17 final size:18
Alignment explanation
Indices: 3786570--3786665 Score: 72
Period size: 17 Copynumber: 5.2 Consensus size: 18
3786560 GATATAACAA
*
3786570 AAAG-AAAAAAGAAAAAT
1 AAAGAAAAAAAGAAAAAG
*
3786587 TAAGAAAAAGATAG-AAAAG
1 AAAGAAAAA-A-AGAAAAAG
*
3786606 AAAAAAATAAGAGAGATAAAAG
1 AAAGAAA-AA-A-AGA-AAAAG
3786628 AAAGAAAAAAAGAAAAAG
1 AAAGAAAAAAAGAAAAAG
* *
3786646 AAAG-AAATAGGAAAAAG
1 AAAGAAAAAAAGAAAAAG
3786663 AAA
1 AAA
3786666 AGATAAAAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
17 17 0.26
18 13 0.20
19 13 0.20
20 9 0.14
21 2 0.03
22 11 0.17
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (18 bp):
AAAGAAAAAAAGAAAAAG
Found at i:3786663 original size:31 final size:32
Alignment explanation
Indices: 3786588--3786677 Score: 62
Period size: 35 Copynumber: 2.7 Consensus size: 32
3786578 AAGAAAAATT
*
3786588 AAGAAAAAGATAG-AAAAGAAAAAAATA-AGA
1 AAGAAAAAGAAAGAAAAAGAAAAAAATAGAGA
*
3786618 GAGATAAAAGAAAGAAAAAAAGAAAAAGAA-AGA-A
1 AAGA-AAAAGAAAG--AAAAAGAAAAA-AATAGAGA
3786652 ATAGGAAAAAGAAAAGATAAAAGAAA
1 A-A-GAAAAAG-AAAGA-AAAAGAAA
3786678 GAAGAGATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
30 3 0.06
31 8 0.17
34 13 0.28
35 17 0.36
36 6 0.13
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.06
Consensus pattern (32 bp):
AAGAAAAAGAAAGAAAAAGAAAAAAATAGAGA
Found at i:3789016 original size:35 final size:35
Alignment explanation
Indices: 3788977--3789071 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 35
3788967 TTTTTTTAAA
*
3788977 AATTGTTTGAGTCCTTCTTAGGACCGTTTTTCTGG
1 AATTGTTTGAGTCCTTCTTAGGACCATTTTTCTGG
* * *
3789012 AATTGTTTGAGTCATTCTTAGTACCATTTTTTTGG
1 AATTGTTTGAGTCCTTCTTAGGACCATTTTTCTGG
* *
3789047 GATGTCGTTTGAGTCCTTTTTAGGA
1 AAT-T-GTTTGAGTCCTTCTTAGGA
3789072 TTGTCTTCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
35 33 0.66
36 1 0.02
37 16 0.32
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (35 bp):
AATTGTTTGAGTCCTTCTTAGGACCATTTTTCTGG
Found at i:3789707 original size:91 final size:92
Alignment explanation
Indices: 3789546--3789722 Score: 286
Period size: 91 Copynumber: 1.9 Consensus size: 92
3789536 GATAAACCAG
*
3789546 TCAACATTTCCAGTGGAAGGATTCATAATGAGAAGAACTCATCCGATGAGGAAGAATAAGTTCAT
1 TCAACATTTCCAGTGGAAGGATTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
3789611 AATGAGAAGAACTTGTTCAACCTTGGC
66 AATGAGAAGAACTTGTTCAACCTTGGC
* * *
3789638 TCAATATTTCCAGTGG-A-GAGTTCATAATGAGAAGAACTTATCCGATGAGGGAGAAGAAGTTCA
1 TCAACATTTCCAGTGGAAGGA-TTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCA
*
3789701 TAATGAGAATAACTTGTTCAAC
65 TAATGAGAAGAACTTGTTCAAC
3789723 ATAATCTCAA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
90 2 0.03
91 62 0.78
92 15 0.19
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (92 bp):
TCAACATTTCCAGTGGAAGGATTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGGC
Found at i:3789937 original size:91 final size:91
Alignment explanation
Indices: 3789777--3789960 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 91
3789767 ACTCGAGGGA
* *
3789777 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAAAAGTTCATA
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATA
* * *
3789842 ATGAGAAGAATTTGTTCAACCTTGGC
66 ATGAGAACAAGTTGTTCAACCTTAGC
* * * *
3789868 TCAATATTTCAAGTGTAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATA
3789933 ATGAGAACAAGTTGTTCAACCTTAGC
66 ATGAGAACAAGTTGTTCAACCTTAGC
3789959 TC
1 TC
3789961 GATTTATCAC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (91 bp):
TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATA
ATGAGAACAAGTTGTTCAACCTTAGC
Found at i:3789972 original size:230 final size:230
Alignment explanation
Indices: 3789546--3790099 Score: 822
Period size: 230 Copynumber: 2.4 Consensus size: 230
3789536 GATAAACCAG
* * *
3789546 TCAACATTTCCAGTGGA-AGGATTCATAATGAGAAGAACTCATCCGATGAGGAAGAATAAGTTCA
1 TCAACATTTCCAGTGGAGA-G-TTCATAATGAGAAGAACTCATCCAATGAGGGAGAAAAAGTTCA
*
3789610 TAATGAGAAGAACTTGTTCAACCTTGGCTCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAAC
64 TAATGAGAAGAACTTGTTCAACCTTGGCTCAATATTTCAAGTGGAGAGTTCATAATGAGAAGAAC
* * * *
3789675 TTATCCGATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACATAATCTCAATTCATCA
129 TCATCCAATGAGGGAGAAGAAGTTCATAATGAGAACAACTTGTTCAACATAAGCTCAATTCATCA
*
3789740 CATATGGAGTTGAATCAGCAACACCTCACTCGAGGGA
194 CATATGGAGTTGAATCAGAAACACCTCACTCGAGGGA
* *
3789777 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAAAAGTTCATA
* *
3789842 ATGAGAAGAATTTGTTCAACCTTGGCTCAATATTTCAAGTGTAGAGTTCATAATGAGAAGAACTC
66 ATGAGAAGAACTTGTTCAACCTTGGCTCAATATTTCAAGTGGAGAGTTCATAATGAGAAGAACTC
* * * * *
3789907 ATCCAATGAGGGAGAAGAAGTTCATAATGAGAACAAGTTGTTCAACCTTAGCTCGATTTATCACA
131 ATCCAATGAGGGAGAAGAAGTTCATAATGAGAACAACTTGTTCAACATAAGCTCAATTCATCACA
*
3789972 TATGGAGTTGAATCAGAAACACCTCACTCGATGGA
196 TATGGAGTTGAATCAGAAACACCTCACTCGAGGGA
** * ** * ** *
3790007 TCAACATTTAAAGTGGAGAGTTCATATTGATCAGAACTCATCCTATGAGGGAGATGAAGTTTATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAAAAGTTCATA
*
3790072 ATGAGAAGAACTTGTTCAACCTTAGCTC
66 ATGAGAAGAACTTGTTCAACCTTGGCTC
3790100 GATTAATCAC
Statistics
Matches: 290, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
230 271 0.93
231 18 0.06
232 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (230 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGCTCAATATTTCAAGTGGAGAGTTCATAATGAGAAGAACTC
ATCCAATGAGGGAGAAGAAGTTCATAATGAGAACAACTTGTTCAACATAAGCTCAATTCATCACA
TATGGAGTTGAATCAGAAACACCTCACTCGAGGGA
Found at i:3790132 original size:139 final size:139
Alignment explanation
Indices: 3789868--3790376 Score: 772
Period size: 139 Copynumber: 3.7 Consensus size: 139
3789858 CAACCTTGGC
* * * *
3789868 TCAATATTTCAAGTGTAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTTAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * *
3789933 ATGAGAACAAGTTGTTCAACCTTAGCTCGATTTATCACATATGGAGTTGAATCAGAAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCTCA
*
3789998 CTCGATGGA
131 CTCGAGGGA
* * ** * * *
3790007 TCAACATTTAAAGTGGAGAGTTCATATTGATCAGAACTCATCCTATGAGGGAGATGAAGTTTATA
1 TCAACATTTTAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
** *
3790072 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATAAAGTTGAATCAGCAACACATCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCTCA
3790137 CTCGAGGGA
131 CTCGAGGGA
3790146 TCAACATTTCTAA-TGGATG-GTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
1 TCAACATTT-TAAGTGGA-GAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
3790209 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCA-CAACACCT
64 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCT
*
3790273 CACGCGAGGGA
129 CACTCGAGGGA
* *
3790284 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTTATA
1 TCAACATTTTAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
*
3790349 ATGAGAAGAACTTGTTCAACTTTAGCTC
66 ATGAGAAGAACTTGTTCAACCTTAGCTC
3790377 ATTTCTATTA
Statistics
Matches: 335, Mismatches: 31, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
137 3 0.01
138 102 0.30
139 227 0.68
140 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (139 bp):
TCAACATTTTAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCTCA
CTCGAGGGA
Found at i:3791983 original size:51 final size:50
Alignment explanation
Indices: 3791889--3792009 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 50
3791879 TTTTATTTTA
* * ** *
3791889 ATTTAATCATTGTTTATTT-TTATTTAGCTATTGTTATTTTGTTTTATGC
1 ATTTAATCACTGTTTATTTATGATTTAGCTACGGTTATTTTGTTTCATGC
* *
3791938 ATTTCAATCACTGTTTATTTATGATTTGGCTACGGTTCTTTTGTTTCATGC
1 ATTT-AATCACTGTTTATTTATGATTTAGCTACGGTTATTTTGTTTCATGC
*
3791989 ATTTTAGTCACTGTTT-TTTAT
1 A-TTTAATCACTGTTTATTTAT
3792010 TTTTGAGTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
49 4 0.07
50 19 0.31
51 35 0.57
52 3 0.05
ACGTcount: A:0.19, C:0.11, G:0.12, T:0.58
Consensus pattern (50 bp):
ATTTAATCACTGTTTATTTATGATTTAGCTACGGTTATTTTGTTTCATGC
Found at i:3798742 original size:54 final size:54
Alignment explanation
Indices: 3798669--3798983 Score: 415
Period size: 54 Copynumber: 5.9 Consensus size: 54
3798659 TTATGTATAC
* * *
3798669 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
* * * *
3798723 TATC-AGCAGTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACTACCG
1 TATCGA-CACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
*
3798777 TATC-AGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGACCA
1 TATCGA-CACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
* *
3798831 TATCGACACTAAGTGTGCAACCCAC-AGAATTCAT-ATAAGTTTATGACCGACTA
1 TATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCA
* * * * *
3798884 TATCGACACTAAGTGTGTAACCCATGGAATTTATAATAAGTTTATGAACGGCCA
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
*
3798938 TATCGACACTAAGTGTGCAACCTACTG-AATTCATAATAAGTTTATG
1 TATCGACACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATG
3798984 CAACACTACA
Statistics
Matches: 231, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
53 46 0.20
54 183 0.79
55 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
Found at i:3798863 original size:108 final size:106
Alignment explanation
Indices: 3798669--3798983 Score: 427
Period size: 107 Copynumber: 2.9 Consensus size: 106
3798659 TTATGTATAC
* * *
3798669 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGATCGTATC-AGCAGT
1 TATC-GCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGA-CACT
* *
3798733 AAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACTACCG
64 AAGTGTGCAACCCACG-AATTCATAATAAGTTTATGAACGACCA
*
3798777 TATCAGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGACCATATCGACACTA
1 TATC-GCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGACACTA
* *
3798842 AGTGTGCAACCCACAGAATTCAT-ATAAGTTTATGACCGACTA
65 AGTGTGCAACCCAC-GAATTCATAATAAGTTTATGAACGACCA
* * * * *
3798884 TATCGACACTAAGTGTGTAACCCATGGAATTTATAATAAGTTTATGAACGGCCATATCGACACTA
1 TATCG-CACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGACACTA
*
3798949 AGTGTGCAACCTACTGAATTCATAATAAGTTTATG
65 AGTGTGCAACCCAC-GAATTCATAATAAGTTTATG
3798984 CAACACTACA
Statistics
Matches: 186, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
106 1 0.01
107 93 0.50
108 90 0.48
109 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (106 bp):
TATCGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCATATCGACACTAA
GTGTGCAACCCACGAATTCATAATAAGTTTATGAACGACCA
Found at i:3798950 original size:161 final size:162
Alignment explanation
Indices: 3798669--3798983 Score: 435
Period size: 161 Copynumber: 2.0 Consensus size: 162
3798659 TTATGTATAC
* * *
3798669 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGATCGTATCAGCAGTA
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGATCATATCAGCACTA
* * *
3798734 AGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACTACCGTATCAGCACTAAGTGTGCAACC
66 AGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCATATCAGCACTAAGTGTGCAACC
3798799 CAC-GAAATTCATAATAAGTTTATGAATGACCA
131 CACTG-AATTCATAATAAGTTTATGAATGACCA
*
3798831 TATCGACACTAAGTGTGCAACCCAC-AGAATTCAT-ATAAGTTTATGACCGA-CTATATC-GACA
1 TATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGATC-ATATCAG-CA
* * * *
3798892 CTAAGTGTGTAACCCATGGAATTTATAATAAGTTTATGAACGGCCATATC-GACACTAAGTGTGC
63 CTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCATATCAG-CACTAAGTGTGC
*
3798956 AACCTACTGAATTCATAATAAGTTTATG
127 AACCCACTGAATTCATAATAAGTTTATG
3798984 CAACACTACA
Statistics
Matches: 136, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
160 3 0.02
161 101 0.74
162 32 0.24
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (162 bp):
TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGATCATATCAGCACTA
AGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCATATCAGCACTAAGTGTGCAACC
CACTGAATTCATAATAAGTTTATGAATGACCA
Done.