Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 123 of 136
Found at i:41848057 original size:23 final size:23
Alignment explanation
Indices: 41848024--41848098 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
41848014 ATAAGTGCCA
*
41848024 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
41848047 CATTGAAATGTAGCTGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
41848070 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
41848093 CACTGA
1 CACTGA
41848099 TCAATAACAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:41850523 original size:3 final size:3
Alignment explanation
Indices: 41850509--41850561 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
41850499 TTGTTTTTCG
* * * **
41850509 TAT TAT TCT TAT TAT TAT TAT CAT TAT TAT TATT TAT TTT TCC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
41850555 TAT TAT T
1 TAT TAT T
41850562 TATTTAGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41852648 original size:128 final size:127
Alignment explanation
Indices: 41852503--41852757 Score: 501
Period size: 128 Copynumber: 2.0 Consensus size: 127
41852493 AACCAGTACG
41852503 AATGATACCATTACAATACTAACTACCATAATTTAAAAACATAAACCTTTACCACTCATTCTAAA
1 AATGATACCATTACAATACTAACTACCATAATTTAAAAACATAAACCTTTACCACTCATTCTAAA
41852568 AAATATAATTGAAGTTTAAAATTTTACTTAATATAAATATATATATATATATAATATATATTT
66 AAATATAATTGAAGTTTAAAATTTTACTTAATATAAATATATATATATATAT-ATATATATTT
41852631 AATGATACCATTACAATACTAACTACCATAATTTAAAAACATAAACCTTTACCACTCATTCTAAA
1 AATGATACCATTACAATACTAACTACCATAATTTAAAAACATAAACCTTTACCACTCATTCTAAA
41852696 AAATATAATTGAAGTTTAAAATTTTACTTAATATAAATATATATATATATATATATATATTT
66 AAATATAATTGAAGTTTAAAATTTTACTTAATATAAATATATATATATATATATATATATTT
41852758 TTGTGTCAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 10 0.08
128 117 0.92
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (127 bp):
AATGATACCATTACAATACTAACTACCATAATTTAAAAACATAAACCTTTACCACTCATTCTAAA
AAATATAATTGAAGTTTAAAATTTTACTTAATATAAATATATATATATATATATATATATTT
Found at i:41852739 original size:2 final size:2
Alignment explanation
Indices: 41852726--41852755 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41852716 ATTTTACTTA
*
41852726 AT AT AA 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
41852756 TTTTGTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41859084 original size:4 final size:4
Alignment explanation
Indices: 41859075--41859125 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
41859065 AGATTACTAT
41859075 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
41859123 ATA
1 ATA
41859126 AACAGATAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:41861920 original size:2 final size:2
Alignment explanation
Indices: 41861913--41861937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41861903 CCAAAGGAAA
41861913 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
41861938 TATACATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41862261 original size:4 final size:4
Alignment explanation
Indices: 41862254--41862303 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
41862244 TGCATATATA
* * *
41862254 TATG TATG TATG TATG TATG CATG TATG TATG CATG TTTG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
41862302 TA
1 TA
41862304 GCCGTTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:41862694 original size:3 final size:3
Alignment explanation
Indices: 41862686--41862738 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
41862676 AAGAATGCAA
41862686 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41862734 AAT AA
1 AAT AA
41862739 AAGAAGCTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41864201 original size:17 final size:17
Alignment explanation
Indices: 41864179--41864213 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41864169 TGTTTGAGAT
41864179 AGTTAAGTTAAGTT-TTG
1 AGTTAA-TTAAGTTGTTG
41864196 AGTTAATTAAGTTGTTG
1 AGTTAATTAAGTTGTTG
41864213 A
1 A
41864214 ATCATATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (17 bp):
AGTTAATTAAGTTGTTG
Found at i:41873245 original size:21 final size:20
Alignment explanation
Indices: 41873206--41873245 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41873196 CAAAATTGTC
*
41873206 AAGAGAAGAGAATTGGAAGA
1 AAGAGAAGAGAAATGGAAGA
*
41873226 AAGAGCAGAGGAAATGGAAG
1 AAGAGAAGA-GAAATGGAAG
41873246 GCAGTAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.07
Consensus pattern (20 bp):
AAGAGAAGAGAAATGGAAGA
Found at i:41879671 original size:131 final size:131
Alignment explanation
Indices: 41879437--41879886 Score: 722
Period size: 131 Copynumber: 3.4 Consensus size: 131
41879427 TAGTAAAGAC
* *
41879437 TGCAGATCTTGTCTCACTAAGCAGTAACGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCCAG
1 TGCAGATCTTGTCTCCCTAAGCAATAACGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCCAG
41879502 GAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
66 GAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
41879567 T
131 T
** * *
41879568 TGCAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATTGAAGATGACGAATCTTATCTTCCCCAG
1 TGCAGATCTTGTCTCCCTAAGCAATAACGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCCAG
41879633 GAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
66 GAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
41879698 T
131 T
* * * *
41879699 TGCAGATCTTGTCTCCCTAAGCAATAATGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCTAG
1 TGCAGATCTTGTCTCCCTAAGCAATAACGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCCAG
* * *
41879764 GAGTAGAGAAACAGATTTAGGCCACAAGTTCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
66 GAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
41879829 T
131 T
* * * * * *
41879830 TGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATC-AATACGGCGAATCTTATCT
1 TGCAGATCTTGTCTCCCTAAGCAATAACGGAGCAGATCGAAGATGGCGAATCTTATCT
41879887 CCCTGAGACT
Statistics
Matches: 297, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
130 17 0.06
131 280 0.94
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (131 bp):
TGCAGATCTTGTCTCCCTAAGCAATAACGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCCAG
GAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAA
T
Found at i:41884099 original size:41 final size:39
Alignment explanation
Indices: 41884054--41884153 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 39
41884044 TTCAATACAC
41884054 CGGCACTTAGCCTGCTAGACATATAGTCTGAAATGTTTCA
1 CGGCA-TTAGCCTGCTAGACATATAGTCTGAAATGTTTCA
* *
41884094 TCGGCATTAAGCCTACTAGACATATAGTCTGAATTGTTTCA
1 -CGGCATT-AGCCTGCTAGACATATAGTCTGAAATGTTTCA
*
41884135 CTGGCAATAAGCCTGCTAG
1 C-GGC-ATTAGCCTGCTAG
41884154 GTGCTAAGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
40 3 0.06
41 47 0.90
42 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (39 bp):
CGGCATTAGCCTGCTAGACATATAGTCTGAAATGTTTCA
Found at i:41890669 original size:24 final size:24
Alignment explanation
Indices: 41890636--41890688 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
41890626 TTCCAATCAA
*
41890636 CAACTACTGAAATTTTTCTCAGAT
1 CAACTACTGAAATTTTGCTCAGAT
* *
41890660 TAACTGCTGAAATTTTGCTCAGAT
1 CAACTACTGAAATTTTGCTCAGAT
41890684 CAACT
1 CAACT
41890689 TTGATGCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (24 bp):
CAACTACTGAAATTTTGCTCAGAT
Found at i:41893870 original size:9 final size:9
Alignment explanation
Indices: 41893856--41893886 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41893846 GTTAAAGAAA
41893856 TCGAGTTAT
1 TCGAGTTAT
*
41893865 TCGAGTTAA
1 TCGAGTTAT
41893874 TCGAGTTAT
1 TCGAGTTAT
41893883 TCGA
1 TCGA
41893887 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:41896565 original size:20 final size:20
Alignment explanation
Indices: 41896526--41896567 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
41896516 ATGTTAGAGT
*
41896526 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
41896546 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
41896566 TA
1 TA
41896568 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:41896596 original size:15 final size:15
Alignment explanation
Indices: 41896576--41896606 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41896566 TACCGTTGTA
41896576 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
41896591 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
41896606 A
1 A
41896607 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:41902245 original size:15 final size:15
Alignment explanation
Indices: 41902225--41902255 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41902215 TACCGTTGTA
41902225 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
41902240 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
41902255 A
1 A
41902256 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:41906791 original size:90 final size:90
Alignment explanation
Indices: 41906638--41906814 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 90
41906628 ATTTTACATT
* * * *
41906638 CAATGCAATCCAAAAAAATGTTCCTCGATGAATAAAATAAGTGTTCGAAGATCAGTGCATCAACT
1 CAATGCAATCCAAAAAAATGCTCCTCGATGAACAAAATAAGTGCTCGAAGATCAATGCATCAACT
*
41906703 ATACAAGGGTCCTCAATTATAAGCA
66 ATACAAGGCTCCTCAATTATAAGCA
* * *
41906728 CAATGCACTCCAAAGAAATGCTCCTC-AGTGAACAAAATAAGTGCTC-ACGAATCAATGCATCAA
1 CAATGCAATCCAAAAAAATGCTCCTCGA-TGAACAAAATAAGTGCTCGAAG-ATCAATGCATCAA
*
41906791 CTATACAAGTCTCCTCAATTATAA
64 CTATACAAGGCTCCTCAATTATAA
41906815 ACAACTAAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
89 3 0.04
90 73 0.96
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (90 bp):
CAATGCAATCCAAAAAAATGCTCCTCGATGAACAAAATAAGTGCTCGAAGATCAATGCATCAACT
ATACAAGGCTCCTCAATTATAAGCA
Found at i:41910348 original size:2 final size:2
Alignment explanation
Indices: 41910341--41910374 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
41910331 TACAGTCCTT
41910341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41910375 GTTTCGCGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:41919588 original size:21 final size:20
Alignment explanation
Indices: 41919546--41919588 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
41919536 AATATTAACA
** *
41919546 ATTTAATTAATTTTCAATTT
1 ATTTAATTAATTCACAAATT
41919566 ATTTATATTAATTCACAAATT
1 ATTTA-ATTAATTCACAAATT
41919587 AT
1 AT
41919589 AACGCAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAATTAATTCACAAATT
Found at i:41921024 original size:22 final size:23
Alignment explanation
Indices: 41920986--41921033 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
41920976 AAGCACATCT
*
41920986 CCTGCCTCTTAACAGTCAAGTAA
1 CCTGCCTCTCAACAGTCAAGTAA
41921009 CCTGCCTC-CAACAGTCAAGTAA
1 CCTGCCTCTCAACAGTCAAGTAA
41921031 CCT
1 CCT
41921034 ACACACACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.23
Consensus pattern (23 bp):
CCTGCCTCTCAACAGTCAAGTAA
Found at i:41921143 original size:154 final size:155
Alignment explanation
Indices: 41920950--41921259 Score: 613
Period size: 154 Copynumber: 2.0 Consensus size: 155
41920940 CCAGTTCCAA
41920950 CAAGGCTTCCCCACAAAAAAAAAAAAAAGCACATCTCCTGCCTCTTAACAGTCAAGTAACCTGCC
1 CAAGGCTTCCCCACAAAAAAAAAAAAAAGCACATCTCCTGCCTCTTAACAGTCAAGTAACCTGCC
41921015 TCCAACAGTCAAGTAACCTACACACACTTGGTTTATCGAATCCAAACAATAATCACAACCTAGAA
66 TCCAACAGTCAAGTAACCTACACACACTTGGTTTATCGAATCCAAACAATAATCACAACCTAGAA
41921080 GGCTAGAACCTACAGCAGTAACATC
131 GGCTAGAACCTACAGCAGTAACATC
41921105 CAAGGCTTCCCCA-AAAAAAAAAAAAAAGCACATCTCCTGCCTCTTAACAGTCAAGTAACCTGCC
1 CAAGGCTTCCCCACAAAAAAAAAAAAAAGCACATCTCCTGCCTCTTAACAGTCAAGTAACCTGCC
41921169 TCCAACAGTCAAGTAACCTACACACACTTGGTTTATCGAATCCAAACAATAATCACAACCTAGAA
66 TCCAACAGTCAAGTAACCTACACACACTTGGTTTATCGAATCCAAACAATAATCACAACCTAGAA
41921234 GGCTAGAACCTACAGCAGTAACATC
131 GGCTAGAACCTACAGCAGTAACATC
41921259 C
1 C
41921260 TAGTAAAAGC
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 142 0.92
155 13 0.08
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.19
Consensus pattern (155 bp):
CAAGGCTTCCCCACAAAAAAAAAAAAAAGCACATCTCCTGCCTCTTAACAGTCAAGTAACCTGCC
TCCAACAGTCAAGTAACCTACACACACTTGGTTTATCGAATCCAAACAATAATCACAACCTAGAA
GGCTAGAACCTACAGCAGTAACATC
Found at i:41921178 original size:22 final size:23
Alignment explanation
Indices: 41921140--41921187 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
41921130 AAGCACATCT
*
41921140 CCTGCCTCTTAACAGTCAAGTAA
1 CCTGCCTCTCAACAGTCAAGTAA
41921163 CCTGCCTC-CAACAGTCAAGTAA
1 CCTGCCTCTCAACAGTCAAGTAA
41921185 CCT
1 CCT
41921188 ACACACACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.23
Consensus pattern (23 bp):
CCTGCCTCTCAACAGTCAAGTAA
Found at i:41942297 original size:28 final size:28
Alignment explanation
Indices: 41942259--41942328 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
41942249 TATTGTTTAT
41942259 GTAGTTAAATAATCTTACACTTCATCTA
1 GTAGTTAAATAATCTTACACTTCATCTA
* *
41942287 GTAGTTAAATAATCTTGCACTTTATCTA
1 GTAGTTAAATAATCTTACACTTCATCTA
*
41942315 CTAGTTAAATAATC
1 GTAGTTAAATAATC
41942329 CGTCCATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (28 bp):
GTAGTTAAATAATCTTACACTTCATCTA
Found at i:41945746 original size:30 final size:31
Alignment explanation
Indices: 41945692--41945750 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
41945682 GAATTACTAT
*
41945692 TAGTGTATTTTAGAAATAAAAAAAATATATG
1 TAGTGTATTTTAAAAATAAAAAAAATATATG
41945723 TAGTGTATTTTAAAAAT-AAAAAAATATA
1 TAGTGTATTTTAAAAATAAAAAAAATATA
41945751 GTTTATATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (31 bp):
TAGTGTATTTTAAAAATAAAAAAAATATATG
Found at i:41946330 original size:22 final size:23
Alignment explanation
Indices: 41946278--41946331 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
41946268 GGCGCCAATG
41946278 AATATTTTTTTTGTTTGAATAAA
1 AATATTTTTTTTGTTTGAATAAA
*
41946301 ATATTATTTTTTATT-TTT-ATTAAA
1 A-A-TATTTTTT-TTGTTTGAATAAA
41946325 AATATTT
1 AATATTT
41946332 AAATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 7 0.26
25 11 0.41
26 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
AATATTTTTTTTGTTTGAATAAA
Found at i:41946748 original size:45 final size:45
Alignment explanation
Indices: 41946692--41946780 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
41946682 TTAAAGAGTT
* *
41946692 TAATGTTGGTTTAGACTCGATGACTTTGTAGTCTACTGATATATA
1 TAATATTGGTTTAGACTCGACGACTTTGTAGTCTACTGATATATA
41946737 TAATATTGGTTTAGACTCGACGACTTTGTAGTCTACTGATATAT
1 TAATATTGGTTTAGACTCGACGACTTTGTAGTCTACTGATATAT
41946781 TCATGCTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (45 bp):
TAATATTGGTTTAGACTCGACGACTTTGTAGTCTACTGATATATA
Found at i:41947294 original size:53 final size:54
Alignment explanation
Indices: 41947231--41947341 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 54
41947221 GAATCAATTT
* *
41947231 AAAAAAAAATTTAATCGCGCTTATCTGACAGACACGAAT-AAATATTTATATTA
1 AAAAAAAAATTTAATCGCGCCTATCTAACAGACACGAATCAAATATTTATATTA
* ** * *
41947284 AAAAAAAAATTTAATCGCGCCTATCTAACAGGCGTGAATCAATTTTTTATATTA
1 AAAAAAAAATTTAATCGCGCCTATCTAACAGACACGAATCAAATATTTATATTA
41947338 AAAA
1 AAAA
41947342 TATTTTTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 34 0.68
54 16 0.32
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (54 bp):
AAAAAAAAATTTAATCGCGCCTATCTAACAGACACGAATCAAATATTTATATTA
Found at i:41948240 original size:35 final size:35
Alignment explanation
Indices: 41948200--41948267 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
41948190 TTTTGTTGGC
* * *
41948200 ATTTTATTTATTAATTTAATTTTTTTTGCCTTTTA
1 ATTTTATTTATCAATTTAATTTATGTTGCCTTTTA
41948235 ATTTTATTTATCAATTTAATTTATGTTGCCTTT
1 ATTTTATTTATCAATTTAATTTATGTTGCCTTT
41948268 GCAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (35 bp):
ATTTTATTTATCAATTTAATTTATGTTGCCTTTTA
Found at i:41948254 original size:18 final size:18
Alignment explanation
Indices: 41948200--41948256 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
41948190 TTTTGTTGGC
*
41948200 ATTTTATTTATTAATTTA
1 ATTTTATTTATCAATTTA
**
41948218 ATTTT-TTT-TGCCTTTTA
1 ATTTTATTTAT-CAATTTA
41948235 ATTTTATTTATCAATTTA
1 ATTTTATTTATCAATTTA
41948253 ATTT
1 ATTT
41948257 ATGTTGCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.03
17 12 0.39
18 17 0.55
19 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTATTTATCAATTTA
Found at i:41948257 original size:17 final size:17
Alignment explanation
Indices: 41948202--41948258 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
41948192 TTGTTGGCAT
*
41948202 TTTATTTATTAATTTAA
1 TTTATTTATCAATTTAA
* **
41948219 TTT-TTTTTGCCTTTTAA
1 TTTATTTAT-CAATTTAA
41948236 TTTTATTTATCAATTTAA
1 -TTTATTTATCAATTTAA
41948254 TTTAT
1 TTTAT
41948259 GTTGCCTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 4 0.13
17 13 0.43
18 9 0.30
19 4 0.13
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTTATCAATTTAA
Found at i:41952724 original size:53 final size:54
Alignment explanation
Indices: 41952661--41952771 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 54
41952651 GAATCAATTT
* *
41952661 AAAAAAAAATTTAATCGCGCTTATCTGACAGACACGAAT-AAATATTTATATTA
1 AAAAAAAAATTTAATCGCGCCTATCTAACAGACACGAATCAAATATTTATATTA
* ** * *
41952714 AAAAAAAAATTTAATCGCGCCTATCTAACAGGCGTGAATCAATTTTTTATATTA
1 AAAAAAAAATTTAATCGCGCCTATCTAACAGACACGAATCAAATATTTATATTA
41952768 AAAA
1 AAAA
41952772 TATTTTTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 34 0.68
54 16 0.32
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (54 bp):
AAAAAAAAATTTAATCGCGCCTATCTAACAGACACGAATCAAATATTTATATTA
Found at i:41953670 original size:35 final size:35
Alignment explanation
Indices: 41953630--41953697 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
41953620 TTTTGTTGGC
* * *
41953630 ATTTTATTTATTAATTTAATTTTTTTTGCCTTTTA
1 ATTTTATTTATCAATTTAATTTATGTTGCCTTTTA
41953665 ATTTTATTTATCAATTTAATTTATGTTGCCTTT
1 ATTTTATTTATCAATTTAATTTATGTTGCCTTT
41953698 GCAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (35 bp):
ATTTTATTTATCAATTTAATTTATGTTGCCTTTTA
Found at i:41953684 original size:18 final size:18
Alignment explanation
Indices: 41953630--41953686 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
41953620 TTTTGTTGGC
*
41953630 ATTTTATTTATTAATTTA
1 ATTTTATTTATCAATTTA
**
41953648 ATTTT-TTT-TGCCTTTTA
1 ATTTTATTTAT-CAATTTA
41953665 ATTTTATTTATCAATTTA
1 ATTTTATTTATCAATTTA
41953683 ATTT
1 ATTT
41953687 ATGTTGCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.03
17 12 0.39
18 17 0.55
19 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTATTTATCAATTTA
Found at i:41953687 original size:17 final size:17
Alignment explanation
Indices: 41953632--41953688 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
41953622 TTGTTGGCAT
*
41953632 TTTATTTATTAATTTAA
1 TTTATTTATCAATTTAA
* **
41953649 TTT-TTTTTGCCTTTTAA
1 TTTATTTAT-CAATTTAA
41953666 TTTTATTTATCAATTTAA
1 -TTTATTTATCAATTTAA
41953684 TTTAT
1 TTTAT
41953689 GTTGCCTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 4 0.13
17 13 0.43
18 9 0.30
19 4 0.13
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTTATCAATTTAA
Found at i:41961507 original size:10 final size:10
Alignment explanation
Indices: 41961494--41961535 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
41961484 GGGCTTTTAG
41961494 TTTCTTTTCC
1 TTTCTTTTCC
*
41961504 TTTCTTTTCT
1 TTTCTTTTCC
41961514 TTTCTTTT-C
1 TTTCTTTTCC
41961523 TTTCCTTTTCC
1 TTT-CTTTTCC
41961534 TT
1 TT
41961536 CTCATCTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTTCC
Found at i:41961514 original size:15 final size:15
Alignment explanation
Indices: 41961494--41961535 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
41961484 GGGCTTTTAG
41961494 TTTCTTTTCCTTTCT
1 TTTCTTTTCCTTTCT
*
41961509 TTTCTTTTCTTTTCT
1 TTTCTTTTCCTTTCT
*
41961524 TTCCTTTTCCTT
1 TTTCTTTTCCTT
41961536 CTCATCTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCCTTTCT
Found at i:41961543 original size:5 final size:5
Alignment explanation
Indices: 41961535--41961562 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41961525 TCCTTTTCCT
41961535 TCTCA TCTCA TCTCA TCTCA TCTCA TCT
1 TCTCA TCTCA TCTCA TCTCA TCTCA TCT
41961563 TATGTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (5 bp):
TCTCA
Found at i:41961904 original size:2 final size:2
Alignment explanation
Indices: 41961897--41961923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41961887 AAAATGGATA
41961897 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
41961924 TCATGATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41967352 original size:23 final size:24
Alignment explanation
Indices: 41967310--41967363 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
41967300 TTAATTGTTA
*
41967310 AAAAATATATTATATATAATATAT
1 AAAATTATATTATATATAATATAT
41967334 AAAATTATATTATAT-TAATATAT
1 AAAATTATATTATATATAATATAT
41967357 AAAATTA
1 AAAATTA
41967364 AAAATAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTATATTATATATAATATAT
Found at i:41970607 original size:21 final size:20
Alignment explanation
Indices: 41970567--41970608 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
41970557 TTGAAAATTT
* *
41970567 TAATAAATTTTTTTATTAAA
1 TAATAAATTTGTTTAATAAA
41970587 TAATAAATTTGGTTTAATAAA
1 TAATAAATTT-GTTTAATAAA
41970608 T
1 T
41970609 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATAAATTTGTTTAATAAA
Found at i:41972799 original size:2 final size:2
Alignment explanation
Indices: 41972792--41972827 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
41972782 CCCTTTCAAG
*
41972792 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41972828 ACAGGCAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:41980442 original size:39 final size:40
Alignment explanation
Indices: 41980362--41980445 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 40
41980352 TTTATTGCTA
41980362 AAACAGAAGAAAAGGAATTTCTCATGACTCATTTAAAGTTT
1 AAACAGAAGAAAAGGAATTTCTCA-GACTCATTTAAAGTTT
41980403 AAACAGAAGAAAAGGAATTTCTCA-ACTCATTTAAAGTTT
1 AAACAGAAGAAAAGGAATTTCTCAGACTCATTTAAAGTTT
41980442 AAAC
1 AAAC
41980446 TTCCAGATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 19 0.44
41 24 0.56
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (40 bp):
AAACAGAAGAAAAGGAATTTCTCAGACTCATTTAAAGTTT
Found at i:41986119 original size:31 final size:32
Alignment explanation
Indices: 41986081--41986142 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
41986071 GGCCCATTTT
41986081 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATCTTTAAAAAATTAAAAAAAG
* *
41986112 TATTTTAAAAATCTTTTAAAATTTAAAAAAA
1 TATTTTAAAAATCTTTAAAAAATTAAAAAAA
41986143 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (32 bp):
TATTTTAAAAATCTTTAAAAAATTAAAAAAAG
Found at i:41986142 original size:42 final size:41
Alignment explanation
Indices: 41986081--41986265 Score: 286
Period size: 42 Copynumber: 4.5 Consensus size: 41
41986071 GGCCCATTTT
*
41986081 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
41986123 TCTTTTAAAATTTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTT-AAAAAAATTAAAAAAAGTATTTTAAAAA
41986165 TATTTTAAAA-TTAAAAAAATTAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATT-AAAAAAAGTATTTTAAAAA
* *
41986206 TATTTTAAAATTTAAAAAAATT-AAAAAAGTATGTAAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
41986246 TATTTTAAAA-TTAAAAAAAT
1 TATTTTAAAATTTAAAAAAAT
41986266 AAATATATTT
Statistics
Matches: 135, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
39 10 0.07
40 35 0.26
41 38 0.28
42 52 0.39
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (41 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:41986256 original size:10 final size:11
Alignment explanation
Indices: 41986081--41986215 Score: 67
Period size: 11 Copynumber: 12.9 Consensus size: 11
41986071 GGCCCATTTT
41986081 TATTTT-AAAA
1 TATTTTAAAAA
41986091 -ATTTTAAAAA
1 TATTTTAAAAA
**
41986101 -ATTAAAAAAA
1 TATTTTAAAAA
41986111 GTATTTTAAAAA
1 -TATTTTAAAAA
*
41986123 TCTTTT--AAA
1 TATTTTAAAAA
*
41986132 -ATTTAAAAAA
1 TATTTTAAAAA
* **
41986142 AATTAAAAAAA
1 TATTTTAAAAA
41986153 GTATTTTAAAAA
1 -TATTTTAAAAA
41986165 TATTTT--AAA
1 TATTTTAAAAA
41986174 -A--TTAAAAA
1 TATTTTAAAAA
* **
41986182 AATTAAAAAAAA
1 TATT-TTAAAAA
41986194 GTATTTTAAAAA
1 -TATTTTAAAAA
41986206 TATTTTAAAA
1 TATTTTAAAA
41986216 TTTAAAAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 27
0.69 0.12 0.20
Matches are distributed among these distances:
6 2 0.02
8 7 0.07
9 12 0.13
10 15 0.16
11 30 0.32
12 26 0.27
13 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:41991060 original size:31 final size:31
Alignment explanation
Indices: 41991022--41991080 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
41991012 AATAAAAGCA
41991022 ATATTAAT-TGAATATTAATTAATATGGTAGT
1 ATATTAATGTGAA-ATTAATTAATATGGTAGT
*
41991053 ATATTAATGTGAAATTAATTAATTTGGT
1 ATATTAATGTGAAATTAATTAATATGGT
41991081 CATATCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (31 bp):
ATATTAATGTGAAATTAATTAATATGGTAGT
Found at i:41991396 original size:24 final size:24
Alignment explanation
Indices: 41991361--41991410 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
41991351 GTACTTTCCA
41991361 TGTATGTAAATTTTGAAATTCATC
1 TGTATGTAAATTTTGAAATTCATC
* *
41991385 TGTATGTGAATTTTGAAATTGATC
1 TGTATGTAAATTTTGAAATTCATC
41991409 TG
1 TG
41991411 ATCATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (24 bp):
TGTATGTAAATTTTGAAATTCATC
Found at i:41991833 original size:133 final size:134
Alignment explanation
Indices: 41991679--41991946 Score: 529
Period size: 133 Copynumber: 2.0 Consensus size: 134
41991669 AATATAATAC
41991679 ATCAAATACACTAAAACATTAAAATAAATGTTTCCCAACAAATTAAAAAAATTAAAAAAAGTATT
1 ATCAAATACACTAAAACATTAAAATAAATGTTTCCCAACAAATTAAAAAAATTAAAAAAAGTATT
41991744 TATACTTAAATAACACTAGGATATGTGCAACTTAACAAGCAAAATGTTTCTAAAATAGTAGCAAA
66 TATACTTAAATAACACTAGGATATGTGCAACTTAACAAGCAAAATGTTTCTAAAATAGTAGCAAA
41991809 ATTA
131 ATTA
41991813 ATCAAATACA-TAAAACATTAAAATAAATGTTTCCCAACAAATTAAAAAAATTAAAAAAAGTATT
1 ATCAAATACACTAAAACATTAAAATAAATGTTTCCCAACAAATTAAAAAAATTAAAAAAAGTATT
41991877 TATACTTAAATAACACTAGGATATGTGCAACTTAACAAGCAAAATGTTTCTAAAATAGTAGCAAA
66 TATACTTAAATAACACTAGGATATGTGCAACTTAACAAGCAAAATGTTTCTAAAATAGTAGCAAA
41991942 ATTA
131 ATTA
41991946 A
1 A
41991947 CAATAAAATA
Statistics
Matches: 134, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 124 0.93
134 10 0.07
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (134 bp):
ATCAAATACACTAAAACATTAAAATAAATGTTTCCCAACAAATTAAAAAAATTAAAAAAAGTATT
TATACTTAAATAACACTAGGATATGTGCAACTTAACAAGCAAAATGTTTCTAAAATAGTAGCAAA
ATTA
Found at i:41995275 original size:31 final size:32
Alignment explanation
Indices: 41995231--41995305 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
41995221 TTAACTTTTT
41995231 CATAATGATAAATA-TAAAAATATATATTTAA
1 CATAATGATAAATATTAAAAATATATATTTAA
*
41995262 CATAATGGA-AAATATTAAAAATATAT-TTTTA
1 CATAAT-GATAAATATTAAAAATATATATTTAA
* *
41995293 TATAATTATAAAT
1 CATAATGATAAAT
41995306 TTATTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 1 0.03
31 24 0.63
32 13 0.34
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.39
Consensus pattern (32 bp):
CATAATGATAAATATTAAAAATATATATTTAA
Found at i:41995300 original size:22 final size:21
Alignment explanation
Indices: 41995275--41995325 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
41995265 AATGGAAAAT
*
41995275 ATTAAAAATATATTTTTATATA
1 ATTAAAAATATATTTATATA-A
* *
41995297 ATTATAAATTTATTTATATAA
1 ATTAAAAATATATTTATATAA
*
41995318 ATAAAAAA
1 ATTAAAAA
41995326 GTTATTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAAAAATATATTTATATAA
Found at i:41998506 original size:29 final size:29
Alignment explanation
Indices: 41998451--41998507 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
41998441 GTTTAATGTG
* *
41998451 TAATTTTATACGTGAATTTTGATTTTGAA
1 TAATTTTATACATGAATTTTGAATTTGAA
*
41998480 TAATTTTATATATGAAATTTT-AATTTGA
1 TAATTTTATACATG-AATTTTGAATTTGA
41998508 TTCAATTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (29 bp):
TAATTTTATACATGAATTTTGAATTTGAA
Found at i:42001648 original size:14 final size:16
Alignment explanation
Indices: 42001619--42001655 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
42001609 TTCTATTTAC
42001619 ATTTGTTATCTTCAAT-
1 ATTT-TTATCTTCAATA
42001635 ATTTTTAT-TTCAATA
1 ATTTTTATCTTCAATA
42001650 ATTTTT
1 ATTTTT
42001656 TATTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 10 0.50
16 4 0.20
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTTATCTTCAATA
Found at i:42004816 original size:155 final size:154
Alignment explanation
Indices: 42004349--42004817 Score: 762
Period size: 153 Copynumber: 3.0 Consensus size: 154
42004339 ATATATATAT
*
42004349 ATATTGACTCTAGATTTAGGTTGATATTTTATTTTTTTTGACTTAATTATATCTAGATTTGAAAT
1 ATATTGCCTCTAGATTTAGGTTGATATTTTA-TTTTTTT-ACTTAATTATATCTAGATTTGAAAT
* * * * *
42004414 TTGTTGTATTTGACATCTCTATCATAACACTATTAGAATATGATGACATGATATTATCGTTCAAT
64 TCGTCGCATTTGGCATCTCTATCATAACATTATTAGAATATGATGACATGATATTATCGTTCAAT
42004479 ATTATGATAATACTTGGCAAGCATAA
129 ATTATGATAATACTTGGCAAGCATAA
42004505 ATATTGCCTCTAGATTTAGGTTGATA-TTT-TTTTTTTACTTAATTATATCTAGATTTGAAATTT
1 ATATTGCCTCTAGATTTAGGTTGATATTTTATTTTTTTACTTAATTATATCTAGATTTGAAA-TT
* * *
42004568 CGTCGCATTTGGCATCTCTGTCGTAACATTATTAGAATACGATGACATGATATTATCGTTCAATA
65 CGTCGCATTTGGCATCTCTATCATAACATTATTAGAATATGATGACATGATATTATCGTTCAATA
42004633 TTATGATAATACTTGGCAAGCATAA
130 TTATGATAATACTTGGCAAGCATAA
42004658 ATATTGCCTCTAGATTTAGGTTGATATTTTATTTTATTTACTTAATTATATCTAGATTTGAAATT
1 ATATTGCCTCTAGATTTAGGTTGATATTTTATTTT-TTTACTTAATTATATCTAGATTTGAAATT
* *
42004723 CGTCGCATTTGGCATATCTATCCTAACATTATTAGAATATGATGACATGATATTATCGTTCAATA
65 CGTCGCATTTGGCATCTCTATCATAACATTATTAGAATATGATGACATGATATTATCGTTCAATA
** *
42004788 TTACAATAACACTTGGCAAGCATAA
130 TTATGATAATACTTGGCAAGCATAA
42004813 ATATT
1 ATATT
42004818 TTTTAAATAT
Statistics
Matches: 293, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
152 24 0.08
153 117 0.40
154 3 0.01
155 97 0.33
156 52 0.18
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (154 bp):
ATATTGCCTCTAGATTTAGGTTGATATTTTATTTTTTTACTTAATTATATCTAGATTTGAAATTC
GTCGCATTTGGCATCTCTATCATAACATTATTAGAATATGATGACATGATATTATCGTTCAATAT
TATGATAATACTTGGCAAGCATAA
Found at i:42006919 original size:15 final size:15
Alignment explanation
Indices: 42006901--42006937 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42006891 AATAAAGGGA
42006901 AAAAAAAAAGAAAAG
1 AAAAAAAAAGAAAAG
*
42006916 AAAAAAACAGAAAAG
1 AAAAAAAAAGAAAAG
42006931 AAAAAAA
1 AAAAAAA
42006938 TTAAATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:42015097 original size:22 final size:22
Alignment explanation
Indices: 42015054--42015097 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42015044 GTTGTTGTTG
* *
42015054 TTTGCTGCCACTTTGATGTTAT
1 TTTGCTACCACTTTGATATTAT
*
42015076 TTTGCTACCACTTTGCTATTAT
1 TTTGCTACCACTTTGATATTAT
42015098 ATTGATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTGCTACCACTTTGATATTAT
Found at i:42023136 original size:2 final size:2
Alignment explanation
Indices: 42023129--42023161 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
42023119 GCTAACATAA
42023129 AT AT AT AT AT AT AT AT AT AGT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
42023162 ATGCTGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:42028365 original size:21 final size:21
Alignment explanation
Indices: 42028336--42028375 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42028326 TGTATACAAG
*
42028336 AAAAGAGGGGGGGGGGGGGAA
1 AAAAAAGGGGGGGGGGGGGAA
42028357 AAAAAAGGGGGGGGGGGGG
1 AAAAAAGGGGGGGGGGGGG
42028376 GGGTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.68, T:0.00
Consensus pattern (21 bp):
AAAAAAGGGGGGGGGGGGGAA
Found at i:42040050 original size:29 final size:29
Alignment explanation
Indices: 42040008--42040069 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
42039998 TAACACCGAA
42040008 GATGCACTCAAGTATTTTTACTTATGCAT
1 GATGCACTCAAGTATTTTTACTTATGCAT
42040037 GATGCACTCAAGTATTTTTACTTATGCAT
1 GATGCACTCAAGTATTTTTACTTATGCAT
42040066 GATG
1 GATG
42040070 TAAACACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (29 bp):
GATGCACTCAAGTATTTTTACTTATGCAT
Found at i:42043835 original size:128 final size:129
Alignment explanation
Indices: 42043646--42043902 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 129
42043636 TTGTTACATA
42043646 AGAAGCATTTTATAATAACTAACAATTTGAACTGGCAATATGAGAAAAGCAGTTCATTTCATATC
1 AGAAGCATTTTATAATAACTAACAATTTGAACTGGCAATATGAGAAAAGCAGTTCATTTCATATC
42043711 CTTTATAATCACATCACCCTCTAAGGGGCAGTTTGATTACTGAATATACCAAATTAAATGCAGC
66 CTTTATAATCACATCACCCTCTAAGGGGCAGTTTGATTACTGAATATACCAAATTAAATGCAGC
42043775 AGAAGCA-TTTATAATAACTAACAATTTGAACTGGCAATATGAGAAAAGCAGTTCATTTCATATC
1 AGAAGCATTTTATAATAACTAACAATTTGAACTGGCAATATGAGAAAAGCAGTTCATTTCATATC
42043839 CTTTATAATCACATCACCCTCTAAGGGGCAGTTTGATTACTGAATATACCAAATTAAATGCAGC
66 CTTTATAATCACATCACCCTCTAAGGGGCAGTTTGATTACTGAATATACCAAATTAAATGCAGC
42043903 TGCTAAAAAT
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 121 0.95
129 7 0.05
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (129 bp):
AGAAGCATTTTATAATAACTAACAATTTGAACTGGCAATATGAGAAAAGCAGTTCATTTCATATC
CTTTATAATCACATCACCCTCTAAGGGGCAGTTTGATTACTGAATATACCAAATTAAATGCAGC
Found at i:42046383 original size:59 final size:59
Alignment explanation
Indices: 42046291--42046472 Score: 364
Period size: 59 Copynumber: 3.1 Consensus size: 59
42046281 CAGTGTAAAG
42046291 ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
1 ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
42046350 ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
1 ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
42046409 ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
1 ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
42046468 ATTAA
1 ATTAA
42046473 TAGAAAAGTT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 123 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.29
Consensus pattern (59 bp):
ATTAAAAATTATCAAATTGAAGAATATCAAATAAATCCACAACTTATACATAGTATGAA
Found at i:42050022 original size:26 final size:28
Alignment explanation
Indices: 42049968--42050028 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
42049958 TATTATCAAG
* *
42049968 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
42049996 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
42050022 AATTATA
1 AATTATA
42050029 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:42050541 original size:16 final size:16
Alignment explanation
Indices: 42050520--42050579 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
42050510 TTGATTTGCT
*
42050520 ATTACACATTTATTCC
1 ATTACACATCTATTCC
*
42050536 ATTACACCTCTATTCC
1 ATTACACATCTATTCC
* *
42050552 ATTACACCTCTAATCC
1 ATTACACATCTATTCC
* *
42050568 AATACACCTCTA
1 ATTACACATCTA
42050580 ATCTAATACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTACACATCTATTCC
Found at i:42050580 original size:16 final size:16
Alignment explanation
Indices: 42050533--42050589 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
42050523 ACACATTTAT
* *
42050533 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
42050549 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
42050565 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
*
42050581 TCTAATACA
1 TCCAATACA
42050590 GCGAACCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:42052670 original size:84 final size:84
Alignment explanation
Indices: 42052572--42052736 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 84
42052562 GTTTCAGGCA
*
42052572 ATTCGGTGTTATTTTTGAAGCTAAAATCATATCCGAAACGAGTCAAAATACCAAAAACACTTTTA
1 ATTCGGTGTTATTTTTGAAGCTAAAATCATATCCGAAACGAGTCAAAATACCAAAAACAATTTTA
42052637 ATTGGTTTCGTCGATTGCC
66 ATTGGTTTCGTCGATTGCC
* *
42052656 ATTCGGTGTTATTTTTGAAGTTAAAATCATATCCGAAACGAGTCAAAATACCAAAAACAATTTTC
1 ATTCGGTGTTATTTTTGAAGCTAAAATCATATCCGAAACGAGTCAAAATACCAAAAACAATTTTA
42052721 ATTGGTTTCGTCGATT
66 ATTGGTTTCGTCGATT
42052737 TTTTTTCTCC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (84 bp):
ATTCGGTGTTATTTTTGAAGCTAAAATCATATCCGAAACGAGTCAAAATACCAAAAACAATTTTA
ATTGGTTTCGTCGATTGCC
Found at i:42062668 original size:32 final size:33
Alignment explanation
Indices: 42062596--42062668 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
42062586 TAGAAAAACT
*
42062596 AATATTTTCTGATGTTTGGATGAATTTGTGTAA
1 AATATTTTCTGATGTTTGGATGAACTTGTGTAA
*
42062629 AATATTTTCTGCTGTTT-GAT-AGACTTGCTG-AA
1 AATATTTTCTGATGTTTGGATGA-ACTTG-TGTAA
42062661 AATATTTT
1 AATATTTT
42062669 ATAAAAGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 17 0.47
33 18 0.50
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (33 bp):
AATATTTTCTGATGTTTGGATGAACTTGTGTAA
Found at i:42067279 original size:14 final size:14
Alignment explanation
Indices: 42067260--42067292 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
42067250 GTTACTTTTT
42067260 TGTTCTATATCAAA
1 TGTTCTATATCAAA
42067274 TGTTCTATATCAAA
1 TGTTCTATATCAAA
42067288 T-TTCT
1 TGTTCT
42067293 CTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (14 bp):
TGTTCTATATCAAA
Found at i:42078660 original size:13 final size:13
Alignment explanation
Indices: 42078621--42078662 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
42078611 AAAATAAGAG
42078621 AATTAAATTATATCA
1 AATTAAATTATA--A
42078636 AATTATAA-TATAA
1 AATTA-AATTATAA
42078649 AATTAAATTATAA
1 AATTAAATTATAA
42078662 A
1 A
42078663 TTTTTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
15 9 0.36
16 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAAATTATAA
Found at i:42083390 original size:39 final size:41
Alignment explanation
Indices: 42083311--42083400 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
42083301 AAAAAAGTGT
* *
42083311 TTATATTAAAAAACACTATCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTATAATAAATAAAATAAATATTTTA
*
42083352 TTATATTAAAAAACAC-A-AATAAATAAAATAAATGTTTTA
1 TTATATTAAAAAACACTATAATAAATAAAATAAATATTTTA
*
42083391 TTGTATTAAA
1 TTATATTAAA
42083401 TATAAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 28 0.62
40 1 0.02
41 16 0.36
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAACACTATAATAAATAAAATAAATATTTTA
Found at i:42086028 original size:24 final size:23
Alignment explanation
Indices: 42086001--42086047 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
42085991 TAACCATGAG
42086001 ACATTT-AAAGTAAGGTAAGTAATA
1 ACATTTGAAAGTAA-GTAAG-AATA
*
42086025 ACATTTGAAATTAAGTAAGAATA
1 ACATTTGAAAGTAAGTAAGAATA
42086048 TGTGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTGAAAGTAAGTAAGAATA
Found at i:42086394 original size:22 final size:23
Alignment explanation
Indices: 42086350--42086394 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
42086340 GGATTTATAT
*
42086350 TATTCTAGGTGTGTTAGGTTGGA
1 TATTCTAGGTGTGTTAGGGTGGA
*
42086373 TATTCT-GGTGTGTTTGGGTGGA
1 TATTCTAGGTGTGTTAGGGTGGA
42086395 ATCCATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.13, C:0.04, G:0.38, T:0.44
Consensus pattern (23 bp):
TATTCTAGGTGTGTTAGGGTGGA
Found at i:42086648 original size:47 final size:47
Alignment explanation
Indices: 42086579--42086720 Score: 268
Period size: 47 Copynumber: 3.0 Consensus size: 47
42086569 TGAAGTGATA
42086579 TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAAGGTTTATGG
1 TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAAGGTTTATGG
42086626 TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAAGGTTTATGG
1 TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAAGGTTTATGG
42086673 TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAA-GTCTTATGG
1 TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAAGGT-TTATGG
42086720 T
1 T
42086721 TGATGTTTGT
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
46 2 0.02
47 92 0.98
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (47 bp):
TATAATTATGTATAATTAGTTTAAATGATTTTTTTAAAGGTTTATGG
Found at i:42087083 original size:36 final size:35
Alignment explanation
Indices: 42087043--42087112 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
42087033 CATCTCCGGA
42087043 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
* *
42087079 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATA
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATA
42087113 AGTTTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:42089158 original size:11 final size:11
Alignment explanation
Indices: 42089124--42089197 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 11
42089114 TAAATATCTC
*
42089124 TAAAATAATAG
1 TAAAATAATAA
*
42089135 CAAAATTAATAA
1 TAAAA-TAATAA
42089147 TAAAATAATAA
1 TAAAATAATAA
* * * *
42089158 TTACACAATAT
1 TAAAATAATAA
* * *
42089169 TTAAACAACAA
1 TAAAATAATAA
42089180 TAAAATAATAA
1 TAAAATAATAA
42089191 TAAAATA
1 TAAAATA
42089198 GTAAAATGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 40 0.82
12 9 0.18
ACGTcount: A:0.65, C:0.07, G:0.01, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:42091891 original size:13 final size:13
Alignment explanation
Indices: 42091873--42091897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42091863 TAATCACACT
42091873 AACAAATAAATAA
1 AACAAATAAATAA
42091886 AACAAATAAATA
1 AACAAATAAATA
42091898 TCTTCAGAGG
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AACAAATAAATAA
Found at i:42094267 original size:22 final size:22
Alignment explanation
Indices: 42094214--42094275 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
42094204 AAATATATAT
*
42094214 TAAAAAATTTAAAAAAATTCAA
1 TAAAAATTTTAAAAAAATTCAA
42094236 TAAAACATTTTGAAAAGAAA-TCAA
1 TAAAA-ATTTT-AAAA-AAATTCAA
* *
42094260 TAAAATTTTTTAAAAA
1 TAAAAATTTTAAAAAA
42094276 TGATTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 8 0.24
23 8 0.24
24 13 0.38
25 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (22 bp):
TAAAAATTTTAAAAAAATTCAA
Found at i:42094534 original size:25 final size:27
Alignment explanation
Indices: 42094491--42094541 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
42094481 TTAATTTTCT
42094491 AAAATTTTAAAAAAATTTATG-TTTTG
1 AAAATTTTAAAAAAATTTATGATTTTG
* *
42094517 AAAA-TTTCAAAATATTTATGATTTT
1 AAAATTTTAAAAAAATTTATGATTTT
42094542 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (27 bp):
AAAATTTTAAAAAAATTTATGATTTTG
Found at i:42098519 original size:6 final size:6
Alignment explanation
Indices: 42098508--42098538 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42098498 CTCATTCAGG
42098508 TACAAA TACAAA TACAAA TACAAA TACAAA T
1 TACAAA TACAAA TACAAA TACAAA TACAAA T
42098539 CATTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (6 bp):
TACAAA
Found at i:42100703 original size:12 final size:12
Alignment explanation
Indices: 42100688--42100712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42100678 TGGGCGTCAC
42100688 GTTGGGCTTGAG
1 GTTGGGCTTGAG
42100700 GTTGGGCTTGAG
1 GTTGGGCTTGAG
42100712 G
1 G
42100713 GAGTGAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.52, T:0.32
Consensus pattern (12 bp):
GTTGGGCTTGAG
Found at i:42101498 original size:83 final size:84
Alignment explanation
Indices: 42101385--42101551 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 84
42101375 ATTTAAATAG
42101385 CTTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATCATTTTTAGGGGGCCAAAGTAT
1 CTTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATCATTTTTAGGGGGCCAAAGTAT
42101450 AATTTTATCTTTACTAGTT
66 AATTTTATCTTTACTAGTT
42101469 CTTATATC-TTATAATTTTTAAAGAATTAAATTAAATTTTTATCATTTTTAGGGGGCCAAAGTAT
1 CTTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATCATTTTTAGGGGGCCAAAGTAT
42101533 AATTTTATCTTTACTAGTT
66 AATTTTATCTTTACTAGTT
42101552 TAAAATTTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 75 0.90
84 8 0.10
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.49
Consensus pattern (84 bp):
CTTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATCATTTTTAGGGGGCCAAAGTAT
AATTTTATCTTTACTAGTT
Found at i:42101949 original size:170 final size:170
Alignment explanation
Indices: 42101658--42102008 Score: 533
Period size: 170 Copynumber: 2.1 Consensus size: 170
42101648 AAGAGAGTAA
*
42101658 CAGTGGCTGAAAATTTTGAACTTTTGCATGTTCCCAAAACTGAAACAATTGCTAAGATTCTTCTT
1 CAGTGGCTGAAAAATTTGAACTTTTGCATGTTCCCAAAACTGAAACAATTGCTAAGATTCTTCTT
** * * * * *
42101723 CTTCTACTGTTTAGCCCAATTAGAGTTCTTAAATTGGGGCCGTTTACACTATGGGATGACATGTC
66 CTTCTACTGTCCAGCCCAACTAGAGTTCTTAAATTAGGGCCGTTTAAACCATGGGATGACAGGTC
* **
42101788 AGCTTTCCGTTATGGACATAAAGAAAAATGGTGAAAAGTT
131 AACTTTCCGTTACAGACATAAAGAAAAATGGTGAAAAGTT
*
42101828 TAGTGGCTGAAAAATTTGAACTTTTGCATGTTCCCAAAACTGAAACAATTG-TAAGGATTCTTCT
1 CAGTGGCTGAAAAATTTGAACTTTTGCATGTTCCCAAAACTGAAACAATTGCTAA-GATTCTTCT
* *
42101892 TCTTTTACTGTCCAGCCCAACTAGGGTTCTTAAATTAGGGCCGTTTAAACCATGGGATGACAGGT
65 TCTTCTACTGTCCAGCCCAACTAGAGTTCTTAAATTAGGGCCGTTTAAACCATGGGATGACAGGT
* *
42101957 CAACTTTCCGTTACAGACGTAACGAAAAATGGTGAAAAGTT
130 CAACTTTCCGTTACAGACATAAAGAAAAATGGTGAAAAGTT
*
42101998 CAATGGCTGAA
1 CAGTGGCTGAA
42102009 TTGTAACTTT
Statistics
Matches: 162, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
169 3 0.02
170 159 0.98
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (170 bp):
CAGTGGCTGAAAAATTTGAACTTTTGCATGTTCCCAAAACTGAAACAATTGCTAAGATTCTTCTT
CTTCTACTGTCCAGCCCAACTAGAGTTCTTAAATTAGGGCCGTTTAAACCATGGGATGACAGGTC
AACTTTCCGTTACAGACATAAAGAAAAATGGTGAAAAGTT
Found at i:42107282 original size:14 final size:15
Alignment explanation
Indices: 42107260--42107336 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42107250 CAATCAAACA
42107260 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
42107274 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
42107289 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
42107309 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
42107323 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
42107337 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:42107301 original size:20 final size:20
Alignment explanation
Indices: 42107276--42107315 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42107266 AATATTTTCC
*
42107276 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42107296 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42107316 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42107321 original size:34 final size:35
Alignment explanation
Indices: 42107264--42107330 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
42107254 CAAACACCAG
*
42107264 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42107299 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42107331 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42107608 original size:36 final size:36
Alignment explanation
Indices: 42107561--42107637 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
42107551 AGTTCGAGTC
42107561 TTATCATGTGTGATTATTATGTATAAATCTTTAATT
1 TTATCATGTGTGATTATTATGTATAAATCTTTAATT
42107597 TTATCATGTGTGATTATTATGTATAAATCTTTAATT
1 TTATCATGTGTGATTATTATGTATAAATCTTTAATT
42107633 TTATC
1 TTATC
42107638 GTCAGTAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.53
Consensus pattern (36 bp):
TTATCATGTGTGATTATTATGTATAAATCTTTAATT
Found at i:42107650 original size:36 final size:36
Alignment explanation
Indices: 42107561--42107651 Score: 121
Period size: 36 Copynumber: 2.5 Consensus size: 36
42107551 AGTTCGAGTC
**
42107561 TTATCATGTGTGATTATTATGTATAAATCTTTAATT
1 TTATCATCAGTGATTATTATGTATAAATCTTTAATT
**
42107597 TTATCATGTGTGATTATTATGTATAAATCTTTAATT
1 TTATCATCAGTGATTATTATGTATAAATCTTTAATT
*
42107633 TTATCGTCAGT-AGTTATTA
1 TTATCATCAGTGA-TTATTA
42107652 CGTGAGAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
35 1 0.02
36 50 0.98
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.52
Consensus pattern (36 bp):
TTATCATCAGTGATTATTATGTATAAATCTTTAATT
Found at i:42108506 original size:111 final size:112
Alignment explanation
Indices: 42108298--42108520 Score: 430
Period size: 111 Copynumber: 2.0 Consensus size: 112
42108288 GGCGTTATGC
42108298 TAACCTAATCTTAAGAAAAAGGAACAAGCTTTATATGGCAAATTGGATCTCTTCCAAGCTCAAAG
1 TAACCTAATCTTAAGAAAAAGGAACAAGCTTTATATGGCAAATTGGATCTCTTCCAAGCTCAAAG
*
42108363 TCGCTGAAACTCTCCTTCAACAGGCAAGTTTTTCCTTCCTTTTCATA
66 TCGCTGAAACTCTCCTTCAACAGGCAAATTTTTCCTTCCTTTTCATA
42108410 TAACCTAATC-TAAGAAAAAGGAACAAGCTTTATATGGCAAATTGGATCTCTTCCAAGCTCAAAG
1 TAACCTAATCTTAAGAAAAAGGAACAAGCTTTATATGGCAAATTGGATCTCTTCCAAGCTCAAAG
42108474 TCGCTGAAACTCTCCTTCAACAGGCAAATTTTTCCTTCCTTTTCATA
66 TCGCTGAAACTCTCCTTCAACAGGCAAATTTTTCCTTCCTTTTCATA
42108521 GTTCTTTTTC
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
111 100 0.91
112 10 0.09
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (112 bp):
TAACCTAATCTTAAGAAAAAGGAACAAGCTTTATATGGCAAATTGGATCTCTTCCAAGCTCAAAG
TCGCTGAAACTCTCCTTCAACAGGCAAATTTTTCCTTCCTTTTCATA
Found at i:42113169 original size:8 final size:8
Alignment explanation
Indices: 42113156--42113191 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
42113146 TATATTATTG
42113156 TTATTATA
1 TTATTATA
42113164 TTATTAT-
1 TTATTATA
42113171 TTGATTATA
1 TT-ATTATA
42113180 TTATTATA
1 TTATTATA
42113188 TTAT
1 TTAT
42113192 GAAATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 2 0.08
8 22 0.85
9 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TTATTATA
Found at i:42113177 original size:16 final size:17
Alignment explanation
Indices: 42113148--42113186 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
42113138 TTATAAAATA
*
42113148 TATTATTGTTATTATAT
1 TATTATTGTGATTATAT
42113165 TATTATT-TGATTATAT
1 TATTATTGTGATTATAT
42113181 TATTAT
1 TATTAT
42113187 ATTATGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
TATTATTGTGATTATAT
Found at i:42113612 original size:16 final size:16
Alignment explanation
Indices: 42113591--42113622 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42113581 CAAAAAAAGA
42113591 AATAGAAACGAAACAG
1 AATAGAAACGAAACAG
42113607 AATAGAAACGAAACAG
1 AATAGAAACGAAACAG
42113623 GGAGAAAAAG
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:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (16 bp):
AATAGAAACGAAACAG
Found at i:42114541 original size:41 final size:37
Alignment explanation
Indices: 42114490--42114590 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 37
42114480 ACTTCGACAT
*
42114490 TAAGTTGATGAGACACTAGGTGTCACTATTTTACTTCGGA
1 TAAGTTGATGAGACACTGGGTGTCAC---TTTACTTCGGA
* * * *
42114530 TAGATTTGATGAGATACTGGGTATCACTTTACTTCGGT
1 TA-AGTTGATGAGACACTGGGTGTCACTTTACTTCGGA
*
42114568 TAAGTCGATGAGACACTGGGTGT
1 TAAGTTGATGAGACACTGGGTGT
42114591 TAGCTTTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
37 17 0.33
38 12 0.24
40 2 0.04
41 20 0.39
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (37 bp):
TAAGTTGATGAGACACTGGGTGTCACTTTACTTCGGA
Found at i:42118660 original size:24 final size:24
Alignment explanation
Indices: 42118632--42118685 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
42118622 TATCTCATGA
42118632 ACATTTAGTTCATGCTTTCTATTC
1 ACATTTAGTTCATGCTTTCTATTC
42118656 ACATTTAGTTCATGCTTTCTATTC
1 ACATTTAGTTCATGCTTTCTATTC
42118680 ACATTT
1 ACATTT
42118686 TCATATTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.50
Consensus pattern (24 bp):
ACATTTAGTTCATGCTTTCTATTC
Found at i:42118717 original size:19 final size:20
Alignment explanation
Indices: 42118675--42118717 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
42118665 TCATGCTTTC
*
42118675 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
42118695 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
42118713 TATTC
1 TATTC
42118718 CACAATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:42119117 original size:18 final size:17
Alignment explanation
Indices: 42119071--42119124 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
42119061 TTTCCAATTC
42119071 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
* *
42119088 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTCACTT
42119106 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
42119124 T
1 T
42119125 TTCATTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:42119133 original size:18 final size:17
Alignment explanation
Indices: 42119074--42119139 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 17
42119064 CCAATTCTCA
42119074 ATTC-AAATTCACTTTC
1 ATTCAAAATTCACTTTC
*
42119090 ATTTCAAAATTTACTTTC
1 A-TTCAAAATTCACTTTC
42119108 AATATC-AAATTCACTTTTTC
1 -AT-TCAAAATTCAC--TTTC
42119128 ATTCAAAATTCA
1 ATTCAAAATTCA
42119140 ATTCAATACT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.02
17 3 0.07
18 21 0.51
19 12 0.29
20 4 0.10
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTCAAAATTCACTTTC
Found at i:42119145 original size:36 final size:36
Alignment explanation
Indices: 42119071--42119147 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
42119061 TTTCCAATTC
* *
42119071 TCAAT-TCAAATTCACTTTCATTTCAAAATTTACTT
1 TCAATATCAAATTCACTTTCATTTCAAAATTCACAT
42119106 TCAATATCAAATTCACTTTTTCA-TTCAAAATTCA-AT
1 TCAATATCAAATTCAC--TTTCATTTCAAAATTCACAT
42119142 TCAATA
1 TCAATA
42119148 CTAACACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 5 0.14
36 17 0.46
37 10 0.27
38 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (36 bp):
TCAATATCAAATTCACTTTCATTTCAAAATTCACAT
Found at i:42119851 original size:12 final size:12
Alignment explanation
Indices: 42119834--42119885 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
42119824 GCCCTTTTTC
42119834 TTTTCTTTCTTT
1 TTTTCTTTCTTT
* *
42119846 TTTTCTCTGTTT
1 TTTTCTTTCTTT
*
42119858 CTTTCTATTTCTTT
1 -TTT-TCTTTCTTT
*
42119872 TTTTGTTTCTTT
1 TTTTCTTTCTTT
42119884 TT
1 TT
42119886 ATGCTTTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 20 0.62
13 6 0.19
14 6 0.19
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:42120282 original size:23 final size:23
Alignment explanation
Indices: 42120256--42120304 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
42120246 GTCTTTTCTT
42120256 AATTT-ATTTCATAATATAATAAC
1 AATTTAATTT-ATAATATAATAAC
42120279 AATTTAATTTATAATATAATAAC
1 AATTTAATTTATAATATAATAAC
42120302 AAT
1 AAT
42120305 AATAACAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATTTATAATATAATAAC
Found at i:42120308 original size:9 final size:9
Alignment explanation
Indices: 42120294--42120318 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42120284 AATTTATAAT
42120294 ATAATAACA
1 ATAATAACA
42120303 ATAATAACA
1 ATAATAACA
42120312 ATAATAA
1 ATAATAA
42120319 TATATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:42120315 original size:23 final size:23
Alignment explanation
Indices: 42120266--42120317 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
42120256 AATTTATTTC
* **
42120266 ATAATATAATAACAATTTAATTT
1 ATAATATAATAACAATATAATCA
42120289 ATAATATAATAACAATAATAA-CA
1 ATAATATAATAACAAT-ATAATCA
42120312 ATAATA
1 ATAATA
42120318 ATATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAATATAATAACAATATAATCA
Found at i:42127716 original size:21 final size:21
Alignment explanation
Indices: 42127691--42127733 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
42127681 TTGAGAAGTA
42127691 AAGAGTTTGATATTATCACCT
1 AAGAGTTTGATATTATCACCT
42127712 AAGAGTTTGATATTATCACCT
1 AAGAGTTTGATATTATCACCT
42127733 A
1 A
42127734 TCTTACTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (21 bp):
AAGAGTTTGATATTATCACCT
Found at i:42130307 original size:22 final size:23
Alignment explanation
Indices: 42130254--42130309 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
42130244 CCCGTTTTTA
* * *
42130254 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
42130277 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
42130299 ATTAAAATTAA
1 ATTAAAATTAA
42130310 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:42130322 original size:16 final size:16
Alignment explanation
Indices: 42130285--42130324 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42130275 TTAATAAAAT
* *
42130285 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
42130301 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
42130317 TAAAATTA
1 TAAAATTA
42130325 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:42141413 original size:86 final size:87
Alignment explanation
Indices: 42141307--42141479 Score: 339
Period size: 86 Copynumber: 2.0 Consensus size: 87
42141297 AAAAATAATA
42141307 ATAATTAAAATACATTATAATATTTAAGGGTATTTTAGTCTATTCATTTTAATAAAAAATCAACA
1 ATAATTAAAATACATTATAATATTTAAGGGTATTTTAGTCTATTCATTTTAATAAAAAATCAACA
42141372 AAAATATACATATGATGAGATT
66 AAAATATACATATGATGAGATT
42141394 ATAATTAAAA-ACATTATAATATTTAAGGGTATTTTAGTCTATTCATTTTAATAAAAAATCAACA
1 ATAATTAAAATACATTATAATATTTAAGGGTATTTTAGTCTATTCATTTTAATAAAAAATCAACA
42141458 AAAATATACATATGATGAGATT
66 AAAATATACATATGATGAGATT
42141480 TGAATCCACG
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 76 0.88
87 10 0.12
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (87 bp):
ATAATTAAAATACATTATAATATTTAAGGGTATTTTAGTCTATTCATTTTAATAAAAAATCAACA
AAAATATACATATGATGAGATT
Found at i:42146059 original size:6 final size:6
Alignment explanation
Indices: 42146045--42146075 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
42146035 CTGACACTCA
42146045 CTGCAAT CTGCAT CTGCAT CTGCAT CTGCAT
1 CTGC-AT CTGCAT CTGCAT CTGCAT CTGCAT
42146076 GTAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (6 bp):
CTGCAT
Found at i:42148045 original size:18 final size:18
Alignment explanation
Indices: 42148022--42148059 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42148012 ATTTATTATT
* *
42148022 TCTTATTTGGATCTGTTA
1 TCTTATTCGAATCTGTTA
42148040 TCTTATTCGAATCTGTTA
1 TCTTATTCGAATCTGTTA
42148058 TC
1 TC
42148060 AAATCCGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (18 bp):
TCTTATTCGAATCTGTTA
Found at i:42160818 original size:21 final size:21
Alignment explanation
Indices: 42160776--42160820 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
42160766 TGTAACAAGA
* *
42160776 TTTTAATTTAATATGTTTAAT
1 TTTTAATTTAATATGATCAAT
42160797 TTTTAATTTAAT-TCGATCAAT
1 TTTTAATTTAATAT-GATCAAT
42160818 TTT
1 TTT
42160821 ACTTGATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTAATTTAATATGATCAAT
Found at i:42164928 original size:12 final size:12
Alignment explanation
Indices: 42164896--42164929 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
42164886 CATTTATTAT
42164896 TTTTTTAAAAGA
1 TTTTTTAAAAGA
*
42164908 TTATTTTAAAATA
1 TT-TTTTAAAAGA
42164921 TTTTTTAAA
1 TTTTTTAAA
42164930 TTGAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTTTTTAAAAGA
Found at i:42168574 original size:20 final size:20
Alignment explanation
Indices: 42168548--42168596 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
42168538 ATGTTTCGTC
*
42168548 AAAAAATAATTTAAAAATTC
1 AAAAAATAATTTAAAAATTA
*
42168568 TAAAAAT-ATTTAAAAATTA
1 AAAAAATAATTTAAAAATTA
42168587 AAAAAATAAT
1 AAAAAATAAT
42168597 GATGAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATAATTTAAAAATTA
Found at i:42171530 original size:113 final size:114
Alignment explanation
Indices: 42171396--42171601 Score: 396
Period size: 113 Copynumber: 1.8 Consensus size: 114
42171386 ATATATGTTA
42171396 ACTTGGGAATGATAGTTTTGGTTTGAACCTAAGCTAATGTTTGATTTTGGGAAGGCTAATGTTCA
1 ACTTGGGAAT-ATAGTTTTGGTTTGAACCTAAGCTAATGTTTGATTTTGGGAAGGCTAATGTTCA
42171461 AATAGATATGTGTATGCTTTGGTAATATGATAGGCTATATATATATATAC
65 AATAGATATGTGTATGCTTTGGTAATATGATAGGCTATATATATATATAC
42171511 ACTTGGGAAT-TAGTTTTGGTTTGAACCTAAGCTAATGTTTGATTTTGGGAAGGCTAATGTTCAA
1 ACTTGGGAATATAGTTTTGGTTTGAACCTAAGCTAATGTTTGATTTTGGGAAGGCTAATGTTCAA
42171575 ATAGATATGTGTATGCTTTGGTAATAT
66 ATAGATATGTGTATGCTTTGGTAATAT
42171602 ATNNNNNNNN
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
113 81 0.89
115 10 0.11
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (114 bp):
ACTTGGGAATATAGTTTTGGTTTGAACCTAAGCTAATGTTTGATTTTGGGAAGGCTAATGTTCAA
ATAGATATGTGTATGCTTTGGTAATATGATAGGCTATATATATATATAC
Found at i:42172634 original size:21 final size:18
Alignment explanation
Indices: 42172610--42172653 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
42172600 TTTTAAATCG
42172610 ATTAATAAAATTTCATTAATT
1 ATTAA-AAAATTTCA--AATT
*
42172631 ATTAAAAACTTTCAAATT
1 ATTAAAAAATTTCAAATT
42172649 ATTAA
1 ATTAA
42172654 CATGCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
20 8 0.36
21 5 0.23
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAAAAATTTCAAATT
Found at i:42176282 original size:33 final size:33
Alignment explanation
Indices: 42176245--42176322 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
42176235 TGGCCCTGCC
*
42176245 ATGGTCTTACACTC-GTAATGCCATAACCCAGTT
1 ATGGTCTTACACTCAG-AATGCCATAACCCAGCT
* *
42176278 ATGGTCTTATCA-TCAGGATGCCATAGCCCAGCT
1 ATGGTCTTA-CACTCAGAATGCCATAACCCAGCT
42176311 ATGGTCTTACAC
1 ATGGTCTTACAC
42176323 ATATACATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 34 0.87
34 3 0.08
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCAGAATGCCATAACCCAGCT
Found at i:42176415 original size:105 final size:101
Alignment explanation
Indices: 42176263--42176459 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 101
42176253 ACACTCGTAA
* ** * *
42176263 TGCCATAACCCAGTTATGGTCTTATCATCAGGATGCCATAGCCCAGCTATGGTCTTACACATATA
1 TGCCATAACCCAGTTATGATCTTATCATCAAAATGCCATAACCCAGCTATGGTCTTACACATAAA
42176328 CATTTACTGCCATGGTCCAACCATGGTCTTACATTCAAGG
66 CATTT--T--CATGGTCCAACCATGGTCTTACATTCAAGG
* * * * *
42176368 TGCCATAACCCAGTTATGATCTTTTCATTAAAATGTCATAACTCAGCTATGGTCTTACATATAAA
1 TGCCATAACCCAGTTATGATCTTATCATCAAAATGCCATAACCCAGCTATGGTCTTACACATAAA
*
42176433 CATTTTCATGGTCCAACTATGGTCTTA
66 CATTTTCATGGTCCAACCATGGTCTTA
42176460 TTCATCAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
101 20 0.25
103 1 0.01
105 60 0.74
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGATCTTATCATCAAAATGCCATAACCCAGCTATGGTCTTACACATAAA
CATTTTCATGGTCCAACCATGGTCTTACATTCAAGG
Found at i:42192621 original size:38 final size:38
Alignment explanation
Indices: 42192574--42192657 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
42192564 TATCGTCATT
*
42192574 ACCAGATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
1 ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
42192612 ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
1 ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
42192650 ACCAAATT
1 ACCAAATT
42192658 TTGAAACATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.25, C:0.36, G:0.06, T:0.33
Consensus pattern (38 bp):
ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
Found at i:42193057 original size:18 final size:18
Alignment explanation
Indices: 42193034--42193070 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42193024 AACAAATTAA
42193034 ACCTAACAATTTAAATAT
1 ACCTAACAATTTAAATAT
*
42193052 ACCTAACAATTTAACTAT
1 ACCTAACAATTTAAATAT
42193070 A
1 A
42193071 AGAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (18 bp):
ACCTAACAATTTAAATAT
Found at i:42202750 original size:13 final size:13
Alignment explanation
Indices: 42202732--42202761 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42202722 TCCAACAACT
42202732 ATGAATTTATTTC
1 ATGAATTTATTTC
*
42202745 ATGAATTTATTTG
1 ATGAATTTATTTC
42202758 ATGA
1 ATGA
42202762 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:42202926 original size:50 final size:50
Alignment explanation
Indices: 42202864--42203098 Score: 326
Period size: 50 Copynumber: 4.7 Consensus size: 50
42202854 AAAGATGTCA
* * *
42202864 CATGTAAGACCATGTCTGGGACACGGTATTGGCACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* *
42202914 CATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATTAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
*
42202964 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
42203014 CCCGTAAGGCCATGTCTGGGACATGGCATGGGCACCGACATGAGAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGGTCC
* *
42203065 CATGTAAGATCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
42203099 TGTTTTTATT
Statistics
Matches: 162, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 130 0.80
51 32 0.20
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:42203338 original size:19 final size:19
Alignment explanation
Indices: 42203314--42203352 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42203304 TAAACAAGCA
42203314 AGAAAACTAGAATGAGATT
1 AGAAAACTAGAATGAGATT
42203333 AGAAAACTAGAATGAGATT
1 AGAAAACTAGAATGAGATT
42203352 A
1 A
42203353 ACTAAAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AGAAAACTAGAATGAGATT
Found at i:42205359 original size:19 final size:19
Alignment explanation
Indices: 42205332--42205369 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42205322 ATGTAATTTA
*
42205332 TATTTTAAAAAATATTAAT
1 TATTGTAAAAAATATTAAT
*
42205351 TATTGTAAAAATTATTAAT
1 TATTGTAAAAAATATTAAT
42205370 AGGATAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TATTGTAAAAAATATTAAT
Found at i:42205843 original size:18 final size:18
Alignment explanation
Indices: 42205822--42205864 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
42205812 TATTCACCTA
**
42205822 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
42205840 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
42205858 AACCCAA
1 AACCCAA
42205865 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Done.