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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 44 of 66
Found at i:15894991 original size:13 final size:13
Alignment explanation
Indices: 15894973--15894997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15894963 GGAAAAATTG
15894973 TGATTTTATAAAA
1 TGATTTTATAAAA
15894986 TGATTTTATAAA
1 TGATTTTATAAA
15894998 TTTTTTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:15900892 original size:23 final size:23
Alignment explanation
Indices: 15900866--15900912 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
15900856 GTTATGAAAA
15900866 ATAACTTAAAAGAACAAATAAAG
1 ATAACTTAAAAGAACAAATAAAG
* *
15900889 ATAACTTAAAAGAATAATTAAAG
1 ATAACTTAAAAGAACAAATAAAG
15900912 A
1 A
15900913 GAAGAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (23 bp):
ATAACTTAAAAGAACAAATAAAG
Found at i:15905401 original size:25 final size:25
Alignment explanation
Indices: 15905367--15905450 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
15905357 TTCCGGTGGC
* *
15905367 AAAATTATCCTTAGATTCTAATAGT
1 AAAATTATCCTTAAATTCTAATGGT
** * *
15905392 AAAATTATCCATCCACTTCTACTGGT
1 AAAATTATCC-TTAAATTCTAATGGT
* *
15905418 AAAATTATTCTTAAATTCTGATGGT
1 AAAATTATCCTTAAATTCTAATGGT
15905443 AAAATTAT
1 AAAATTAT
15905451 TATCCACTTC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 28 0.61
26 18 0.39
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (25 bp):
AAAATTATCCTTAAATTCTAATGGT
Found at i:15905419 original size:26 final size:26
Alignment explanation
Indices: 15905300--15905425 Score: 119
Period size: 26 Copynumber: 4.9 Consensus size: 26
15905290 TGGGTGTTCG
*
15905300 TCCACTTCTGGTGGTAAAATTATCCA
1 TCCACTTCTAGTGGTAAAATTATCCA
* * * *
15905326 TCTACTTTTTGTGGCAAAATTATCCA
1 TCCACTTCTAGTGGTAAAATTATCCA
** * *
15905352 TCCACTTCCGGTGGCAAAATTATCCT
1 TCCACTTCTAGTGGTAAAATTATCCA
** * *
15905378 TAGA-TTCTAATAGTAAAATTATCCA
1 TCCACTTCTAGTGGTAAAATTATCCA
*
15905403 TCCACTTCTACTGGTAAAATTAT
1 TCCACTTCTAGTGGTAAAATTAT
15905426 TCTTAAATTC
Statistics
Matches: 78, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
25 17 0.22
26 61 0.78
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (26 bp):
TCCACTTCTAGTGGTAAAATTATCCA
Found at i:15905422 original size:51 final size:51
Alignment explanation
Indices: 15905341--15905461 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 51
15905331 TTTTTGTGGC
*** *
15905341 AAAATTATCCATCCACTTCCGGTGGCAAAATTATCCTTAGATTCTAATAGT
1 AAAATTATCCATCCACTTCTACTGGCAAAATTATCCTTAAATTCTAATAGT
* * * *
15905392 AAAATTATCCATCCACTTCTACTGGTAAAATTATTCTTAAATTCTGATGGT
1 AAAATTATCCATCCACTTCTACTGGCAAAATTATCCTTAAATTCTAATAGT
*
15905443 AAAATTAT-TATCCACTTCT
1 AAAATTATCCATCCACTTCT
15905462 TCCATATCCA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 10 0.16
51 51 0.84
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (51 bp):
AAAATTATCCATCCACTTCTACTGGCAAAATTATCCTTAAATTCTAATAGT
Found at i:15905461 original size:25 final size:25
Alignment explanation
Indices: 15905390--15905461 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
15905380 GATTCTAATA
*
15905390 GTAAAATTATCCATCCACTTCTACTG
1 GTAAAATTAT-TATCCACTTCTACTG
* ** *
15905416 GTAAAATTATTCTTAAATTCTGA-TG
1 GTAAAATTATTATCCACTTCT-ACTG
15905441 GTAAAATTATTATCCACTTCT
1 GTAAAATTATTATCCACTTCT
15905462 TCCATATCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
25 25 0.69
26 11 0.31
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (25 bp):
GTAAAATTATTATCCACTTCTACTG
Found at i:15906016 original size:23 final size:23
Alignment explanation
Indices: 15905982--15906028 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
15905972 GTTATGAAAA
15905982 ATAACTTAAAAGAACAACTAAAG
1 ATAACTTAAAAGAACAACTAAAG
* * *
15906005 ATAACTTGAAAGAATAATTAAAG
1 ATAACTTAAAAGAACAACTAAAG
15906028 A
1 A
15906029 GAAGAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.21
Consensus pattern (23 bp):
ATAACTTAAAAGAACAACTAAAG
Found at i:15906470 original size:2 final size:2
Alignment explanation
Indices: 15906463--15906506 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
15906453 AGTCACTCTC
15906463 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
15906505 AT
1 AT
15906507 TAAATCCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15906993 original size:147 final size:146
Alignment explanation
Indices: 15906777--15907069 Score: 577
Period size: 147 Copynumber: 2.0 Consensus size: 146
15906767 TAATTATTAT
15906777 ATAAAATTTTTATGTAATTTAATTAAATTTGATCATCTAAATTGGTATCACTTGACTCACAATGT
1 ATAAAATTTTTATGTAATTTAATTAAATTTGATCATCTAAATTGGTATCACTTGACTCACAATGT
15906842 CAAACTCAACAATTGATTTTAATAACAGTATCAATTACTATTTCTTCCATTACCCTTAATCTAAA
66 CAAACTCAACAATTGATTTTAATAACAGTATCAATTACTATTTCTTCCATTACCCTTAATCTAAA
15906907 TCCATCTTTAGGCATA
131 TCCATCTTTAGGCATA
15906923 NATAAAATTTTTATGTAATTTAATTAAATTTGATCATCTAAATTGGTATCACTTGACTCACAATG
1 -ATAAAATTTTTATGTAATTTAATTAAATTTGATCATCTAAATTGGTATCACTTGACTCACAATG
15906988 TCAAACTCAACAATTGATTTTAATAACAGTATCAATTACTATTTCTTCCATTACCCTTAATCTAA
65 TCAAACTCAACAATTGATTTTAATAACAGTATCAATTACTATTTCTTCCATTACCCTTAATCTAA
15907053 ATCCATCTTTAGGCATA
130 ATCCATCTTTAGGCATA
15907070 CTATTTTATC
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (146 bp):
ATAAAATTTTTATGTAATTTAATTAAATTTGATCATCTAAATTGGTATCACTTGACTCACAATGT
CAAACTCAACAATTGATTTTAATAACAGTATCAATTACTATTTCTTCCATTACCCTTAATCTAAA
TCCATCTTTAGGCATA
Found at i:15907203 original size:95 final size:91
Alignment explanation
Indices: 15907064--15907368 Score: 288
Period size: 95 Copynumber: 3.3 Consensus size: 91
15907054 TCCATCTTTA
* * * * *
15907064 GGCATACTATTTTATCTCTCAAAATGATGGTACTAAAGTTTAATAGCTTCCATTGCCCTAGTCTA
1 GGCATACT-TTTTATCTCTCAAAGTGATGGTATTTAAGTCTAATAGCTTCCATTGCCCTACTCTA
*
15907129 AATCCCTCTTATAACCCATTTGATTGAAATG
65 AAT-CCTC--A-AACCCATTTGATTGAAATT
* *
15907160 GGCATACTTTTTATCTCTCCAAGTGATGGTATTTAAGTCTAATAGGTTCCATTGCCCTACTCT--
1 GGCATACTTTTTATCTCTCAAAGTGATGGTATTTAAGTCTAATAGCTTCCATTGCCCTACTCTAA
15907223 -T-C-C-AACCCA-TTGAATTG-AATT
66 ATCCTCAAACCCATTTG-ATTGAAATT
** * * *
15907244 CACATGCTTTTTCTCTCTCAAAGTGATGGTATTTAAGTCTAATAATAGCTTTCATTGCCCTTACT
1 GGCATACTTTTTATCTCTCAAAGTGATGGTATTTAAGTC---TAATAGCTTCCATTGCCC-TACT
* *
15907309 TTAAATCTATCCCAAA-CCATTTGATT-AAATT
62 CTAAATC---CTCAAACCCATTTGATTGAAATT
15907340 GGCATACTTTTTATCTCTCAAAGTGATGG
1 GGCATACTTTTTATCTCTCAAAGTGATGG
15907369 CAAATGGGAC
Statistics
Matches: 173, Mismatches: 20, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
84 40 0.23
85 10 0.06
87 16 0.09
88 5 0.03
89 1 0.01
90 1 0.01
91 1 0.01
92 1 0.01
95 49 0.28
96 44 0.25
97 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (91 bp):
GGCATACTTTTTATCTCTCAAAGTGATGGTATTTAAGTCTAATAGCTTCCATTGCCCTACTCTAA
ATCCTCAAACCCATTTGATTGAAATT
Found at i:15908587 original size:95 final size:94
Alignment explanation
Indices: 15908407--15908598 Score: 267
Period size: 95 Copynumber: 2.0 Consensus size: 94
15908397 ATGAAGTAAG
* * *
15908407 AAGGCAAGGTTAGATCGAGTTACAGTCTAGTAAGGCAATTCTAAGCTAACTAAAACAAGTTTGAA
1 AAGGCAAGGTTAGATCGAGTTACAGTATAATAAGGCAACTCTAAGCTAACTAAAACAAGTTTGAA
* * * *
15908472 AAGTTGAATTTTTTAGATTTTCAAGCTTC
66 AACTTGAACTTTTCAGATTTTAAAGCTTC
* * *
15908501 AAGGCAAGGTTGGATCGAGTTTTCAGTATAATAAGGCAACTCTAAGCTAACTAAAACAAGTTTGG
1 AAGGCAAGGTTAGATCGAG-TTACAGTATAATAAGGCAACTCTAAGCTAACTAAAACAAGTTTGA
* *
15908566 AAACTTGAGCTTTTCATATTTTAAAGCTTC
65 AAACTTGAACTTTTCAGATTTTAAAGCTTC
15908596 AAG
1 AAG
15908599 AGTCAAGTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
94 18 0.21
95 67 0.79
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (94 bp):
AAGGCAAGGTTAGATCGAGTTACAGTATAATAAGGCAACTCTAAGCTAACTAAAACAAGTTTGAA
AACTTGAACTTTTCAGATTTTAAAGCTTC
Found at i:15910699 original size:2 final size:2
Alignment explanation
Indices: 15910692--15910721 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15910682 CTTGATTAGC
15910692 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
15910722 TACTTAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15914243 original size:104 final size:104
Alignment explanation
Indices: 15914062--15914270 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 104
15914052 AAAAACAAAC
* * * *
15914062 ACAACTCTATTCAAAGCACCACATAGGGTCTAGGTAACTCTTATATACCATTAAACCTTTTCAGA
1 ACAACTCTATTCAAAGCACCAAATAGGGTCCAAGTAACTCTTATATACAATTAAACCTTTTCAGA
* *
15914127 TGTGATCTATCGTTTCAAATCTTCAACGTTAGCATCACA
66 TGTGATCCATCGTTTCAAATCTACAACGTTAGCATCACA
** *
15914166 ACAACTCTATTCAAAGTGCCAAATAGGGTCCAAGTAACTCTTATGTACAATTAAACCTTTTCAGA
1 ACAACTCTATTCAAAGCACCAAATAGGGTCCAAGTAACTCTTATATACAATTAAACCTTTTCAGA
15914231 TGTGATCCATCGTTTCAAATCTACAACGTTAGCATCACA
66 TGTGATCCATCGTTTCAAATCTACAACGTTAGCATCACA
15914270 A
1 A
15914271 TTGACCCATG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (104 bp):
ACAACTCTATTCAAAGCACCAAATAGGGTCCAAGTAACTCTTATATACAATTAAACCTTTTCAGA
TGTGATCCATCGTTTCAAATCTACAACGTTAGCATCACA
Found at i:15920155 original size:12 final size:13
Alignment explanation
Indices: 15920135--15920232 Score: 71
Period size: 12 Copynumber: 7.5 Consensus size: 13
15920125 ACCTTCCTTC
*
15920135 CTTTCTCTTT-TT
1 CTTTTTCTTTCTT
15920147 CTTTTTCTTTCTT
1 CTTTTTCTTTCTT
15920160 CTTTCTTTCTTTCTT
1 C-TT-TTTCTTTCTT
*
15920175 -TCTTTCTTTCTT
1 CTTTTTCTTTCTT
15920187 CTTCTTCTCTTT-TT
1 CTT-TT-TCTTTCTT
*
15920201 -TCTTTCTTTCTT
1 CTTTTTCTTTCTT
*
15920213 CTCCTTTCTCTT-TT
1 CT-TTTTCT-TTCTT
15920227 CTTTTT
1 CTTTTT
15920233 GGTTATGGGC
Statistics
Matches: 71, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
11 5 0.07
12 23 0.32
13 10 0.14
14 16 0.23
15 17 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTTCTTTCTT
Found at i:15920159 original size:4 final size:4
Alignment explanation
Indices: 15920150--15920230 Score: 91
Period size: 4 Copynumber: 20.8 Consensus size: 4
15920140 TCTTTTTCTT
15920150 TTTC TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTTC -TTC -TTC TTCTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC
*
15920196 TTT- TTTC TTTC TTTC TTCTCC TTTC TCT- TTTC TTT
1 TTTC TTTC TTTC TTTC TT-T-C TTTC TTTC TTTC TTT
15920231 TTGGTTATGG
Statistics
Matches: 68, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
3 14 0.21
4 45 0.66
5 6 0.09
6 3 0.04
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:15920349 original size:20 final size:22
Alignment explanation
Indices: 15920324--15920365 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
15920314 CAAGGCCACA
15920324 TTCTTTTC-CATTA-TTTTCTT
1 TTCTTTTCTCATTACTTTTCTT
*
15920344 TTCTTTTCTCTTTACTTTTCTT
1 TTCTTTTCTCATTACTTTTCTT
15920366 GCATGGGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTTTCTCATTACTTTTCTT
Found at i:15924549 original size:17 final size:17
Alignment explanation
Indices: 15924524--15924556 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15924514 TCTGTAGGTA
15924524 TTTAATGAAAGAAGAAT
1 TTTAATGAAAGAAGAAT
*
15924541 TTTATTGAAAGAAGAA
1 TTTAATGAAAGAAGAA
15924557 GAGCAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (17 bp):
TTTAATGAAAGAAGAAT
Found at i:15925049 original size:17 final size:16
Alignment explanation
Indices: 15925019--15925052 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
15925009 GATTTTTCTA
*
15925019 TCTTTTTTTTTTAGTT
1 TCTTTTTTTCTTAGTT
15925035 TCTTATTTTTCTTAGTT
1 TCTT-TTTTTCTTAGTT
15925052 T
1 T
15925053 GATTTTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (16 bp):
TCTTTTTTTCTTAGTT
Found at i:15927465 original size:6 final size:6
Alignment explanation
Indices: 15927457--15927506 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
15927447 AGTTAGCCAT
* *
15927457 ATACAT ATACAT ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
15927505 AT
1 AT
15927507 TAACGAGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (6 bp):
ATACAC
Found at i:15938658 original size:28 final size:27
Alignment explanation
Indices: 15938622--15938674 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
15938612 ATATCCTGGT
*
15938622 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
15938649 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
15938675 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:15938744 original size:20 final size:20
Alignment explanation
Indices: 15938719--15938764 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
15938709 CTTCTAAACC
15938719 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
15938739 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
15938759 TCAAAT
1 TCAAAT
15938765 GGGGCGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:15941227 original size:5 final size:5
Alignment explanation
Indices: 15941217--15941241 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15941207 TGAAAGTGAT
15941217 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
15941242 TTTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:15942101 original size:2 final size:2
Alignment explanation
Indices: 15942094--15942142 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
15942084 GAAACGCTTG
* *
15942094 CT CT CT CT CT CT CT CT CT CT CT TT C- CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15942135 CT CT CT CT
1 CT CT CT CT
15942143 GTTTTGGCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:15942208 original size:2 final size:2
Alignment explanation
Indices: 15942201--15942248 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
15942191 GAGAAAATGN
*
15942201 CT CT CT CT CT CT CT CT CT CT CT -T C- CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15942241 CT CT CT CT
1 CT CT CT CT
15942249 GTTTTGGCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:15942249 original size:106 final size:106
Alignment explanation
Indices: 15942092--15942305 Score: 412
Period size: 106 Copynumber: 2.0 Consensus size: 106
15942082 AAGAAACGCT
15942092 TGCTCTCTCTCTCTCTCTCTCTCTTTCCTCTTTCTCTCTCTCTCTCTCTCTGTTTTGGCGTAAGC
1 TGCTCTCTCTCTCTCTCTCTCTCTTTCCTCTTTCTCTCTCTCTCTCTCTCTGTTTTGGCGTAAGC
15942157 AAATGGAGCAGAAAAGCTGACGCTATATTTTCTCGAGAAAA
66 AAATGGAGCAGAAAAGCTGACGCTATATTTTCTCGAGAAAA
15942198 TGNCTCTCTCTCTCTCTCTCTCTC-TTCCTCTTTCTCTCTCTCTCTCTCTCTGTTTTGGCGTAAG
1 TG-CTCTCTCTCTCTCTCTCTCTCTTTCCTCTTTCTCTCTCTCTCTCTCTCTGTTTTGGCGTAAG
15942262 CAAATGGAGCAGAAAAGCTGACGCTATATTTTCTCGAGAAAA
65 CAAATGGAGCAGAAAAGCTGACGCTATATTTTCTCGAGAAAA
15942304 TG
1 TG
15942306 AAAGAAAGGA
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
106 86 0.80
107 21 0.20
ACGTcount: A:0.18, C:0.29, G:0.14, T:0.38
Consensus pattern (106 bp):
TGCTCTCTCTCTCTCTCTCTCTCTTTCCTCTTTCTCTCTCTCTCTCTCTCTGTTTTGGCGTAAGC
AAATGGAGCAGAAAAGCTGACGCTATATTTTCTCGAGAAAA
Found at i:15949400 original size:3 final size:3
Alignment explanation
Indices: 15949392--15949446 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
15949382 CAGAGATCAA
* *
15949392 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15949440 AA- AAT AA
1 AAT AAT AA
15949447 AATTCCAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:15959625 original size:375 final size:375
Alignment explanation
Indices: 15958935--15960060 Score: 2164
Period size: 375 Copynumber: 3.0 Consensus size: 375
15958925 CTACAAACAC
*
15958935 TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGCGGAAGTAGGCCAGAACGTA
1 TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGTGGAAGTAGGCCAGAACGTA
15959000 TCAATTCATGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
66 TCAATTCATGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
15959065 TTTGACTGTATTACTTTCTTTCTGTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
131 TTTGACTGTATTACTTTCTTTCTGTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
15959130 AAGCTAAATCTGAACCCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCC-
196 AAGCTAAATCTGAA-CCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCCT
15959194 TTTCCTTCCTCTAAAGCCATAAACCATTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTAA
260 TTTCCTTCCTCTAAAGCCATAAACCATTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTAA
15959259 AACCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
325 AACCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
15959310 TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGTGGAAGTAGGCCAGAACGTA
1 TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGTGGAAGTAGGCCAGAACGTA
15959375 TCAATTCATGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
66 TCAATTCATGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
15959440 TTTGACTGTATTACTTTCTTTCTGTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
131 TTTGACTGTATTACTTTCTTTCTGTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
15959505 AAGCTAAATCTGAACCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCCTT
196 AAGCTAAATCTGAACCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCCTT
15959570 TTCCTTCCTCTAAAGCCATAAACCATTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTAAA
261 TTCCTTCCTCTAAAGCCATAAACCATTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTAAA
15959635 ACCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
326 ACCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
*
15959685 TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGTGGAAGTAGGCCAGAAAGTA
1 TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGTGGAAGTAGGCCAGAACGTA
*
15959750 TCAATTCAAGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
66 TCAATTCATGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
*
15959815 TTTGACTGTATTACTTTCTTTCTTTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
131 TTTGACTGTATTACTTTCTTTCTGTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
15959880 AAGCTAAATCTGAACCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCCTT
196 AAGCTAAATCTGAACCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCCTT
* * *
15959945 TTCCTTCCTCTTAAGCCATAAACCGTTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTGAA
261 TTCCTTCCTCTAAAGCCATAAACCATTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTAAA
*
15960010 GCCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
326 ACCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
15960060 T
1 T
15960061 ATAACTCTAT
Statistics
Matches: 742, Mismatches: 8, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
374 49 0.07
375 693 0.93
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (375 bp):
TCTCAACCATTAAGGAACTAGTAGAATGAGTGAGAAAAGGATCCGTGGAAGTAGGCCAGAACGTA
TCAATTCATGGTGGTTTGTTCTTACAGTATAATGAGAATGAAAGGATCAAATCAAACTGGTTACT
TTTGACTGTATTACTTTCTTTCTGTTTTGTACTTTTGTCTGTGCATCAAAAGACCTTCAATGAAG
AAGCTAAATCTGAACCTCTCATAAAATCTGCTGCCGGAATATCAGATGATGCCTGTTATATCCTT
TTCCTTCCTCTAAAGCCATAAACCATTTCTATCAAAACTATGATCTAGATTTGCAAAGTTCTAAA
ACCAGCTGACTCATCTAATTTTTTTTTCATTTCTTTCGTTACTATTTCAT
Found at i:15976111 original size:13 final size:13
Alignment explanation
Indices: 15976093--15976125 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
15976083 AAAGTTTAGC
15976093 CTTTATTGACAGT
1 CTTTATTGACAGT
*
15976106 CTTTATTGATAGT
1 CTTTATTGACAGT
15976119 CTTTATT
1 CTTTATT
15976126 CTTGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (13 bp):
CTTTATTGACAGT
Found at i:15978877 original size:22 final size:22
Alignment explanation
Indices: 15978842--15978923 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
15978832 ACTTAATCAC
15978842 TGCGTGACT-AGTTTTTAGGCAT
1 TGCGTGACTGA-TTTTTAGGCAT
* * *
15978864 TACGTGATTG-GTTTTAGGCAT
1 TGCGTGACTGATTTTTAGGCAT
* *
15978885 TGTGTGACTGATTTTTAGGAAT
1 TGCGTGACTGATTTTTAGGCAT
15978907 TGCGTGACTGATTTTTA
1 TGCGTGACTGATTTTTA
15978924 AGTAATGCCT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.35
22 32 0.65
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (22 bp):
TGCGTGACTGATTTTTAGGCAT
Found at i:15978961 original size:23 final size:23
Alignment explanation
Indices: 15978935--15979041 Score: 73
Period size: 23 Copynumber: 4.7 Consensus size: 23
15978925 GTAATGCCTA
*
15978935 AGTCACACAATGCTTTACTAACT
1 AGTCACACAATGCCTTACTAACT
*
15978958 AGTCACGCAATGCCTTACTAA-T
1 AGTCACACAATGCCTTACTAACT
*
15978980 -G--ACGCAATGCC-TA-TCAACT
1 AGTCACACAATGCCTTACT-AACT
* * *
15978999 AGTTACGCAATGCCTTATCAGAAACT
1 AGTCACACAATGCCTTA-C--TAACT
*
15979025 AGTCACGCAATGCCTTA
1 AGTCACACAATGCCTTA
15979042 TCAAAAACTA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 4 0.06
19 11 0.16
20 1 0.01
21 1 0.01
22 11 0.16
23 21 0.30
26 20 0.29
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (23 bp):
AGTCACACAATGCCTTACTAACT
Found at i:15978984 original size:19 final size:19
Alignment explanation
Indices: 15978962--15979015 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 19
15978952 CTAACTAGTC
15978962 ACGCAATGCCTTACTAATG
1 ACGCAATGCCTTACTAATG
* *
15978981 ACGCAATGCCTATCAACTAGTT
1 ACGCAATGCCT-T--ACTAATG
15979003 ACGCAATGCCTTA
1 ACGCAATGCCTTA
15979016 TCAGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 12 0.40
20 1 0.03
21 1 0.03
22 16 0.53
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (19 bp):
ACGCAATGCCTTACTAATG
Found at i:15979025 original size:26 final size:25
Alignment explanation
Indices: 15978954--15979207 Score: 190
Period size: 26 Copynumber: 10.8 Consensus size: 25
15978944 ATGCTTTACT
*
15978954 AACTAGTCACGCAATGCCTTA-C-T
1 AACTAGTCACGCAATGCCTTATCAA
15978977 AA-T-G--ACGCAATGCC-TATC--
1 AACTAGTCACGCAATGCCTTATCAA
*
15978995 AACTAGTTACGCAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCA-A
15979021 AACTAGTCACGCAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATC-AA
*
15979047 AACTAGTCACGCATTGCC----C-A
1 AACTAGTCACGCAATGCCTTATCAA
*
15979067 AAGTCAGTCACGCAATGCC-TATC--
1 AACT-AGTCACGCAATGCCTTATCAA
* *
15979090 AATTAGTCACGTAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCA-A
*
15979116 AACTAATCACGCAATGCC-TA--AA
1 AACTAGTCACGCAATGCCTTATCAA
** *
15979138 GTC-AGTCACGTAATGCCTTATCAGA
1 AACTAGTCACGCAATGCCTTATCA-A
*
15979163 AACTAGTCACACAATGCCTTATCAAA
1 AACTAGTCACGCAATGCCTTATC-AA
* *
15979189 AACTAGTTAAGCAATGCCT
1 AACTAGTCACGCAATGCCT
15979208 AAAGTCAGTC
Statistics
Matches: 187, Mismatches: 20, Indels: 45
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.02
19 12 0.06
20 5 0.03
21 26 0.14
22 29 0.16
23 14 0.07
24 2 0.01
25 4 0.02
26 89 0.48
27 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (25 bp):
AACTAGTCACGCAATGCCTTATCAA
Found at i:15979108 original size:69 final size:71
Alignment explanation
Indices: 15978981--15979218 Score: 293
Period size: 73 Copynumber: 3.3 Consensus size: 71
15978971 CTTACTAATG
* *
15978981 ACGCAATGCCTATCAACT-AGTTACGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTATCA
1 ACGCAATGCCTA--AAGTCAGTCACGCAATGCCTTATC--AAACTAGTCACGCAATGCCTTATCA
15979045 AAAACTAGTC
62 AAAACTAGTC
* * * * *
15979055 ACGCATTGCCCAAAGTCAGTCACGCAATGCC-TATC-AATTAGTCACGTAATGCCTTATCAGAAA
1 ACGCAATGCCTAAAGTCAGTCACGCAATGCCTTATCAAACTAGTCACGCAATGCCTTATCAAAAA
*
15979118 CTAATC
66 CTAGTC
* *
15979124 ACGCAATGCCTAAAGTCAGTCACGTAATGCCTTATCAGAAACTAGTCACACAATGCCTTATCAAA
1 ACGCAATGCCTAAAGTCAGTCACGCAATGCCTTATC--AAACTAGTCACGCAATGCCTTATCAAA
*
15979189 AACTAGTT
64 AACTAGTC
*
15979197 AAGCAATGCCTAAAGTCAGTCA
1 ACGCAATGCCTAAAGTCAGTCA
15979219 TACAATGTCC
Statistics
Matches: 141, Mismatches: 18, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
69 58 0.41
70 4 0.03
72 7 0.05
73 62 0.44
74 10 0.07
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (71 bp):
ACGCAATGCCTAAAGTCAGTCACGCAATGCCTTATCAAACTAGTCACGCAATGCCTTATCAAAAA
CTAGTC
Found at i:15979152 original size:21 final size:21
Alignment explanation
Indices: 15979051--15979155 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 21
15979041 ATCAAAAACT
* *
15979051 AGTCACGCATTGCCCA-AAGTC
1 AGTCACGCAATGCCTACAA-TC
*
15979072 AGTCACGCAATGCCTATCAATT
1 AGTCACGCAATGCCTA-CAATC
* *
15979094 AGTCACGTAATGCCTTATCAGAAAC
1 AGTCACGCAATGCC-TA-C--AATC
*
15979119 TAATCACGCAATGCCTA-AAGTC
1 -AGTCACGCAATGCCTACAA-TC
*
15979141 AGTCACGTAATGCCT
1 AGTCACGCAATGCCT
15979156 TATCAGAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
21 29 0.44
22 15 0.23
23 6 0.09
25 4 0.06
26 12 0.18
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (21 bp):
AGTCACGCAATGCCTACAATC
Found at i:15979154 original size:47 final size:47
Alignment explanation
Indices: 15979074--15979181 Score: 164
Period size: 47 Copynumber: 2.3 Consensus size: 47
15979064 CCAAAGTCAG
*
15979074 TCACGCAATGCCTATCAATTAGTCACGTAATGCCTTATCAGAAACTAA
1 TCACGCAATGCCTA-CAATCAGTCACGTAATGCCTTATCAGAAACTAA
*
15979122 TCACGCAATGCCTA-AAGTCAGTCACGTAATGCCTTATCAGAAACTAG
1 TCACGCAATGCCTACAA-TCAGTCACGTAATGCCTTATCAGAAACTAA
*
15979169 TCACACAATGCCT
1 TCACGCAATGCCT
15979182 TATCAAAAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.04
47 40 0.71
48 14 0.25
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (47 bp):
TCACGCAATGCCTACAATCAGTCACGTAATGCCTTATCAGAAACTAA
Found at i:15979172 original size:95 final size:93
Alignment explanation
Indices: 15978954--15979134 Score: 240
Period size: 95 Copynumber: 1.9 Consensus size: 93
15978944 ATGCTTTACT
** * * *
15978954 AACTAGTCACGCAATG-CCTTACT-AATGACGCAATGCCTATCAACTAGTTACGCAATGCCTTAT
1 AACTAGTCACGCAATGCCCAAACTCAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTAT
*
15979017 CAGAAACTAGTCACGCAATGCCTTATCAAA
66 CAGAAACTAATCACGCAATGCC-T-TCAAA
* * * *
15979047 AACTAGTCACGCATTGCCCAAAGTCAGTCACGCAATGCCTATCAATTAGTCACGTAATGCCTTAT
1 AACTAGTCACGCAATGCCCAAACTCAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTAT
15979112 CAGAAACTAATCACGCAATGCCT
66 CAGAAACTAATCACGCAATGCCT
15979135 AAAGTCAGTC
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
93 15 0.20
94 5 0.07
95 56 0.74
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (93 bp):
AACTAGTCACGCAATGCCCAAACTCAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTAT
CAGAAACTAATCACGCAATGCCTTCAAA
Found at i:15979232 original size:21 final size:21
Alignment explanation
Indices: 15979200--15979252 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
15979190 ACTAGTTAAG
15979200 CAATGCCTAAAGTCAGTCATA
1 CAATGCCTAAAGTCAGTCATA
* *
15979221 CAATGTCC-AAAGTTAGTCATG
1 CAATG-CCTAAAGTCAGTCATA
15979242 CAATGCCTAAA
1 CAATGCCTAAA
15979253 AACTAGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (21 bp):
CAATGCCTAAAGTCAGTCATA
Found at i:15979261 original size:22 final size:22
Alignment explanation
Indices: 15979186--15979263 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
15979176 ATGCCTTATC
* *
15979186 AAAAACTAGTTAAGCAATGCCT
1 AAAAACTAGTCATGCAATGCCT
** *
15979208 AAAGTC-AGTCATACAATGTCC-
1 AAAAACTAGTCATGCAATG-CCT
**
15979229 -AAAGTTAGTCATGCAATGCCT
1 AAAAACTAGTCATGCAATGCCT
15979250 AAAAACTAGTCATG
1 AAAAACTAGTCATG
15979264 TAATTCTCAA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
20 4 0.10
21 20 0.49
22 17 0.41
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (22 bp):
AAAAACTAGTCATGCAATGCCT
Found at i:15982764 original size:33 final size:33
Alignment explanation
Indices: 15982674--15982764 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 33
15982664 TTCGTTAATG
* * *
15982674 GCATTCACATCATCATTACCAACCCCAATAGCA
1 GCATCCACATCATCATCACCAACTCCAATAGCA
** *
15982707 ATATCCACATCATCACCACCAACTCCAATAGCA
1 GCATCCACATCATCATCACCAACTCCAATAGCA
*
15982740 GCATCCACATCATCATCACTAACTC
1 GCATCCACATCATCATCACCAACTC
15982765 TCGTAGCACC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.36, C:0.38, G:0.04, T:0.21
Consensus pattern (33 bp):
GCATCCACATCATCATCACCAACTCCAATAGCA
Found at i:15986505 original size:20 final size:20
Alignment explanation
Indices: 15986467--15986505 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15986457 AAAATTTTAG
* **
15986467 GGAAAAGCCTTTGGGAATTA
1 GGAAAAGACTTTGAAAATTA
15986487 GGAAAAGACTTTGAAAATT
1 GGAAAAGACTTTGAAAATT
15986506 GATTGTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (20 bp):
GGAAAAGACTTTGAAAATTA
Found at i:15986602 original size:22 final size:22
Alignment explanation
Indices: 15986577--15986628 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
15986567 GTAAAAATCT
15986577 AATTCTTTAAATTTTCTTATCA
1 AATTCTTTAAATTTTCTTATCA
15986599 AATTCTTTAAATTTTCTTATCA
1 AATTCTTTAAATTTTCTTATCA
15986621 AATTCTTT
1 AATTCTTT
15986629 TCTACCTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTCTTTAAATTTTCTTATCA
Found at i:15987482 original size:27 final size:28
Alignment explanation
Indices: 15987452--15987514 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
15987442 GCCCAGGAGT
*
15987452 GTTCCTAACAGGGAAGTGCCAAAGGG-A
1 GTTCCTAACAGGGAAATGCCAAAGGGCA
* * * *
15987479 GTTCTTAGCATGGAAATGCCTAAGGGCA
1 GTTCCTAACAGGGAAATGCCAAAGGGCA
15987507 -TTCCTAAC
1 GTTCCTAAC
15987515 GTGGAAGCAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (28 bp):
GTTCCTAACAGGGAAATGCCAAAGGGCA
Found at i:15987616 original size:13 final size:13
Alignment explanation
Indices: 15987594--15987669 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
15987584 GATAACAAAA
*
15987594 AAAAAGAATAAAT
1 AAAAATAATAAAT
15987607 AAAAATAATAAAT
1 AAAAATAATAAAT
15987620 ATAAAA-AATAAAT
1 A-AAAATAATAAAT
*
15987633 AAGAA-AA-AAAT
1 AAAAATAATAAAT
*
15987644 AAAAGT-A-AAAT
1 AAAAATAATAAAT
15987655 AATAAATATATAAAT
1 AA-AAATA-ATAAAT
15987670 TTGCAAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
11 14 0.27
12 8 0.15
13 21 0.40
14 5 0.10
15 4 0.08
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:15987623 original size:15 final size:15
Alignment explanation
Indices: 15987605--15987669 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
15987595 AAAAGAATAA
15987605 ATAAAAATAATAAAT
1 ATAAAAATAATAAAT
15987620 AT-AAAA-AATAAAT
1 ATAAAAATAATAAAT
*
15987633 A-AGAAAAAAATAAA-
1 ATA-AAAATAATAAAT
15987647 AGT-AAAATAATAAAT
1 A-TAAAAATAATAAAT
*
15987662 ATATAAAT
1 ATAAAAAT
15987670 TTGCAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 8 0.20
14 20 0.49
15 13 0.32
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
ATAAAAATAATAAAT
Found at i:15987658 original size:29 final size:27
Alignment explanation
Indices: 15987595--15987662 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 27
15987585 ATAACAAAAA
*
15987595 AAAAGAATAAAT-AAAAATAATAAATAT
1 AAAA-AATAAATAAAAAAAAATAAATAT
15987622 AAAAAATAAATAAGAAAAAAATAAA-AGT
1 AAAAAATAAATAA-AAAAAAATAAATA-T
15987650 AAAATAATAAATA
1 AAAA-AATAAATA
15987663 TATAAATTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 7 0.19
27 6 0.17
28 15 0.42
29 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.19
Consensus pattern (27 bp):
AAAAAATAAATAAAAAAAAATAAATAT
Found at i:15987667 original size:22 final size:22
Alignment explanation
Indices: 15987603--15987668 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
15987593 AAAAAAGAAT
15987603 AAATAAAAATAATAAATATA-AA
1 AAAT-AAAATAATAAATATATAA
* * *
15987625 AAAT-AAATAAGAAAAAAATAA
1 AAATAAAATAATAAATATATAA
*
15987646 AAGTAAAATAATAAATATATAA
1 AAATAAAATAATAAATATATAA
15987668 A
1 A
15987669 TTTGCAAACT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.31
21 5 0.14
22 19 0.54
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (22 bp):
AAATAAAATAATAAATATATAA
Found at i:15998318 original size:17 final size:18
Alignment explanation
Indices: 15998296--15998352 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 18
15998286 AAGTAATTAT
15998296 ATTAAAAATATATA-AAA
1 ATTAAAAATATATATAAA
15998313 ATTAAAAA-ATATATAAA
1 ATTAAAAATATATATAAA
15998330 ATTAAAAATA-ATTAATAAA
1 ATTAAAAATATA-T-ATAAA
15998349 ATTA
1 ATTA
15998353 TTTGTTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.14
17 20 0.56
18 2 0.06
19 9 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAAATATATATAAA
Found at i:15999819 original size:43 final size:43
Alignment explanation
Indices: 15999766--15999867 Score: 168
Period size: 43 Copynumber: 2.4 Consensus size: 43
15999756 TAACACTACA
* *
15999766 GATCATGGATATCAAGCATAATGATTTGAACTGTATCATTAAC
1 GATCAAGGATATCAAGCATAATGATTTGAACTATATCATTAAC
* *
15999809 GATTAAGGATATCAAGCATAATGATTTGAACTATATCATTATC
1 GATCAAGGATATCAAGCATAATGATTTGAACTATATCATTAAC
15999852 GATCAAGGATATCAAG
1 GATCAAGGATATCAAG
15999868 TATTATGCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (43 bp):
GATCAAGGATATCAAGCATAATGATTTGAACTATATCATTAAC
Found at i:15999844 original size:24 final size:24
Alignment explanation
Indices: 15999774--15999846 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
15999764 CAGATCATGG
15999774 ATATCAAGCATAATGATTTGAACT
1 ATATCAAGCATAATGATTTGAACT
* * * **
15999798 GTATC-A--TTAACGA-TT-AAGG
1 ATATCAAGCATAATGATTTGAACT
15999817 ATATCAAGCATAATGATTTGAACT
1 ATATCAAGCATAATGATTTGAACT
15999841 ATATCA
1 ATATCA
15999847 TTATCGATCA
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
19 6 0.18
20 3 0.09
21 5 0.15
22 5 0.15
23 3 0.09
24 12 0.35
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (24 bp):
ATATCAAGCATAATGATTTGAACT
Found at i:16002253 original size:43 final size:43
Alignment explanation
Indices: 16002178--16002271 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
16002168 ACGATATATT
* * * *
16002178 AAGGATATCAAACATTGTAATTGAATCTGTAGCACCTCAGATC
1 AAGGATATCAAACATTATAATTGAAACTGTAGCACCACAAATC
* *
16002221 AAGGATATCAAACATTATACTTGGAAAC-GTAGCAGCACAAATC
1 AAGGATATCAAACATTATAATT-GAAACTGTAGCACCACAAATC
16002264 AAGGATAT
1 AAGGATAT
16002272 AATTAAGCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (43 bp):
AAGGATATCAAACATTATAATTGAAACTGTAGCACCACAAATC
Found at i:16002838 original size:43 final size:43
Alignment explanation
Indices: 16002791--16002905 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
16002781 GTAGTACCCA
*
16002791 AGATCAAAGATATCAAGCATTAGGCTTGGAAGC-GTAACACTAG
1 AGATCAAAGATATCAAGCATTATGCTTGGAA-CTGTAACACTAG
** * * * * *
16002834 AGATCATTGATATCAAGCATAATGATTTGAACTGTATCACTAT
1 AGATCAAAGATATCAAGCATTATGCTTGGAACTGTAACACTAG
16002877 AGATC-AAGACTATCAAGCATTATGCTTGG
1 AGATCAAAGA-TATCAAGCATTATGCTTGG
16002906 TACCATAACA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
42 3 0.05
43 54 0.95
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (43 bp):
AGATCAAAGATATCAAGCATTATGCTTGGAACTGTAACACTAG
Found at i:16003014 original size:43 final size:43
Alignment explanation
Indices: 16002937--16003074 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 43
16002927 GGTGTCATCT
* * * *
16002937 ATTATGCTTGGAACTGTAGTA-TCCAAGATCAAGGATATCAAGC
1 ATTATGCTTGAAAGTGTAGCACTACAA-ATCAAGGATATCAAGC
* * *
16002980 ATTAGGCTTGAAAGTGTAGCACTACAAATTAAGGATATCAAAC
1 ATTATGCTTGAAAGTGTAGCACTACAAATCAAGGATATCAAGC
* * ** * * * *
16003023 ATAATGATTTTAATTGTATCACTATAAATCAAGGATATCAAGT
1 ATTATGCTTGAAAGTGTAGCACTACAAATCAAGGATATCAAGC
16003066 ATTATGCTT
1 ATTATGCTT
16003075 AGTACTATAA
Statistics
Matches: 74, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
43 70 0.95
44 4 0.05
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (43 bp):
ATTATGCTTGAAAGTGTAGCACTACAAATCAAGGATATCAAGC
Found at i:16003045 original size:171 final size:171
Alignment explanation
Indices: 16002760--16003094 Score: 456
Period size: 171 Copynumber: 2.0 Consensus size: 171
16002750 ATCAAAGATA
* * *
16002760 TCATCTATTATTCTTGGATCCGTAGTACCCAAGATCAAAGATATCAAGCATTAGGCTTGGAAGCG
1 TCATCTATTATGCTTGGAACCGTAGTACCCAAGATCAAAGATATCAAGCATTAGGCTTGAAAGCG
* * ** * *
16002825 TAACACTAGAGATCATTGATATCAAGCATAATGATTTGAACTGTATCACTATAGATCAA-GACTA
66 TAACACTACAAATCAAGGATATCAAACATAATGATTTGAACTGTATCACTATAAATCAAGGA-TA
* *
16002889 TCAAGCATTATGCTTGGTACCATAACACCTTATATTAAGGTG
130 TCAAGCATTATGCTTAGTACCATAACACCCTATATTAAGGTG
* * * *
16002931 TCATCTATTATGCTTGGAACTGTAGTATCCAAGATCAAGGATATCAAGCATTAGGCTTGAAAGTG
1 TCATCTATTATGCTTGGAACCGTAGTACCCAAGATCAAAGATATCAAGCATTAGGCTTGAAAGCG
* * * *
16002996 TAGCACTACAAATTAAGGATATCAAACATAATGATTTTAATTGTATCACTATAAATCAAGGATAT
66 TAACACTACAAATCAAGGATATCAAACATAATGATTTGAACTGTATCACTATAAATCAAGGATAT
* * *
16003061 CAAGTATTATGCTTAGTACTATAACGCCCTATAT
131 CAAGCATTATGCTTAGTACCATAACACCCTATAT
16003095 CAAATATATC
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
171 139 0.99
172 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (171 bp):
TCATCTATTATGCTTGGAACCGTAGTACCCAAGATCAAAGATATCAAGCATTAGGCTTGAAAGCG
TAACACTACAAATCAAGGATATCAAACATAATGATTTGAACTGTATCACTATAAATCAAGGATAT
CAAGCATTATGCTTAGTACCATAACACCCTATATTAAGGTG
Found at i:16004307 original size:18 final size:19
Alignment explanation
Indices: 16004284--16004326 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
16004274 AAAAATATTA
16004284 GAAAAAGA-AAGAACAACAT
1 GAAAAAGACAA-AACAACAT
16004303 GAAAAAGACAAAACAACAT
1 GAAAAAGACAAAACAACAT
*
16004322 TAAAA
1 GAAAA
16004327 CAAATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.70, C:0.12, G:0.12, T:0.07
Consensus pattern (19 bp):
GAAAAAGACAAAACAACAT
Found at i:16005375 original size:13 final size:12
Alignment explanation
Indices: 16005350--16005390 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
16005340 ATCCCATTTC
16005350 TTTTTTCTTCTT
1 TTTTTTCTTCTT
16005362 TTTTTTCTTCCTT
1 TTTTTTCTT-CTT
*
16005375 TTGTTTCTTTCTT
1 TTTTTTC-TTCTT
16005388 TTT
1 TTT
16005391 ATTTATCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 14 0.56
14 2 0.08
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:16021775 original size:21 final size:21
Alignment explanation
Indices: 16021751--16021792 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16021741 TAATAAATTA
*
16021751 TTAAAAAATAAATATTTTAAT
1 TTAAAAAATAAATATTATAAT
* *
16021772 TTAAAAATTAGATATTATAAT
1 TTAAAAAATAAATATTATAAT
16021793 AAAAGGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAAAATAAATATTATAAT
Found at i:16028691 original size:23 final size:23
Alignment explanation
Indices: 16028647--16028691 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
16028637 ATTAGATTAA
* *
16028647 TCAAATCTCTATTTAATTAATCT
1 TCAAATCTCTAATTAATCAATCT
* *
16028670 TCAATTCTCTAATTGATCAATC
1 TCAAATCTCTAATTAATCAATC
16028692 CATACTCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (23 bp):
TCAAATCTCTAATTAATCAATCT
Found at i:16032757 original size:29 final size:29
Alignment explanation
Indices: 16032725--16032810 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
16032715 ACATATTTAT
*
16032725 AATATCTACAATAGCTAAACAAGATATAC
1 AATATCTACAATAGCTAAGCAAGATATAC
* * *
16032754 AATATCCATAGTAGCTAAGCAAGATATAC
1 AATATCTACAATAGCTAAGCAAGATATAC
16032783 AATAT-T-CATAGTAGCTAAGCAAGATATA
1 AATATCTACA-A-TAGCTAAGCAAGATATA
16032811 TTACATATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 1 0.02
29 47 0.98
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.26
Consensus pattern (29 bp):
AATATCTACAATAGCTAAGCAAGATATAC
Found at i:16033369 original size:20 final size:20
Alignment explanation
Indices: 16033344--16033419 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
16033334 TAAATTTGCT
16033344 AAATATTAATATTTAACTTA
1 AAATATTAATATTTAACTTA
* *
16033364 AAATATTAA-A--AAAATTAAA
1 AAATATTAATATTTAACTT--A
*
16033383 AATATATTAATATTCAACTTA
1 AA-ATATTAATATTTAACTTA
16033404 AAATATTAATATTTAA
1 AAATATTAATATTTAA
16033420 ATTATTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 4 0.09
19 4 0.09
20 29 0.64
21 4 0.09
23 4 0.09
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATTAATATTTAACTTA
Found at i:16033636 original size:63 final size:64
Alignment explanation
Indices: 16033550--16033672 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 64
16033540 AATGATATGA
* * * *
16033550 TGAATACATATAAGTATAGGTTTTAAATATCTTACACAATTAAT-AATATTGATATTTTTACAG
1 TGAAAACACATAAATATAGGTTTTAAATATCTTACACAATTAATAAATATTAATATTTTTACAG
** * * **
16033613 TGAAAACACATAAATATAGGTTTTGGATGTGTTACACAATTGTTAAATATTAATATTTTT
1 TGAAAACACATAAATATAGGTTTTAAATATCTTACACAATTAATAAATATTAATATTTTT
16033673 CGTGTTATGG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
63 35 0.71
64 14 0.29
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (64 bp):
TGAAAACACATAAATATAGGTTTTAAATATCTTACACAATTAATAAATATTAATATTTTTACAG
Found at i:16043560 original size:15 final size:15
Alignment explanation
Indices: 16043542--16043588 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
16043532 TATTGTTTGA
*
16043542 AATCACATTAATTAT
1 AATCATATTAATTAT
*
16043557 AATCATATTACTTAT
1 AATCATATTAATTAT
16043572 AA-CATATTACATTAT
1 AATCATATTA-ATTAT
16043587 AA
1 AA
16043589 AATATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
AATCATATTAATTAT
Found at i:16043593 original size:15 final size:15
Alignment explanation
Indices: 16043548--16043595 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
16043538 TTGAAATCAC
16043548 ATTA-ATTATAATCAT
1 ATTACATTATAA-CAT
16043563 ATTAC-TTATAACAT
1 ATTACATTATAACAT
*
16043577 ATTACATTATAAAAT
1 ATTACATTATAACAT
16043592 ATTA
1 ATTA
16043596 AATAGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTACATTATAACAT
Found at i:16048283 original size:60 final size:58
Alignment explanation
Indices: 16048215--16048329 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 58
16048205 AGTTCAAAAT
16048215 AAGTTAAATGACCATATAGATTCAGAAAATTTCAAATATTAGAAAATTTTCTTTTTTAA
1 AAGTTAAATGACCATATAGATTCAGAAAATTTCAAATATTAGAAAA-TTTCTTTTTTAA
16048274 NAAGTTAAATGACCATATAGATTCAGAAAATTTCAAATATTAGAAAATTTCTTTTT
1 -AAGTTAAATGACCATATAGATTCAGAAAATTTCAAATATTAGAAAATTTCTTTTT
16048330 AATTTTTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 9 0.16
60 46 0.84
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (58 bp):
AAGTTAAATGACCATATAGATTCAGAAAATTTCAAATATTAGAAAATTTCTTTTTTAA
Found at i:16051046 original size:25 final size:25
Alignment explanation
Indices: 16051014--16051067 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
16051004 TCCATGTCTC
*
16051014 AAAAGCTTCTCTTTTA-AAGCACCCA
1 AAAAGCTTCTCTCTTATAA-CACCCA
16051039 AAAAGCTTCTCTCTTATAACACCCA
1 AAAAGCTTCTCTCTTATAACACCCA
16051064 AAAA
1 AAAA
16051068 TGTAAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.26
Consensus pattern (25 bp):
AAAAGCTTCTCTCTTATAACACCCA
Found at i:16053146 original size:85 final size:85
Alignment explanation
Indices: 16053051--16053209 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 85
16053041 ATGGTCTCAA
* * * * *
16053051 GTTGTTATATAGACGTTTTATTGGCTGAAT-AAATTTTTTTTCTTCTTTTATTTATTTTTTATGT
1 GTTGTCATATAGACATTTTATTGGCTAAATGAAA-GTGTTTTCTTCTTTTATTTATTTTTTATGT
*
16053115 ACTTTTTATTGAGTACTAGTT
65 ACCTTTTATTGAGTACTAGTT
*
16053136 GTTGTCATATAGACATTTTATTGGCTAAATGAAAGTGTTTTCTTCTTTTGTTTATTTTTTATGTA
1 GTTGTCATATAGACATTTTATTGGCTAAATGAAAGTGTTTTCTTCTTTTATTTATTTTTTATGTA
16053201 CCTTTTATT
66 CCTTTTATT
16053210 AACTTCTAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 63 0.95
86 3 0.05
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.57
Consensus pattern (85 bp):
GTTGTCATATAGACATTTTATTGGCTAAATGAAAGTGTTTTCTTCTTTTATTTATTTTTTATGTA
CCTTTTATTGAGTACTAGTT
Found at i:16061635 original size:13 final size:13
Alignment explanation
Indices: 16061619--16061650 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16061609 TTTTACGAAA
*
16061619 AAATTTTCGTTTG
1 AAATTTTCGTTGG
16061632 AAATTTTCGTTGG
1 AAATTTTCGTTGG
16061645 AAATTT
1 AAATTT
16061651 CCAACAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (13 bp):
AAATTTTCGTTGG
Found at i:16061829 original size:87 final size:87
Alignment explanation
Indices: 16061718--16061917 Score: 255
Period size: 87 Copynumber: 2.3 Consensus size: 87
16061708 TTCAATGGAA
* * * * * *
16061718 AATTTTCAACGAAAAAA-TTCCGTTGGAAATTTGTTGGAAAAATTATTGGCGAGCCAAAAAAGAG
1 AATTTCCAACGAAAAAATTTCCGTTGGAAATCTGTTGAAAAAATTATTGGCAAGCAAAAAAAGAC
* *
16061782 AGAAGACAACCAATTCTGACGG
66 AGAAGACAACCAATTCCGACAG
*
16061804 AATTTCCAACGAAAAAATTTCCGTTGGAAATCTGTTGAAAAAATTTTTGGCAAGCAAAAAAAGAC
1 AATTTCCAACGAAAAAATTTCCGTTGGAAATCTGTTGAAAAAATTATTGGCAAGCAAAAAAAGAC
* * *
16061869 AGGAGACCACCATTTCCGACAG
66 AGAAGACAACCAATTCCGACAG
*
16061891 AATTTCCAAC---AGAATTTCCGTTGGAAA
1 AATTTCCAACGAAAAAATTTCCGTTGGAAA
16061918 ATTCCAATGG
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
84 16 0.16
86 16 0.16
87 68 0.68
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (87 bp):
AATTTCCAACGAAAAAATTTCCGTTGGAAATCTGTTGAAAAAATTATTGGCAAGCAAAAAAAGAC
AGAAGACAACCAATTCCGACAG
Found at i:16061897 original size:12 final size:12
Alignment explanation
Indices: 16061880--16061910 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16061870 GGAGACCACC
16061880 ATTTCCGACAGA
1 ATTTCCGACAGA
*
16061892 ATTTCCAACAGA
1 ATTTCCGACAGA
16061904 ATTTCCG
1 ATTTCCG
16061911 TTGGAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (12 bp):
ATTTCCGACAGA
Found at i:16063216 original size:76 final size:76
Alignment explanation
Indices: 16063129--16063516 Score: 433
Period size: 76 Copynumber: 5.1 Consensus size: 76
16063119 ATAACTCAAA
* * * * * *
16063129 TGGAAATCCCTATCCACCTCGTGAGACACTTTCCCCAAATCTTTCAACCCACCTTCCCTTCTTCT
1 TGGAAATCCCTAGCCACCGCCTGAGTCACTTTCCCCAAATCTCTCAACCCGCCTTCCCTTCTTCT
16063194 GCCTACATTCG
66 GCCTACATTCG
* ** * *
16063205 TGGAAATCCCTAGCCACCGCACT-CGTCACGGTCCCCAAATCTGTCAACCCGCCTTCCCTTTTTC
1 TGGAAATCCCTAGCCACCGC-CTGAGTCACTTTCCCCAAATCTCTCAACCCGCCTTCCCTTCTTC
16063269 TG-CTGACATTCG
65 TGCCT-ACATTCG
* * ** *
16063281 TGGAAATCCCTAGCCACCACACT-CGTCACGGTCCCCAAATCTGTCAACCCGCCTTCCCTTCTTC
1 TGGAAATCCCTAGCCACCGC-CTGAGTCACTTTCCCCAAATCTCTCAACCCGCCTTCCCTTCTTC
* *
16063345 T-ACTAACAGTCG
65 TGCCT-ACATTCG
* * ** * *
16063357 TGGAAATCACTGGCCACCGTGTGAGTCACTTTCCCGAAATCTCTCAACCCGCCTTCCCTTTTTCT
1 TGGAAATCCCTAGCCACCGCCTGAGTCACTTTCCCCAAATCTCTCAACCCGCCTTCCCTTCTTCT
* *
16063422 GCCGACATTCA
66 GCCTACATTCG
* * *
16063433 TGAAAATCCCTAGCCACCGCATGAGTCACTTTCCCCAAATCTCTCAACCTGCCTTCCCTTCTTCT
1 TGGAAATCCCTAGCCACCGCCTGAGTCACTTTCCCCAAATCTCTCAACCCGCCTTCCCTTCTTCT
* *
16063498 GCCAACAGTCG
66 GCCTACATTCG
16063509 TGGAAATC
1 TGGAAATC
16063517 TCGTTACCGA
Statistics
Matches: 266, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
75 3 0.01
76 261 0.98
77 2 0.01
ACGTcount: A:0.21, C:0.38, G:0.13, T:0.27
Consensus pattern (76 bp):
TGGAAATCCCTAGCCACCGCCTGAGTCACTTTCCCCAAATCTCTCAACCCGCCTTCCCTTCTTCT
GCCTACATTCG
Found at i:16071943 original size:30 final size:30
Alignment explanation
Indices: 16071907--16071974 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
16071897 CTTGATTGAG
*
16071907 GATGAAGACGATGACATGCAAAGAGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
* *
16071937 GATGAAGAAGATGACATGGAAATAGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
*
16071967 AATGAAGA
1 GATGAAGA
16071975 TGACGATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.29, T:0.15
Consensus pattern (30 bp):
GATGAAGAAGATGACATGCAAAGAGATGAA
Found at i:16071984 original size:18 final size:18
Alignment explanation
Indices: 16071961--16071995 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16071951 CATGGAAATA
16071961 GATGAA-AATGAAGATGAC
1 GATGAAGAA-GAAGATGAC
16071979 GATGAAGAAGAAGATGA
1 GATGAAGAAGAAGATGA
16071996 ATTTGAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.51, C:0.03, G:0.31, T:0.14
Consensus pattern (18 bp):
GATGAAGAAGAAGATGAC
Found at i:16072734 original size:21 final size:20
Alignment explanation
Indices: 16072710--16072767 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
16072700 GTATGTTGTC
*
16072710 TTAAGATATTTCTAATATTTG
1 TTAAGAAATTT-TAATATTTG
16072731 TTAATGAAATTGTT-ATATTTG
1 TTAA-GAAATT-TTAATATTTG
16072752 TTAA-AAATTTTAATAT
1 TTAAGAAATTTTAATAT
16072768 ATAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 9 0.27
21 15 0.45
22 6 0.18
23 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (20 bp):
TTAAGAAATTTTAATATTTG
Found at i:16080841 original size:3 final size:3
Alignment explanation
Indices: 16080815--16080877 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
16080805 CAGTTTTGGT
* * *
16080815 TTA TT- TTA TTT TTA TTA TTT TTA TTA TTA TT- TTA CT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16080860 TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA T-TA TT
16080878 CTTTTCCCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:16081026 original size:16 final size:16
Alignment explanation
Indices: 16081007--16081063 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
16080997 TTTAGAATTT
16081007 TGTTAGTTTATTTACA
1 TGTTAGTTTATTTACA
* *
16081023 TGTTTTATTTGTGATTTGCA
1 TG--TTAGTT-T-ATTTACA
16081043 TTGTTAGTTTATTTACA
1 -TGTTAGTTTATTTACA
16081060 TGTT
1 TGTT
16081064 TTATTTGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 6 0.19
19 6 0.19
20 6 0.19
21 2 0.06
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (16 bp):
TGTTAGTTTATTTACA
Found at i:16081039 original size:20 final size:20
Alignment explanation
Indices: 16081016--16081085 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
16081006 TTGTTAGTTT
16081016 ATTTACATGTTTTATTTGTG
1 ATTTACATGTTTTATTTGTG
* * *
16081036 ATTTGCAT-TGTTAGTT-T-
1 ATTTACATGTTTTATTTGTG
16081053 ATTTACATGTTTTATTTGTG
1 ATTTACATGTTTTATTTGTG
*
16081073 ATTTGCATGTTTT
1 ATTTACATGTTTT
16081086 GTTGTGTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
19 7 0.17
20 19 0.47
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.60
Consensus pattern (20 bp):
ATTTACATGTTTTATTTGTG
Found at i:16081056 original size:37 final size:37
Alignment explanation
Indices: 16081006--16081080 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
16080996 GTTTAGAATT
16081006 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
1 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
16081043 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
1 TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
16081080 T
1 T
16081081 GTTTTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (37 bp):
TTGTTAGTTTATTTACATGTTTTATTTGTGATTTGCA
Found at i:16082447 original size:20 final size:20
Alignment explanation
Indices: 16082418--16082460 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16082408 ATTAGGTTAC
16082418 TTTTAAGTTAGTTATTTTAA
1 TTTTAAGTTAGTTATTTTAA
* * *
16082438 TTTTATGTTATTTCTTTTAA
1 TTTTAAGTTAGTTATTTTAA
16082458 TTT
1 TTT
16082461 GTTTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTAAGTTAGTTATTTTAA
Found at i:16087528 original size:21 final size:22
Alignment explanation
Indices: 16087474--16087530 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
16087464 TAATCACCGT
* *
16087474 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGATTTTAGGCATTAC
*
16087496 GTGA-TTGATTTTAGGCATTAC
1 GTGACTAGATTTTAGGCATTAC
*
16087517 GTGACTAGTTTTTA
1 GTGACTAGATTTTA
16087531 TATATTGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.46
Consensus pattern (22 bp):
GTGACTAGATTTTAGGCATTAC
Found at i:16087656 original size:26 final size:25
Alignment explanation
Indices: 16087564--16087835 Score: 198
Period size: 26 Copynumber: 11.2 Consensus size: 25
16087554 ACAATGCCTA
* *
16087564 AGTCACACAATGCCTTA-C-GAACT
1 AGTCACGCAATGCCTTATCAAAACT
* * *
16087587 AGTCATG-AATGCCTTA-C-TAACA
1 AGTCACGCAATGCCTTATCAAAACT
*
16087609 AGTCATGCAATGCC-TATC--AACT
1 AGTCACGCAATGCCTTATCAAAACT
*
16087631 AGTCATGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
*
16087657 AGTCACGCAATACCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
16087683 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
* * *
16087709 AGTCAAGCAATACCTTATAAAAAACT
1 AGTCACGCAATGCCTTAT-CAAAACT
* *
16087735 AGTCACGTAATGCC----C-AAAGT
1 AGTCACGCAATGCCTTATCAAAACT
*
16087755 CAGTCACGCAATGCC-TAT--TAACT
1 -AGTCACGCAATGCCTTATCAAAACT
* * *
16087778 AGTCAAGCATTGCTTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
* *
16087804 AGTCACTCAATGCCTTATTAAAAACT
1 AGTCACGCAATGCCTTA-TCAAAACT
16087830 AGTCAC
1 AGTCAC
16087836 ATAATTCTCA
Statistics
Matches: 203, Mismatches: 28, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
20 4 0.02
21 13 0.06
22 50 0.25
23 22 0.11
25 1 0.00
26 109 0.54
27 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (25 bp):
AGTCACGCAATGCCTTATCAAAACT
Found at i:16087693 original size:52 final size:51
Alignment explanation
Indices: 16087627--16087835 Score: 220
Period size: 52 Copynumber: 4.2 Consensus size: 51
16087617 AATGCCTATC
*
16087627 AACTAGTCATGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTATCAAA
1 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTAT-AAA
*
16087679 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCAAGCAATACCTTATAAAA
1 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTAT-AAA
* * * *
16087731 AACTAGTCACGTAATGCC----C--AAAGTCAGTCACGCAATGCC-TAT--T
1 AACTAGTCACGCAATGCCTTATCAGAAACT-AGTCACGCAATACCTTATAAA
* * * * *
16087774 AACTAGTCAAGCATTGCTTTATCAGAAACTAGTCACTCAATGCCTTATTAAA
1 AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTA-TAAA
16087826 AACTAGTCAC
1 AACTAGTCAC
16087836 ATAATTCTCA
Statistics
Matches: 130, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
43 14 0.11
46 7 0.05
47 13 0.10
48 14 0.11
49 6 0.05
50 1 0.01
52 75 0.58
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.25
Consensus pattern (51 bp):
AACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTATAAA
Found at i:16100039 original size:2 final size:2
Alignment explanation
Indices: 16100032--16100069 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16100022 ACAGTTGCAA
*
16100032 AG AG AG AG AA 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
16100070 TAAAGTACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16100045 original size:10 final size:10
Alignment explanation
Indices: 16100030--16100074 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
16100020 AAACAGTTGC
16100030 AAAGAGAGAG
1 AAAGAGAGAG
16100040 AAAGAGAGAG
1 AAAGAGAGAG
*
16100050 AGAGAGAGAG
1 AAAGAGAGAG
*
16100060 AGAGAGAGAG
1 AAAGAGAGAG
16100070 TAAAG
1 -AAAG
16100075 TACCATGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 29 0.91
11 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (10 bp):
AAAGAGAGAG
Found at i:16101325 original size:25 final size:25
Alignment explanation
Indices: 16101295--16101348 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
16101285 AATTAATAAT
*
16101295 ATTAATCTTCAT-GCAATAAATTAAC
1 ATTAATCTTCATAG-AATAAATAAAC
*
16101320 ATTAATCTTTATAGAATAAATAAAC
1 ATTAATCTTCATAGAATAAATAAAC
16101345 ATTA
1 ATTA
16101349 GTTTAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTAATCTTCATAGAATAAATAAAC
Found at i:16101767 original size:12 final size:12
Alignment explanation
Indices: 16101750--16101790 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
16101740 GACAAATCAA
* *
16101750 ATAAATTAAATT
1 ATAAATAAAACT
16101762 ATAAATAAAACT
1 ATAAATAAAACT
16101774 ATAAATAAAACT
1 ATAAATAAAACT
16101786 ATAAA
1 ATAAA
16101791 AAGAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAAATAAAACT
Found at i:16105308 original size:17 final size:17
Alignment explanation
Indices: 16105286--16105318 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16105276 AAGGAAGGGG
16105286 AAGAG-AAGAAAAGAGGA
1 AAGAGAAAG-AAAGAGGA
16105303 AAGAGAAAGAAAGAGG
1 AAGAGAAAGAAAGAGG
16105319 GAGCTGCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AAGAGAAAGAAAGAGGA
Found at i:16106110 original size:15 final size:14
Alignment explanation
Indices: 16106067--16106123 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
16106057 GTAAGACATC
16106067 AAAAAA-TATTTTT
1 AAAAAATTATTTTT
*
16106080 AAAATATTAAATTTTTT
1 AAAAAATT--A-TTTTT
16106097 AAAAAATTNATTTTT
1 AAAAAATT-ATTTTT
16106112 AAAAAATTATTT
1 AAAAAATTATTT
16106124 AAATTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 13 0.35
16 2 0.05
17 12 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAAAATTATTTTT
Found at i:16106166 original size:18 final size:18
Alignment explanation
Indices: 16106145--16106180 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16106135 TTATTGTATT
16106145 ATTTATAAAT-ATTTTTAA
1 ATTTA-AAATCATTTTTAA
16106163 ATTTAAAATCATTTTTAA
1 ATTTAAAATCATTTTTAA
16106181 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAATCATTTTTAA
Found at i:16113193 original size:3 final size:3
Alignment explanation
Indices: 16113185--16113253 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
16113175 CAAATGATTG
* *
16113185 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
16113233 CCA TTA ATA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
16113254 ATCTCCAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:16114015 original size:2 final size:2
Alignment explanation
Indices: 16114010--16114050 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16114000 TTTTTTTTNT
16114010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16114051 GTAAAAGGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16115149 original size:5 final size:5
Alignment explanation
Indices: 16115130--16115166 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
16115120 AATTAACCTT
*
16115130 TAATA TTATA T-ATA TAATA TAATA TAATA T-ATA TAAT
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
16115167 CCATTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
TAATA
Found at i:16115154 original size:19 final size:19
Alignment explanation
Indices: 16115130--16115166 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16115120 AATTAACCTT
*
16115130 TAATATTATATATATAATA
1 TAATATAATATATATAATA
16115149 TAATATAATATATATAAT
1 TAATATAATATATATAAT
16115167 CCATTTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATATAATATATATAATA
Found at i:16116459 original size:60 final size:60
Alignment explanation
Indices: 16116388--16116504 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
16116378 TCAGGTCGCT
** *
16116388 CTTTACCTACTCGTGGGAACTGCCCACACCACTTAATGTGAATCGGGGCTTCAAGTCTCC
1 CTTTACCTACTCGTGGGAACTGCCCACACCACCCAATATGAATCGGGGCTTCAAGTCTCC
* *
16116448 CTTTACCTACTCGTGGGAACTGCCCACGCCACCCAATATGAATTGGGGCTTCAAGTC
1 CTTTACCTACTCGTGGGAACTGCCCACACCACCCAATATGAATCGGGGCTTCAAGTC
16116505 CCTCTTTTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (60 bp):
CTTTACCTACTCGTGGGAACTGCCCACACCACCCAATATGAATCGGGGCTTCAAGTCTCC
Found at i:16118341 original size:35 final size:35
Alignment explanation
Indices: 16118302--16118439 Score: 177
Period size: 35 Copynumber: 3.9 Consensus size: 35
16118292 TTAATTGTTT
*
16118302 AATTTAATCGATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * * *
16118337 AATTTAATTAATTAAGCCTAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
16118372 AATTTAATCAATTAGGCCAAATGACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
16118407 AAATTTAATTAATTAGGCCCAAAAACTTAATTA
1 -AATTTAATCAATTAGGCCCAATAACTTAATTA
16118440 TNNNNNNNNN
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 58 0.67
36 28 0.33
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:16118376 original size:70 final size:71
Alignment explanation
Indices: 16118302--16118439 Score: 206
Period size: 70 Copynumber: 2.0 Consensus size: 71
16118292 TTAATTGTTT
* * * * *
16118302 AATTTAATCGATTAGGCCCAATAACTTAATTAAAC-AATTTAATTAATTAAGCCTAACAATTTAA
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAAATTTAATTAATTAAGCCCAAAAACTTAA
16118366 TTAAAC
66 TTAAAC
* *
16118372 AATTTAATCAATTAGGCCAAATGACTTAATTAAACAAATTTAATTAATTAGGCCCAAAAACTTAA
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAAATTTAATTAATTAAGCCCAAAAACTTAA
16118437 TTA
66 TTA
16118440 TNNNNNNNNN
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
70 32 0.53
71 28 0.47
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (71 bp):
AATTTAATCAATTAGGCCAAATAACTTAATTAAACAAATTTAATTAATTAAGCCCAAAAACTTAA
TTAAAC
Found at i:16119069 original size:35 final size:35
Alignment explanation
Indices: 16119044--16119299 Score: 284
Period size: 35 Copynumber: 7.3 Consensus size: 35
16119034 TTAATTGTTT
*
16119044 AATTTAATCGATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * * *
16119079 AATTTAATTAATTAAGCCTAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
16119114 AATTTTAATCAATTAGGCCCAATGACTTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ***
16119150 AAATTTAATCAATTAGGCCAAATAACTTAATTATTT
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
16119186 AATTTAATTAATTAGGCCCAATGACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
16119221 AATTTAATTAATTAGGCCCAATGATTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
16119256 AATTTAATTAATTAGG--C-ACAACTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
16119288 AATTTTAATCAA
1 AA-TTTAATCAA
16119300 GTGCTTGAGA
Statistics
Matches: 189, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
32 14 0.07
33 9 0.05
35 109 0.58
36 55 0.29
37 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:16119133 original size:71 final size:70
Alignment explanation
Indices: 16119043--16119292 Score: 308
Period size: 71 Copynumber: 3.6 Consensus size: 70
16119033 CTTAATTGTT
* * * *
16119043 TAATTTAATCGATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCTAACAATTTAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGGCCAAATAATTTAA
16119108 TTAAA
66 TTAAA
* * * *
16119113 CAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTAATCAATTAGGCCAAATAACTT
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAATTAATTAGGCCAAATAATTT
**
16119178 AATTATT
64 AATTAAA
* * * *
16119185 TAATTTAATTAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCCAATGATTTAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGGCCAAATAATTTAA
16119250 TTAAA
66 TTAAA
* * *
16119255 TAATTTAATTAATTAGG--C-ACAACTTAATTAAATAATTT
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
16119293 TAATCAAGTG
Statistics
Matches: 157, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
67 17 0.11
68 1 0.01
70 47 0.30
71 63 0.40
72 29 0.18
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (70 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGGCCAAATAATTTAA
TTAAA
Found at i:16119187 original size:142 final size:138
Alignment explanation
Indices: 16119030--16119299 Score: 387
Period size: 142 Copynumber: 1.9 Consensus size: 138
16119020 GAAGCATAAT
* *
16119030 TAACTTAATTGTTTAATTTAATCGATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAG
1 TAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAG
* *
16119095 CCTAACAATTTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTAATC
66 CCCAACAATTTAATTAAACAA-TTTAATCAATTAGGCAC-A--ACTTAATTAAACAAATTTAATC
16119160 AATTAGGCCAAA
127 AATTAGGCCAAA
* * *
16119172 TAACTTAATTATTTAATTTAATTAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGG
1 TAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAG
** * * * *
16119237 CCCAATGATTTAATTAAATAATTTAATTAATTAGGCACAACTTAATTAAATAATTTTAATCAA
66 CCCAACAATTTAATTAAACAATTTAATCAATTAGGCACAACTTAATTAAACAAATTTAATCAA
16119300 GTGCTTGAGA
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
138 22 0.19
140 1 0.01
141 15 0.13
142 77 0.67
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (138 bp):
TAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAG
CCCAACAATTTAATTAAACAATTTAATCAATTAGGCACAACTTAATTAAACAAATTTAATCAATT
AGGCCAAA
Found at i:16125116 original size:60 final size:60
Alignment explanation
Indices: 16124952--16125126 Score: 203
Period size: 60 Copynumber: 3.0 Consensus size: 60
16124942 CATCATCACT
* * * * *
16124952 TACTTGTGGGAACTGCCTACGCCATC--ATATGAATTGGGGCTTCAGGTCCCCCTTTACC
1 TACTCGTGGGAACTACCTACGCCACCATATATAAATTAGGGCTTCAGGTCCCCCTTTACC
* * * **
16125010 TACTCGTAGGAACTACCTACACCACCATATATAAA-TCGAGATTTCAGGTCCCCCTTTACC
1 TACTCGTGGGAACTACCTACGCCACCATATATAAATTAG-GGCTTCAGGTCCCCCTTTACC
* * *
16125070 TACTCGTGGGAACTACCCACGCCACCATATATAAATTAGGGCTTCAGATCCCTCTTT
1 TACTCGTGGGAACTACCTACGCCACCATATATAAATTAGGGCTTCAGGTCCCCCTTT
16125127 TTAAATTAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
58 21 0.22
59 2 0.02
60 71 0.74
61 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (60 bp):
TACTCGTGGGAACTACCTACGCCACCATATATAAATTAGGGCTTCAGGTCCCCCTTTACC
Found at i:16126080 original size:35 final size:35
Alignment explanation
Indices: 16126041--16126123 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
16126031 TCTCAAAACT
*
16126041 GGCAGCACAACCTTTCCTTTCTCCCTCACAAACCC
1 GGCAGCACAACCCTTCCTTTCTCCCTCACAAACCC
* *
16126076 GGCAGCACAACCCTTCTTTTTTCCCTCACAAACCC
1 GGCAGCACAACCCTTCCTTTCTCCCTCACAAACCC
* *
16126111 GACAGCAAAACCC
1 GGCAGCACAACCC
16126124 CTTATTTCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.27, C:0.43, G:0.10, T:0.20
Consensus pattern (35 bp):
GGCAGCACAACCCTTCCTTTCTCCCTCACAAACCC
Found at i:16126178 original size:35 final size:34
Alignment explanation
Indices: 16126058--16126180 Score: 117
Period size: 35 Copynumber: 3.5 Consensus size: 34
16126048 CAACCTTTCC
*
16126058 TTTCTCCCTCACAAACCCGGCAGC-ACAACCCTTCT
1 TTTCTCCCTCACAAACCCGACAGCAACAACCC-T-T
*
16126093 TTTTTCCCTCACAAACCCGACAGCAA-AACCCCTT
1 TTTCTCCCTCACAAACCCGACAGCAACAA-CCCTT
** * *
16126127 ATTTCTCTTTCTCAAA-CCAACAGCAACAACTCCTAT
1 -TTTCTCCCTCACAAACCCGACAGCAACAAC-CCT-T
16126163 TTTCTCCCTCACAAACCC
1 TTTCTCCCTCACAAACCC
16126181 TATAACACCA
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
34 11 0.15
35 53 0.75
36 7 0.10
ACGTcount: A:0.28, C:0.41, G:0.05, T:0.26
Consensus pattern (34 bp):
TTTCTCCCTCACAAACCCGACAGCAACAACCCTT
Found at i:16131199 original size:19 final size:19
Alignment explanation
Indices: 16131175--16131273 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
16131165 TGCCCGTGTG
16131175 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
16131194 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
16131213 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
16131232 CACGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
16131253 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
16131272 CA
1 CA
16131274 TGAGTCGGGT
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 3 0.05
19 33 0.59
20 9 0.16
21 11 0.20
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.21
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:16131213 original size:38 final size:40
Alignment explanation
Indices: 16131171--16131273 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 40
16131161 ATAGTGCCCG
*
16131171 TGTGCACGATGTGGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGATA
* *
16131209 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
16131249 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
16131274 TGAGTCGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 28 0.48
39 4 0.07
40 26 0.45
ACGTcount: A:0.19, C:0.17, G:0.42, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
Found at i:16142672 original size:24 final size:24
Alignment explanation
Indices: 16142622--16142673 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
16142612 AGATGACAGG
* **
16142622 AATTCTATGGAACCTAAAAGGCCA
1 AATTCTATGGAACATAAAAGGAAA
* *
16142646 AATTCTATGGGACATGAAAGGAAA
1 AATTCTATGGAACATAAAAGGAAA
16142670 AATT
1 AATT
16142674 TAGGAAGCCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (24 bp):
AATTCTATGGAACATAAAAGGAAA
Found at i:16145973 original size:2 final size:2
Alignment explanation
Indices: 16145961--16145990 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
16145951 TACCAACGAA
16145961 TG TG ATG 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 TG T
16145991 ATACATAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16154706 original size:27 final size:27
Alignment explanation
Indices: 16154674--16154805 Score: 135
Period size: 27 Copynumber: 5.0 Consensus size: 27
16154664 GGTGTTTTTG
*
16154674 CGCTTGGAACACCCCTGGGCACTTCCA
1 CGCTTGGAACACCCCTGGGCGCTTCCA
*
16154701 CACTTGGAACACCCCT-GGCGCTTCC-
1 CGCTTGGAACACCCCTGGGCGCTTCCA
* * ***
16154726 TGCTTGGAACAACCCTGGGTATTTCCA
1 CGCTTGGAACACCCCTGGGCGCTTCCA
* * * *
16154753 TG-TGTGGAACTCCCCTGGGTGCTTCCG
1 CGCT-TGGAACACCCCTGGGCGCTTCCA
16154780 CGCTTGGAACACCCCTGGGCGCTTCC
1 CGCTTGGAACACCCCTGGGCGCTTCC
16154806 GCGTTTATAA
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
25 13 0.15
26 15 0.18
27 56 0.66
28 1 0.01
ACGTcount: A:0.15, C:0.36, G:0.25, T:0.23
Consensus pattern (27 bp):
CGCTTGGAACACCCCTGGGCGCTTCCA
Found at i:16159462 original size:39 final size:40
Alignment explanation
Indices: 16159393--16159468 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
16159383 GTCGTGATGC
* *
16159393 TTTTTCTCTTGGGGGTGTTCTGAATACTACTTGCAATGGT
1 TTTTTCTCTTGGGGGTGTTCCGAATACTACTCGCAATGGT
* * *
16159433 TTTTTTTC-TGGGGGTGTTCCGGATTCTACTCGCAAT
1 TTTTTCTCTTGGGGGTGTTCCGAATACTACTCGCAAT
16159469 TCTTCCTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 24 0.77
40 7 0.23
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (40 bp):
TTTTTCTCTTGGGGGTGTTCCGAATACTACTCGCAATGGT
Found at i:16160300 original size:93 final size:95
Alignment explanation
Indices: 16160186--16160369 Score: 318
Period size: 93 Copynumber: 1.9 Consensus size: 95
16160176 CTGTGTGCGG
*
16160186 CTAAAAAGGGATTCTTAGCTTCTTATTGGGGAGAATAATCCTCAACCTAATAAGAAGGAGAATGA
1 CTAAAAAGGGATTCTTAGCTTCTTATTAGGGAGAATAATCCTCAACCTAATAAGAAGGAGAATGA
*
16160251 CATATTAC-GAGCGTTTAAAGCTGTACGAC
66 CATATTACAGAGCATTTAAAGCTGTACGAC
*
16160280 CTAAAAA-GGATTCTTAGCTTCTTATTAGGGAGAATAATCCTCAACCTAATAGGAAGGAGAATGA
1 CTAAAAAGGGATTCTTAGCTTCTTATTAGGGAGAATAATCCTCAACCTAATAAGAAGGAGAATGA
16160344 CATATTACATGAGCATTTAAAGCTGT
66 CATATTACA-GAGCATTTAAAGCTGT
16160370 GGCCTTTTTA
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
93 63 0.74
94 7 0.08
95 15 0.18
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (95 bp):
CTAAAAAGGGATTCTTAGCTTCTTATTAGGGAGAATAATCCTCAACCTAATAAGAAGGAGAATGA
CATATTACAGAGCATTTAAAGCTGTACGAC
Found at i:16160587 original size:14 final size:14
Alignment explanation
Indices: 16160568--16160594 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16160558 TACGGCTGAA
16160568 AATGAATTTACTTG
1 AATGAATTTACTTG
16160582 AATGAATTTACTT
1 AATGAATTTACTT
16160595 TAACATACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (14 bp):
AATGAATTTACTTG
Found at i:16162908 original size:27 final size:27
Alignment explanation
Indices: 16162870--16162986 Score: 103
Period size: 27 Copynumber: 4.3 Consensus size: 27
16162860 GTGTTTTTGA
*
16162870 GCTTGGAACACCCTTGAGCGCTTTCGC
1 GCTTGGAACACCCTTGAGCGCTTCCGC
* * *
16162897 GCTTGGATCACCCCT-AGGCGCTTCCGT
1 GCTTGGAACACCCTTGA-GCGCTTCCGC
* * *
16162924 GCTTAGAACTCCCTTGGGCGCTTCCGC
1 GCTTGGAACACCCTTGAGCGCTTCCGC
* * *
16162951 TCTTGGAACACCCGT-AGGCACTTCCGC
1 GCTTGGAACACCCTTGA-GCGCTTCCGC
*
16162978 GCCTGGAAC
1 GCTTGGAAC
16162987 GCCTTCGGGT
Statistics
Matches: 69, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 68 0.99
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.24
Consensus pattern (27 bp):
GCTTGGAACACCCTTGAGCGCTTCCGC
Found at i:16162963 original size:54 final size:54
Alignment explanation
Indices: 16162870--16162976 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
16162860 GTGTTTTTGA
* * * *
16162870 GCTTGGAACACCCTTGAGCGCTTTCGCGCTTGGATCACCCCTAGGCGCTTCCGT
1 GCTTAGAACACCCTTGAGCGCTTCCGCGCTTGGAACACCCCTAGGCACTTCCGT
* * * *
16162924 GCTTAGAACTCCCTTGGGCGCTTCCGCTCTTGGAACACCCGTAGGCACTTCCG
1 GCTTAGAACACCCTTGAGCGCTTCCGCGCTTGGAACACCCCTAGGCACTTCCG
16162977 CGCCTGGAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.14, C:0.36, G:0.25, T:0.25
Consensus pattern (54 bp):
GCTTAGAACACCCTTGAGCGCTTCCGCGCTTGGAACACCCCTAGGCACTTCCGT
Found at i:16165169 original size:17 final size:17
Alignment explanation
Indices: 16165137--16165170 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16165127 GCGCTTTATT
*
16165137 TCTTCTTCCTTGTCTAG
1 TCTTCTTCCTTATCTAG
*
16165154 TCTTCTTCTTTATCTAG
1 TCTTCTTCCTTATCTAG
16165171 CCTCTTGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.26, G:0.09, T:0.56
Consensus pattern (17 bp):
TCTTCTTCCTTATCTAG
Found at i:16173820 original size:21 final size:22
Alignment explanation
Indices: 16173790--16173836 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
16173780 GGATATGTTC
16173790 ATGCAATTCATGACAAAGACTA
1 ATGCAATTCATGACAAAGACTA
*
16173812 ATGC-ATTCATGACAAAGACTG
1 ATGCAATTCATGACAAAGACTA
16173833 ATGC
1 ATGC
16173837 CTCCATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (22 bp):
ATGCAATTCATGACAAAGACTA
Found at i:16175323 original size:29 final size:30
Alignment explanation
Indices: 16175291--16175375 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 30
16175281 TTTTTTTTAA
*
16175291 ATTTAAAAAAAATTTCAAGAAAAATATAT-
1 ATTTAAAAAAAATTTCAAAAAAAATATATC
* * *
16175320 ATTTCAAAAAAA-TTCAAAAAAAAAATTTC
1 ATTTAAAAAAAATTTCAAAAAAAATATATC
* *
16175349 ATATCAAAAAATATTTCAAAAAAAATA
1 AT-TTAAAAAAAATTTCAAAAAAAATA
16175376 AAAAAAGTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 13 0.29
29 13 0.29
30 7 0.16
31 12 0.27
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.28
Consensus pattern (30 bp):
ATTTAAAAAAAATTTCAAAAAAAATATATC
Found at i:16175328 original size:28 final size:30
Alignment explanation
Indices: 16175296--16175375 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
16175286 TTTAAATTTA
* *
16175296 AAAAAAATTTCAAGAAAAATATAT-ATTTC
1 AAAAAAATTTCAAAAAAAATATATCATATC
* *
16175325 AAAAAAA-TTCAAAAAAAAAATTTCATATC
1 AAAAAAATTTCAAAAAAAATATATCATATC
16175354 AAAAAATATTTCAAAAAAAATA
1 AAAAAA-ATTTCAAAAAAAATA
16175376 AAAAAAGTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 13 0.30
29 17 0.40
30 1 0.02
31 12 0.28
ACGTcount: A:0.65, C:0.07, G:0.01, T:0.26
Consensus pattern (30 bp):
AAAAAAATTTCAAAAAAAATATATCATATC
Found at i:16175340 original size:41 final size:40
Alignment explanation
Indices: 16175295--16175381 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 40
16175285 TTTTAAATTT
*
16175295 AAAAAAAATTTCA-AGAAAAATATATATTTCAAAAAAATTCAA
1 AAAAAAAATTTCATAGAAAAA-A-ATATTTCAAAAAAAAT-AA
**
16175337 AAAAAAAATTTCATATCAAAAAATATTTCAAAAAAAATAA
1 AAAAAAAATTTCATAGAAAAAAATATTTCAAAAAAAATAA
16175377 AAAAA
1 AAAAA
16175382 GTGGTCAGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 7 0.17
41 15 0.37
42 14 0.34
43 5 0.12
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.24
Consensus pattern (40 bp):
AAAAAAAATTTCATAGAAAAAAATATTTCAAAAAAAATAA
Found at i:16175666 original size:8 final size:8
Alignment explanation
Indices: 16175648--16175700 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
16175638 TCATTTGGAC
*
16175648 TACCCATT
1 TACCCACT
*
16175656 TACCCCCT
1 TACCCACT
16175664 TACCCACT
1 TACCCACT
*
16175672 TACCTACT
1 TACCCACT
* *
16175680 AACCCATT
1 TACCCACT
16175688 TACCCA-T
1 TACCCACT
16175695 TACCCA
1 TACCCA
16175701 ACAAAAACTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
7 7 0.19
8 30 0.81
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.28
Consensus pattern (8 bp):
TACCCACT
Found at i:16175669 original size:16 final size:16
Alignment explanation
Indices: 16175648--16175700 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
16175638 TCATTTGGAC
*
16175648 TACCCATTTACCCCCT
1 TACCCATTTACCCACT
* *
16175664 TACCCACTTACCTACT
1 TACCCATTTACCCACT
*
16175680 AACCCATTTACCCA-T
1 TACCCATTTACCCACT
16175695 TACCCA
1 TACCCA
16175701 ACAAAAACTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 6 0.20
16 24 0.80
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.28
Consensus pattern (16 bp):
TACCCATTTACCCACT
Found at i:16180074 original size:17 final size:17
Alignment explanation
Indices: 16180048--16180082 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
16180038 AATCAACTGA
*
16180048 GAGACGGCTGGTTGTTG
1 GAGACAGCTGGTTGTTG
16180065 GAGACAGCTGGTTGTTG
1 GAGACAGCTGGTTGTTG
16180082 G
1 G
16180083 GTCAGTTGCA
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:0.11, G:0.46, T:0.29
Consensus pattern (17 bp):
GAGACAGCTGGTTGTTG
Found at i:16185192 original size:23 final size:23
Alignment explanation
Indices: 16185162--16185215 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
16185152 TACATATGCT
16185162 CATCATCATCATGCACACCATCC
1 CATCATCATCATGCACACCATCC
* *
16185185 CATCATCATCATGCACACCGTCT
1 CATCATCATCATGCACACCATCC
16185208 CATCATCA
1 CATCATCA
16185216 CCAGCTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.41, G:0.06, T:0.24
Consensus pattern (23 bp):
CATCATCATCATGCACACCATCC
Found at i:16185257 original size:43 final size:43
Alignment explanation
Indices: 16185210--16185341 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 43
16185200 CACCGTCTCA
** ***
16185210 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAACCAAG
* * *
16185253 TCATCACTGAG-TTATGCGTACTCCCTACTCGCACATAACCAAG
1 TCATCAC-CAGCTCATGCGCACTCCCTACTCGCACATAACCAAG
* * * *
16185296 TCATCATCGGC-CTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCACCAGCTC-ATGCGCACTCCCTACTCGCACATAACCAAG
16185339 TCA
1 TCA
16185342 ATATAATTAC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 1 0.01
43 68 0.96
44 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (43 bp):
TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAACCAAG
Done.