Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008624.1 Hibiscus syriacus cultivar Beakdansim tig00111587_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 642794
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:360297 original size:2 final size:2
Alignment explanation
Indices: 360292--360325 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
360282 GTATGTGTGG
360292 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
360326 GAAAGGTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:364442 original size:21 final size:21
Alignment explanation
Indices: 364416--364460 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
364406 TGATTTTGGG
* *
364416 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
364437 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
364458 CAA
1 CAA
364461 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:365332 original size:32 final size:32
Alignment explanation
Indices: 365291--365386 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
365281 GAGTCGAGGG
365291 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
365323 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * *
365354 TATACATATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
365386 T
1 T
365387 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
31 25 0.46
32 29 0.54
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:365377 original size:31 final size:31
Alignment explanation
Indices: 365297--365385 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
365287 AGGGTTTACC
* * *
365297 TATGTTCTACGGAACATATGGACAGTTTTACC
1 TATGTTCTAAGGAACATATGGACAG-TATACA
***
365329 TATG-TCTTTCGAGACATATGGACAGTATACA
1 TATGTTCTAAGGA-ACATATGGACAGTATACA
365360 TATGTTCTAAGGAACATATGGACAGT
1 TATGTTCTAAGGAACATATGGACAGT
365386 TACCGAGGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
31 26 0.55
32 21 0.45
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (31 bp):
TATGTTCTAAGGAACATATGGACAGTATACA
Found at i:365468 original size:29 final size:30
Alignment explanation
Indices: 365378--365469 Score: 152
Period size: 29 Copynumber: 3.1 Consensus size: 30
365368 AAGGAACATA
365378 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
365408 T-GACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* *
365437 TGGACAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
365466 TGGA
1 TGGA
365470 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
29 47 0.80
30 12 0.20
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:366742 original size:20 final size:20
Alignment explanation
Indices: 366717--366757 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
366707 AATTTTGGGT
366717 TGAAGAACTTAGTTGATTAC
1 TGAAGAACTTAGTTGATTAC
366737 TGAAGAACTTAGTTGATTAC
1 TGAAGAACTTAGTTGATTAC
366757 T
1 T
366758 ACCCGCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
TGAAGAACTTAGTTGATTAC
Found at i:367262 original size:14 final size:15
Alignment explanation
Indices: 367226--367263 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
367216 GAAATCATTG
367226 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
367241 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
367256 AAAAATTA
1 AAAAATTA
367264 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:367465 original size:21 final size:21
Alignment explanation
Indices: 367431--367493 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
367421 TTACGAAATT
*
367431 AAATT-CGCGTTGCGAATTTG
1 AAATTCCGCGCTGCGAATTTG
*
367451 AAATTCCGCGGTGCGAATTTG
1 AAATTCCGCGCTGCGAATTTG
367472 AAATTCCGCGCTGCGAATTTG
1 AAATTCCGCGCTGCGAATTTG
367493 A
1 A
367494 CTATCGCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 5 0.12
21 35 0.88
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (21 bp):
AAATTCCGCGCTGCGAATTTG
Found at i:367508 original size:20 final size:20
Alignment explanation
Indices: 367483--367535 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
367473 AATTCCGCGC
367483 TGCGAATTTGACTATCGCAT
1 TGCGAATTTGACTATCGCAT
* **
367503 TGCGAATTTGAGTATCGTGT
1 TGCGAATTTGACTATCGCAT
*
367523 TTCGAATTTGACT
1 TGCGAATTTGACT
367536 TATGTGTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (20 bp):
TGCGAATTTGACTATCGCAT
Found at i:367569 original size:20 final size:20
Alignment explanation
Indices: 367541--367607 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
367531 TGACTTATGT
* *
367541 GTTGTGATTTACAAATTCAC
1 GTTGCGATTTACAGATTCAC
**
367561 GTTGCGATTTACAGATTCGT
1 GTTGCGATTTACAGATTCAC
*
367581 GTTGCGATTTACAGATTCAG
1 GTTGCGATTTACAGATTCAC
367601 GTTGCGA
1 GTTGCGA
367608 ATTTGGAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCAC
Found at i:367628 original size:21 final size:21
Alignment explanation
Indices: 367604--367649 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
367594 GATTCAGGTT
367604 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
367625 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
367646 GCGA
1 GCGA
367650 TTTATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:367837 original size:13 final size:13
Alignment explanation
Indices: 367819--367845 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
367809 ATTCGGTACA
367819 CCTCAAAATGTAG
1 CCTCAAAATGTAG
367832 CCTCAAAATGTAG
1 CCTCAAAATGTAG
367845 C
1 C
367846 TTCTCTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (13 bp):
CCTCAAAATGTAG
Found at i:370771 original size:16 final size:16
Alignment explanation
Indices: 370750--370783 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
370740 CTAGTAGTTC
370750 GAAAAATCTCATAATT
1 GAAAAATCTCATAATT
*
370766 GAAAAATCTTATAATT
1 GAAAAATCTCATAATT
370782 GA
1 GA
370784 GCACCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (16 bp):
GAAAAATCTCATAATT
Found at i:372547 original size:20 final size:20
Alignment explanation
Indices: 372495--372535 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
372485 TATATTGAAC
372495 GTGTCGATACTTTAATATAA
1 GTGTCGATACTTTAATATAA
372515 GTGTCGATACTTTAATATAA
1 GTGTCGATACTTTAATATAA
372535 G
1 G
372536 GATCGACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (20 bp):
GTGTCGATACTTTAATATAA
Found at i:372691 original size:20 final size:20
Alignment explanation
Indices: 372639--372679 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
372629 TATATTGAAC
372639 GTGTCGATACTTTAATATAA
1 GTGTCGATACTTTAATATAA
372659 GTGTCGATACTTTAATATAA
1 GTGTCGATACTTTAATATAA
372679 G
1 G
372680 GATCGACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (20 bp):
GTGTCGATACTTTAATATAA
Found at i:372691 original size:144 final size:143
Alignment explanation
Indices: 372431--372718 Score: 567
Period size: 144 Copynumber: 2.0 Consensus size: 143
372421 TATAACATGT
372431 AAAAATATGATAAAACCGGTCACGAAAAGACAATACCGATAAAGCTCAACAGGATATATTGAACG
1 AAAAATATGATAAAACCGGTCACGAAAAGACAATACCGATAAAGCTCAACAGGATATATTGAACG
372496 TGTCGATACTTTAATATAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTTAAAA
66 TGTCGATACTTTAATATAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAA-TTTAAAA
372561 GATAAGCAGTTTTA
130 GATAAGCAGTTTTA
372575 AAAAATATGATAAAACCGGTCACGAAAAGACAATACCGATAAAGCTCAACAGGATATATTGAACG
1 AAAAATATGATAAAACCGGTCACGAAAAGACAATACCGATAAAGCTCAACAGGATATATTGAACG
372640 TGTCGATACTTTAATATAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAG
66 TGTCGATACTTTAATATAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAG
372705 ATAAGCAGTTTTA
131 ATAAGCAGTTTTA
372718 A
1 A
372719 CGTCTATAAA
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
143 22 0.15
144 122 0.85
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (143 bp):
AAAAATATGATAAAACCGGTCACGAAAAGACAATACCGATAAAGCTCAACAGGATATATTGAACG
TGTCGATACTTTAATATAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAG
ATAAGCAGTTTTA
Found at i:372979 original size:20 final size:19
Alignment explanation
Indices: 372956--373001 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
372946 CGATATAACA
372956 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
372976 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
372996 GATAAA
1 GGTAAA
373002 GCGCTACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:375240 original size:21 final size:21
Alignment explanation
Indices: 375216--375280 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
375206 AAGACAATCA
*
375216 AGAGTCAAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
375237 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
375258 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
375279 AG
1 AG
375281 GCATAATGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:376587 original size:4 final size:4
Alignment explanation
Indices: 376578--376610 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
376568 TAAGAGATTG
376578 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
376611 AAAGGACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:377802 original size:201 final size:200
Alignment explanation
Indices: 377449--378418 Score: 1471
Period size: 200 Copynumber: 4.8 Consensus size: 200
377439 AAAAATAAGT
* * * *
377449 AACCAT-ATGTGTCGAT-TCATATATAAAAAT-TATCGATCTCAGAAACATCGAAACCAATAAGT
1 AACCATAAAGTGTCGATCT-ATTTAT-AAAATGTATCGATCCCAGAAACATCGAAACCCATAAGT
* * * * *
377511 ATAATGTAATTGGTAATTTTTCAATATAACCGGTACAAATATACCGGTTTTATGAGAGAATAAGT
64 ATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAGGT
377576 CTACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCTAGAATGAATGCCAAAA
129 CTACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCTAGAATGAATGCC-AAA
* **
377641 AATGGGAA
193 AAGGGGGC
*
377649 AACCATAAAGTGTCGATCTATTTATAAAATGTATCGATCACAGAAACATCGAAACCCATAAGTAT
1 AACCATAAAGTGTCGATCTATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
* * * *
377714 AATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGATTTTACGAGAGAATAGGTCT
66 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAGGTCT
* *
377779 ACAACATATATCGACACTTTTTAATTTTGTTTCGATACTTTTGGTCTAGAATGAATGCCAAAAAG
131 ACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCTAGAATGAATGCCAAAAAG
377844 GGGGC
196 GGGGC
* * * *
377849 AACCATAAAATATCGATATATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
1 AACCATAAAGTGTCGATCTATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
* *
377914 AATGTAATATGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCT
66 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAGGTCT
* * *
377979 ACAACATGTATCGACACTTTTTAATTTTCTCTCGATACTTTTGGTCCAGGATGAATGCCAAAAAG
131 ACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCTAGAATGAATGCCAAAAA-
378044 GGGGGC
195 GGGGGC
* * * *
378050 AACCATAAAGTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCAAAACCCATAAGTAT
1 AACCATAAAGTGTCGATCTATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
* *
378115 AATGTAATTGGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTATGAGAGAATAGGTCT
66 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAGGTCT
* * *
378180 ACAACATGTATCGACACTTTTTAATTTTGTGTCAATATTTTTGGT-TCAGAATGAATGCCAAAAA
131 ACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCT-AGAATGAATGCCAAAAA
*
378244 GGGTGC
195 GGGGGC
*
378250 AACCATAAAGTGTCGATCCATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
1 AACCATAAAGTGTCGATCTATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
* * **
378315 AATGTAATAGGTAATTTTTCAATGTAATCGATATAAATTTACCGGTTTTATGAGAGAATAAATCT
66 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAGGTCT
*
378380 ACAACATGTATCGACACTTTTTAATTTTGTGTCGATACT
131 ACAACATGTATCGACACTTTTTAATTTTGTCTCGATACT
378419 AATTTAAATA
Statistics
Matches: 709, Mismatches: 56, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
200 364 0.51
201 344 0.49
202 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (200 bp):
AACCATAAAGTGTCGATCTATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTAT
AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAGGTCT
ACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCTAGAATGAATGCCAAAAAG
GGGGC
Found at i:377959 original size:401 final size:401
Alignment explanation
Indices: 377460--378418 Score: 1499
Period size: 401 Copynumber: 2.4 Consensus size: 401
377450 ACCATATGTG
* * * * *
377460 TCGATTCATATATAAAAATTATCGATCTCAGAAACATCGAAACCAATAAGTATAATGTAAT-TGG
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAT-G
* * *
377524 TAATTTTTCAATATAACCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTACAACATGTAT
65 TAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAAGTCTACAACATGTAT
* *
377589 CGACACTTTTTAATTTTGTCTCGATACTTTTGGTCTAGAATGAATGCCAAAAAATGGGAAAACCA
130 CGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAAGGGGAAAACCA
* * *
377654 TAAAGTGTCGATCTATTTATAAAATGTATCGATCACAGAAACATCGAAACCCATAAGTATAATGT
195 TAAAGTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCAAAACCCATAAGTATAATGT
*
377719 AATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGATTTTACGAGAGAATAGGTCTACAAC
260 AATAGGTAAATTTTCAATGTAACCGATATAAATATACCGATTTTACGAGAGAATAGGTCTACAAC
* *
377784 ATATATCGACACTTTTTAATTTTGTTTCGATACTTTTGG-TCTAGAATGAATGCCAAAAAGGGGG
325 ATATATCGACACTTTTTAATTTTGTGTCAATACTTTTGGTTC-AGAATGAATGCCAAAAAGGGGG
377848 CAACCATAAAATA
389 CAACCATAAAATA
*
377861 TCGATATATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATATGT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATATGT
* *
377926 AATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAACATGTATC
66 AATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAAGTCTACAACATGTATC
* * * **
377991 GACACTTTTTAATTTTCTCTCGATACTTTTGGTCCAGGATGAATGCCAAAAAGGGGGGCAACCAT
131 GACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAAGGGGAAAACCAT
* *
378056 AAAGTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCAAAACCCATAAGTATAATGTA
196 AAAGTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCAAAACCCATAAGTATAATGTA
* * * * *
378121 ATTGGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTATGAGAGAATAGGTCTACAACA
261 ATAGGTAAATTTTCAATGTAACCGATATAAATATACCGATTTTACGAGAGAATAGGTCTACAACA
* * *
378186 TGTATCGACACTTTTTAATTTTGTGTCAATATTTTTGGTTCAGAATGAATGCCAAAAAGGGTGCA
326 TATATCGACACTTTTTAATTTTGTGTCAATACTTTTGGTTCAGAATGAATGCCAAAAAGGGGGCA
* *
378251 ACCATAAAGTG
391 ACCATAAAATA
* * *
378262 TCGATCCATTTATAAAATGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATATGT
* * *
378327 AATTTTTCAATGTAATCGATATAAATTTACCGGTTTTATGAGAGAATAAATCTACAACATGTATC
66 AATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAAGTCTACAACATGTATC
*
378392 GACACTTTTTAATTTTGTGTCGATACT
131 GACACTTTTTAATTTTGTCTCGATACT
378419 AATTTAAATA
Statistics
Matches: 509, Mismatches: 47, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
401 506 0.99
402 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (401 bp):
TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATATGT
AATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTATGAGAGAATAAGTCTACAACATGTATC
GACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAAGGGGAAAACCAT
AAAGTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCAAAACCCATAAGTATAATGTA
ATAGGTAAATTTTCAATGTAACCGATATAAATATACCGATTTTACGAGAGAATAGGTCTACAACA
TATATCGACACTTTTTAATTTTGTGTCAATACTTTTGGTTCAGAATGAATGCCAAAAAGGGGGCA
ACCATAAAATA
Found at i:384541 original size:200 final size:196
Alignment explanation
Indices: 384186--384894 Score: 691
Period size: 200 Copynumber: 3.5 Consensus size: 196
384176 ACCTAAATAT
* * * *
384186 GTGTCGATACATTT-TCTACAAGTATCGA-CCCAAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCTC--AAAACATCGAAACCGATAATTATAATGTAA
* * *
384249 TATGTAAATTAACAATGTAACCGGTGTAAATATACCGGTTAATTA-GAAAACATA--TCAACATA
63 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTT--TTATGAAAA-ATAGGTC-ACATA
* * *
384311 ATGTATCGACACTTGTGGAATTTATGTCGATACTTATTGTCCAGGATGAATGCACAAACAAGGTG
124 ATGTATCGACACTTGT-AAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCACAAACAAGGTG
*
384376 CATGCATAAA
187 CAAGCATAAA
* *
384386 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAATATCGAAACCGATAATTATAATGTATTAG
1 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAACATCGAAACCGATAATTATAATGTAATAG
* * * *
384451 CTAAATTTACAATGTAACTGATATAAATATATCGGTTTTATGATAAAATAGGTCAGCATCAA-GT
66 GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-AAAATAGGTCA-CAT-AATGT
* *
384515 ATCGACACTTGCTAAATTTGTGTCGATACTTTTGGTCCATAATGAATGC-CAAA-AGGGGTGCAA
128 ATCGACACTTG-TAAATTTGTGTCGATACTTTT-GTCCAGAATGAATGCACAAACA-AGGTGCAA
*
384578 CCATAAA
190 GCATAAA
* * * * * *
384585 GTGTCGATATATTTATAAAAAGTATCGATCTCGTAATCATCGAAACCTATAAGTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCTC-AAAACATCGAAACCGATAATTATAATGTAATA
** ** * * *
384650 GGTAAATTTTTAATGTAACCGGTATAAATATACCAATTTTATGAGAGACTAGGTCTAAATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-AAAATAGGTC-ACATAATGT
* * * * * *
384715 ATCGACACTTTGTTAGTTTGTGTCGATACTTTTTTCCAGAATAAAATATGAATTCCTAAACCAGG
128 ATCGACAC-TTGTAAATTTGTGTCGATACTTTTGTCCAGAAT--GA-ATGCA---C-AAACAAGG
384780 TGCAAGCATAAA
185 TGCAAGCATAAA
* * * *
384792 GTGTCGATATATTTA--AAATTGTATCGATCTAAAAAACATCGAAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCT-CAAAACATCGAAACCGATAATTATAATGTAAT
* *
384855 AGGTAAATTTACAATGTTACCGGTATAAGTATACCGGTTT
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
384895 ACTTCGAAAA
Statistics
Matches: 421, Mismatches: 62, Indels: 46
0.80 0.12 0.09
Matches are distributed among these distances:
197 3 0.01
198 6 0.01
199 120 0.29
200 173 0.41
201 11 0.03
202 3 0.01
205 3 0.01
206 71 0.17
207 31 0.07
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (196 bp):
GTGTCGATACATTTATTAAAAGTATCGATCTCAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAATAGGTCACATAATGTATC
GACACTTGTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCACAAACAAGGTGCAAGCATAA
A
Found at i:385046 original size:23 final size:23
Alignment explanation
Indices: 384996--385040 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
384986 TGCCTATTTT
*
384996 ATTATATAAACGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
* *
385019 ATTATATAAGCTCTACCTAATA
1 ATTATATAAACGCTACCTAATA
385041 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:385058 original size:87 final size:87
Alignment explanation
Indices: 384912--385074 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
384902 AAATAGGTCA
* *
384912 ATATAAGCGCTACCTATTACATTATTTAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
384977 CCAGTTAAATGCCTATTTTATT
66 CCAGTTAAATGCCTATTTTATT
**
384999 ATATAAACGCTACCTATTACATTATATAAGCTCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
385064 TCGGTTAAATG
66 CCAGTTAAATG
385075 ATATAACATT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATGCCTATTTTATT
Found at i:385138 original size:20 final size:18
Alignment explanation
Indices: 385093--385140 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
385083 TTACCGATAA
385093 AATTTTTAACCGATCACT
1 AATTTTTAACCGATCACT
*
385111 --TATTTAACCGATCACAT
1 AATTTTTAACCGATCAC-T
385128 CAATTTTTAACCG
1 -AATTTTTAACCG
385141 TTGCACAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
20 9 0.38
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (18 bp):
AATTTTTAACCGATCACT
Found at i:387362 original size:2 final size:2
Alignment explanation
Indices: 387355--387396 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
387345 AAATAAATAA
387355 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
387397 TACATAAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:390041 original size:58 final size:60
Alignment explanation
Indices: 389953--390072 Score: 145
Period size: 58 Copynumber: 2.0 Consensus size: 60
389943 TAAATATTTT
* * * **
389953 AAATTCATCCCCAAACTATAATTTTCATTCTAAATCGGTTCTTAAAC-TTTGAAAATTCC
1 AAATTCATCCCCAAACTATAACTCTCATTCTAAATCGGTCCCCAAACTTTTGAAAATTCC
* * * *
390012 AAATTCAT-CCCTAACTATGACTCTCATTCTAAATTGGTCCCCAAACTTTTGAACATTCC
1 AAATTCATCCCCAAACTATAACTCTCATTCTAAATCGGTCCCCAAACTTTTGAAAATTCC
390071 AA
1 AA
390073 TATCTTCCCC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 30 0.59
59 21 0.41
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (60 bp):
AAATTCATCCCCAAACTATAACTCTCATTCTAAATCGGTCCCCAAACTTTTGAAAATTCC
Found at i:393914 original size:3 final size:3
Alignment explanation
Indices: 393893--393999 Score: 84
Period size: 3 Copynumber: 37.3 Consensus size: 3
393883 GAAATTCCCC
* * * **
393893 TAA TTA TAA T-A TGA TAA TAA TAA TAA -AA TAA -AA -AA TAA TGA TGG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
393937 TGA TAA T-A TAC T-A TAAA TAA TAAA TAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
393981 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
394000 TAGGGATTCA
Statistics
Matches: 87, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
2 13 0.15
3 69 0.79
4 5 0.06
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:394898 original size:40 final size:40
Alignment explanation
Indices: 394809--395018 Score: 162
Period size: 40 Copynumber: 5.1 Consensus size: 40
394799 ATTCGAACCC
* * *
394809 ACTTTTTATCTTTATAATTGAAGCCATTACTTTTTTTCAATCT
1 ACTTTTTATATTTATAATTGAGGCC-TTA-ATTTTTT-AATCT
*
394852 -CTTTTTTATATTTATACTTGAGGCCTTAATTTTTTAATCT
1 AC-TTTTTATATTTATAATTGAGGCCTTAATTTTTTAATCT
*
394892 ACTTTTTA-ACTTTATAATTGAGGCCTTAA-TTTTCAATCT
1 ACTTTTTATA-TTTATAATTGAGGCCTTAATTTTTTAATCT
* * * * *
394931 -CATTTTCTATCTTATAA-CGATGCCCATAATTTTTTAATCT
1 ACTTTTTATAT-TTATAATTGA-GGCCTTAATTTTTTAATCT
* * *
394971 CACTTTTAAT-TTTATAATTGAGCCCTTATGTTTTTTCAATCT
1 -ACTTTTTATATTTATAATTGAGGCCTTA-ATTTTTT-AATCT
395013 CACTTT
1 -ACTTT
395019 CTACCTTTAC
Statistics
Matches: 137, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
38 8 0.06
39 23 0.17
40 50 0.36
41 16 0.12
42 20 0.15
43 20 0.15
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (40 bp):
ACTTTTTATATTTATAATTGAGGCCTTAATTTTTTAATCT
Found at i:395230 original size:38 final size:39
Alignment explanation
Indices: 395181--395323 Score: 132
Period size: 38 Copynumber: 3.6 Consensus size: 39
395171 TCAATCTCTT
*
395181 TTTTATATTTATACTTGA-GCCTTAATTTTTTAATCCTA-
1 TTTTA-ATTTATAATTGAGGCCTTAATTTTTTAATCCTAC
* *
395219 TTTTAACTTTATAATTGAGGCCTTAA-TTTTTAATCTTAT
1 TTTTAA-TTTATAATTGAGGCCTTAATTTTTTAATCCTAC
* * * *
395258 TTTCTATCTTTATAATCGATGCCCATAATTTTTTAAT-CTCAC
1 TTT-TA-ATTTATAATTGA-GGCCTTAATTTTTTAATCCT-AC
*
395300 TTTTAATTTATAATTGAGCCCTTA
1 TTTTAATTTATAATTGAGGCCTTA
395324 TGTTTTTTCA
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
37 1 0.01
38 26 0.30
39 16 0.19
40 22 0.26
41 9 0.10
42 12 0.14
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (39 bp):
TTTTAATTTATAATTGAGGCCTTAATTTTTTAATCCTAC
Found at i:395249 original size:80 final size:85
Alignment explanation
Indices: 395139--395346 Score: 210
Period size: 80 Copynumber: 2.6 Consensus size: 85
395129 CGAACCCACT
* * * * *
395139 TTTTATCTTTA-AATTGAAGCCATTACTTTTTTTCAATCTCT-TTTT-TATATTTATACTTGA-G
1 TTTTAACTTTATAATTGAGGCC-TTAATTTTTTTCAATCTCTATTTTCTATATTTATAATCGATG
*
395200 -CCTTAATTTTTTAATC-CTA-
65 CCCATAATTTTTTAATCTC-AC
*
395219 TTTTAACTTTATAATTGAGGCCTTAA--TTTTT-AATCT-TATTTTCTATCTTTATAATCGATGC
1 TTTTAACTTTATAATTGAGGCCTTAATTTTTTTCAATCTCTATTTTCTATATTTATAATCGATGC
395280 CCATAATTTTTTAATCTCAC
66 CCATAATTTTTTAATCTCAC
* *
395300 TTTTAA-TTTATAATTGAGCCCTT-ATGTTTTTTCAATCTC-ACTTTCTA
1 TTTTAACTTTATAATTGAGGCCTTAAT-TTTTTTCAATCTCTATTTTCTA
395347 CCTTTACAGT
Statistics
Matches: 107, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
76 1 0.01
77 9 0.08
78 17 0.16
79 2 0.02
80 45 0.42
81 16 0.15
82 5 0.05
83 12 0.11
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (85 bp):
TTTTAACTTTATAATTGAGGCCTTAATTTTTTTCAATCTCTATTTTCTATATTTATAATCGATGC
CCATAATTTTTTAATCTCAC
Found at i:395293 original size:326 final size:326
Alignment explanation
Indices: 394698--395353 Score: 1164
Period size: 326 Copynumber: 2.0 Consensus size: 326
394688 CAGACCAGGC
*
394698 TACTAGGGGAGCGCCCTGAGCGATTGTGACCAGGCCCCATTTTCAACTTTTAATTATGTCTTTAA
1 TACTAGGGGAGCGCCCTGAGCGATTGTGACCAGGCCCCATTTTCAACTTATAATTATGTCTTTAA
394763 TTTTTTTTTTTGCCTTTATAATTGATATTTAATATTATTCGAACCCACTTTTTATCTTTATAATT
66 TTTTTTTTTTTGCCTTTATAATTGATATTTAATATTATTCGAACCCACTTTTTATCTTTATAATT
394828 GAAGCCATTACTTTTTTTCAATCTCTTTTTTATATTTATACTTGAGGCCTTAATTTTTTAATCTA
131 GAAGCCATTACTTTTTTTCAATCTCTTTTTTATATTTATACTTGAGGCCTTAATTTTTTAATCTA
394893 CTTTTTAACTTTATAATTGAGGCCTTAATTTTCAATCTCATTTTCTATCTTATAACGATGCCCAT
196 C-TTTTAACTTTATAATTGAGGCCTTAATTTTCAATCTCATTTTCTATCTTATAACGATGCCCAT
394958 AATTTTTTAATCTCACTTTTAATTTTATAATTGAGCCCTTATGTTTTTTCAATCTCACTTTCTAC
260 AATTTTTTAATCTCACTTTTAA-TTTATAATTGAGCCCTTATGTTTTTTCAATCTCACTTTCTAC
395023 CTT
324 CTT
395026 TACTAGGGGAGCGCCCTGAGCGATTGTGACCAGGCCCCTATTTTTC-ACTTAT-ATTATGTC-TT
1 TACTAGGGGAGCGCCCTGAGCGATTGTGACCAGGCCCC-A-TTTTCAACTTATAATTATGTCTTT
395088 AA-TTTTTTTTTTGCCTTTATAATTGATATTTTAATATTATTCGAACCCACTTTTTATCTTTA-A
64 AATTTTTTTTTTTGCCTTTATAATTGATA-TTTAATATTATTCGAACCCACTTTTTATCTTTATA
395151 ATTGAAGCCATTACTTTTTTTCAATCTCTTTTTTATATTTATACTTGA-GCCTTAATTTTTTAAT
128 ATTGAAGCCATTACTTTTTTTCAATCTCTTTTTTATATTTATACTTGAGGCCTTAATTTTTTAAT
* *
395215 CCTA-TTTTAACTTTATAATTGAGGCCTTAATTTTTAATCTTATTTTCTATCTTTATAATCGATG
193 -CTACTTTTAACTTTATAATTGAGGCCTTAATTTTCAATCTCATTTTCTATC-TTATAA-CGATG
395279 CCCATAATTTTTTAATCTCACTTTTAATTTATAATTGAGCCCTTATGTTTTTTCAATCTCACTTT
255 CCCATAATTTTTTAATCTCACTTTTAATTTATAATTGAGCCCTTATGTTTTTTCAATCTCACTTT
395344 CTACCTT
320 CTACCTT
395351 TAC
1 TAC
395354 AGTTGAGTCC
Statistics
Matches: 319, Mismatches: 3, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
324 45 0.14
325 70 0.22
326 110 0.34
327 37 0.12
328 46 0.14
329 6 0.02
330 5 0.02
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (326 bp):
TACTAGGGGAGCGCCCTGAGCGATTGTGACCAGGCCCCATTTTCAACTTATAATTATGTCTTTAA
TTTTTTTTTTTGCCTTTATAATTGATATTTAATATTATTCGAACCCACTTTTTATCTTTATAATT
GAAGCCATTACTTTTTTTCAATCTCTTTTTTATATTTATACTTGAGGCCTTAATTTTTTAATCTA
CTTTTAACTTTATAATTGAGGCCTTAATTTTCAATCTCATTTTCTATCTTATAACGATGCCCATA
ATTTTTTAATCTCACTTTTAATTTATAATTGAGCCCTTATGTTTTTTCAATCTCACTTTCTACCT
T
Found at i:395310 original size:40 final size:39
Alignment explanation
Indices: 395166--395343 Score: 157
Period size: 40 Copynumber: 4.4 Consensus size: 39
395156 AGCCATTACT
** *
395166 TTTTTTCAATCTCTTTTTTATATTTATACTTGAG-CCTTAA
1 TTTTTT-AATCTCACTTTTA-ATTTATAATTGAGCCCTTAA
*
395206 TTTTTTAATC-CTA-TTTTAACTTTATAATTGAGGCCTTAA
1 TTTTTTAATCTC-ACTTTTAA-TTTATAATTGAGCCCTTAA
* * * * *
395245 -TTTTTAATCTTATTTTCTATCTTTATAATCGATGCCCATAA
1 TTTTTTAATCTCACTTT-TA-ATTTATAATTGA-GCCCTTAA
*
395286 TTTTTTAATCTCACTTTTAATTTATAATTGAGCCCTTATG
1 TTTTTTAATCTCACTTTTAATTTATAATTGAGCCCTTA-A
395326 TTTTTTCAATCTCACTTT
1 TTTTTT-AATCTCACTTT
395344 CTACCTTTAC
Statistics
Matches: 114, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
37 1 0.01
38 27 0.24
39 19 0.17
40 34 0.30
41 19 0.17
42 14 0.12
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.54
Consensus pattern (39 bp):
TTTTTTAATCTCACTTTTAATTTATAATTGAGCCCTTAA
Found at i:395379 original size:44 final size:44
Alignment explanation
Indices: 395325--395429 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
395315 GAGCCCTTAT
* * **
395325 GTTTTTTCAATCTCACTTTCTACCTTTACAGTTGA-GTCCCCTGA
1 GTTTTTTCAATCTCAATTTCTACCTTTACAATTGAGGT-CCCAAA
*
395369 GTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGGTCCCAAA
1 GTTTTTTCAATCTCAATTTCTACCTTTACAATTGAGGTCCCAAA
395413 GTTTTTTC-ATCTCAATT
1 GTTTTTTCAATCTCAATT
395430 ATACTGAGGC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 9 0.16
44 44 0.80
45 2 0.04
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (44 bp):
GTTTTTTCAATCTCAATTTCTACCTTTACAATTGAGGTCCCAAA
Found at i:395882 original size:66 final size:69
Alignment explanation
Indices: 395805--395939 Score: 249
Period size: 66 Copynumber: 2.0 Consensus size: 69
395795 AAAATAAATA
395805 GACGACCGAATAAATAATTTACCCCAG-AAAAAACTATGAGCCA-C-CACCCTTTGTTAACGTGT
1 GACGACCGAATAAATAATTTACCCCAGAAAAAAACTATGAGCCACCACACCCTTTGTTAACGTGT
395867 CATC
66 CATC
395871 GACGACCGAATAAATAATTTACCCCAGAAAAAAACTATGAGCCACCACACCCTTTGTTAACGTGT
1 GACGACCGAATAAATAATTTACCCCAGAAAAAAACTATGAGCCACCACACCCTTTGTTAACGTGT
395936 CATC
66 CATC
395940 CTCAAACATC
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
66 27 0.41
67 16 0.24
68 1 0.02
69 22 0.33
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.22
Consensus pattern (69 bp):
GACGACCGAATAAATAATTTACCCCAGAAAAAAACTATGAGCCACCACACCCTTTGTTAACGTGT
CATC
Found at i:396349 original size:2 final size:2
Alignment explanation
Indices: 396342--396367 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
396332 GGATTGAAGG
396342 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
396368 TGACTCTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399264 original size:122 final size:120
Alignment explanation
Indices: 399011--399308 Score: 325
Period size: 122 Copynumber: 2.5 Consensus size: 120
399001 AGCGGTGTTT
* * * **
399011 TTTTA-ACAAACGCCGGTAAATACTCGT-CATTTAGTGGCGTTTTTATATAAACGCTGCTAAATA
1 TTTTATACAAACGCCGCTAAATACTCGTACA-TTAGTGGCATTTTTATACAAACGCCACTAAATA
* *
399074 CTATATCTTAGTGGAGTTTTTGTACAAACGCCGCAAACAATCGTACATTAGTGGAG
65 CTATATCTTAGTGGAGTTTTTGTACAAACGCCGCAAACAATCGTACTTTAGTGGTG
* * *
399130 TTTTAAGCACAAACGCCGCTAAATACTCGTACATTAGTGGCATTTTTGTACACACGCCACTAAAT
1 TTTT-A-TACAAACGCCGCTAAATACTCGTACATTAGTGGCATTTTTATACAAACGCCACTAAAT
* * * *
399195 ACTCATA-CTTTAGTGGAGTTTTTGTATAAACGCTGCTAAA-TATTGTACTTTAGTGGTG
64 ACT-ATATC-TTAGTGGAGTTTTTGTACAAACGCCGC-AAACAATCGTACTTTAGTGGTG
* * * * * *
399253 TTTGTATACAAACGCCGCCAAAGACTTGTACTTTAGTGGCGTTTCTATACAAACGC
1 TTT-TATACAAACGCCGCTAAATACTCGTACATTAGTGGCATTTTTATACAAACGC
399309 AAACACCACT
Statistics
Matches: 149, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
119 4 0.03
120 1 0.01
122 92 0.62
123 48 0.32
124 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (120 bp):
TTTTATACAAACGCCGCTAAATACTCGTACATTAGTGGCATTTTTATACAAACGCCACTAAATAC
TATATCTTAGTGGAGTTTTTGTACAAACGCCGCAAACAATCGTACTTTAGTGGTG
Found at i:399302 original size:41 final size:41
Alignment explanation
Indices: 399010--399457 Score: 347
Period size: 41 Copynumber: 10.9 Consensus size: 41
399000 TAGCGGTGTT
*
399010 TTTTTA-ACAAACGCCGGTAAATACTCGT-CATTTAGTGGCG
1 TTTTTATACAAACGCCGCTAAATACTCGTAC-TTTAGTGGCG
* * * *
399050 TTTTTATATAAACGCTGCTAAATACT-ATA-TCTTAGTGGAG
1 TTTTTATACAAACGCCGCTAAATACTCGTACT-TTAGTGGCG
* * * * *
399090 TTTTTGTACAAACGCCGC-AAACAATCGTACATTAGTGGAG
1 TTTTTATACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
* * * *
399130 TTTTAAGCACAAACGCCGCTAAATACTCGTACATTAGTGGCA
1 TTTTTA-TACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
* * * * *
399172 TTTTTGTACACACGCCACTAAATACTCATACTTTAGTGGAG
1 TTTTTATACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
* * * * *
399213 TTTTTGTATAAACGCTGCTAAATA-TTGTACTTTAGTGGTG
1 TTTTTATACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
* * * *
399253 TTTGTATACAAACGCCGCCAAAGACTTGTACTTTAGTGGCG
1 TTTTTATACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
* * *
399294 TTTCTATACAAACGCAAACACCACTAAAGACTCGTACTTTAGTGGCG
1 TTTTTATACAAACG------CCGCTAAATACTCGTACTTTAGTGGCG
* * * *
399341 TTTTAAGCACAAACGCCGCTAAATACGAC-TACTTTAGTGACG
1 TTTTTA-TACAAACGCCGCTAAATAC-TCGTACTTTAGTGGCG
* * * * *
399383 GTTTTATACAAATGCTGCCAAAGACTCGTACTTTAGTGGC-
1 TTTTTATACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
* * *
399423 TTTTTATATAATCGCCGCTAAATA-TTGTACTTTAG
1 TTTTTATACAAACGCCGCTAAATACTCGTACTTTAG
399458 ATTATCTTAT
Statistics
Matches: 321, Mismatches: 70, Indels: 35
0.75 0.16 0.08
Matches are distributed among these distances:
39 16 0.05
40 94 0.29
41 128 0.40
42 47 0.15
43 1 0.00
47 28 0.09
48 7 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (41 bp):
TTTTTATACAAACGCCGCTAAATACTCGTACTTTAGTGGCG
Found at i:401338 original size:19 final size:18
Alignment explanation
Indices: 401316--401383 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
401306 TTTATAGTAG
401316 ATAAATTTATAATAATTTT
1 ATAAATTT-TAATAATTTT
* *
401335 ATAATCTTTTAATAAATTTA
1 ATAA-ATTTTAAT-AATTTT
401355 ATAAGTATTTT-ATAATTTT
1 ATAA--ATTTTAATAATTTT
*
401374 TTAAATTTTA
1 ATAAATTTTA
401384 TTGACGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 5 0.12
19 16 0.40
20 14 0.35
21 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
ATAAATTTTAATAATTTT
Found at i:401368 original size:31 final size:30
Alignment explanation
Indices: 401316--401377 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
401306 TTTATAGTAG
401316 ATAAATTTATAATAATTTTATAATCTTTTA
1 ATAAATTTATAATAATTTTATAATCTTTTA
*
401346 ATAAATTTAATAAGT-ATTTTATAATTTTTTA
1 ATAAATTT-ATAA-TAATTTTATAATCTTTTA
401377 A
1 A
401378 ATTTTATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.28
31 20 0.69
32 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
ATAAATTTATAATAATTTTATAATCTTTTA
Found at i:401374 original size:9 final size:10
Alignment explanation
Indices: 401321--401384 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 10
401311 AGTAGATAAA
401321 TTTATAATAAT
1 TTTATAAT-AT
*
401332 TTTATAATCT
1 TTTATAATAT
401342 TTTAATAA-AT
1 TTT-ATAATAT
*
401352 TTAATAAGTAT
1 TTTATAA-TAT
401363 TTTATAAT-T
1 TTTATAATAT
401372 TTT-TAA-AT
1 TTTATAATAT
401380 TTTAT
1 TTTAT
401385 TGACGAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 7 0.16
9 9 0.20
10 8 0.18
11 20 0.45
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTATAATAT
Found at i:402140 original size:31 final size:30
Alignment explanation
Indices: 402093--402177 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 30
402083 TCAATAAAAT
*
402093 TTAAAAAATTAAAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
402124 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
402155 TCT-AAATACTATAAAATAATTAT
1 T-TAAAAAATTATAAAAT-ATTAT
402178 ATATTCGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 41 0.91
32 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:406381 original size:93 final size:93
Alignment explanation
Indices: 406222--406408 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
406212 CACAACAACG
406222 TCATTCACCATCAAACCGGGATTATATCTTAACAATCAATCTAACATTAATATTATAATTATTTG
1 TCATTCACCATCAAACCGGGATTATATCTTAACAATCAATCTAACATTAATATTATAATTATTTG
406287 TCAATTTGCAATTTCAATTAATCTTCAA
66 TCAATTTGCAATTTCAATTAATCTTCAA
406315 TCATTCACCATCAAACCGGGATTATATCTTAACAATCAATCTAACATTAATATTATAATTATTTG
1 TCATTCACCATCAAACCGGGATTATATCTTAACAATCAATCTAACATTAATATTATAATTATTTG
406380 TCAATTTGCAATTTCAATTAATCTTCAA
66 TCAATTTGCAATTTCAATTAATCTTCAA
406408 T
1 T
406409 AAGAAAATAC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (93 bp):
TCATTCACCATCAAACCGGGATTATATCTTAACAATCAATCTAACATTAATATTATAATTATTTG
TCAATTTGCAATTTCAATTAATCTTCAA
Found at i:406497 original size:37 final size:36
Alignment explanation
Indices: 406406--406584 Score: 288
Period size: 36 Copynumber: 4.9 Consensus size: 36
406396 ATTAATCTTC
* *
406406 AATAAG-AAAATACCCAAATTTGTTATGAAATCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
406441 ATTAAGAAAAATACCCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
406477 AATAAGAAAAAATACTCAAATTTCTTATGAAACCTTT
1 AATAAG-AAAAATACCCAAATTTCTTATGAAACCTTT
406514 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
*
406550 AATAAGAAAAAATACCCAAATTTCTTATAAAACCT
1 AATAAG-AAAAATACCCAAATTTCTTATGAAACCT
406585 AATTTGGTGA
Statistics
Matches: 134, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
35 5 0.04
36 67 0.50
37 62 0.46
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (36 bp):
AATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
Found at i:406497 original size:73 final size:73
Alignment explanation
Indices: 406412--406584 Score: 301
Period size: 73 Copynumber: 2.4 Consensus size: 73
406402 CTTCAATAAG
* * *
406412 AAAATACCCAAATTTGTTATGAAATCTTTATTAAGAAAAATACCCAAATTTCTTATGAAACCTTT
1 AAAATACCCAAATTTCTTATGAAACCTTTAATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
406477 AATAAGAA
66 AATAAGAA
*
406485 AAAATACTCAAATTTCTTATGAAACCTTTAATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
1 AAAATACCCAAATTTCTTATGAAACCTTTAATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
406550 AATAAGAA
66 AATAAGAA
*
406558 AAAATACCCAAATTTCTTATAAAACCT
1 AAAATACCCAAATTTCTTATGAAACCT
406585 AATTTGGTGA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 94 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (73 bp):
AAAATACCCAAATTTCTTATGAAACCTTTAATAAGAAAAATACCCAAATTTCTTATGAAACCTTT
AATAAGAA
Found at i:415865 original size:20 final size:22
Alignment explanation
Indices: 415824--415866 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
415814 ATTTCAGGGT
415824 ACAAGTATCGATAATGGGATGA
1 ACAAGTATCGATAATGGGATGA
*
415846 ACAA-TATCGAT-ATTGGATGA
1 ACAAGTATCGATAATGGGATGA
415866 A
1 A
415867 GTGGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (22 bp):
ACAAGTATCGATAATGGGATGA
Found at i:417412 original size:42 final size:43
Alignment explanation
Indices: 417329--417475 Score: 127
Period size: 42 Copynumber: 3.4 Consensus size: 43
417319 TAATTAACAA
* *
417329 CGTTTGTGGCAAAAAAAAGTACACTAAAAATAAGAGAATTAGTGG
1 CGTTTGTGGC--AAAAAAGTACACTAAAAACAAGAGAATTAGCGG
* * * *
417374 CGTTTGTGGCAAAAAAGT-CAGTAAAGACAGGATAATTAGCGG
1 CGTTTGTGGCAAAAAAGTACACTAAAAACAAGAGAATTAGCGG
* * * * * *
417416 CATTTGTGCCCAAAAAA-TACCATTAAAAATAACAGAATTAGTGG
1 CGTTTGTG-GCAAAAAAGTA-CACTAAAAACAAGAGAATTAGCGG
*
417460 CGTTTATGGCAAAAAA
1 CGTTTGTGGCAAAAAA
417476 TGCCACTATT
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 26 0.32
43 22 0.27
44 23 0.28
45 10 0.12
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (43 bp):
CGTTTGTGGCAAAAAAGTACACTAAAAACAAGAGAATTAGCGG
Found at i:417475 original size:44 final size:43
Alignment explanation
Indices: 417329--417475 Score: 143
Period size: 44 Copynumber: 3.4 Consensus size: 43
417319 TAATTAACAA
417329 CGTTTGTGGCAAAAAAAAGTACACTAAAAATAAGAGAATTAGTGG
1 CGTTTGTGGC-AAAAAAA-TACACTAAAAATAAGAGAATTAGTGG
* * * * * * *
417374 CGTTTGTGGCAAAAAAGT-CAGTAAAGACAGGATAATTAGCGG
1 CGTTTGTGGCAAAAAAATACACTAAAAATAAGAGAATTAGTGG
* * * * *
417416 CATTTGTGCCCAAAAAATACCATTAAAAATAACAGAATTAGTGG
1 CGTTTGTGGCAAAAAAATA-CACTAAAAATAAGAGAATTAGTGG
*
417460 CGTTTATGGCAAAAAA
1 CGTTTGTGGCAAAAAA
417476 TGCCACTATT
Statistics
Matches: 78, Mismatches: 22, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
42 32 0.41
43 1 0.01
44 35 0.45
45 10 0.13
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (43 bp):
CGTTTGTGGCAAAAAAATACACTAAAAATAAGAGAATTAGTGG
Found at i:423988 original size:3 final size:3
Alignment explanation
Indices: 423980--424065 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
423970 GGGTAATGTT
423980 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
424028 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
424066 GGGTAAAGTA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:424323 original size:35 final size:34
Alignment explanation
Indices: 424277--424389 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
424267 AAAACAATCC
*
424277 TCAATTTCATTCTAAACCATAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-TAAATTCCAAAATAAT
424312 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAA-CCTAAATTCCAAAATAAT
* * * *
424347 TCAATTACATTCTAAAACTCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCT-AAATTCCAAAATAAT
424382 TCAATTTC
1 TCAATTTC
424390 TGTCTTTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
34 2 0.03
35 66 0.94
36 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCTAAATTCCAAAATAAT
Found at i:425467 original size:35 final size:35
Alignment explanation
Indices: 425419--425530 Score: 172
Period size: 35 Copynumber: 3.2 Consensus size: 35
425409 ATTCCTCCTT
* *
425419 AAATTGAAATATTTTAGAATTT-GGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTAGGG-TTTAGAATG
*
425454 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
*
425489 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
425524 AAATTGA
1 AAATTGA
425531 GGAATGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 68 0.96
36 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
Found at i:426198 original size:15 final size:15
Alignment explanation
Indices: 426178--426234 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
426168 AACCGGGTAT
426178 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
426193 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
426210 TGGGTACCCGATTAC
1 CGGGTACCCGATTAC
*
426225 CGTGTACCCG
1 CGGGTACCCG
426235 TAACATCCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 19 0.58
16 4 0.12
17 10 0.30
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:427422 original size:15 final size:16
Alignment explanation
Indices: 427402--427431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
427392 AATATTTAGT
427402 ATATAA-TCAATAAAA
1 ATATAATTCAATAAAA
427417 ATATAATTCAATAAA
1 ATATAATTCAATAAA
427432 TGATAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAATTCAATAAAA
Found at i:427708 original size:22 final size:19
Alignment explanation
Indices: 427668--427711 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
427658 TTAATTTACG
*
427668 ATTATAATTGTAAAGTTTT
1 ATTATAATTCTAAAGTTTT
427687 ATTATAATTCTGAATAGCTTTT
1 ATTATAATTCT-AA-AG-TTTT
427709 ATT
1 ATT
427712 TTTAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 2 0.10
21 2 0.10
22 7 0.33
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (19 bp):
ATTATAATTCTAAAGTTTT
Found at i:429161 original size:26 final size:28
Alignment explanation
Indices: 429132--429189 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
429122 TAGATTTTCA
429132 TATAATTTAATTAAT-T-TTTT-ATTTTT
1 TATAATTTAA-TAATATGTTTTAATTTTT
429158 TAT-A-TTAATAATATGTTTTAATTTTT
1 TATAATTTAATAATATGTTTTAATTTTT
429184 TATAAT
1 TATAAT
429190 ATTAGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
23 4 0.15
24 5 0.19
25 5 0.19
26 12 0.44
27 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TATAATTTAATAATATGTTTTAATTTTT
Found at i:432440 original size:2 final size:2
Alignment explanation
Indices: 432433--432483 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
432423 ATTATATTTC
* * *
432433 AT AT AT AT AT AT AT AT AT AT AA AT AA AT AA 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
432475 AT AT AT AT A
1 AT AT AT AT A
432484 ATGCAAGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:433464 original size:25 final size:25
Alignment explanation
Indices: 433436--433495 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
433426 ATTTTTTACG
433436 ATTACTTTAAAATAATAA-TAT-TAAA
1 ATTA-TTTAAAATAA-AATTATATAAA
433461 ATTATATTGAAAATAAAATTATATAAA
1 ATTAT-TT-AAAATAAAATTATATAAA
433488 ATTATTTA
1 ATTATTTA
433496 GAGAATCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 1 0.03
25 9 0.29
26 12 0.39
27 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTTAAAATAAAATTATATAAA
Found at i:433675 original size:17 final size:17
Alignment explanation
Indices: 433643--433692 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
433633 CTCTAAATAA
433643 TTTTAATATAATTTTAT
1 TTTTAATATAATTTTAT
433660 TTTTCAATATAATTTATAT
1 TTTT-AATATAATTT-TAT
433679 ATTATTAA-ATAATT
1 -TT-TTAATATAATT
433693 GTAAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 9 0.31
20 4 0.14
21 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAATATAATTTTAT
Found at i:433808 original size:2 final size:2
Alignment explanation
Indices: 433801--433828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
433791 TAATAAATTG
433801 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
433829 GAAATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:438250 original size:7 final size:7
Alignment explanation
Indices: 438218--438264 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
438208 TCTTTACCAT
438218 CGCCGTC
1 CGCCGTC
*
438225 CGACGTC
1 CGCCGTC
*
438232 CGCCGAC
1 CGCCGTC
*
438239 AGCCGTC
1 CGCCGTC
438246 CGCCGTC
1 CGCCGTC
*
438253 CGCCGCC
1 CGCCGTC
438260 CGCCG
1 CGCCG
438265 CCCACCGCCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.06, C:0.55, G:0.30, T:0.09
Consensus pattern (7 bp):
CGCCGTC
Found at i:438264 original size:21 final size:21
Alignment explanation
Indices: 438218--438264 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
438208 TCTTTACCAT
438218 CGCCGTCCGACGTCCGCCGAC
1 CGCCGTCCGACGTCCGCCGAC
* * *
438239 AGCCGTCCGCCGTCCGCCGCC
1 CGCCGTCCGACGTCCGCCGAC
438260 CGCCG
1 CGCCG
438265 CCCACCGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.55, G:0.30, T:0.09
Consensus pattern (21 bp):
CGCCGTCCGACGTCCGCCGAC
Found at i:447178 original size:38 final size:38
Alignment explanation
Indices: 447135--447249 Score: 221
Period size: 38 Copynumber: 3.0 Consensus size: 38
447125 TGTGATTTTG
447135 TCTTTGTAAACCATTAAGTGAATCCTTCAAATTATTTA
1 TCTTTGTAAACCATTAAGTGAATCCTTCAAATTATTTA
*
447173 TCTTTGTAAATCATTAAGTGAATCCTTCAAATTATTTA
1 TCTTTGTAAACCATTAAGTGAATCCTTCAAATTATTTA
447211 TCTTTGTAAACCATTAAGTGAATCCTTCAAATTATTTA
1 TCTTTGTAAACCATTAAGTGAATCCTTCAAATTATTTA
447249 T
1 T
447250 TAATCCAGTA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (38 bp):
TCTTTGTAAACCATTAAGTGAATCCTTCAAATTATTTA
Found at i:447313 original size:51 final size:51
Alignment explanation
Indices: 447225--447828 Score: 545
Period size: 51 Copynumber: 11.9 Consensus size: 51
447215 TGTAAACCAT
* * * * * *
447225 TAAGTGAATCCT-TCAAATTATTTATTAATCCAGTATTGATTAAATACGTGC
1 TAAGTGAATCCTCT-AAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * *
447276 TAAGTGAATCCTCCAAAGTATTTGTAAACCCAATATTGATTAAACACGTGT
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * *** * * *
447327 TAAGTGAATCCTCCAAAGCAGAAGTCAGCCCAATACTGATTAGACACGTGC
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * * * *
447378 TAAATG-ATCCTCTAAAGTATTTATCAACTCAATATTGATTCAACATGTGT
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * * *
447428 TAAGTGAAT-TTTTAAAGTATTTATCAATCCATTATTGATTAAACACGTGC
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * * * * *
447478 TAAATAAATCCTCTAACGTATTCGTCAACCTAATACTGATTAAACATGTGC
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * * * *
447529 TAAAT-AATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGT
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * * *
447579 TAAGTGAATCTTCTAAAGTATTTGTCAACTCATTATTGATTAAACACATGG
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * *
447630 TAAGTG-ATCCTCTAAAGTATTTATCAACTCAATACTGATTAAACATGTGC
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * * * * *
447680 TAAGTGAATCCTCCAAAGTATTTCTCGACCCAATACTAATTGAACACGTAC
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * * *
447731 TAAGTGAATCCTCTAAAGTATTTGTCAACCTAATACTAATTAAACATGTGC
1 TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
* * ** * *
447782 TAAAT-AGATCCTATAAAGTATTTGTCAACTAAATACTAATTAAACAC
1 TAAGTGA-ATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACAC
447829 ATATTAAATA
Statistics
Matches: 450, Mismatches: 97, Indels: 12
0.81 0.17 0.02
Matches are distributed among these distances:
50 159 0.35
51 291 0.65
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (51 bp):
TAAGTGAATCCTCTAAAGTATTTGTCAACCCAATATTGATTAAACACGTGC
Found at i:447428 original size:101 final size:102
Alignment explanation
Indices: 447225--447828 Score: 567
Period size: 101 Copynumber: 6.0 Consensus size: 102
447215 TGTAAACCAT
* * * * * * *
447225 TAAGTGAATCCT-TCAAATTATTTATTAATCCAGTATTGATTAAATACGTGCTAAGTGAATCCTC
1 TAAGTGAATCCTCT-AAAGTATTTATCAACCCAATACTGATTAAACACGTGCTAAATGAATCCTC
* * * *
447289 CAAAGTATTTGTAAACCCAATATTGATTAAACACGTGT
65 TAAAGTATTTGTCAACTCAATATTGATTAAACACGTGC
* * ** * *
447327 TAAGTGAATCCTCCAAAGCA-GAAGTCAGCCCAATACTGATTAGACACGTGCTAAATG-ATCCTC
1 TAAGTGAATCCTCTAAAGTATTTA-TCAACCCAATACTGATTAAACACGTGCTAAATGAATCCTC
* * * *
447390 TAAAGTATTTATCAACTCAATATTGATTCAACATGTGT
65 TAAAGTATTTGTCAACTCAATATTGATTAAACACGTGC
* * * * * *
447428 TAAGTGAAT-TTTTAAAGTATTTATCAATCCATTATTGATTAAACACGTGCTAAATAAATCCTCT
1 TAAGTGAATCCTCTAAAGTATTTATCAACCCAATACTGATTAAACACGTGCTAAATGAATCCTCT
* * * *
447492 AACGTATTCGTCAAC-CTAATACTGATTAAACATGTGC
66 AAAGTATTTGTCAACTC-AATATTGATTAAACACGTGC
* * * * * * * *
447529 TAAAT-AATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCT
1 TAAGTGAATCCTCTAAAGTATTTATCAACCCAATACTGATTAAACACGTGCTAAATGAATCCTCT
* * *
447593 AAAGTATTTGTCAACTCATTATTGATTAAACACATGG
66 AAAGTATTTGTCAACTCAATATTGATTAAACACGTGC
* * * *
447630 TAAGTG-ATCCTCTAAAGTATTTATCAACTCAATACTGATTAAACATGTGCTAAGTGAATCCTCC
1 TAAGTGAATCCTCTAAAGTATTTATCAACCCAATACTGATTAAACACGTGCTAAATGAATCCTCT
* * * * * * *
447694 AAAGTATTTCTCGACCCAATACTAATTGAACACGTAC
66 AAAGTATTTGTCAACTCAATATTGATTAAACACGTGC
* * * * *
447731 TAAGTGAATCCTCTAAAGTATTTGTCAACCTAATACTAATTAAACATGTGCTAAAT-AGATCCTA
1 TAAGTGAATCCTCTAAAGTATTTATCAACCCAATACTGATTAAACACGTGCTAAATGA-ATCCTC
* * *
447795 TAAAGTATTTGTCAACTAAATACTAATTAAACAC
65 TAAAGTATTTGTCAACTCAATATTGATTAAACAC
447829 ATATTAAATA
Statistics
Matches: 406, Mismatches: 86, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
100 37 0.09
101 250 0.62
102 119 0.29
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (102 bp):
TAAGTGAATCCTCTAAAGTATTTATCAACCCAATACTGATTAAACACGTGCTAAATGAATCCTCT
AAAGTATTTGTCAACTCAATATTGATTAAACACGTGC
Found at i:447513 original size:151 final size:151
Alignment explanation
Indices: 447232--447828 Score: 608
Period size: 151 Copynumber: 3.9 Consensus size: 151
447222 CATTAAGTGA
* * * * * * * * *
447232 ATCCTTCAAATTATTTATTAA-TCCAGTATTGATTAAATACGTGCTAAGTGAATCCTCCAAAGTA
1 ATCCTCCAAAGTATTTATCAACT-CAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTA
* * * * * * *** * **
447296 TTTGTAAACCCAATATTGATTAAACACGTGTTAAGTGAATCCTCCAAAGCAGAAGTCAGCCCAAT
65 TTTGTCAA-CCAATATTGATTAAACACGTGCTAAATAAATCCTCTAAAGTATTTGTCAACTAAAT
*
447361 ACTGATTAGACACGTGCTAAATG
129 ACTGATTAAACACGTGCTAAATG
* * *
447384 ATCCTCTAAAGTATTTATCAACTCAATATTGATTCAACATGTGTTAAGTGAAT-TTTTAAAGTAT
1 ATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTAT
* * * *
447448 TTATCAATCCATTATTGATTAAACACGTGCTAAATAAATCCTCTAACGTATTCGTCAACCT-AAT
66 TTGTCAA-CCAATATTGATTAAACACGTGCTAAATAAATCCTCTAAAGTATTTGTCAA-CTAAAT
* *
447512 ACTGATTAAACATGTGCTAAATA
129 ACTGATTAAACACGTGCTAAATG
447535 ATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTAT
1 ATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTAT
* * * * * * *
447600 TTGTCAACTCATTATTGATTAAACACATGGTAAGT-GATCCTCTAAAGTATTTATCAACTCAATA
66 TTGTCAAC-CAATATTGATTAAACACGTGCTAAATAAATCCTCTAAAGTATTTGTCAACTAAATA
* *
447664 CTGATTAAACATGTGCTAAGTG
130 CTGATTAAACACGTGCTAAATG
* * * * * * ** *
447686 AATCCTCCAAAGTATTTCTCGACCCAATACTAATTGAACACGTACTAAGTGAATCCTCTAAAGTA
1 -ATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTA
* * * * *
447751 TTTGTCAACCTAATACTAATTAAACATGTGCTAAATAGATCCTATAAAGTATTTGTCAACTAAAT
65 TTTGTCAACC-AATATTGATTAAACACGTGCTAAATAAATCCTCTAAAGTATTTGTCAACTAAAT
*
447816 ACTAATTAAACAC
129 ACTGATTAAACAC
447829 ATATTAAATA
Statistics
Matches: 373, Mismatches: 64, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
150 2 0.01
151 170 0.46
152 164 0.44
153 37 0.10
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (151 bp):
ATCCTCCAAAGTATTTATCAACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTAT
TTGTCAACCAATATTGATTAAACACGTGCTAAATAAATCCTCTAAAGTATTTGTCAACTAAATAC
TGATTAAACACGTGCTAAATG
Found at i:447520 original size:202 final size:202
Alignment explanation
Indices: 447224--447905 Score: 669
Period size: 202 Copynumber: 3.4 Consensus size: 202
447214 TTGTAAACCA
* * * * *
447224 TTAAGTGAATCCTTCAAATTATTTATTAATCCAGTATTGATTAAATACGTGCTAAGTGAATCCTC
1 TTAAGTGAATCCTTTAAAGTATTTATCAATCCAATATTGATTAAACACGTGCTAAGTGAATCCTC
* * * * * **
447289 CAAAGTATTTGTAAACCCAATATTGATTAAACACGTGTTAAGTGAATCCTCCAAAGCAGAAGTCA
66 CAAAGTATTCGTCAACCCAATACTGATTAAACACGTGCTAAGTGAATCCTCCAAAGTATTAGTCA
* * *
447354 GCCCAATACTGATTAGACACGTGCTAAATGATCCTCTAAAGTATTTATCAACTCAATATTGATTC
131 ACCCAATACTGATTA-ACACGTGCTAAATGATCCTCTAAAGTATTTGTCAACTCAATATTGATTA
**
447419 AACATGTG
195 AACACATG
* * * *
447427 TTAAGTGAAT-TTTTAAAGTATTTATCAATCCATTATTGATTAAACACGTGCTAAATAAATCCTC
1 TTAAGTGAATCCTTTAAAGTATTTATCAATCCAATATTGATTAAACACGTGCTAAGTGAATCCTC
* * * * *
447491 TAACGTATTCGTCAACCTAATACTGATTAAACATGTGCTAAAT-AATCCTCCAAAGTATTTA-TC
66 CAAAGTATTCGTCAACCCAATACTGATTAAACACGTGCTAAGTGAATCCTCCAAAGTA-TTAGTC
* * * * * *
447554 AACTCAATATTGATTCAACACGTGTTAAGTGAATCTTCTAAAGTATTTGTCAACTCATTATTGAT
130 AACCCAATACTGATT-AACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACTCAATATTGAT
447619 TAAACACATG
193 TAAACACATG
* * * *
447629 GTAAGTG-ATCCTCTAAAGTATTTATCAA-CTCAATACTGATTAAACATGTGCTAAGTGAATCCT
1 TTAAGTGAATCCTTTAAAGTATTTATCAATC-CAATATTGATTAAACACGTGCTAAGTGAATCCT
* * * * * *
447692 CCAAAGTATTTC-TCGACCCAATACTAATTGAACACGTACTAAGTGAATCCTCTAAAGTATTTGT
65 CCAAAGTA-TTCGTCAACCCAATACTGATTAAACACGTGCTAAGTGAATCCTCCAAAGTATTAGT
* * * * * * *
447756 CAACCTAATACTAATTAAACATGTGCTAAATAGATCCTATAAAGTATTTGTCAACTAAATACTAA
129 CAACCCAATACTGATT-AACACGTGCTAAAT-GATCCTCTAAAGTATTTGTCAACTCAATATTGA
*
447821 TTAAACACATA
192 TTAAACACATG
* * * * * * * * * *
447832 TTAAAT-AGTTCCTATAAAATATTTGTTAATCCAATACTAATTAAACACATGCTAAGT-AGATCA
1 TTAAGTGA-ATCCTTTAAAGTATTTATCAATCCAATATTGATTAAACACGTGCTAAGTGA-ATCC
*
447895 TTCAAAGTATT
64 TCCAAAGTATT
447906 TATCAATTCG
Statistics
Matches: 389, Mismatches: 77, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
201 42 0.11
202 202 0.52
203 93 0.24
204 51 0.13
205 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (202 bp):
TTAAGTGAATCCTTTAAAGTATTTATCAATCCAATATTGATTAAACACGTGCTAAGTGAATCCTC
CAAAGTATTCGTCAACCCAATACTGATTAAACACGTGCTAAGTGAATCCTCCAAAGTATTAGTCA
ACCCAATACTGATTAACACGTGCTAAATGATCCTCTAAAGTATTTGTCAACTCAATATTGATTAA
ACACATG
Found at i:447837 original size:51 final size:50
Alignment explanation
Indices: 447263--447927 Score: 442
Period size: 51 Copynumber: 13.1 Consensus size: 50
447253 TCCAGTATTG
* * * * * * *
447263 ATTAAATACGTGCTAAGTGAATCCTCCAAAGTATTTGTAAACCCAATATTG
1 ATTAAACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACTCAATACTA
* * * * *** * * *
447314 ATTAAACACGTGTTAAGTGAATCCTCCAAAGCAGAAGTCAGCCCAATACTG
1 ATTAAACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACTCAATACTA
* * * *
447365 ATTAGACACGTGCTAAATGATCCTCTAAAGTATTTATCAACTCAATATTG
1 ATTAAACACGTGCTAAATGATCCTCTAAAGTATTTGTCAACTCAATACTA
* * * * * * * * * *
447415 ATTCAACATGTGTTAAGTGAAT-TTTTAAAGTATTTATCAA-TCCATTATTG
1 ATTAAACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACT-CAATACTA
* * * *
447465 ATTAAACACGTGCTAAATAAATCCTCTAACGTATTCGTCAAC-CTAATACTG
1 ATTAAACACGTGCTAAAT-GATCCTCTAAAGTATTTGTCAACTC-AATACTA
* * * * * *
447516 ATTAAACATGTGCTAAATAATCCTCCAAAGTATTTATCAACTCAATATTG
1 ATTAAACACGTGCTAAATGATCCTCTAAAGTATTTGTCAACTCAATACTA
* * * * * * *
447566 ATTCAACACGTGTTAAGTGAATCTTCTAAAGTATTTGTCAACTCATTATTG
1 ATTAAACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACTCAATACTA
* * * * *
447617 ATTAAACACATGGTAAGTGATCCTCTAAAGTATTTATCAACTCAATACTG
1 ATTAAACACGTGCTAAATGATCCTCTAAAGTATTTGTCAACTCAATACTA
* * * * * *
447667 ATTAAACATGTGCTAAGTGAATCCTCCAAAGTATTTCTCGACCCAATACTA
1 ATTAAACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACTCAATACTA
* * *
447718 ATTGAACACGTACTAAGTGAATCCTCTAAAGTATTTGTCAAC-CTAATACTA
1 ATTAAACACGTGCTAAATG-ATCCTCTAAAGTATTTGTCAACTC-AATACTA
* * *
447769 ATTAAACATGTGCTAAATAGATCCTATAAAGTATTTGTCAACTAAATACTA
1 ATTAAACACGTGCTAAAT-GATCCTCTAAAGTATTTGTCAACTCAATACTA
* ** * * * *
447820 ATTAAACACATATTAAATAGTTCCTATAAAATATTTGTTAA-TCCAATACTA
1 ATTAAACACGTGCTAAAT-GATCCTCTAAAGTATTTGTCAACT-CAATACTA
* * * * * * *
447871 ATTAAACACATGCTAAGTAGATCAT-TCAAAGTATTTATCAATTCGATTCTA
1 ATTAAACACGTGCTAAAT-GATCCTCT-AAAGTATTTGTCAACTCAATACTA
447922 ATTAAA
1 ATTAAA
447928 TATGTACAGG
Statistics
Matches: 498, Mismatches: 101, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.00
50 161 0.32
51 334 0.67
52 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (50 bp):
ATTAAACACGTGCTAAATGATCCTCTAAAGTATTTGTCAACTCAATACTA
Found at i:448042 original size:29 final size:29
Alignment explanation
Indices: 447980--448044 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
447970 TTAGGGCCCC
* * *
447980 CAATTTTTTGTATTTATATTTAAGACTCT
1 CAATTTTTTATATTTATAATTAAGACCCT
448009 CAATTTTTTATATTTATAATT-AGAGCCCT
1 CAATTTTTTATATTTATAATTAAGA-CCCT
*
448038 TAATTTT
1 CAATTTT
448045 ATAATTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (29 bp):
CAATTTTTTATATTTATAATTAAGACCCT
Found at i:448138 original size:117 final size:118
Alignment explanation
Indices: 448008--448253 Score: 317
Period size: 117 Copynumber: 2.1 Consensus size: 118
447998 TTTAAGACTC
* *
448008 TCAATTTTTTATATTTATAATTA-GAGCCCTTAA-TTTTATAATTTCATAA-AGTTTTTAGTTTT
1 TCAATTTTTTATATTAATAATTAGGA-CCC-TAATTTTTATAATTTCATAATA-TGTTTAG-TTT
* * *
448070 TTA-TCTTATTTTTTCATTTCTCTTATTAATTCAT-C-CAATTTTGAATTAAATTTAA
62 TTACCCTCATTTTCT-ATTTCTCTTATTAATTCATGCTCAATTTTGAATTAAATTTAA
448125 TCAATTTTTTATATTAATAATTAGGACCCTAATTTTTATAATTTCATAATATGTTTAGTTTTTAC
1 TCAATTTTTTATATTAATAATTAGGACCCTAATTTTTATAATTTCATAATATGTTTAGTTTTTAC
* *
448190 CCTCATTTTCTATTTCTTTTATTTATTCATGCATTCAATTTTGAATTAAATTTAA
66 CCTCATTTTCTATTTCTCTTATTAATTCATGC--TCAATTTTGAATTAAATTTAA
448245 TC-ATTTTTT
1 TCAATTTTTT
448254 CTCTTTTTTT
Statistics
Matches: 114, Mismatches: 7, Indels: 14
0.84 0.05 0.10
Matches are distributed among these distances:
116 26 0.23
117 56 0.49
118 3 0.03
119 7 0.06
120 22 0.19
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.55
Consensus pattern (118 bp):
TCAATTTTTTATATTAATAATTAGGACCCTAATTTTTATAATTTCATAATATGTTTAGTTTTTAC
CCTCATTTTCTATTTCTCTTATTAATTCATGCTCAATTTTGAATTAAATTTAA
Found at i:451957 original size:35 final size:35
Alignment explanation
Indices: 451911--451985 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
451901 CGTAACGTAC
*
451911 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
451946 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
451981 AGTAA
1 AGTAA
451986 TCTTCCTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:452099 original size:23 final size:23
Alignment explanation
Indices: 452067--452127 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
452057 ATTCAAGTTA
452067 AATATCATATCA-AATCCAGGTC
1 AATATCATATCAGAATCCAGGTC
* *
452089 ATGTATCATATCAGAATCCATGTC
1 A-ATATCATATCAGAATCCAGGTC
452113 AATATCATATCAGAA
1 AATATCATATCAGAA
452128 ATCAGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 23 0.68
24 10 0.29
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (23 bp):
AATATCATATCAGAATCCAGGTC
Found at i:454612 original size:18 final size:18
Alignment explanation
Indices: 454589--454630 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
454579 ACCGGTCTAC
454589 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
454607 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
454625 GGTCAA
1 GGTCAA
454631 GTTGGAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:455506 original size:16 final size:16
Alignment explanation
Indices: 455485--455515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
455475 TATAAACAGT
455485 AACAATAACAGCTAGA
1 AACAATAACAGCTAGA
*
455501 AACAATAATAGCTAG
1 AACAATAACAGCTAG
455516 GATGTCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (16 bp):
AACAATAACAGCTAGA
Found at i:456028 original size:32 final size:32
Alignment explanation
Indices: 455938--456103 Score: 187
Period size: 31 Copynumber: 5.3 Consensus size: 32
455928 CGGCTAGTGT
* * *
455938 ATAAGGCACAACATAGTC-ATATT-CATTTAG
1 ATAATGCACAACAGAGTCAATATTGCATTCAG
* * *
455968 ATAATGCACAACAAAAT-AGTATTGCATTCAG
1 ATAATGCACAACAGAGTCAATATTGCATTCAG
455999 ATAATGCACAACAGAGTCAATATTGCATTCAG
1 ATAATGCACAACAGAGTCAATATTGCATTCAG
* *
456031 AT-ATGCATAACAGAGTCAATATTGCATTCAT
1 ATAATGCACAACAGAGTCAATATTGCATTCAG
* * * * *
456062 ATAATGCATAGCAGAGTTAGTGTTGCATTCAG
1 ATAATGCACAACAGAGTCAATATTGCATTCAG
456094 ATAATGCACA
1 ATAATGCACA
456104 GAAGCATCAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
30 18 0.16
31 50 0.43
32 48 0.41
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (32 bp):
ATAATGCACAACAGAGTCAATATTGCATTCAG
Found at i:456057 original size:63 final size:63
Alignment explanation
Indices: 455938--456103 Score: 185
Period size: 63 Copynumber: 2.7 Consensus size: 63
455928 CGGCTAGTGT
* * * *
455938 ATAAGGCACAACATAGTC-ATATT-CATTTAGATAATGCACAACAAAATAGTATTGCATTCAG
1 ATAATGCACAACAGAGTCAATATTGCATTCAGATAATGCACAACAAAATAATATTGCATTCAG
* * * *
455999 ATAATGCACAACAGAGTCAATATTGCATTCAGAT-ATGCATAACAGAGTCAATATTGCATTCAT
1 ATAATGCACAACAGAGTCAATATTGCATTCAGATAATGCACAACAAAAT-AATATTGCATTCAG
* * * * *
456062 ATAATGCATAGCAGAGTTAGTGTTGCATTCAGATAATGCACA
1 ATAATGCACAACAGAGTCAATATTGCATTCAGATAATGCACA
456104 GAAGCATCAG
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
61 16 0.18
62 16 0.18
63 49 0.56
64 6 0.07
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (63 bp):
ATAATGCACAACAGAGTCAATATTGCATTCAGATAATGCACAACAAAATAATATTGCATTCAG
Found at i:456864 original size:21 final size:22
Alignment explanation
Indices: 456816--456871 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
456806 TACTCGAGGT
*
456816 AGTATCGGTACTATCATGTAGA
1 AGTATCGATACTATCATGTAGA
*
456838 AGTATCGATACTA-CA-GTTAGG
1 AGTATCGATACTATCATG-TAGA
456859 AGTATCGATACTA
1 AGTATCGATACTA
456872 AGGGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.03
21 18 0.58
22 12 0.39
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (22 bp):
AGTATCGATACTATCATGTAGA
Found at i:459936 original size:24 final size:26
Alignment explanation
Indices: 459892--459942 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
459882 TCCGTCGTTG
*
459892 TCGTGGTCTGTTCTTCCTCTCTTTCT
1 TCGTGGTCTGTTCTTCCTCTCTCTCT
*
459918 TCGTGGT-TG-TCTTCTTCTCTCTCT
1 TCGTGGTCTGTTCTTCCTCTCTCTCT
459942 T
1 T
459943 TTTTATAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 2 0.09
26 7 0.30
ACGTcount: A:0.00, C:0.29, G:0.16, T:0.55
Consensus pattern (26 bp):
TCGTGGTCTGTTCTTCCTCTCTCTCT
Found at i:460383 original size:3 final size:3
Alignment explanation
Indices: 460375--460436 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
460365 AATATTTATT
* * *
460375 TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA TGTA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
460422 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
460437 AAAAATAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
3 47 0.92
4 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:460398 original size:16 final size:16
Alignment explanation
Indices: 460377--460436 Score: 97
Period size: 16 Copynumber: 3.8 Consensus size: 16
460367 TATTTATTTA
460377 ATAATAATAATAATGT
1 ATAATAATAATAATGT
460393 ATAATAATAATAATGT
1 ATAATAATAATAATGT
460409 ATAATAATAAT-A-GT
1 ATAATAATAATAATGT
460423 AATAATAATAATAA
1 -ATAATAATAATAA
460437 AAAAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.05
15 12 0.29
16 28 0.67
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
ATAATAATAATAATGT
Found at i:460747 original size:45 final size:45
Alignment explanation
Indices: 460676--460989 Score: 454
Period size: 45 Copynumber: 7.0 Consensus size: 45
460666 TCAAAAAGCT
* * *
460676 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATAA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
460723 CCCTG-AGGCTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCC-GAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
460768 CCCGAAGGTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
460813 TCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
460858 CTCGAAGGTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
460903 CCC-AAGGTTTTGAAAACATCATG-ACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
460946 CCCGAAGGTTTTGAAAGCATCATGCACTGAAGGAGTTACAGATG
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
460990 TGGGAAATAG
Statistics
Matches: 245, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
43 22 0.09
44 39 0.16
45 177 0.72
47 6 0.02
48 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:465797 original size:21 final size:20
Alignment explanation
Indices: 465773--465813 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
465763 TCTAATTAGA
465773 TGCCTTCAATCTTGCTTTGCT
1 TGCCTTCAATC-TGCTTTGCT
**
465794 TGCCTTGGATCTGCTTTGCT
1 TGCCTTCAATCTGCTTTGCT
465814 GGGGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.07, C:0.27, G:0.20, T:0.46
Consensus pattern (20 bp):
TGCCTTCAATCTGCTTTGCT
Found at i:465960 original size:8 final size:8
Alignment explanation
Indices: 465947--466014 Score: 77
Period size: 8 Copynumber: 8.4 Consensus size: 8
465937 GGTTCAATTC
465947 TTTCCTTT
1 TTTCCTTT
465955 TTTCCTTTTT
1 TTTCC--TTT
465965 TTTCCTTT
1 TTTCCTTT
465973 TTTCCTTT
1 TTTCCTTT
*
465981 TTTTCTGTT
1 TTTCCT-TT
465990 TTT-CTTT
1 TTTCCTTT
465997 TTTCC-TT
1 TTTCCTTT
*
466004 TTCCCTTT
1 TTTCCTTT
466012 TTT
1 TTT
466015 TCAAGTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
7 11 0.21
8 28 0.54
9 5 0.10
10 8 0.15
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTCCTTT
Found at i:465967 original size:10 final size:10
Alignment explanation
Indices: 465952--465984 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
465942 AATTCTTTCC
465952 TTTTTTCCTT
1 TTTTTTCCTT
465962 TTTTTTCC--
1 TTTTTTCCTT
465970 TTTTTTCCTT
1 TTTTTTCCTT
465980 TTTTT
1 TTTTT
465985 CTGTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:465970 original size:18 final size:17
Alignment explanation
Indices: 465947--466016 Score: 85
Period size: 18 Copynumber: 4.2 Consensus size: 17
465937 GGTTCAATTC
465947 TTTCCTTTTTTCCTTTTT
1 TTTCCTTTTTTCC-TTTT
465965 TTTCCTTTTTTCCTTTT
1 TTTCCTTTTTTCCTTTT
465982 TTT-CTGTTTTT-C-TTT
1 TTTCCT-TTTTTCCTTTT
*
465997 TTTCC-TTTTCCCTTTT
1 TTTCCTTTTTTCCTTTT
466013 TTTC
1 TTTC
466017 AAGTATAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 4 0.09
15 7 0.15
16 11 0.23
17 12 0.26
18 13 0.28
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTCCTTTTTTCCTTTT
Found at i:468784 original size:14 final size:15
Alignment explanation
Indices: 468759--468793 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
468749 ATGTAAATAC
468759 AAATGTAAAATGTAA
1 AAATGTAAAATGTAA
468774 AAATG-AAAATGTAA
1 AAATGTAAAATGTAA
*
468788 ATATGT
1 AAATGT
468794 GAATATGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (15 bp):
AAATGTAAAATGTAA
Found at i:472819 original size:3 final size:3
Alignment explanation
Indices: 472811--472853 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
472801 AATATTTATT
* *
472811 TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
472854 AAGCAAACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:473953 original size:16 final size:17
Alignment explanation
Indices: 473922--473955 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
473912 GGATATTTTT
*
473922 TTATTGTTTATTTTAAA
1 TTATTGTTTATATTAAA
473939 TTATT-TTTATATTAAA
1 TTATTGTTTATATTAAA
473955 T
1 T
473956 AATACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATTGTTTATATTAAA
Found at i:477731 original size:17 final size:18
Alignment explanation
Indices: 477701--477749 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
477691 AATTATACCG
*
477701 TTTTTATTGAATTTTATT-
1 TTTTTATT-TATTTTATTA
477719 TTTTTATTTATTTTATTA
1 TTTTTATTTATTTTATTA
*
477737 TATTT-TTTATTTT
1 TTTTTATTTATTTT
477750 GTTCACTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTATTTATTTTATTA
Found at i:486110 original size:2 final size:2
Alignment explanation
Indices: 486103--486149 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
486093 AGCATCTGCT
* * * *
486103 TA TA TA TA TA TA TA TA TA CA CA TA T- TA TA TA CA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
486144 TA TA TA
1 TA TA TA
486150 AAGCTTTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:486133 original size:13 final size:14
Alignment explanation
Indices: 486110--486147 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
486100 GCTTATATAT
486110 ATATATATATACAC
1 ATATATATATACAC
*
486124 ATAT-TATATACAT
1 ATATATATATACAC
*
486137 ATACATATATA
1 ATATATATATA
486148 TAAAGCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATATATACAC
Found at i:487318 original size:43 final size:43
Alignment explanation
Indices: 487270--487397 Score: 147
Period size: 43 Copynumber: 3.0 Consensus size: 43
487260 AACTCGTAAT
* *
487270 TTGCACCGAAGTGCCACATAATTGTCCCGAAAGACCACATAGG
1 TTGCACCAAAGTGCCACATAATTGTCCCGAAAGACCACATAGA
* * * *
487313 TTGCACCAAAGTGCCACATATTTATCCCGGAGGACCACATA-A
1 TTGCACCAAAGTGCCACATAATTGTCCCGAAAGACCACATAGA
487355 TTGTC-CCAAAAGAT--CACATAATTGTCCCGAAAGACCACATAGA
1 TTG-CACC-AAAG-TGCCACATAATTGTCCCGAAAGACCACATAGA
487398 CCCTCGACTC
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 28 0.39
43 42 0.59
44 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.20
Consensus pattern (43 bp):
TTGCACCAAAGTGCCACATAATTGTCCCGAAAGACCACATAGA
Found at i:487387 original size:21 final size:21
Alignment explanation
Indices: 487283--487395 Score: 113
Period size: 21 Copynumber: 5.3 Consensus size: 21
487273 CACCGAAGTG
487283 CCACATAATTGTCCCGAAAGA
1 CCACATAATTGTCCCGAAAGA
* *
487304 CCACATAGGTTG-CACC-AAAGTG
1 CCACATA-ATTGTC-CCGAAAG-A
* * * *
487326 CCACATATTTATCCCGGAGGA
1 CCACATAATTGTCCCGAAAGA
*
487347 CCACATAATTGTCCCAAAAGA
1 CCACATAATTGTCCCGAAAGA
*
487368 TCACATAATTGTCCCGAAAGA
1 CCACATAATTGTCCCGAAAGA
487389 CCACATA
1 CCACATA
487396 GACCCTCGAC
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
21 57 0.79
22 15 0.21
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAAGA
Found at i:487988 original size:55 final size:55
Alignment explanation
Indices: 487904--488094 Score: 312
Period size: 55 Copynumber: 3.5 Consensus size: 55
487894 TCATACTTGG
*
487904 GGGTATCGATACACTCCTCAGTGTACTGATACA-AAATTAGCACTCGATGTTTTAA
1 GGGTATCGATACACTCCTCAGTGTACTGATACACAAA-TAGCACTCGATGTTTTGA
*
487959 GGGTATCGATACACTCCTCAGTGTACTGATACACAAATAGCACTTGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACTGATACACAAATAGCACTCGATGTTTTGA
* * *
488014 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACTGATACACAAATAGCACTCGATGTTTTGA
*
488069 GGGTATCGATACACTCCTCGGTGTAC
1 GGGTATCGATACACTCCTCAGTGTAC
488095 CAAAACACAC
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
55 125 0.98
56 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACTGATACACAAATAGCACTCGATGTTTTGA
Found at i:494252 original size:22 final size:23
Alignment explanation
Indices: 494227--494278 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
494217 TCTCAAAAGA
* *
494227 CCACATA-GGTTGTATCGAAGTG
1 CCACATAGGGTTGTACCAAAGTG
494249 CCACATAGGGTTGTACCAAAGTG
1 CCACATAGGGTTGTACCAAAGTG
494272 CCACATA
1 CCACATA
494279 TTTATCCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CCACATAGGGTTGTACCAAAGTG
Found at i:494298 original size:21 final size:21
Alignment explanation
Indices: 494272--494320 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
494262 TACCAAAGTG
* * *
494272 CCACATATTTATCCTGGAGGA
1 CCACATAATTATCCCGAAGGA
*
494293 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAAGGA
494314 CCACATA
1 CCACATA
494321 GACCCTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGGA
Found at i:494869 original size:55 final size:55
Alignment explanation
Indices: 494784--494960 Score: 248
Period size: 55 Copynumber: 3.2 Consensus size: 55
494774 ATACTTAGAA
* *
494784 GTATCGATACACT-CTACAGTGTACCGATACATAATTAGCACTCGATGTTTTGAGG
1 GTATCGATACACTCCT-CAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
* * * * *
494839 GTATCGATACACTCCTCAGTGTACCAATACACAAATAGCACTCAATATTTTTAAG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
* * *
494894 GTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTTGATGTTTTGAGG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
494949 GTATCGATACAC
1 GTATCGATACAC
494961 AAATGACATT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 104 0.98
56 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (55 bp):
GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
Found at i:494964 original size:35 final size:35
Alignment explanation
Indices: 494918--494995 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
494908 CTCAGTGTAC
* *
494918 CGATACACAAATGGCATTTGATGTTTTGAGGGTAT
1 CGATACACAAATGACATTCGATGTTTTGAGGGTAT
494953 CGATACACAAATGACATTCGATGTTTTGAGGGTAT
1 CGATACACAAATGACATTCGATGTTTTGAGGGTAT
494988 CGATACAC
1 CGATACAC
494996 TCCTCAGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (35 bp):
CGATACACAAATGACATTCGATGTTTTGAGGGTAT
Found at i:495233 original size:29 final size:29
Alignment explanation
Indices: 495199--495263 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
495189 CTTGTACAAT
495199 TTAAAACTCTCAAACATCCCAAATTCTCA
1 TTAAAACTCTCAAACATCCCAAATTCTCA
495228 TTAAAACTCTCAAACATCCCAAATTCTCA
1 TTAAAACTCTCAAACATCCCAAATTCTCA
*
495257 TTTAAAC
1 TTAAAAC
495264 ACTTGAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (29 bp):
TTAAAACTCTCAAACATCCCAAATTCTCA
Found at i:497404 original size:39 final size:39
Alignment explanation
Indices: 497350--497500 Score: 284
Period size: 39 Copynumber: 3.9 Consensus size: 39
497340 TTTATTATCA
497350 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
497389 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
*
497428 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTT
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
*
497467 TATGCAAATATAGAAAGAAAGAAACCTATAAGGG
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGG
497501 TTTTTTTAAA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.19
Consensus pattern (39 bp):
TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
Found at i:498266 original size:25 final size:25
Alignment explanation
Indices: 498232--498285 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
498222 TTAATTACAG
498232 GATCACTTGCATGCATACGTACCTA
1 GATCACTTGCATGCATACGTACCTA
*
498257 GATCACTTGCTTGCATACGTACCTA
1 GATCACTTGCATGCATACGTACCTA
498282 GATC
1 GATC
498286 CAACAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (25 bp):
GATCACTTGCATGCATACGTACCTA
Found at i:510487 original size:117 final size:113
Alignment explanation
Indices: 510281--510503 Score: 358
Period size: 117 Copynumber: 1.9 Consensus size: 113
510271 AATCCGACAG
510281 ATCCGATCCATTTTTCAATTTATAGTTCGGATCGGGTATCCGATTTTTTTCGGATTTTCGGATCG
1 ATCCGATCCATTTTTCAATTTATAGTTCGGATCGGGTATCCGATTTTTTTCGGATTTTCGGATCG
510346 GATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAATTTGGAT
66 GATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAATTTGGAT
*
510394 ATCCGATCCGTTTTTCAATTTTCGGATAGTTCGGATC-GGTATCCGAATTTTTTTCGGATTTTCG
1 ATCCGATCCATTTTTCAA-TTT---ATAGTTCGGATCGGGTATCCG-ATTTTTTTCGGATTTTCG
* * *
510458 GATCGGATACGGATTGATCAAAATTCAATTTCGGATTATCCGAAAA
61 GATCGGATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAA
510504 CCCGAAAAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
113 17 0.17
114 3 0.03
116 8 0.08
117 73 0.72
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (113 bp):
ATCCGATCCATTTTTCAATTTATAGTTCGGATCGGGTATCCGATTTTTTTCGGATTTTCGGATCG
GATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAATTTGGAT
Found at i:514182 original size:20 final size:20
Alignment explanation
Indices: 514157--514209 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
514147 TTTTCCTAAT
514157 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
514177 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
514197 TCGCAACGCGAAT
1 TCGCAATGCGAAT
514210 CTGACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:514219 original size:20 final size:20
Alignment explanation
Indices: 514196--514298 Score: 161
Period size: 20 Copynumber: 5.2 Consensus size: 20
514186 GAATACGTAA
* *
514196 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
514216 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
514236 ATCGCAACGAGATTCTGATT
1 ATCGCAACGAGATTCTGACT
*
514256 ATCGTAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
514276 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
514296 ATC
1 ATC
514299 ACAATACTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:515196 original size:24 final size:24
Alignment explanation
Indices: 515145--515198 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
515135 GTATTCGAAA
*
515145 TTTGATCTTGGTCAATACCCTGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
515169 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
515193 TTTGAT
1 TTTGAT
515199 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:517637 original size:20 final size:19
Alignment explanation
Indices: 517612--517703 Score: 112
Period size: 20 Copynumber: 4.6 Consensus size: 19
517602 GACATTCATT
*
517612 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACACGAA-A
* *
517632 TGACTATCGCAATACAAAAA
1 TGACTATCGCAACAC-GAAA
517652 TGACTATCGCAACACGAAA
1 TGACTATCGCAACACGAAA
*
517671 TTGACTATCGCAACGCGGAAA
1 -TGACTATCGCAACAC-GAAA
517692 TGACTATCGCAA
1 TGACTATCGCAA
517704 TGAGAGAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.05
20 54 0.86
21 6 0.10
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (19 bp):
TGACTATCGCAACACGAAA
Found at i:517727 original size:33 final size:33
Alignment explanation
Indices: 517677--517772 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
517667 GAAATTGACT
* **
517677 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGAGAGA
*
517711 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
517744 ATCGCAATGCGAAAATGAAAATCGCAATG
1 ATCGCAATGCG-AAATGAAAATCGCAATG
517773 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
Found at i:517768 original size:20 final size:19
Alignment explanation
Indices: 517710--517776 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
517700 GCAATGAGAG
517710 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
517729 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
517743 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
517763 AATCGCAATGCGAA
1 AATCGCAATGCGAA
517777 TTTAGTTTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 14 0.35
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:517793 original size:19 final size:20
Alignment explanation
Indices: 517765--517814 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
517755 AAAATGAAAA
*
517765 TCGCAATGCGAATTT-AGTT
1 TCGCATTGCGAATTTCAGTT
* * *
517784 TCGCGTTGCGATTTTCATTT
1 TCGCATTGCGAATTTCAGTT
517804 TCGCATTGCGA
1 TCGCATTGCGA
517815 TTCTCTCGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGAATTTCAGTT
Found at i:517830 original size:34 final size:34
Alignment explanation
Indices: 517787--517882 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
517777 TTTAGTTTCG
517787 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
517821 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** ** * *
517854 ATTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
517883 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:518007 original size:14 final size:14
Alignment explanation
Indices: 517988--518024 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
517978 CATCAATTAA
517988 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
518002 ACAAATCATCTTTT
1 ACAAATCAACATTT
518016 ACAAATCAA
1 ACAAATCAA
518025 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:520026 original size:20 final size:20
Alignment explanation
Indices: 520001--520089 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
519991 GAAACTTAAA
*
520001 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
520021 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
520041 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
520061 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
520081 ATCGCAACG
1 ATCGCAACG
520090 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:520153 original size:34 final size:34
Alignment explanation
Indices: 520112--520267 Score: 143
Period size: 34 Copynumber: 4.4 Consensus size: 34
520102 TGCGATTTTC
520112 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
* *
520146 AATTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC---TTT-CGTTGCGATAGTCA
* * * * **
520186 TTTTCGCATTGCGATTTTTTTGTTGCGGTTTTC-
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
* *
520219 ATTTTGCATTGCGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
* *
520253 TTTTCGCGTTGCGAT
1 ATTTCGCATTGCGAT
520268 AGTCATTTTC
Statistics
Matches: 94, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
33 25 0.27
34 34 0.36
35 3 0.03
36 2 0.02
38 1 0.01
39 3 0.03
40 26 0.28
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:520159 original size:20 final size:20
Alignment explanation
Indices: 520134--520290 Score: 133
Period size: 20 Copynumber: 8.5 Consensus size: 20
520124 GATTCTTTCG
**
520134 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
520154 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
520174 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
520194 TTGCGAT--T--TTTTTG--
1 TTGCGATAGTCATTTTCGCA
* **
520208 TTGCGGTTTTCATTTT-GCA
1 TTGCGATAGTCATTTTCGCA
*
520227 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
520241 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
520261 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
520281 TTGCAATAGT
1 TTGCGATAGT
520291 AAACTATTCT
Statistics
Matches: 113, Mismatches: 11, Indels: 26
0.75 0.07 0.17
Matches are distributed among these distances:
14 13 0.12
15 2 0.02
16 9 0.08
17 3 0.03
18 9 0.08
19 6 0.05
20 71 0.63
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:522186 original size:20 final size:20
Alignment explanation
Indices: 522163--522232 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
522153 TCTGAAACTT
522163 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
522183 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
522203 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
522222 AAAATCGCAAC
1 AAAATCGCAAC
522233 GACAGAATCG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 14 0.31
20 31 0.69
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:522631 original size:22 final size:22
Alignment explanation
Indices: 522569--522634 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
522559 TGACCGTGAA
* *
522569 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
522591 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
522613 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
522635 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:522853 original size:20 final size:20
Alignment explanation
Indices: 522830--522962 Score: 239
Period size: 20 Copynumber: 6.7 Consensus size: 20
522820 CGATAGTCAG
*
522830 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
522850 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
522870 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
522890 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
522910 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
522930 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
522950 ATTCGCATTGCGA
1 ATTCGCATTGCGA
522963 ATTAGGAAAG
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 108 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:522983 original size:21 final size:21
Alignment explanation
Indices: 522959--523004 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
522949 TATTCGCATT
*
522959 GCGAATTAGGAAAGTCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
522980 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
523001 GCGA
1 GCGA
523005 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:523831 original size:29 final size:29
Alignment explanation
Indices: 523799--523867 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
523789 ATTTTGAAAT
523799 AACCCTTAAACTTTGAAATCTTTCATTTC
1 AACCCTTAAACTTTGAAATCTTTCATTTC
523828 AACCCTTAAACTTTGAAATCTTTCATTTC
1 AACCCTTAAACTTTGAAATCTTTCATTTC
*
523857 AACCCCTAAAC
1 AACCCTTAAAC
523868 CTACGTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (29 bp):
AACCCTTAAACTTTGAAATCTTTCATTTC
Found at i:526285 original size:2 final size:2
Alignment explanation
Indices: 526280--526365 Score: 129
Period size: 2 Copynumber: 43.5 Consensus size: 2
526270 ACACACACAA
* * * *
526280 AG AG AG GG AG AG GG AG AG GG AG AG GG AG AG -G AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
526321 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
526363 AG A
1 AG A
526366 TAATTAGGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:529427 original size:50 final size:50
Alignment explanation
Indices: 529354--529453 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
529344 TCATTAAAAA
* *
529354 CAAAATTATGATCTTTTGCAGTGATAGTGTGATACTTACAATCAAACAGC
1 CAAAATTATGATATTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
529404 CAAAATTATGATATTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
1 CAAAATTATGATATTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
529454 TAAGACAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (50 bp):
CAAAATTATGATATTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
Done.