Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004015.1 Hibiscus syriacus cultivar Beakdansim tig00008767_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: 64629
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3290 original size:24 final size:24
Alignment explanation
Indices: 3263--3345 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
3253 AGAAATCAAA
3263 AACAGAATTCAGATCAGATATCAG
1 AACAGAATTCAGATCAGATATCAG
* * * *
3287 AACATAATCCAGTTCAGAAATCAG
1 AACAGAATTCAGATCAGATATCAG
* * *
3311 AACATAATTCAGGTAATG-TATCAG
1 AACAGAATTCAGATCA-GATATCAG
3335 AACAGAATTCA
1 AACAGAATTCA
3346 AGTTGAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (24 bp):
AACAGAATTCAGATCAGATATCAG
Found at i:8440 original size:52 final size:52
Alignment explanation
Indices: 8377--8481 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
8367 AAGATTGGAC
* * *
8377 GCACAGAAATAGGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAG
1 GCACAAAAATAGGAAACTAGCATAGAGTTAGGGGATTACAACTAATTACAAG
8429 GCACAAAAATAGGAAACTAGCATAGAGTTAGGGGATTACAACTAATTACAAG
1 GCACAAAAATAGGAAACTAGCATAGAGTTAGGGGATTACAACTAATTACAAG
8481 G
1 G
8482 ATATTATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (52 bp):
GCACAAAAATAGGAAACTAGCATAGAGTTAGGGGATTACAACTAATTACAAG
Found at i:9075 original size:100 final size:100
Alignment explanation
Indices: 8971--9821 Score: 743
Period size: 100 Copynumber: 8.6 Consensus size: 100
8961 CTATAAGTAT
* * * *
8971 GTTTTAATAATATAAACGGTTAAAACCTTATAACTTAACCGATTCACAATACAACAAGGTGAAAT
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGATTCACAAAACAACAAGGTGCAAC
* *
9036 CTATTATGTTACCATTACAACTGGATTTTTAATAG
66 CTATTATGTTACCATCACAACTGAATTTTTAATAG
* ** * * * *
9071 GTTTTAATAATATAAATGGTTACAA-CCTTATAACTTAATTGGTTTACAAAACAACAAGGCGTAA
1 GTTTTAATAATATAAACGGTTA-AAGCCTTATAACTTAACCGATTCACAAAACAACAAGGTGCAA
*
9135 CCTATTA----A--ATCACAACCGAATTTTTAATAG
65 CCTATTATGTTACCATCACAACTGAATTTTTAATAG
* * * * * * * *
9165 CTTTTAATAATATAAACGATTACAA-TCTTATAACTTAACTGATTAAAAATAAAAATAAGGTGCA
1 GTTTTAATAATATAAACGGTTA-AAGCCTTATAACTTAACCGATTCACAA-AACAACAAGGTGCA
* * * * *
9229 ACCAATTATGTTACCATCGCAAC-CAATTATTAATAA
64 ACCTATTATGTTACCATCACAACTGAATTTTTAATAG
* * * *
9265 GTTTTAGTAATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAAGGCGAAAC
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGATTCACAAAACAACAAGGTGCAAC
* *
9330 CTATTATGTTACCATCACAACCGGATTTTTAATAG
66 CTATTATGTTACCATCACAACTGAATTTTTAATAG
* ** * ** * * *
9365 GTTTTAATAATTTAAATAGTTAAAGCCTTGTAACTTAATTGGTTGACAAAACAACAAGGCGCAAC
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGATTCACAAAACAACAAGGTGCAAC
* ** ** *
9430 ATATTACCTTATAATCACAA-TCGAATTTTTAATAA
66 CTATTATGTTACCATCACAACT-GAATTTTTAATAG
* * * * * *
9465 GTTCTAATAATATAAACAGTTACAGCCTTATAACTTAA-CAAGTT-AAAATAAAAACAAGGTGCA
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGA-TTCACAA-AACAACAAGGTGCA
** * **
9528 ACCTATTAAT-TT-CCATTGCAAC-AAGATTAGTAATAG
64 ACCTATT-ATGTTACCATCACAACTGA-ATTTTTAATAG
*
9564 GTTTTAATAATACAAACGGTTAAAGCCTTATAACTTAACC-AGTTCACAAAACAA-AATGGTG-A
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGA-TTCACAAAACAACAA-GGTGCA
* * * *
9626 CACCTATTACGTTATCATCACAA-TCAGATATTTAATAG
64 -ACCTATTATGTTACCATCACAACTGA-ATTTTTAATAG
* * *
9664 ATTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACC-AGTTCACAAAACAATAAGGAGCAA
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGA-TTCACAAAACAACAAGGTGCAA
* * * *
9728 CCTATTACGTTACGATCGCAACTGAACTTTTAATAG
65 CCTATTATGTTACCATCACAACTGAATTTTTAATAG
** ** * * *
9764 ACTTTAATAATATAAATTGTTAAAGTCTTATAAATTAATCGATTCACAAAACAACAAG
1 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGATTCACAAAACAACAAG
9822 TCTTATATAA
Statistics
Matches: 607, Mismatches: 117, Indels: 54
0.78 0.15 0.07
Matches are distributed among these distances:
94 60 0.10
95 17 0.03
96 1 0.00
98 5 0.01
99 105 0.17
100 403 0.66
101 16 0.03
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31
Consensus pattern (100 bp):
GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCGATTCACAAAACAACAAGGTGCAAC
CTATTATGTTACCATCACAACTGAATTTTTAATAG
Found at i:9278 original size:194 final size:196
Alignment explanation
Indices: 8972--9779 Score: 590
Period size: 199 Copynumber: 4.1 Consensus size: 196
8962 TATAAGTATG
* * * * *
8972 TTTTAATAATATAAACGGTTAAAACCTTATAACTTAACCGATTCACAATACAACAAGGTGAAATC
1 TTTTAATAATATAAACGATTAAAACCTTATAACTTAACCGATTAAAAATAAAACAAGGTGAAACC
* * ** * * *
9037 TATTATGTTACCATTACAACTGGATTTTTAATAGGTTTTAATAATATAAATGGTTACAA-CCTTA
66 AATTATGTTACCATCACAACTCAATTATTAATAAGTTTTAATAATATAAACGGTTA-AAGCCTTA
**** * *
9101 TAACTTAATTGGTTTACAAAACAACAAGGCGTAACCTATTA-A-ATCACAACCGAATTTTTAATA
130 TAACTTAACCAATTCACAAAACAACAAGGCGAAACCTATTATACATCACAACCGAATTTTTAATA
9164 GC
195 GC
* * * * *
9166 TTTTAATAATATAAACGATTACAATCTTATAACTTAACTGATTAAAAATAAAAATAAGGTGCAAC
1 TTTTAATAATATAAACGATTAAAACCTTATAACTTAACCGATTAAAAAT-AAAACAAGGTGAAAC
* *
9231 CAATTATGTTACCATCGCAAC-CAATTATTAATAAGTTTTAGTAATATAAACGGTTAAAGCCTTA
65 CAATTATGTTACCATCACAACTCAATTATTAATAAGTTTTAATAATATAAACGGTTAAAGCCTTA
*
9295 TAACTTAACCAATTCACAAAACAACAAGGCGAAACCTATTATGTTACCATCACAACCGGATTTTT
130 TAACTTAACCAATTCACAAAACAACAAGGCGAAACCTATTA---TA-CATCACAACCGAATTTTT
*
9360 AATAGG
191 AATAGC
* * * * ** * * * * *
9366 TTTTAATAATTTAAA-TAGTTAAAGCCTTGTAACTTAATTGGTTGACAAA-ACAACAAGGCGCAA
1 TTTTAATAATATAAACGA-TTAAAACCTTATAACTTAACCGATT-AAAAATAAAACAAGGTGAAA
** ** * * * *
9429 -CATATTACCTTATAATCACAA-TCGAATTTTTAATAAGTTCTAATAATATAAACAGTTACAGCC
64 CCA-ATTATGTTACCATCACAACTC-AATTATTAATAAGTTTTAATAATATAAACGGTTAAAGCC
* * * * * ** *
9492 TTATAACTTAA-CAAGTT-AAAATAAAAACAAGGTGCAACCTATTAATTTCCATTGCAA-CAAGA
127 TTATAACTTAACCAA-TTCACAA-AACAACAAGGCGAAACCTATT-A--TACATCACAACCGA-A
** *
9554 TTAGTAATAGG
186 TTTTTAATAGC
* * * * * *
9565 TTTTAATAATACAAACGGTTAAAGCCTTATAACTTAACC-AGTTCACAAAA-CAAA-ATGGTGAC
1 TTTTAATAATATAAACGATTAAAACCTTATAACTTAACCGA-TT-A-AAAATAAAACAAGGTGAA
* * *
9627 ACCTATTACGTTATCATCACAA-TCAGA-TATTTAAT-AGATTTTAATAATATAAACGGTTAAAG
63 ACCAATTATGTTACCATCACAACTCA-ATTA-TTAATAAG-TTTTAATAATATAAACGGTTAAAG
* * * * * *
9689 CCTTATAACTTAACCAGTTCACAAAACAATAAGGAGCAACCTATTACGTTACGATCGCAACTGAA
125 CCTTATAACTTAACCAATTCACAAAACAACAAGGCGAAACCTATTA---TAC-ATCACAACCGAA
*
9754 CTTTTAATAGAC
186 TTTTTAATAG-C
9766 -TTTAATAATATAAA
1 TTTTAATAATATAAA
9780 TTGTTAAAGT
Statistics
Matches: 485, Mismatches: 99, Indels: 54
0.76 0.16 0.08
Matches are distributed among these distances:
193 2 0.00
194 112 0.23
195 29 0.06
198 9 0.02
199 168 0.35
200 159 0.33
201 6 0.01
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31
Consensus pattern (196 bp):
TTTTAATAATATAAACGATTAAAACCTTATAACTTAACCGATTAAAAATAAAACAAGGTGAAACC
AATTATGTTACCATCACAACTCAATTATTAATAAGTTTTAATAATATAAACGGTTAAAGCCTTAT
AACTTAACCAATTCACAAAACAACAAGGCGAAACCTATTATACATCACAACCGAATTTTTAATAG
C
Found at i:9401 original size:294 final size:294
Alignment explanation
Indices: 8850--9734 Score: 997
Period size: 294 Copynumber: 3.0 Consensus size: 294
8840 TTTAGTTAAC
* * * * * *
8850 ATCAC-ACCAAATTTTTAATATGTTTTAATAATATAAAAAATTACATCCTTATAACTTAATCAA-
1 ATCACAACCGAATTTTTAATAAGTTCTAATAATATAAACAGTTACAACCTTATAACTTAA-CAAG
* * * * ** * * *
8913 ATACAATAAAAACAAGGCT-CAACCTACTACATTAT-CATCTTAAC-CGAACTA-TAAGTATGTT
65 TTAAAATAAAAACAAGG-TGCAACCAATTA-ATT-TCCATCGCAACAAG-ATTAGTAA-TAAGTT
* * * *
8974 TTAATAATATAAACGGTTAAAACCTTATAACTTAACCGATTCACAATACAACAAGGTGAAATCTA
125 TTAATAATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAAGGTGAAACCTA
* *
9039 TTATGTTACCATTACAACTGGATTTTTAATAGGTTTTAATAATATAAATGGTTACAA-CCTTATA
190 TTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTA-AAGCCTTATA
* *
9103 ACTTAATTGGTTTACAAAACAACAAGGCGTAACCTATTA-A
254 ACTTAATTGGTTCACAAAACAACAAGGCGCAACCTATTATA
* * *
9143 ATCACAACCGAATTTTTAAT-AGCTTTTAATAATATAAAC-GATTACAATCTTATAACTTAAC-T
1 ATCACAACCGAATTTTTAATAAG-TTCTAATAATATAAACAG-TTACAACCTTATAACTTAACAA
* * *
9205 GATTAAAAATAAAAATAAGGTGCAACCAATT-ATGTTACCATCGCAACCA-ATTATTAATAAGTT
64 G-TT-AAAATAAAAACAAGGTGCAACCAATTAAT-TT-CCATCGCAACAAGATTAGTAATAAGTT
* *
9268 TTAGTAATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAAGGCGAAACCTA
125 TTAATAATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAAGGTGAAACCTA
* * *
9333 TTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATTTAAATAGTTAAAGCCTTGTAA
190 TTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTAAAGCCTTATAA
* *
9398 CTTAATTGGTTGACAAAACAACAAGGCGCAACATATTACCTTATA
255 CTTAATTGGTTCACAAAACAACAAGGCGCAAC---CTA--TTATA
* *
9443 ATCACAATCGAATTTTTAATAAGTTCTAATAATATAAACAGTTACAGCCTTATAACTTAACAAGT
1 ATCACAACCGAATTTTTAATAAGTTCTAATAATATAAACAGTTACAACCTTATAACTTAACAAGT
* * *
9508 TAAAATAAAAACAAGGTGCAACCTATTAATTTCCATTGCAACAAGATTAGTAATAGGTTTTAATA
66 TAAAATAAAAACAAGGTGCAACCAATTAATTTCCATCGCAACAAGATTAGTAATAAGTTTTAATA
* * * *
9573 ATACAAACGGTTAAAGCCTTATAACTTAACCAGTTCACAAAACAA-AATGGTGACACCTATTACG
131 ATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAA-GGTGAAACCTATTATG
* * * * * *
9637 TTATCATCACAATCAGATATTTAATAGATTTTAATAATATAAACGGTTAAAGCCTTATAACTTAA
195 TTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTAAAGCCTTATAACTTAA
*** * *
9702 CCAGTTCACAAAACAATAAGGAGCAACCTATTA
260 TTGGTTCACAAAACAACAAGGCGCAACCTATTA
9735 CGTTACGATC
Statistics
Matches: 503, Mismatches: 64, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
293 12 0.02
294 205 0.41
295 30 0.06
296 2 0.00
297 2 0.00
298 12 0.02
299 179 0.36
300 57 0.11
301 4 0.01
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (294 bp):
ATCACAACCGAATTTTTAATAAGTTCTAATAATATAAACAGTTACAACCTTATAACTTAACAAGT
TAAAATAAAAACAAGGTGCAACCAATTAATTTCCATCGCAACAAGATTAGTAATAAGTTTTAATA
ATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAAGGTGAAACCTATTATGT
TACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTAAAGCCTTATAACTTAAT
TGGTTCACAAAACAACAAGGCGCAACCTATTATA
Found at i:9634 original size:299 final size:293
Alignment explanation
Indices: 8845--9779 Score: 993
Period size: 299 Copynumber: 3.1 Consensus size: 293
8835 AGCCTTTTAG
* * * * * *
8845 TTAACATCACACCAAATTTTTAATATGTTTTAATAATATAAAAAATTACATCCTTATAACTTAAT
1 TTAA-ATCACAACGAATTTTTAATAAGTTTTAATAATATAAACAGTTACAACCTTATAACTTAA-
* * * * * * *
8910 CAA-ATACAATAAAAACAAGGCT-CAACCTACTACATTAT-CATCT-TAACCGAACTATAAGTAT
64 CAAGTTAAAATAAAAACAAGG-TGCAACCTATTA-ATT-TCCAT-TGCAACAG-ATTATAA-TAA
* *
8971 GTTTTAATAATATAAACGGTTAAAACCTTATAACTTAACC-GATTCACAATACAACAAGGTGAAA
123 GTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCAG-TTCACAAAACAACAAGGTGAAA
* * *
9035 TCTATTATGTTACCATTACAACTGGATTTTTAATAGGTTTTAATAATATAAATGGTTACAA-CCT
187 CCTATTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTA-AAGCCT
* * *
9099 TATAACTTAATTGGTTTACAAAACAACAAGGCGTAAC--CTA-
251 TATAACTTAATTGGTTCACAAAACAACAAGGCGCAACTATTAC
*
9139 TTAAATCACAACCGAATTTTTAAT-AGCTTTTAATAATATAAAC-GATTACAATCTTATAACTTA
1 TTAAATCACAA-CGAATTTTTAATAAG-TTTTAATAATATAAACAG-TTACAACCTTATAACTTA
* * * *
9202 AC-TGATTAAAAATAAAAATAAGGTGCAACCAATT-ATGTTACCATCGCAACCA-ATTATTAATA
63 ACAAG-TT-AAAATAAAAACAAGGTGCAACCTATTAAT-TT-CCATTGCAA-CAGATTA-TAATA
* * *
9264 AGTTTTAGTAATATAAACGGTTAAAGCCTTATAACTTAACCAATTCACAAAACAACAAGGCGAAA
122 AGTTTTAATAATATAAACGGTTAAAGCCTTATAACTTAACCAGTTCACAAAACAACAAGGTGAAA
* *
9329 CCTATTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATTTAAATAGTTAAAGCCTT
187 CCTATTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTAAAGCCTT
* *
9394 GTAACTTAATTGGTTGACAAAACAACAAGGCGCAACATATTACC
252 ATAACTTAATTGGTTCACAAAACAACAAGGCGCAAC-TATTA-C
* *
9438 TTATAATCACAATCGAATTTTTAATAAGTTCTAATAATATAAACAGTTACAGCCTTATAACTTAA
1 TTA-AATCACAA-CGAATTTTTAATAAGTTTTAATAATATAAACAGTTACAACCTTATAACTTAA
*
9503 CAAGTTAAAATAAAAACAAGGTGCAACCTATTAATTTCCATTGCAACAAGATTAGTAATAGGTTT
64 CAAGTTAAAATAAAAACAAGGTGCAACCTATTAATTTCCATTGCAAC-AGATTA-TAATAAGTTT
* *
9568 TAATAATACAAACGGTTAAAGCCTTATAACTTAACCAGTTCACAAAACAA-AATGGTGACACCTA
127 TAATAATATAAACGGTTAAAGCCTTATAACTTAACCAGTTCACAAAACAACAA-GGTGAAACCTA
* * * * * * *
9632 TTACGTTATCATCACAATCAGATATTTAATAGATTTTAATAATATAAACGGTTAAAGCCTTATAA
191 TTATGTTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTAAAGCCTTATAA
*** * *
9697 CTTAACCAGTTCACAAAACAATAAGGAGCAACCTATTAC
256 CTTAATTGGTTCACAAAACAACAAGGCGCAA-CTATTAC
* * * *
9736 GTTACGATCGCAACTGAACTTTTAAT-AGACTTTAATAATATAAA
1 -TTA-AATCACAAC-GAATTTTTAATAAG-TTTTAATAATATAAA
9780 TTGTTAAAGT
Statistics
Matches: 540, Mismatches: 69, Indels: 59
0.81 0.10 0.09
Matches are distributed among these distances:
293 13 0.02
294 203 0.38
295 28 0.05
296 1 0.00
297 3 0.01
298 15 0.03
299 215 0.40
300 58 0.11
301 4 0.01
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (293 bp):
TTAAATCACAACGAATTTTTAATAAGTTTTAATAATATAAACAGTTACAACCTTATAACTTAACA
AGTTAAAATAAAAACAAGGTGCAACCTATTAATTTCCATTGCAACAGATTATAATAAGTTTTAAT
AATATAAACGGTTAAAGCCTTATAACTTAACCAGTTCACAAAACAACAAGGTGAAACCTATTATG
TTACCATCACAACCGGATTTTTAATAGGTTTTAATAATATAAATGGTTAAAGCCTTATAACTTAA
TTGGTTCACAAAACAACAAGGCGCAACTATTAC
Found at i:13952 original size:20 final size:20
Alignment explanation
Indices: 13927--13966 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13917 TTATTATTCC
* *
13927 CAAGGAACTTGTCACTCCGG
1 CAAGGAACTCGTCACGCCGG
13947 CAAGGAACTCGTCACGCCGG
1 CAAGGAACTCGTCACGCCGG
13967 AGTGACAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (20 bp):
CAAGGAACTCGTCACGCCGG
Found at i:18363 original size:14 final size:15
Alignment explanation
Indices: 18344--18384 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
18334 AAATTATTAG
18344 CTTTTAGGTTTA-A-T
1 CTTTTA-GTTTAGATT
18358 CTTTTAGTTTAGATT
1 CTTTTAGTTTAGATT
18373 CTTTTAGTTTAG
1 CTTTTAGTTTAG
18385 TCCATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.59
Consensus pattern (15 bp):
CTTTTAGTTTAGATT
Found at i:18451 original size:14 final size:14
Alignment explanation
Indices: 18432--18462 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18422 TTAGATCTAA
18432 TTTCACCTTAGTCC
1 TTTCACCTTAGTCC
18446 TTTCACCTTAGTCC
1 TTTCACCTTAGTCC
18460 TTT
1 TTT
18463 AATTTAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.32, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTCACCTTAGTCC
Found at i:18647 original size:87 final size:86
Alignment explanation
Indices: 18546--18739 Score: 282
Period size: 87 Copynumber: 2.2 Consensus size: 86
18536 AATTGGTTAA
* * *
18546 AATTAATTAAGTTAATAATTAGAGCATTAAGTTTAAATTCTTCACAATTTAGTCCTTTAGCTTTT
1 AATTAATTAGGTTAATAATTAGAACATTAACTTTAAATTCTTCACAATTTAGTCCTTTAGCTTTT
*
18611 AATTAGATATT-ATTTTTACAT
66 AATTAGATATTCA-TTTGACAT
* * * *
18632 AATTAATTAGGGTTAACAATTAGAACCTTAACTTTAGATTCTTCACAATTTAGTCCTTTATCTTT
1 AATTAATTA-GGTTAATAATTAGAACATTAACTTTAAATTCTTCACAATTTAGTCCTTTAGCTTT
*
18697 TAATTATATATTCATTTGACAT
65 TAATTAGATATTCATTTGACAT
18719 AATTAATTAGGTTAATAATTA
1 AATTAATTAGGTTAATAATTA
18740 CTGCTTTCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
86 20 0.21
87 75 0.78
88 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.45
Consensus pattern (86 bp):
AATTAATTAGGTTAATAATTAGAACATTAACTTTAAATTCTTCACAATTTAGTCCTTTAGCTTTT
AATTAGATATTCATTTGACAT
Found at i:24007 original size:14 final size:14
Alignment explanation
Indices: 23956--24009 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
23946 TCAAAGTCAA
*
23956 CGAGTTGACTCTGTT
1 CGAGTTGACTC-GAT
* *
23971 CGAGTTGAATCAAT
1 CGAGTTGACTCGAT
23985 CGAGTTGACTCGAT
1 CGAGTTGACTCGAT
23999 CGAGTTGACTC
1 CGAGTTGACTC
24010 AGTTCGACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (14 bp):
CGAGTTGACTCGAT
Found at i:24016 original size:29 final size:29
Alignment explanation
Indices: 23952--24006 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
23942 TTAGTCAAAG
*
23952 TCAA-CGAGTTGACTCTGTTCGAGTTGAA
1 TCAATCGAGTTGACTCTGATCGAGTTGAA
23980 TCAATCGAGTTGACTC-GATCGAGTTGA
1 TCAATCGAGTTGACTCTGATCGAGTTGA
24007 CTCAGTTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (29 bp):
TCAATCGAGTTGACTCTGATCGAGTTGAA
Found at i:24783 original size:21 final size:21
Alignment explanation
Indices: 24759--24806 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
24749 TCATATGGTG
24759 AGCTAATAGAATTAATGAATA
1 AGCTAATAGAATTAATGAATA
*
24780 AGCTAATAGAATTAGTGAATA
1 AGCTAATAGAATTAATGAATA
24801 AGCTAA
1 AGCTAA
24807 AAGTGCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (21 bp):
AGCTAATAGAATTAATGAATA
Found at i:25618 original size:32 final size:32
Alignment explanation
Indices: 25574--25650 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
25564 ATAATATCTT
* *
25574 ATATT-AT-AATATAATTGATTATTTTATTA-TA
1 ATATTAATAAATATAA-T-ATTATATTATTAGAA
25605 ATATTAA-AAATATAATATTATATTATTAGAA
1 ATATTAATAAATATAATATTATATTATTAGAA
25636 ATATTAATAAATATA
1 ATATTAATAAATATA
25651 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 11 0.28
31 14 0.35
32 15 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
ATATTAATAAATATAATATTATATTATTAGAA
Found at i:25626 original size:22 final size:23
Alignment explanation
Indices: 25598--25644 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
25588 TTGATTATTT
25598 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
25620 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
25643 TA
1 TA
25645 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:25649 original size:22 final size:22
Alignment explanation
Indices: 25606--25649 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25596 TTTATTATAA
*
25606 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
25628 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
25650 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:26199 original size:17 final size:18
Alignment explanation
Indices: 26177--26217 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
26167 TTTCAGATTT
*
26177 AGATTCCAATT-CTTGAC
1 AGATTCCAATTCCTTCAC
26194 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
26212 AGATTC
1 AGATTC
26218 TAATCCCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:26866 original size:39 final size:39
Alignment explanation
Indices: 26772--26887 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 39
26762 TGTATATTGG
* * * *
26772 ATAAGCACTTCAGTACAAAGGATCAACACAGCCTTATGT
1 ATAAGCACTTCAGTGCAAAGGATCAACGCAACCTTATGC
* * * *
26811 GTAAGTAGGTT-TGTGCAAAGGATCAACGCAACCTTATGC
1 ATAAGCA-CTTCAGTGCAAAGGATCAACGCAACCTTATGC
* **
26850 ATAAGCACTTCGGTGCAAAGGATTGACGCAACCTTATG
1 ATAAGCACTTCAGTGCAAAGGATCAACGCAACCTTATG
26888 TGTAAGTACT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
38 2 0.03
39 57 0.93
40 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (39 bp):
ATAAGCACTTCAGTGCAAAGGATCAACGCAACCTTATGC
Found at i:26899 original size:39 final size:39
Alignment explanation
Indices: 26823--26945 Score: 131
Period size: 39 Copynumber: 3.1 Consensus size: 39
26813 AAGTAGGTTT
** * *
26823 GTGCAAAGGATCAACGCAACCTTATGCATAAGCACTTCG
1 GTGCAAAGGATTGACGCAACCTTATGCGTAAGTACTTCG
*
26862 GTGCAAAGGATTGACGCAACCTTATGTGTAAGTACTTCG
1 GTGCAAAGGATTGACGCAACCTTATGCGTAAGTACTTCG
** * *
26901 AAGCAAAAAGGGTTGATGCAACCTTATGCGTAA-TCACTTCG
1 GTGC--AAAGGATTGACGCAACCTTATGCGTAAGT-ACTTCG
26942 GTGC
1 GTGC
26946 GACTCGAATA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 36 0.52
40 1 0.01
41 32 0.46
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (39 bp):
GTGCAAAGGATTGACGCAACCTTATGCGTAAGTACTTCG
Found at i:26907 original size:78 final size:79
Alignment explanation
Indices: 26772--26945 Score: 181
Period size: 78 Copynumber: 2.2 Consensus size: 79
26762 TGTATATTGG
* * * * * *
26772 ATAAGCACTTCAGTACAAAGGATCAACACAGCCTTATGTGTAAGTAGGTTTGTGC-AAAGGATCA
1 ATAAGCACTTCGGTGCAAAGGATCAACACAACCTTATGTGTAAGTAGCTTCGAGCAAAAGGATCA
26836 ACGCAACCTTATGC
66 ACGCAACCTTATGC
** * *
26850 ATAAGCACTTCGGTGCAAAGGATTGACGCAACCTTATGTGTAAGTA-CTTCGAAGCAAAAAGGGT
1 ATAAGCACTTCGGTGCAAAGGATCAACACAACCTTATGTGTAAGTAGCTTCG-AGC-AAAAGGAT
** *
26914 TGATGCAACCTTATGC
64 CAACGCAACCTTATGC
* *
26930 GTAATCACTTCGGTGC
1 ATAAGCACTTCGGTGC
26946 GACTCGAATA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
77 3 0.04
78 42 0.54
80 33 0.42
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (79 bp):
ATAAGCACTTCGGTGCAAAGGATCAACACAACCTTATGTGTAAGTAGCTTCGAGCAAAAGGATCA
ACGCAACCTTATGC
Found at i:27933 original size:3 final size:3
Alignment explanation
Indices: 27911--27964 Score: 72
Period size: 3 Copynumber: 17.0 Consensus size: 3
27901 CTATATATAT
*
27911 TTA TTA CTA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
27959 TTA TTA
1 TTA TTA
27965 CTAGTACTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 38 0.83
4 7 0.15
5 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28380 original size:22 final size:22
Alignment explanation
Indices: 28346--28388 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28336 GTAAAGAAAC
28346 GAAAAAACAAAG-AGATAAAATT
1 GAAAAAACAAAGAAGA-AAAATT
28368 GAAAAAA-AGAAGAAGAAAAAT
1 GAAAAAACA-AAGAAGAAAAAT
28389 AGAGGAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.05
22 15 0.79
23 3 0.16
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.09
Consensus pattern (22 bp):
GAAAAAACAAAGAAGAAAAATT
Found at i:35971 original size:54 final size:54
Alignment explanation
Indices: 35878--36511 Score: 790
Period size: 54 Copynumber: 11.8 Consensus size: 54
35868 AAACAATATT
* * *
35878 ATGTTTTCAAATGAAGTTTGAAAGAAGCTAAGCCCGATTTTCAAGGGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * * *
35932 ATGTCTTT-AAATGAAGTTTGAAAGAAACTAAGCCTGATTTTTTAGGGGTTTCTTG
1 ATGT-TTTCAAATGAATTTTTAAAGAAGCTAAGCCTGA-TTTTCAAGGGTTTCTTG
* * *
35987 ATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * *
36041 ATGTTTTCAAATGAATATTTAAAGAAGCTAAGGCAGATTTTCAAGGGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * * *
36095 ATGTCTTCAAATGAATTTTAAAAGAATCTAAGTCTGATTTTCAAGAGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * * *
36149 ATGTCTTCAAATGAATTTTGAAAGAAGCTAAGACTAATTTTCAGGGGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * *
36203 ATGTTTTCAAAAGAATTTTTAAATAAGTTAAGCCTAATTTTCAAGGGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * * * *
36257 ATGTCTTCAAATGAATTTTGAAATAAACTAAGCCTGATTTACAAGGGTTTCTTT
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * *
36311 ATGTTTTCAAATGAAATTTTAAAGAAGCTAAGCCTAATTTTCATGGGTTTATTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* * * * *
36365 ATATTTTAAAATGAATTTTTAAAGGAGCTAAGCTTGATTTTC-AGGGCTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
* *
36418 ATGTTTTCAAATGAATTTTTAAAGGAGCTACA-CCTGATTTTCAGGGGTTTCTTG
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTA-AGCCTGATTTTCAAGGGTTTCTTG
* *
36472 ATGTCTTCAAATGAATTTTTAAAGAAGATAAGCCT-ATTTT
1 ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTT
36512 TTAGGGATTT
Statistics
Matches: 507, Mismatches: 67, Indels: 13
0.86 0.11 0.02
Matches are distributed among these distances:
53 51 0.10
54 407 0.80
55 49 0.10
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (54 bp):
ATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTG
Found at i:42458 original size:39 final size:39
Alignment explanation
Indices: 42403--42568 Score: 233
Period size: 39 Copynumber: 4.2 Consensus size: 39
42393 TGTATATTGG
**
42403 ATAAGCACTTCGGTGCAAAGGATATACGCAACCTTATGC
1 ATAAGCACTTCGGTGCAAAGGATCGACGCAACCTTATGC
* *
42442 GTAAGCACTTCAGTGCAAAGGATCGACGCAACCTTATGC
1 ATAAGCACTTCGGTGCAAAGGATCGACGCAACCTTATGC
* *
42481 ATAAACACTTCGGTGCAAAGGATCGACGCAACATTATGC
1 ATAAGCACTTCGGTGCAAAGGATCGACGCAACCTTATGC
* * *
42520 GTAAGCACTTCGATGCAAAAAGGGTCGACGCAACCTTATGC
1 ATAAGCACTTCGGTGC--AAAGGATCGACGCAACCTTATGC
42561 ATAAGCAC
1 ATAAGCAC
42569 ATAGGTGCGA
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 83 0.75
41 28 0.25
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (39 bp):
ATAAGCACTTCGGTGCAAAGGATCGACGCAACCTTATGC
Found at i:43924 original size:55 final size:54
Alignment explanation
Indices: 43787--44635 Score: 895
Period size: 55 Copynumber: 15.5 Consensus size: 54
43777 TTCCATGGTT
* * * * ** *
43787 TTGCACACATAGTGCCTATACGGTAATCCACAAACTCATTATGAATTACATTGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATT-TGTGGGG
* * * * * *
43842 -TGCACAGATATTGCCAATA-TGATAATTCATAAAATCATTATGAATTATATGGTG
1 TTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTATGAATT-TGTGGGG
* * * *
43896 TTGCACACATAGTACCAATACGGAAATTCATAAACACGTTATGAATTTCAT-GGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT-GTGGGG
*
43950 TTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTATGAATTTTGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAA-TTTGTGGGG
* * * * * *
44005 TTGCACACATAATGCTAACACGAAAATTCATAAAATAATTATGAATTTTGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAA-TTTGTGGGG
* * *
44060 TTGTACACATAGTGTCAATACGGAGATTCAT-AACTCATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT-GTGGGG
* * *
44114 TTGCACTCATGGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGA
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT-GTGGGG
* * * *
44169 TTGTACACATAGTTCCAATACGAAAATTCATAAACTAATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT-GTGGGG
* *** *
44224 TTGCACACATAGCGCCAATATACAAATTCATAAATTCATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT-GTGGGG
* *
44279 TTGCACACATAGTGCCAATAC-GATAATTCATAATCTCATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTATGAATT-TGTGGGG
* * * * **
44334 TTGAAAACATAATGCAAATATAGAAATTCATAAACTCATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT-GTGGGG
* * *
44389 TTGCACACATAGTGCCAATAC-GATAAATCATAAACTTATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTATGAATT-TGTGGGG
* * ** * * * *
44444 TTGCACACATAATGCAAATATAGAAATTAAAAAACTCAATATGAATTAGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTGTGGGG
*
44498 TTGCACACATAGTGCCAATACGGAAATTCAGAAACTCATTATGAATTTTGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAA-TTTGTGGGG
** *
44553 TTGCACACATAGTG-CATATACAAAAATTCATTAACTCATTATGAAATTCT-TGGGG
1 TTGCACACATAGTGCCA-ATACGGAAATTCATAAACTCATTATG-AATT-TGTGGGG
* *
44608 TTGCACACATAGTGTCAATACAGAAATT
1 TTGCACACATAGTGCCAATACGGAAATT
44636 GAAACATATA
Statistics
Matches: 670, Mismatches: 104, Indels: 40
0.82 0.13 0.05
Matches are distributed among these distances:
53 4 0.01
54 178 0.27
55 477 0.71
56 11 0.02
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTGTGGGG
Found at i:44263 original size:110 final size:110
Alignment explanation
Indices: 43764--44633 Score: 955
Period size: 109 Copynumber: 7.9 Consensus size: 110
43754 TGAATATATT
* * * ** * ** * * *
43764 AACTCATTATAAATTCCATGGTTTTGCACACATAGTGCCTATACGGTAATCCACAAACTCATTAT
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTAT
* * * * * * *
43829 GAATTACATTGGG-TGCACAGATATTGCCAATATGATAATTCATA
66 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * * ** * *
43873 AAATCATTATGAATTAT-ATGGTGTTGCACACATAGTACCAATACGGAAATTCATAAACACGTTA
1 AACTCATTATGAATT-TCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTA
* * *
43937 TGAATTTCAT-GGGTTGCACACATAGTGCCAATATGGAAATTCATA
65 TGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * * * * *
43982 AACTCATTATGAATTTTGTGGGGTTGCACACATAATGCTAACA-CGAAAATTCATAAAATAATTA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAG-AAATTCATAAACTCATTA
* * * * *
44046 TGAATTTTGTGGGGTTGTACACATAGTGTCAATACGGAGATTCAT-
65 TGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * **
44091 AACTCATTATGAATTTCGTGGGGTTGCACTCATGGTGCCAATACGGAAATTCATAAACTCATTAT
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTAT
* * *
44156 GAATTTCGTGGGATTGTACACATAGTTCCAATACGAAAATTCATA
66 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
44201 AACTAATTATGAATTTCGTGGGGTTGCACACATAGCGCCAATATACAAATTCATAAATTCATTAT
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTAT
*
44266 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGATAATTCATA
66 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * * * *
44311 ATCTCATTATGAATTACGTGGGGTTGAAAACATAATGCAAATATAGAAATTCATAAACTCATTAT
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTAT
44376 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGATAAA-TCATA
66 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGA-AAATTCATA
* * * * * * *
44421 AACTTATTATGAATTACGTGGGGTTGCACACATAATGCAAATATAGAAATTAAAAAACTCAATAT
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTAT
* * *
44486 GAA-TTAGTGGGGTTGCACACATAGTGCCAATACGGAAATTCAGA
66 GAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
* * * *
44530 AACTCATTATGAATTTTGTGGGGTTGCACACATAGTG-CATATACAAAAATTCATTAACTCATTA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA-ATATAGAAATTCATAAACTCATTA
* * *
44594 TGAAATTCTTGGGGTTGCACACATAGTGTCAATACAGAAA
65 TGAATTTCGTGGGGTTGCACACATAGTGCCAATAC-GAAA
44634 TTGAAACATA
Statistics
Matches: 652, Mismatches: 97, Indels: 22
0.85 0.13 0.03
Matches are distributed among these distances:
108 9 0.01
109 325 0.50
110 313 0.48
111 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (110 bp):
AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATATAGAAATTCATAAACTCATTAT
GAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATA
Found at i:44635 original size:164 final size:164
Alignment explanation
Indices: 43764--44635 Score: 943
Period size: 164 Copynumber: 5.3 Consensus size: 164
43754 TGAATATATT
* ** * * * *
43764 AACTCATTAT-AAATTCCATGGTTTTGCACACATAGTGCCTATACGGTAATCCACAAACTCATTA
1 AACTCATTATGAAATT-CGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTA
* * * * * * * *
43828 TGAATTACATTGGG-TGCACAGATATTGCCAATA-TGATAATTCATAAAATCATTATGAATTATA
65 TGAATTA-GTGGGGTTGCACACATAATGCCAATACGGA-AATTCATAAACTCATTATGAATTTTG
* * *
43891 TGGTGTTGCACACATAGTACCAATACGGAAATTCATA
128 TGGGGTTGCACACATAGTGCCAATACAGAAATTCATA
* * * * *
43928 AACACGTTATGAATTTCAT-GGGTTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTAT
1 AACTCATTATGAAATTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTAT
* * * * * *
43992 GAATTTTGTGGGGTTGCACACATAATGCTAACACGAAAATTCATAAAATAATTATGAATTTTGTG
66 GAA-TTAGTGGGGTTGCACACATAATGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTG
* * * *
44057 GGGTTGTACACATAGTGTCAATACGGAGATTCAT-
130 GGGTTGCACACATAGTGCCAATACAGAAATTCATA
* * *
44091 AACTCATTATGAATTTCGTGGGGTTGCACTCATGGTGCCAATACGGAAATTCATAAACTCATTAT
1 AACTCATTATGAAATTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTAT
* * * * * * * *
44156 GAATTTCGTGGGATTGTACACATAGTTCCAATACGAAAATTCATAAACTAATTATGAATTTCGTG
66 GAA-TTAGTGGGGTTGCACACATAATGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTG
* * *
44221 GGGTTGCACACATAGCGCCAATATACAAATTCATA
130 GGGTTGCACACATAGTGCCAATACAGAAATTCATA
* * *
44256 AATTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATAC-GATAATTCATAATCTCATTA
1 AACTCATTATGAAATTCGTGGGGTTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTA
* * * ** *
44320 TGAATTACGTGGGGTTGAAAACATAATGCAAATATAGAAATTCATAAACTCATTATGAATTTCGT
65 TGAATTA-GTGGGGTTGCACACATAATGCCAATACGGAAATTCATAAACTCATTATGAATTTTGT
*
44385 GGGGTTGCACACATAGTGCCAATAC-GATAAATCATA
129 GGGGTTGCACACATAGTGCCAATACAGA-AATTCATA
* * * ** * * *
44421 AACTTATTATG-AATTACGTGGGGTTGCACACATAATGCAAATATAGAAATTAAAAAACTCAATA
1 AACTCATTATGAAATT-CGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTA
* *
44485 TGAATTAGTGGGGTTGCACACATAGTGCCAATACGGAAATTCAGAAACTCATTATGAATTTTGTG
65 TGAATTAGTGGGGTTGCACACATAATGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTG
* *
44550 GGGTTGCACACATAGTG-CATATACAAAAATTCATT
130 GGGTTGCACACATAGTGCCA-ATACAGAAATTCATA
* * *
44585 AACTCATTATGAAATTCTTGGGGTTGCACACATAGTGTCAATACAGAAATT
1 AACTCATTATGAAATTCGTGGGGTTGCACACATAGTGCCAATACGGAAATT
44636 GAAACATATA
Statistics
Matches: 599, Mismatches: 95, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
163 63 0.11
164 332 0.55
165 202 0.34
166 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (164 bp):
AACTCATTATGAAATTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTAT
GAATTAGTGGGGTTGCACACATAATGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTGG
GGTTGCACACATAGTGCCAATACAGAAATTCATA
Found at i:50857 original size:51 final size:52
Alignment explanation
Indices: 50796--50899 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 52
50786 CCATGGTTTT
* * *
50796 ACACACATAGTACCGATATGGTAATTCACAAAATC-ATGAATTACGTGGGGC
1 ACACAAATAGTACCAATACGGTAATTCACAAAATCTATGAATTACGTGGGGC
* * *
50847 ACACAAATAGTGCCAATACGGTAATTCATAAACTCGTTATGAATTACGTGGGG
1 ACACAAATAGTACCAATACGGTAATTCACAAAATC--TATGAATTACGTGGGG
50900 TTGCGCACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 29 0.66
54 15 0.34
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (52 bp):
ACACAAATAGTACCAATACGGTAATTCACAAAATCTATGAATTACGTGGGGC
Found at i:50928 original size:55 final size:55
Alignment explanation
Indices: 50831--51532 Score: 985
Period size: 55 Copynumber: 12.8 Consensus size: 55
50821 TCACAAAATC
* ** * * * *
50831 ATGAATTACGTGGGG-CACACAAATAGTGCCAATACGGTAATTCATAAACTCGTT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * ** *
50885 ATGAATTACGTGGGGTTGCGCACATAGTATCAATACAGAAATTCACAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * *
50940 ATGAATTTCATGGGGCTGCACACATAGTGCCAATGCAGAAATTCATAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * *
50995 ATGAATTTCGTGGGGTTGTACTCATAGTGCCAATAGAGAAATTCATAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * *
51050 ATGAATTTCGTGGGGTTGTACACTTAGTGCCAATACGGAAATTCATAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* **
51105 ATGAATTTCGTGGGGCTGCACACATAGTGTTAATACAGAAATTCATAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * *
51160 TTGAATTTCGTGGGGTTGCACACATAGTGTCAATACAGAAATTCACAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* *
51215 ATGAATTTCGTGGGGTTGTACACATAGTGCCAATACAGAAATTCATAAACTCAAT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * *
51270 ATGAATTTCGTGGGGTTGCACACATAATGCCAATACGGTAATTCATAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* * * * ** *
51325 ATGAATTACGTGAGATTGAACACATAGTGCCAATATGGAAATTCACAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* *
51380 ATGAATTAT-GTGGGGTTTCACACATAGTGCCAATACGGAAATTCATAAACTCATT
1 ATGAATT-TCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
* *
51435 CTGAATTTCGTGGGGTTGCACACATAGTACCAATACAGAAATTCATAAACTCATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
*
51490 ATGAATTTCGTGGGGTTACACACATAGTGCCAATACAGAAATT
1 ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATT
51533 GCAGCATATA
Statistics
Matches: 575, Mismatches: 70, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
54 16 0.03
55 559 0.97
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (55 bp):
ATGAATTTCGTGGGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATT
Found at i:52226 original size:20 final size:21
Alignment explanation
Indices: 52183--52226 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
52173 CAACTAACTT
** *
52183 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
52204 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
52224 ACA
1 ACA
52227 CTCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:61589 original size:19 final size:19
Alignment explanation
Indices: 61565--61631 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
61555 GGATTCTATT
61565 TAATATATATATATATATA
1 TAATATATATATATATATA
*
61584 TAATATATTTATATATATA
1 TAATATATATATATATATA
* * * *
61603 TAATTTTTCAAAAATATATA
1 TAATATAT-ATATATATATA
61623 TAATATATA
1 TAATATATA
61632 GTTTTGAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 25 0.64
20 14 0.36
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATATATATATATATATA
Found at i:61591 original size:17 final size:17
Alignment explanation
Indices: 61569--61602 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61559 TCTATTTAAT
61569 ATATATATATATATATA
1 ATATATATATATATATA
*
61586 ATATATTTATATATATA
1 ATATATATATATATATA
61603 TAATTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:61624 original size:2 final size:2
Alignment explanation
Indices: 61567--61604 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
61557 ATTCTATTTA
*
61567 AT AT AT AT AT AT AT AT AT A- AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61605 ATTTTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61636 original size:26 final size:24
Alignment explanation
Indices: 61593--61641 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
61583 ATAATATATT
*
61593 TATATATATATAATTTTTCAAAAA
1 TATATATATATAAGTTTTCAAAAA
*
61617 TATATATAATATATAGTTTTGAAAA
1 TATATAT-ATATA-AGTTTTCAAAA
61642 CATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (24 bp):
TATATATATATAAGTTTTCAAAAA
Found at i:61714 original size:37 final size:37
Alignment explanation
Indices: 61608--61966 Score: 284
Period size: 36 Copynumber: 9.5 Consensus size: 37
61598 ATATATAATT
* *
61608 TTTCAAAAATATATATAATATATAG-TTTTGAAAACA
1 TTTCGAAAATATATATAATATATAGTTTTTGAAAAAA
** * *
61644 TTTTAAAAATTTGTATAATATATAG-TTTT-AAAAAA
1 TTTCGAAAATATATATAATATATAGTTTTTGAAAAAA
** *
61679 AATCGAAAATATATATAATATATAGTTTTTGAAAAAT
1 TTTCGAAAATATATATAATATATAGTTTTTGAAAAAA
** **
61716 TTTAAAAATATATATATAATATATAGTTTTTGAAAACC
1 TTTCGAAA-ATATATATAATATATAGTTTTTGAAAAAA
61754 TTTCGAAAATATATATATAATATATAGTTTTT-AAAAACA
1 TTTCG-AAA-ATATATATAATATATAGTTTTTGAAAAA-A
* *
61793 TTTTGAAAATATATAT-A-ATATAGTTTTTAATATATAATATTA
1 TTTCGAAAATATATATAATATATAGTTTTT--GA-A-AA-A--A
* * * *
61835 GTTTTGAAAACATTTTAATATATATATAG-TTTTGAAAACA
1 -TTTCGAAAATA-TAT-ATA-ATATATAGTTTTTGAAAAAA
* * * *
61875 TTTTGAAAATATATATAATATATAGTTTTTTACAACA
1 TTTCGAAAATATATATAATATATAGTTTTTGAAAAAA
* * *
61912 TTTTGAAAATAGATATAATATATAG-TTTTGAAAACA
1 TTTCGAAAATATATATAATATATAGTTTTTGAAAAAA
*
61948 TTTTGAAAATATATATAAT
1 TTTCGAAAATATATATAAT
61967 TTTAAAATGT
Statistics
Matches: 269, Mismatches: 35, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
35 35 0.13
36 66 0.25
37 53 0.20
38 40 0.15
39 41 0.15
40 3 0.01
41 1 0.00
42 1 0.00
43 12 0.04
44 3 0.01
45 3 0.01
47 5 0.02
48 6 0.02
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (37 bp):
TTTCGAAAATATATATAATATATAGTTTTTGAAAAAA
Found at i:61742 original size:73 final size:73
Alignment explanation
Indices: 61613--61964 Score: 313
Period size: 73 Copynumber: 4.6 Consensus size: 73
61603 TAATTTTTCA
* *
61613 AAAATATATATAATATATAGTTTTGAAAACATTTTAAAA-ATTTGTATAATATATAG-TTTTAAA
1 AAAATATATATAATATATAGTTTTGAAAACATTTTAAAATATATATATAATATATAGTTTTTAAA
61676 AAAAATCG
66 AAAAATCG
61684 AAAATATATATAATATATAGTTTTTGAAAA-ATTTTAAAAATATATATATAATATATAGTTTTTG
1 AAAATATATATAATATATAG-TTTTGAAAACATTTT-AAAATATATATATAATATATAGTTTTT-
****
61748 AAAACCTTTCG
63 AAAAAAAATCG
* *
61759 AAAATATATATATAATATATAGTTTTTAAAAACATTTTGAAA-ATATATAT-A-ATATAGTTTTT
1 -AAA-ATATATATAATATATAG-TTTTGAAAACATTTTAAAATATATATATAATATATAGTTTTT
*
61821 AATATATAATATTAGTTTTG
63 AA-A-A-AA-A--A---TCG
* * *
61841 AAAACATTTTAATATATATATAGTTTTGAAAACATTTTGAAA-ATATATATAATATATAGTTTTT
1 AAAATA-TAT-ATA-ATATATAGTTTTGAAAACATTTTAAAATATATATATAATATATAG-TTTT
* * ** *
61905 TACAACATTTTG
62 TAAAAAAAATCG
*
61917 AAAATAGATATAATATATAGTTTTGAAAACATTTTGAAAATATATATA
1 AAAATATATATAATATATAGTTTTGAAAACATTTT-AAAATATATATA
61965 ATTTTAAAAT
Statistics
Matches: 232, Mismatches: 24, Indels: 46
0.77 0.08 0.15
Matches are distributed among these distances:
71 25 0.11
72 13 0.06
73 40 0.17
74 22 0.09
75 17 0.07
76 19 0.08
77 29 0.12
78 5 0.02
80 2 0.01
81 5 0.02
82 32 0.14
83 10 0.04
84 7 0.03
85 6 0.03
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (73 bp):
AAAATATATATAATATATAGTTTTGAAAACATTTTAAAATATATATATAATATATAGTTTTTAAA
AAAAATCG
Found at i:61855 original size:28 final size:28
Alignment explanation
Indices: 61817--61891 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
61807 ATAATATAGT
61817 TTTTAATATATAATATTAGTTTTGAAAACA
1 TTTTAATATAT-ATA-TAGTTTTGAAAACA
61847 TTTTAATATATATATAGTTTTGAAAACA
1 TTTTAATATATATATAGTTTTGAAAACA
*
61875 TTTTGAAAATATATATA
1 TTTT-AATATATATATA
61892 ATATATAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
28 18 0.42
29 14 0.33
30 11 0.26
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (28 bp):
TTTTAATATATATATAGTTTTGAAAACA
Found at i:61887 original size:29 final size:29
Alignment explanation
Indices: 61829--61993 Score: 111
Period size: 37 Copynumber: 5.2 Consensus size: 29
61819 TTAATATATA
*
61829 ATAT-TAGTTTTGAAAACATTTT-AATAT
1 ATATATAGTTTTGAAAACATTTTGAAAAT
61856 ATATATAGTTTTGAAAACATTTTGAAAATATATAT
1 ATATATAGTTTTGAAAACATTTTG---A-A-A-AT
* *
61891 AATATATAGTTTTTTACAACATTTTGAAAATAGATAT
1 -ATATATAG-TTTTGAAAACATTTTG---A-A-A-AT
61928 AATATATAGTTTTGAAAACATTTTGAAAAT
1 -ATATATAGTTTTGAAAACATTTTGAAAAT
* **
61958 ATATATAATTTT-AAAATGTTTTTGAAAAT
1 ATATATAGTTTTGAAAA-CATTTTGAAAAT
61987 ATATATA
1 ATATATA
61994 ATATATATAG
Statistics
Matches: 118, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
27 4 0.03
28 22 0.19
29 28 0.24
30 2 0.02
31 1 0.01
32 2 0.02
33 2 0.02
35 2 0.02
36 22 0.19
37 33 0.28
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (29 bp):
ATATATAGTTTTGAAAACATTTTGAAAAT
Found at i:62048 original size:12 final size:12
Alignment explanation
Indices: 62027--62081 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 12
62017 TTTCGAAAAC
62027 ATTTTT-TTATT
1 ATTTTTATTATT
62038 ATTTTTATTATT
1 ATTTTTATTATT
*
62050 -TATTTATTTATTT
1 ATTTTTA-TTA-TT
*
62063 ATTTTTATTTTT
1 ATTTTTATTATT
62075 CATTTTT
1 -ATTTTT
62082 TTCTATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 11 0.31
12 10 0.28
13 10 0.28
14 5 0.14
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:62070 original size:25 final size:24
Alignment explanation
Indices: 62026--62079 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
62016 GTTTCGAAAA
*
62026 CATTTTTTTATTATTTTTATTATTT
1 CATTTATTTATTATTTTTATT-TTT
62051 -ATTTATTTATTTATTTTTATTTTT
1 CATTTATTTA-TTATTTTTATTTTT
62075 CATTT
1 CATTT
62080 TTTTCTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (24 bp):
CATTTATTTATTATTTTTATTTTT
Found at i:62079 original size:7 final size:6
Alignment explanation
Indices: 62027--62081 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
62017 TTTCGAAAAC
* *
62027 ATTTTT -TTATT ATTTTT ATTATTT ATTTATT -TATTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATT-TTT ATTT-TT ATTTTT ATTTTT ATTTTT
62075 CATTTTT
1 -ATTTTT
62082 TTCTATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
5 6 0.15
6 20 0.50
7 14 0.35
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:62775 original size:23 final size:23
Alignment explanation
Indices: 62749--62802 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
62739 TGGGTTTTTC
*
62749 CGGCTACCGGAGGCTACGATCAG
1 CGGCCACCGGAGGCTACGATCAG
* *
62772 CGGCCATCGGAGGCTGCGATCAG
1 CGGCCACCGGAGGCTACGATCAG
*
62795 CTGCCACC
1 CGGCCACC
62803 AGGCGTTGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.35, G:0.33, T:0.13
Consensus pattern (23 bp):
CGGCCACCGGAGGCTACGATCAG
Done.