Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 29 of 31
Found at i:13309645 original size:12 final size:12
Alignment explanation
Indices: 13309613--13309683 Score: 60
Period size: 13 Copynumber: 5.9 Consensus size: 12
13309603 AAATATTATT
* *
13309613 ATATAAAAATTA
1 ATATATAAATAA
13309625 ATAATATAAATAA
1 AT-ATATAAATAA
13309638 ATATATAAAATAA
1 ATATAT-AAATAA
13309651 A-ATATAAATATTA
1 ATATATAAATA--A
13309664 ATA-ATAAATAA
1 ATATATAAATAA
13309675 A-ATA-AAATA
1 ATATATAAATA
13309684 TATGACATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
10 6 0.12
11 8 0.16
12 10 0.20
13 26 0.51
14 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATATATAAATAA
Found at i:13309657 original size:29 final size:29
Alignment explanation
Indices: 13309625--13309769 Score: 91
Period size: 29 Copynumber: 4.9 Consensus size: 29
13309615 ATAAAAATTA
13309625 ATAATATAAATAAATATATAAAATAAAAT
1 ATAATATAAATAAATATATAAAATAAAAT
* *
13309654 ATAAATATTAAT-AATAAATAAAATAAAAT
1 AT-AATATAAATAAATATATAAAATAAAAT
* * * **
13309683 ATATGACATTAAA-ATATATTTAAGAA-ATGAT
1 ATA--ATA-TAAATAAATATATAA-AATAAAAT
*
13309714 ATTATATAAA-ATAATAATATAAAATATAAAT
1 ATAATATAAATA-AAT-ATATAAAATA-AAAT
* * *
13309745 ATATTAAAAATAAAAATATAAAATA
1 ATAATATAAATAAATATATAAAATA
13309770 TTTAATAATA
Statistics
Matches: 86, Mismatches: 19, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
28 6 0.07
29 26 0.30
30 26 0.30
31 25 0.29
32 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (29 bp):
ATAATATAAATAAATATATAAAATAAAAT
Found at i:13309666 original size:17 final size:19
Alignment explanation
Indices: 13309612--13309678 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
13309602 AAAATATTAT
*
13309612 TATATAAAAATTAATAATA
1 TATATAAATATTAATAATA
*
13309631 TAAATAAATATATAA-AATAA
1 TATATAAATAT-TAATAAT-A
*
13309651 AATATAAATATTAATAATA
1 TATATAAATATTAATAATA
*
13309670 AATA-AAATA
1 TATATAAATA
13309679 AAATATATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 20 0.49
20 16 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TATATAAATATTAATAATA
Found at i:13309683 original size:17 final size:17
Alignment explanation
Indices: 13309499--13309683 Score: 50
Period size: 20 Copynumber: 10.7 Consensus size: 17
13309489 TAAAACAAAT
13309499 TAAAATAAAATATATAATA
1 TAAAATAAAATA-ATAA-A
*
13309518 TAAAA-AAATATTAAAGAAA
1 TAAAATAAA-A-T-AATAAA
13309537 TGAAAATAAAAT-AT--A
1 T-AAAATAAAATAATAAA
* *
13309552 TAAAATTATATAATAAA
1 TAAAATAAAATAATAAA
*
13309569 TAAAAATAAAATATATGACAT
1 T-AAAATAAAATA-AT-A-AA
* * *
13309590 TAAAATATATTCA-AAA
1 TAAAATAAAATAATAAA
** * *
13309606 TATTATTATATAA-AAA
1 TAAAATAAAATAATAAA
*
13309622 TTAATAATATAAATAAATATA
1 -TAA-AATA-AAAT-AATAAA
13309643 TAAAATAAAAT-ATAAA
1 TAAAATAAAATAATAAA
*
13309659 T---AT-TAATAATAAA
1 TAAAATAAAATAATAAA
13309672 TAAAATAAAATA
1 TAAAATAAAATA
13309684 TATGACATTA
Statistics
Matches: 118, Mismatches: 26, Indels: 46
0.62 0.14 0.24
Matches are distributed among these distances:
12 3 0.03
13 8 0.07
14 8 0.07
15 4 0.03
16 17 0.14
17 10 0.08
18 18 0.15
19 19 0.16
20 23 0.19
21 8 0.07
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAATAAAATAATAAA
Found at i:13309761 original size:23 final size:23
Alignment explanation
Indices: 13309729--13309910 Score: 107
Period size: 23 Copynumber: 7.8 Consensus size: 23
13309719 ATAAAATAAT
13309729 AATATAAAATATAAATATATTAAA
1 AATA-AAAATATAAATATATTAAA
*
13309753 AATAAAAATATAAAATATTTAATAATA
1 AATAAAAATAT-AAATA--TATTAA-A
*
13309780 AATAAAAATA-AAATATA-T-GA
1 AATAAAAATATAAATATATTAAA
* *
13309800 CATTAAAA-AT--ATAT-TTAAGA
1 AATAAAAATATAAATATATTAA-A
** *
13309820 AATGATATTATATAAA-A-ATTAAT
1 AAT-A-AAAATATAAATATATTAAA
13309843 AATAAAAATATAAATATATTAAA
1 AATAAAAATATAAATATATTAAA
13309866 AAT-AAAATATAAAATATTATAATAATA
1 AATAAAAATAT-AAATA-TAT--TAA-A
13309893 AATAAAAATA-AAATATAT
1 AATAAAAATATAAATATAT
13309911 GACATTAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 43
0.69 0.07 0.24
Matches are distributed among these distances:
18 5 0.04
19 1 0.01
20 10 0.08
21 8 0.07
22 12 0.10
23 27 0.22
24 17 0.14
25 9 0.07
26 13 0.11
27 15 0.12
28 6 0.05
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAAAAATATAAATATATTAAA
Found at i:13310031 original size:336 final size:319
Alignment explanation
Indices: 13309539--13310195 Score: 1070
Period size: 336 Copynumber: 2.0 Consensus size: 319
13309529 TAAAGAAATG
13309539 AAAATAAAATATATAAAATTATATAATAAATAAAAATAAAATATATGACATTAAAATATATTCAA
1 AAAATAAAATATATAAAATTATATAATAAATAAAAATAAAATATATGACATTAAAATATATTCAA
*
13309604 AATATTATTATATAAAAATTAATAATATAAATAAATATATAAAATAAAATATAAATATTAATAAT
66 AATATTATTATATAAAAATTAATAATAAAAATAAATATATAAAATAAAATATAAATATTAATAAT
13309669 AAATAAAATAAAATATATGACATTAAAATATATTTAAGAAATGATATTATATAAAA-TAATAATA
131 AAATAAAATAAAATATATGACATTAAAATATATTTAAGAAATGATATTATATAAAATTAATAATA
13309733 TAAAATATAAATATATTAAAAATAAAAATATAAAATATT-TAATAATAAATAAAAATAAAATATA
196 -AAAATATAAATATATTAAAAAT-AAAA-A-AAAATATTATAATAATAAATAAAAAT-AAATATA
13309797 TGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATAT
256 TGACATTAAAAAT-TATTTAAG-AATGATATTATATAAAAATTAATAATAAAAATATAAA-ATAT
13309862 TA
318 TA
13309864 AAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATT
1 AAAATAAAATATATAAA-ATTAT-ATAATAAATAAAAATAAAATATATGACATT-AAAATATATT
13309928 CAAAATATGATATTATATAAAAATTAATAATAAAAATATAAATATATTAAAAATAAAATATAAAA
63 CAAAATAT--TATTATATAAAAATTAATAAT-AAAA-ATAAATATA-T-AAAATAAAATAT-AAA
13309993 TACTATAATAATAAATAAAA-ATAAATATATGACATTAAAATATATTTAAGAAATGATATTATAT
121 TA-T-TAATAATAAATAAAATA-AAATATATGACATTAAAATATATTTAAGAAATGATATTATAT
13310057 AAAATTAATAATAAAAATATAAATATATTAAAAATAAAAAAAAATATTATAATAATAAATAAAAA
183 AAAATTAATAATAAAAATATAAATATATTAAAAATAAAAAAAAATATTATAATAATAAATAAAAA
* *
13310122 TAAATATATGATATTAAAAATTATTTAAGAATGATATTATATAGAAATTAATAATAAAAATATAA
248 TAAATATATGACATTAAAAATTATTTAAGAATGATATTATATAAAAATTAATAATAAAAATATAA
13310187 AATATTA
313 AATATTA
13310194 AA
1 AA
13310196 CTTATATTTT
Statistics
Matches: 314, Mismatches: 3, Indels: 25
0.92 0.01 0.07
Matches are distributed among these distances:
324 3 0.01
325 18 0.06
326 30 0.10
327 18 0.06
329 21 0.07
330 11 0.04
331 45 0.14
332 9 0.03
333 39 0.12
334 23 0.07
335 6 0.02
336 83 0.26
337 8 0.03
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (319 bp):
AAAATAAAATATATAAAATTATATAATAAATAAAAATAAAATATATGACATTAAAATATATTCAA
AATATTATTATATAAAAATTAATAATAAAAATAAATATATAAAATAAAATATAAATATTAATAAT
AAATAAAATAAAATATATGACATTAAAATATATTTAAGAAATGATATTATATAAAATTAATAATA
AAAATATAAATATATTAAAAATAAAAAAAAATATTATAATAATAAATAAAAATAAATATATGACA
TTAAAAATTATTTAAGAATGATATTATATAAAAATTAATAATAAAAATATAAAATATTA
Found at i:13310101 original size:10 final size:10
Alignment explanation
Indices: 13310057--13310127 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
13310047 GATATTATAT
*
13310057 AAAATTAATA
1 AAAATAAATA
*
13310067 ATAA-AAATA
1 AAAATAAATA
* *
13310076 TAAATATATTA
1 AAAATA-AATA
*
13310087 AAAATAAAAA
1 AAAATAAATA
*
13310097 AAAATATTATA
1 AAAATA-AATA
*
13310108 ATAATAAATA
1 AAAATAAATA
13310118 AAAATAAATA
1 AAAATAAATA
13310128 TATGATATTA
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
9 6 0.13
10 24 0.53
11 15 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATAAATA
Found at i:13310103 original size:21 final size:21
Alignment explanation
Indices: 13310060--13310130 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 21
13310050 ATTATATAAA
*
13310060 ATTAATAATAAAAATATAAATAT
1 ATTAAAAATAAAAA-A-AAATAT
13310083 ATTAAAAATAAAAAAAAATATT
1 ATTAAAAATAAAAAAAAATA-T
*
13310105 ATAATAATAAATAAAAATAAATAT
1 AT--TAA-AAATAAAAAAAAATAT
13310129 AT
1 AT
13310131 GATATTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.12
22 4 0.10
23 13 0.31
24 6 0.14
25 14 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAAAAATAAAAAAAAATAT
Found at i:13310105 original size:19 final size:21
Alignment explanation
Indices: 13310062--13310123 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
13310052 TATATAAAAT
13310062 TAATAATAAAAATATAAATA-TA
1 TAATAATAAAAA-A-AAATATTA
*
13310084 TTAAAAATAAAAAAAAATATTA
1 -TAATAATAAAAAAAAATATTA
*
13310106 TAATAATAAATAAAAATA
1 TAATAATAAAAAAAAATA
13310124 AATATATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 21 0.60
22 3 0.09
23 11 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAATAATAAAAAAAAATATTA
Found at i:13310110 original size:29 final size:29
Alignment explanation
Indices: 13309539--13310022 Score: 228
Period size: 30 Copynumber: 16.7 Consensus size: 29
13309529 TAAAGAAATG
*
13309539 AAAATAAAATATATAAAATTATATAATAAATA
1 AAAAT-AAA-ATATAAAA-TATATAATATATA
* *
13309571 AAAATAAAATATATGACAT-TAAAATATATTCA
1 AAAATAAAATATA--AAATATATAATATA-T-A
**
13309603 AAATATTATTATATAAAA-AT-TAATA-ATA
1 AAA-A-TAAAATATAAAATATATAATATATA
*
13309631 TAAATAAATATATAAAATA-A-AATATA-A
1 AAAATAAA-ATATAAAATATATAATATATA
*
13309658 ATATTAATAATAA-ATAAAATA-A-AATATATG
1 A-A--AATAA-AATATAAAATATATAATATATA
* * * *
13309688 ACATTAAAATATATTTAAGAAATGATATTATAT-
1 AAAATAAAATATA---AA-ATAT-ATAATATATA
13309721 AAAATAATAATATAAAATATA-AATATATTA
1 AAAATAA-AATATAAAATATATAATATA-TA
*
13309751 AAAATAAAAATATAAAATATTTAATA-AT-
1 AAAAT-AAAATATAAAATATATAATATATA
* *
13309779 -AAATAAAA-ATAAAATATATGACAT-TA
1 AAAATAAAATATAAAATATATAATATATA
* * *
13309805 AAAAT-ATATTTAAGAA-ATGATATTATATA
1 AAAATAAAATATAA-AATAT-ATAATATATA
13309834 AAAATTAATAATA-AAAATATA-AATATATTA
1 AAAA-TAA-AATATAAAATATATAATATA-TA
13309864 AAAATAAAATATAAAATAT-T-ATA-ATA
1 AAAATAAAATATAAAATATATAATATATA
* *
13309890 ATAAATAAAA-ATAAAATATATGACAT-TA
1 A-AAATAAAATATAAAATATATAATATATA
* *
13309918 AAAAT-ATAT-TCAAAATATGATATTATATA
1 AAAATAAAATAT-AAAATAT-ATAATATATA
13309947 AAAATTAATAATA-AAAATATA-AATATATTA
1 AAAA-TAA-AATATAAAATATATAATATA-TA
13309977 AAAATAAAATATAAAATACTATAATA-AT-
1 AAAATAAAATATAAAATA-TATAATATATA
13310005 -AAATAAAA-AT-AAATATAT
1 AAAATAAAATATAAAATATAT
13310023 GACATTAAAA
Statistics
Matches: 354, Mismatches: 39, Indels: 126
0.68 0.08 0.24
Matches are distributed among these distances:
24 3 0.01
25 18 0.05
26 27 0.08
27 63 0.18
28 37 0.10
29 61 0.17
30 64 0.18
31 37 0.10
32 18 0.05
33 7 0.02
34 19 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATAAAATATAAAATATATAATATATA
Found at i:13310516 original size:79 final size:79
Alignment explanation
Indices: 13310285--13310517 Score: 376
Period size: 79 Copynumber: 2.9 Consensus size: 79
13310275 TGTTATCTTC
*
13310285 CCTGCATTTTAATCATTATTTTGCTTACATACCAAACATTGTAATATTATTTTTCCTGTCATCAC
1 CCTGCATTTTAATCATTATTTTGCTTACATACCAAACATTGTAATATTATTTTTCCTGTAATCAC
*
13310350 ATTGCTTACACTTT
66 ATTGCTTGCACTTT
* *
13310364 TCTGCATTTTAATCATTATTTTGCTTACATACCAAACATTGTAATATTATTTTCCCTGTAATCAC
1 CCTGCATTTTAATCATTATTTTGCTTACATACCAAACATTGTAATATTATTTTTCCTGTAATCAC
13310429 ATTGCTTGCACTTT
66 ATTGCTTGCACTTT
* * * * *
13310443 CCTGCATTTTAATCATTATTTTACTTACATACCAAATATTGTAATATTATTTTTTCTATAATCAT
1 CCTGCATTTTAATCATTATTTTGCTTACATACCAAACATTGTAATATTATTTTTCCTGTAATCAC
*
13310508 ATTACTTGCA
66 ATTGCTTGCA
13310518 ATCATATTAC
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 142 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (79 bp):
CCTGCATTTTAATCATTATTTTGCTTACATACCAAACATTGTAATATTATTTTTCCTGTAATCAC
ATTGCTTGCACTTT
Found at i:13310522 original size:15 final size:15
Alignment explanation
Indices: 13310502--13310536 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
13310492 TTTTTTCTAT
*
13310502 AATCATATTACTTGC
1 AATCATATTACTTAC
13310517 AATCATATTACTTAC
1 AATCATATTACTTAC
13310532 AATCA
1 AATCA
13310537 CATTTTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (15 bp):
AATCATATTACTTAC
Found at i:13315614 original size:7 final size:7
Alignment explanation
Indices: 13315602--13315628 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13315592 TTTTTTAAAT
13315602 AATTTTA
1 AATTTTA
13315609 AATTTTA
1 AATTTTA
13315616 AATTTTA
1 AATTTTA
13315623 AATTTT
1 AATTTT
13315629 TTTTTCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:13319130 original size:74 final size:74
Alignment explanation
Indices: 13319049--13319187 Score: 215
Period size: 74 Copynumber: 1.9 Consensus size: 74
13319039 AAACCTATAC
* * * *
13319049 TTATAAATATGTATTTATTAAATAAAGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATAAAGATCATTGAAATATTTTTTAATATAATTATTAATAAGAT
13319114 ATAAACTTA
66 ATAAACTTA
* * *
13319123 TTATAAATATGTATTCATCGAATGATGATCATTGAAATATTTTTTAATATAATTATTAATAAGAT
1 TTATAAATATGTATTCATCAAATAAAGATCATTGAAATATTTTTTAATATAATTATTAATAAGAT
13319188 TTATTTCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 58 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATAAAGATCATTGAAATATTTTTTAATATAATTATTAATAAGAT
ATAAACTTA
Found at i:13332200 original size:6 final size:6
Alignment explanation
Indices: 13332191--13332218 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13332181 ATTAAAAGGA
13332191 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
13332219 GCTAGAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:13333159 original size:23 final size:23
Alignment explanation
Indices: 13333113--13333176 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
13333103 TAATTTATTA
* *
13333113 ATAGATGTTCTT-TATA-TATCG
1 ATAGATGATCTTATCTATTATCG
13333134 ATAGATGATCTTATCTATTATCG
1 ATAGATGATCTTATCTATTATCG
13333157 ATAGATGATCTTATCTATTA
1 ATAGATGATCTTATCTATTA
13333177 ATAGATGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.28
22 3 0.08
23 25 0.64
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (23 bp):
ATAGATGATCTTATCTATTATCG
Found at i:13333182 original size:20 final size:20
Alignment explanation
Indices: 13333108--13333184 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 20
13333098 ACTACTAATT
* *
13333108 TATTAATAGATGTTCTTTATA
1 TATTAATAGATGATC-TTATC
**
13333129 TATCGATAGATGATCTTATC
1 TATTAATAGATGATCTTATC
13333149 TATTATCGATAGATGATCTTATC
1 TATTA---ATAGATGATCTTATC
13333172 TATTAATAGATGA
1 TATTAATAGATGA
13333185 AGAACATCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 15 0.32
21 12 0.26
23 20 0.43
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (20 bp):
TATTAATAGATGATCTTATC
Found at i:13333516 original size:15 final size:15
Alignment explanation
Indices: 13333477--13333532 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
13333467 TTTACAATGC
*
13333477 AATGTGATTACAAGT
1 AATGTGATTGCAAGT
* *
13333492 AA-GCGATTGCAGGT
1 AATGTGATTGCAAGT
**
13333506 AATGTGATTGCAAAC
1 AATGTGATTGCAAGT
*
13333521 AATGTCATTGCA
1 AATGTGATTGCA
13333533 GAGAAAATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:13333765 original size:15 final size:15
Alignment explanation
Indices: 13333733--13333798 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
13333723 CATCTCTTAA
* *
13333733 ATATATTTTTAATGTC
1 ATATA-TTTTATTTTC
13333749 ATATATTTTATTTTC
1 ATATATTTTATTTTC
*
13333764 ATTTATTATTATAATCTT-
1 ATATATT-TTAT--T-TTC
13333782 ATATATTTTATTTTC
1 ATATATTTTATTTTC
13333797 AT
1 AT
13333799 TTCTTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.05
15 17 0.41
16 9 0.22
17 4 0.10
18 7 0.17
19 2 0.05
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (15 bp):
ATATATTTTATTTTC
Found at i:13333821 original size:34 final size:33
Alignment explanation
Indices: 13333749--13333822 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
13333739 TTTTAATGTC
*
13333749 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATATTTTATTTTCATTTATTAATATAATCTT
* *
13333782 ATATATTTTATTTTCATTTCTTTAATATAATTTT
1 ATATATTTTATTTTCATTT-ATTAATATAATCTT
*
13333816 TTATATT
1 ATATATT
13333823 ATAGATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTATTAATATAATCTT
Found at i:13333894 original size:15 final size:15
Alignment explanation
Indices: 13333876--13333943 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 15
13333866 TAATTTTTTA
13333876 TAATTTATTTTATTT
1 TAATTTATTTTATTT
*
13333891 TAATTTTTGATTCTTATAT
1 TAA--TTT-ATT-TTATTT
*
13333910 T-ATATATTTTATTT
1 TAATTTATTTTATTT
13333924 TAATATT-TTTTATTT
1 TAAT-TTATTTTATTT
13333939 TAATT
1 TAATT
13333944 ATAATATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
14 7 0.16
15 20 0.47
16 3 0.07
17 3 0.07
18 4 0.09
19 6 0.14
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (15 bp):
TAATTTATTTTATTT
Found at i:13333907 original size:24 final size:24
Alignment explanation
Indices: 13333862--13333912 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
13333852 TATTATATAA
* *
13333862 ATTTTAATTTTTTATAATTTATTTT
1 ATTTTAATTTTTGAT-ATTTATATT
13333887 ATTTTAATTTTTGAT-TCTTATATT
1 ATTTTAATTTTTGATAT-TTATATT
13333911 AT
1 AT
13333913 ATATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 8 0.35
25 14 0.61
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
ATTTTAATTTTTGATATTTATATT
Found at i:13333945 original size:33 final size:34
Alignment explanation
Indices: 13333881--13333951 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
13333871 TTTTATAATT
13333881 TATTTTATTTTAATTTTTGATTCTTATATTAT-A
1 TATTTTATTTTAATTTTTGATTCTTATATTATAA
*
13333914 TATTTTATTTTAATATTTTTTATT-TTA-ATTATAA
1 TATTTTATTTT-A-ATTTTTGATTCTTATATTATAA
13333948 TATT
1 TATT
13333952 ATAAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 16 0.47
34 9 0.26
35 9 0.26
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (34 bp):
TATTTTATTTTAATTTTTGATTCTTATATTATAA
Found at i:13337404 original size:20 final size:20
Alignment explanation
Indices: 13337368--13337405 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13337358 AAAAGAACAC
**
13337368 AAATAATAAAATTTAAATTT
1 AAATAATAAAAAATAAATTT
13337388 AAATAATAAAAAATAAAT
1 AAATAATAAAAAATAAAT
13337406 ATCTCCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAAAATAAATTT
Found at i:13337668 original size:17 final size:17
Alignment explanation
Indices: 13337646--13337693 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
13337636 AATGGGAAGT
*
13337646 AAATATATTTATATTTA
1 AAATATATATATATTTA
13337663 AAATATATATATA-TTA
1 AAATATATATATATTTA
13337679 AAAGTATATATATAT
1 AAA-TATATATATAT
13337694 CTATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AAATATATATATATTTA
Found at i:13339578 original size:7 final size:7
Alignment explanation
Indices: 13339532--13339575 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
13339522 CAGCACCAAA
13339532 TCGCCAG
1 TCGCCAG
13339539 TCGCCAG
1 TCGCCAG
13339546 TCGCCAG
1 TCGCCAG
13339553 TCGCCAG
1 TCGCCAG
13339560 TCGCCAG
1 TCGCCAG
*
13339567 TCACCAG
1 TCGCCAG
13339574 TC
1 TC
13339576 ACCCACCCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.43, G:0.25, T:0.16
Consensus pattern (7 bp):
TCGCCAG
Found at i:13344076 original size:2 final size:2
Alignment explanation
Indices: 13344069--13344093 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13344059 CGTGAGCAAC
13344069 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
13344094 AATGAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13345356 original size:45 final size:47
Alignment explanation
Indices: 13345263--13345409 Score: 194
Period size: 47 Copynumber: 3.2 Consensus size: 47
13345253 TGTGACAAGG
* *
13345263 CTGTGACATGGCAAG-GTTCAGAGTTTGTGACACGCCATGGAGGGAAT
1 CTGTGACAT-GCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGAAAT
* *
13345310 CTGTGACATGCTAGAGTTCAGAG-TT-TGACACGTCATGGAGAAAAT
1 CTGTGACATGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGAAAT
* *
13345355 CTATGACACT-CTAGAGTTCAGAGTTTGTGACACGCCATGAAGGAAAT
1 CTGTGACA-TGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGAAAT
13345402 CTGTGACA
1 CTGTGACA
13345410 CACCATGAAG
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
45 37 0.43
46 9 0.10
47 41 0.47
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (47 bp):
CTGTGACATGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGGAAAT
Found at i:13345408 original size:23 final size:23
Alignment explanation
Indices: 13345380--13345434 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
13345370 GTTCAGAGTT
13345380 TGTGACACGCCATGAAGGAAATC
1 TGTGACACGCCATGAAGGAAATC
* *
13345403 TGTGACACACCATGAAGGGAATC
1 TGTGACACGCCATGAAGGAAATC
*
13345426 TATGACACG
1 TGTGACACG
13345435 TCAGAGTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (23 bp):
TGTGACACGCCATGAAGGAAATC
Found at i:13345410 original size:47 final size:48
Alignment explanation
Indices: 13345278--13345410 Score: 193
Period size: 45 Copynumber: 2.9 Consensus size: 48
13345268 ACATGGCAAG
*
13345278 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACA-TGCTAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGAAATCTGTGACACTGCTAGA
* * *
13345325 GTTCAGAG-TT-TGACACGTCATGGAGAAAATCTATGACACT-CTAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGAAATCTGTGACACTGCTAGA
*
13345370 GTTCAGAGTTTGTGACACGCCATGAAGGAAATCTGTGACAC
1 GTTCAGAGTTTGTGACACGCCATGGAGGAAATCTGTGACAC
13345411 ACCATGAAGG
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 37 0.49
46 5 0.07
47 33 0.44
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
GTTCAGAGTTTGTGACACGCCATGGAGGAAATCTGTGACACTGCTAGA
Found at i:13345469 original size:45 final size:45
Alignment explanation
Indices: 13345405--13345688 Score: 273
Period size: 45 Copynumber: 6.2 Consensus size: 45
13345395 AGGAAATCTG
* * * *
13345405 TGACACACCATGAAGGGAATCTATGACACGTCAGAGTTCAGAGTT
1 TGACACGCCATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* * *
13345450 TGACTCGCCATGGACGGAATCTGTGACACATCAGTGTTCAGAGTTT
1 TGACACGCCATGGAGGGAATCTGTGACACGTCAGTGTTCAGAG-TT
* * *
13345496 GTGACACGACATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTT
1 -TGACACGCCATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* * * * *
13345542 TAACACGCCATAGAGGGAATCTGTGACATGCCAGTGTTCAAAGTTT
1 TGACACGCCATGGAGGGAATCTGTGACACGTCAGTGTTCAGAG-TT
* * * *
13345588 GTGACACACCACGGAGGGAATTTGTGACACGTTAGTGTTCAGAGTT
1 -TGACACGCCATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* ** ** * *
13345634 TAACACGCCATAAAGAAAATCTGTGACAAG-CTAGGGTTCAGAGTT
1 TGACACGCCATGGAGGGAATCTGTGACACGTC-AGTGTTCAGAGTT
*
13345679 TGACATGCCA
1 TGACACGCCA
13345689 GCATTCACGG
Statistics
Matches: 193, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
45 114 0.59
46 8 0.04
47 71 0.37
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (45 bp):
TGACACGCCATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
Found at i:13345490 original size:115 final size:115
Alignment explanation
Indices: 13345288--13345525 Score: 320
Period size: 115 Copynumber: 2.1 Consensus size: 115
13345278 GTTCAGAGTT
* * * * *
13345288 TGTGACACGCCATGGAGGGAATCTGTGACATGCTAGAGTTCAGAGTTTGACACGTCATGGAGAAA
1 TGTGACACACCATGAAGGGAATCTATGACACGCTAGAGTTCAGAGTTTGACACGCCATGGAGAAA
*
13345353 ATCTATGACACTCTAGAGTTCAGAGTTTGTGACACGCCATGAAGGAAATC
66 ATCTATGACACTCTAGAGTTCAGAGTTTGTGACACGACATGAAGGAAATC
*
13345403 TGTGACACACCATGAAGGGAATCTATGACACG-TCAGAGTTCAGAGTTTGACTCGCCATGGACG-
1 TGTGACACACCATGAAGGGAATCTATGACACGCT-AGAGTTCAGAGTTTGACACGCCATGGA-GA
* * * * *
13345466 GAATCTGTGACACATC-AGTGTTCAGAGTTTGTGACACGACATGGAGGGAATC
64 AAATCTATGACAC-TCTAGAGTTCAGAGTTTGTGACACGACATGAAGGAAATC
13345518 TGTGACAC
1 TGTGACAC
13345526 GCCAGAGTTC
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
114 1 0.01
115 104 0.96
116 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (115 bp):
TGTGACACACCATGAAGGGAATCTATGACACGCTAGAGTTCAGAGTTTGACACGCCATGGAGAAA
ATCTATGACACTCTAGAGTTCAGAGTTTGTGACACGACATGAAGGAAATC
Found at i:13345523 original size:47 final size:47
Alignment explanation
Indices: 13345403--13345634 Score: 242
Period size: 47 Copynumber: 5.0 Consensus size: 47
13345393 GAAGGAAATC
* * *
13345403 TGTGACAC-ACCATGAAGGGAATCTATGACACGTCAGAGTTCAGAG-T
1 TGTGACACGA-CATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* * * *
13345449 T-TGACTCGCCATGGACGGAATCTGTGACACATCAGTGTTCAGAGTT
1 TGTGACACGACATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* *
13345495 TGTGACACGACATGGAGGGAATCTGTGACACGCCAGAGTTCAGAG-T
1 TGTGACACGACATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* * * * * *
13345541 T-TAACACGCCATAGAGGGAATCTGTGACATGCCAGTGTTCAAAGTT
1 TGTGACACGACATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
* * *
13345587 TGTGACAC-ACCACGGAGGGAATTTGTGACACGTTAGTGTTCAGAGTT
1 TGTGACACGA-CATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
13345634 T
1 T
13345635 AACACGCCAT
Statistics
Matches: 152, Mismatches: 28, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
45 72 0.47
46 7 0.05
47 73 0.48
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
TGTGACACGACATGGAGGGAATCTGTGACACGTCAGTGTTCAGAGTT
Found at i:13345655 original size:92 final size:91
Alignment explanation
Indices: 13345403--13345680 Score: 335
Period size: 92 Copynumber: 3.0 Consensus size: 91
13345393 GAAGGAAATC
* * * * * *
13345403 TGTGACACACCATGAAGGGAATCTATGACACGTCAGAGTTCAGAGTTTGACTCGCCATGGACGGA
1 TGTGACACACCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTAACACGCCAT-AAAGGA
*
13345468 ATCTGTGACACA-TCAGTGTTCAGAGTT
65 ATCTGTGACA-AGCCAGTGTTCAGAGTT
* *
13345495 TGTGACACGA-CATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTTAACACGCCATAGAGGG
1 TGTGACAC-ACCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTAACACGCCATA-AAGG
* *
13345559 AATCTGTGACATGCCAGTGTTCAAAGTT
64 AATCTGTGACAAGCCAGTGTTCAGAGTT
* * * * *
13345587 TGTGACACACCACGGAGGGAATTTGTGACACGTTAGTGTTCAGAGTTTAACACGCCATAAAGAAA
1 TGTGACACACCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTAACACGCCATAAAG-GA
* *
13345652 ATCTGTGACAAGCTAGGGTTCAGAGTT
65 ATCTGTGACAAGCCAGTGTTCAGAGTT
13345679 TG
1 TG
13345681 ACATGCCAGC
Statistics
Matches: 160, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
91 3 0.02
92 156 0.98
93 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (91 bp):
TGTGACACACCATGGAGGGAATCTGTGACACGTCAGAGTTCAGAGTTTAACACGCCATAAAGGAA
TCTGTGACAAGCCAGTGTTCAGAGTT
Found at i:13346312 original size:31 final size:31
Alignment explanation
Indices: 13346277--13346577 Score: 424
Period size: 31 Copynumber: 9.7 Consensus size: 31
13346267 GTTTTGCTTC
* * * *
13346277 TGCATGGCGTGTCACGACATTTGACTTGATA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
13346308 TGCATGGCGTGTGACCACATTTTACTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
*
13346339 TGCATGGCATGTGACCACATTTTACTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
* * *
13346370 TGCATGACGTGTGACGACCTTTTACTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
* *
13346401 TGCATGCCGTGTGACCACATTTTAGTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
13346432 TGCATGGCGTGTGACCACATTTTACTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
* *
13346463 TGCATGGCATGTGACCACCTTTTACTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
* *
13346494 TGCATGGCGTGTCACTACATTTTACTTGTTA
1 TGCATGGCGTGTGACCACATTTTACTTGTTA
* **
13346525 TGCATGGTGTGTGATTAC-TTTTCACTTGTTA
1 TGCATGGCGTGTGACCACATTTT-ACTTGTTA
*
13346556 TGCATGGCGTGTAACCACATTT
1 TGCATGGCGTGTGACCACATTT
13346578 GTGCCATATT
Statistics
Matches: 240, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
30 4 0.02
31 233 0.97
32 3 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
TGCATGGCGTGTGACCACATTTTACTTGTTA
Found at i:13350013 original size:2 final size:2
Alignment explanation
Indices: 13350006--13350037 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13349996 GTCTTAGGTT
13350006 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
13350038 CTACCTCGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13353937 original size:28 final size:28
Alignment explanation
Indices: 13353875--13353930 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
13353865 TAAAAAAACT
* *
13353875 TTTTA-TTATAAATATTATTTATTTTTA
1 TTTTATTTTTAAATATTATATATTTTTA
13353902 TTTTATTTTTAAATATTA-ATA-TTTTA
1 TTTTATTTTTAAATATTATATATTTTTA
13353928 TTT
1 TTT
13353931 ATAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.31
27 7 0.27
28 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTATTTTTAAATATTATATATTTTTA
Found at i:13354516 original size:17 final size:18
Alignment explanation
Indices: 13354482--13354523 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
13354472 TTGTAAAATA
13354482 TTAATATTTTATTTATAAT
1 TTAA-ATTTTATTTATAAT
13354501 TTAAATTTTA-TTATAAT
1 TTAAATTTTATTTATAAT
*
13354518 TAAAAT
1 TTAAAT
13354524 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 6 0.27
19 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTTTATTTATAAT
Found at i:13360267 original size:31 final size:31
Alignment explanation
Indices: 13360232--13360503 Score: 175
Period size: 31 Copynumber: 8.9 Consensus size: 31
13360222 TAGAGAACAA
* *
13360232 TTATACCTCCATTGTAATAGGTAGTGCAAGG
1 TTATACCTCCATTGTAAAAGGTAGTGTAAGG
* ** *
13360263 TTATACCT---TTATACAAATGGTAAAG-AATGA
1 TTATACCTCCATTGTA-AAA-GGTAGTGTAA-GG
* * *
13360293 TTATAACTTCATTGTAAAAGGAAGTGTAAGG
1 TTATACCTCCATTGTAAAAGGTAGTGTAAGG
* * ** * * *
13360324 TTATACCTTC-GTACAAAAAGTAGAG-AACAG
1 TTATACCTCCATTGTAAAAGGTAGTGTAA-GG
* * *
13360354 TTATAACTTCATTGTAAAAGGTAGTATAAGG
1 TTATACCTCCATTGTAAAAGGTAGTGTAAGG
* * * * *
13360385 TTATGCTTCCATAG-AAAAGGTAGAGAAAGG
1 TTATACCTCCATTGTAAAAGGTAGTGTAAGG
* *
13360415 TTATACCTCCTTTATAAAAGGTAGTGTACA-G
1 TTATACCTCCATTGTAAAAGGTAGTGTA-AGG
*
13360446 TTATACCTCTATTGTAAAAGGTAGTGTAAGG
1 TTATACCTCCATTGTAAAAGGTAGTGTAAGG
*
13360477 TTATACCTCC-TTGAGAAAAGGTAGTGT
1 TTATACCTCCATTG-TAAAAGGTAGTGT
13360504 GTTAAAAGTT
Statistics
Matches: 180, Mismatches: 47, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
28 4 0.02
29 6 0.03
30 58 0.32
31 100 0.56
32 8 0.04
33 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (31 bp):
TTATACCTCCATTGTAAAAGGTAGTGTAAGG
Found at i:13360306 original size:61 final size:60
Alignment explanation
Indices: 13360203--13360453 Score: 227
Period size: 61 Copynumber: 4.1 Consensus size: 60
13360193 GGATATTATA
* * * * *
13360203 ATACCTTTATTGCAAAAGGTAGAGAACAATTATACCTCCATTGTAATAGGTAGTGCAAGGTT
1 ATACCTTTA-TACAAAAGGTAGAGAA-AATTATAACTTCATTGTAAAAGGTAGTGTAAGGTT
* * * *
13360265 ATACCTTTATACAAATGGTAAAGAATGATTATAACTTCATTGTAAAAGGAAGTGTAAGGTT
1 ATACCTTTATACAAAAGGTAGAGAA-AATTATAACTTCATTGTAAAAGGTAGTGTAAGGTT
** * * *
13360326 ATACCTTCGTACAAAAAGTAGAGAACAGTTATAACTTCATTGTAAAAGGTAGTATAAGGTT
1 ATACCTTTATACAAAAGGTAGAGAA-AATTATAACTTCATTGTAAAAGGTAGTGTAAGGTT
* * * * * * * *
13360387 AT-GCTTCCATAGAAAAGGTAGAGAAAGGTTATACCTCCTTTATAAAAGGTAGTGTACA-GTT
1 ATACCTT-TATACAAAAGGTAGAGAAA-ATTATAACTTCATTGTAAAAGGTAGTGTA-AGGTT
13360448 ATACCT
1 ATACCT
13360454 CTATTGTAAA
Statistics
Matches: 155, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
60 4 0.03
61 139 0.90
62 12 0.08
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (60 bp):
ATACCTTTATACAAAAGGTAGAGAAAATTATAACTTCATTGTAAAAGGTAGTGTAAGGTT
Found at i:13360433 original size:122 final size:122
Alignment explanation
Indices: 13360215--13360453 Score: 275
Period size: 122 Copynumber: 2.0 Consensus size: 122
13360205 ACCTTTATTG
* * * * *
13360215 CAAAAGGTAGAGAACAATTATACCTCCATTGTAATAGGTAGTGCAAGGTTATACCTTTATACAAA
1 CAAAAAGTAGAGAACAATTATAACTCCATTGTAAAAGGTAGTACAAGGTTATACCTTCATACAAA
* * * *
13360280 TGGTAAAGAATGATTATAACTTCATTGTAAAAGGAAGTGTA-AGGTTATACCTTCGTA
66 AGGTAAAGAAAGATTATAACTCCATTATAAAAGGAAGTGTACA-GTTATACCTTCGTA
* * * * *
13360337 CAAAAAGTAGAGAACAGTTATAACTTCATTGTAAAAGGTAGTATAAGGTTAT-GCTTCCATAGAA
1 CAAAAAGTAGAGAACAATTATAACTCCATTGTAAAAGGTAGTACAAGGTTATACCTT-CATACAA
* * * * *
13360401 AAGGTAGAGAAAGGTTATACCTCCTTTATAAAAGGTAGTGTACAGTTATACCT
65 AAGGTAAAGAAAGATTATAACTCCATTATAAAAGGAAGTGTACAGTTATACCT
13360454 CTATTGTAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
121 3 0.03
122 92 0.96
123 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (122 bp):
CAAAAAGTAGAGAACAATTATAACTCCATTGTAAAAGGTAGTACAAGGTTATACCTTCATACAAA
AGGTAAAGAAAGATTATAACTCCATTATAAAAGGAAGTGTACAGTTATACCTTCGTA
Found at i:13371076 original size:19 final size:18
Alignment explanation
Indices: 13371043--13371079 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
13371033 GCATTCAAAT
*
13371043 AAGTGCTTTTTCTAACAG
1 AAGTGCTTTTCCTAACAG
13371061 AAGTGACTTTTCCTAACAG
1 AAGTG-CTTTTCCTAACAG
13371080 TTGACTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (18 bp):
AAGTGCTTTTCCTAACAG
Found at i:13377129 original size:15 final size:16
Alignment explanation
Indices: 13377094--13377131 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13377084 GTAGGAGTCC
* *
13377094 ATACAATTCTTTGGTG
1 ATACAATTATATGGTG
13377110 ATACAATTATATGG-G
1 ATACAATTATATGGTG
13377125 ATACAAT
1 ATACAAT
13377132 GTGTATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (16 bp):
ATACAATTATATGGTG
Found at i:13384087 original size:38 final size:38
Alignment explanation
Indices: 13383996--13384098 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 38
13383986 AGGTGCACCG
* * * *
13383996 ATTGTCCAA-GAGTGATGGGCACTATACCATTGCTTACA
1 ATTGTCCAAGGA-TGATGGGGATTATACCATCGCTAACA
* * *
13384034 ATTGTTCAAGCATGATGGGGATTATACCATCGCTAAGA
1 ATTGTCCAAGGATGATGGGGATTATACCATCGCTAACA
* *
13384072 GTTGTCCAAGGATGATAGGGATTATAC
1 ATTGTCCAAGGATGATGGGGATTATAC
13384099 TATCACCACT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 52 0.98
39 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (38 bp):
ATTGTCCAAGGATGATGGGGATTATACCATCGCTAACA
Found at i:13386759 original size:22 final size:22
Alignment explanation
Indices: 13386716--13386759 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13386706 ATCACTTTAT
***
13386716 CCTTTTTCTTTTTCTTTCTTTC
1 CCTTTTTCTTTTTCTCAATTTC
13386738 CCTTTTTCTTTTTCTCAATTTC
1 CCTTTTTCTTTTTCTCAATTTC
13386760 ATACCTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (22 bp):
CCTTTTTCTTTTTCTCAATTTC
Found at i:13390394 original size:21 final size:21
Alignment explanation
Indices: 13390352--13390417 Score: 107
Period size: 21 Copynumber: 3.1 Consensus size: 21
13390342 ACCTTCCTTC
13390352 CTTTCCTCTCATTTCTTTCTTT
1 CTTTCCTCTCATTTC-TTCTTT
13390374 CTTTCCTCTCATTTCTTCTTT
1 CTTTCCTCTCATTTCTTCTTT
*
13390395 CTTTCCTCTCCTTTC-TCTTT
1 CTTTCCTCTCATTTCTTCTTT
13390415 CTT
1 CTT
13390418 CTTAGTTATG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 8 0.19
21 20 0.47
22 15 0.35
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (21 bp):
CTTTCCTCTCATTTCTTCTTT
Found at i:13392652 original size:54 final size:54
Alignment explanation
Indices: 13392570--13392684 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 54
13392560 TGCTTTTTTT
* * * * *
13392570 TCTTGAATTTGCTTGTCAACTGTTTCAATCACTGTTTTATTCTCAATAGGCTTA
1 TCTTGAATTTGCTTGTCAACTGTCTCAATCACCGTTTCATTCTCAACAGACTTA
* ** *
13392624 TCTTGAATTTGCTTGTTAGTTGTCTCAATCACCGTTTCATTTTCAACAGACTTA
1 TCTTGAATTTGCTTGTCAACTGTCTCAATCACCGTTTCATTCTCAACAGACTTA
13392678 TCTTGAA
1 TCTTGAA
13392685 GATTGTCTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (54 bp):
TCTTGAATTTGCTTGTCAACTGTCTCAATCACCGTTTCATTCTCAACAGACTTA
Found at i:13395691 original size:20 final size:21
Alignment explanation
Indices: 13395656--13395696 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13395646 CAATTTTTCT
13395656 TAAAGTAAATTAAAAC-AAAA
1 TAAAGTAAATTAAAACTAAAA
13395676 TAAAGTAAAATT-AAACTAAAA
1 TAAAGT-AAATTAAAACTAAAA
13395697 CAACTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (21 bp):
TAAAGTAAATTAAAACTAAAA
Found at i:13397736 original size:15 final size:15
Alignment explanation
Indices: 13397716--13397746 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13397706 TCAAAATAAT
*
13397716 TTGTTTTGAATTAAA
1 TTGTTTTGAATCAAA
13397731 TTGTTTTGAATCAAA
1 TTGTTTTGAATCAAA
13397746 T
1 T
13397747 CAAATGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (15 bp):
TTGTTTTGAATCAAA
Found at i:13402544 original size:14 final size:14
Alignment explanation
Indices: 13402499--13402544 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
13402489 CTTCTTCTCT
*
13402499 CTCTCTCTCTCTCG
1 CTCTCTCTCTCTAG
* *
13402513 CTCGCTCTCTCTTG
1 CTCTCTCTCTCTAG
*
13402527 CTCTCTTTCTCTAG
1 CTCTCTCTCTCTAG
13402541 CTCT
1 CTCT
13402545 AAACACATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.02, C:0.43, G:0.09, T:0.46
Consensus pattern (14 bp):
CTCTCTCTCTCTAG
Found at i:13408830 original size:16 final size:16
Alignment explanation
Indices: 13408801--13408842 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
13408791 ATTTATTAAC
*
13408801 TATTTTTT-ACTTTTA
1 TATTTTTTAATTTTTA
13408816 TATTTTTTAATTTTTA
1 TATTTTTTAATTTTTA
*
13408832 TATATTTTAAT
1 TATTTTTTAAT
13408843 ATAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTTAATTTTTA
Found at i:13408850 original size:25 final size:26
Alignment explanation
Indices: 13408822--13408875 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
13408812 TTTATATTTT
*
13408822 TTAATT-T-TTATATATTTTAATATAA
1 TTAATTATATTATA-ATTTTAATAAAA
*
13408847 TTAATTATATTATAATTTTTATAAAA
1 TTAATTATATTATAATTTTAATAAAA
13408873 TTA
1 TTA
13408876 TAAAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 14 0.56
27 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTAATTATATTATAATTTTAATAAAA
Found at i:13410819 original size:53 final size:53
Alignment explanation
Indices: 13410739--13410842 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
13410729 TCAAAGTTGA
* *
13410739 AAAAAGTATCATTTACTCCATTGATGAACCTAAAAACCATA-CTTTTCTTATTG
1 AAAAAGTATCAGTTAATCCATTGATGAACCTAAAAACCATATC-TTTCTTATTG
* * * *
13410792 AAAAAGTATTAGTTAATTCATTTATGAACCTAAAAATCATATCTTTCTTAT
1 AAAAAGTATCAGTTAATCCATTGATGAACCTAAAAACCATATCTTTCTTAT
13410843 ACTGATGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 43 0.98
54 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (53 bp):
AAAAAGTATCAGTTAATCCATTGATGAACCTAAAAACCATATCTTTCTTATTG
Found at i:13416123 original size:34 final size:36
Alignment explanation
Indices: 13416085--13416160 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
13416075 CCTGCTCCCA
* *
13416085 TGAAAAGGCAATT-TGTGGGTT-TTGGTTAAACTCG
1 TGAAAAGACAATTGTGAGGGTTGTTGGTTAAACTCG
* * *
13416119 TGAAAA-ACCATTGTGAGGGTTGTTGGTTGATCTCG
1 TGAAAAGACAATTGTGAGGGTTGTTGGTTAAACTCG
13416154 TGAAAAG
1 TGAAAAG
13416161 CTTTTTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
33 4 0.12
34 13 0.38
35 17 0.50
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (36 bp):
TGAAAAGACAATTGTGAGGGTTGTTGGTTAAACTCG
Found at i:13416560 original size:4 final size:4
Alignment explanation
Indices: 13416551--13416581 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
13416541 ATACTTTCTC
*
13416551 TATG TATG TAAG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
13416582 ATCTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:13420156 original size:16 final size:17
Alignment explanation
Indices: 13420135--13420172 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
13420125 GATTTTACAC
13420135 AATAGTTAAAT-ATATA
1 AATAGTTAAATAATATA
13420151 AATAGTTAAATAATATA
1 AATAGTTAAATAATATA
13420168 AATAG
1 AATAG
13420173 AAAGAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (17 bp):
AATAGTTAAATAATATA
Found at i:13421601 original size:5 final size:6
Alignment explanation
Indices: 13421586--13421618 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13421576 CCAAAAAACA
*
13421586 AAAAAC AAAAAG AAAAAG AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
13421619 CATTGAGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:13430657 original size:21 final size:20
Alignment explanation
Indices: 13430633--13430672 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13430623 TATTGTTCAT
*
13430633 TCATATCATGCATTTACATAA
1 TCATATAATGCATTT-CATAA
*
13430654 TCATATAATGTATTTCATA
1 TCATATAATGCATTTCATA
13430673 TTTAACTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (20 bp):
TCATATAATGCATTTCATAA
Found at i:13433291 original size:13 final size:13
Alignment explanation
Indices: 13433273--13433297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13433263 CAAAATCCTC
13433273 AAGACTCCACATA
1 AAGACTCCACATA
13433286 AAGACTCCACAT
1 AAGACTCCACAT
13433298 GTTTCATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (13 bp):
AAGACTCCACATA
Found at i:13433605 original size:21 final size:21
Alignment explanation
Indices: 13433569--13433623 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
13433559 AAAGTGGTCA
* *
13433569 AAATTGCTTCAATGATCTTTG
1 AAATTGTTTGAATGATCTTTG
* * *
13433590 AACTTGTTTGAATGATTTTTT
1 AAATTGTTTGAATGATCTTTG
*
13433611 AAATTTTTTGAAT
1 AAATTGTTTGAAT
13433624 ATGTTTTTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (21 bp):
AAATTGTTTGAATGATCTTTG
Found at i:13433630 original size:21 final size:21
Alignment explanation
Indices: 13433596--13433637 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13433586 TTTGAACTTG
13433596 TTTGAATGATTTTTTAAATTT
1 TTTGAATGATTTTTTAAATTT
13433617 TTTGAAT-ATGTTTTTAAATTT
1 TTTGAATGAT-TTTTTAAATTT
13433638 AATTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTGAATGATTTTTTAAATTT
Found at i:13433794 original size:22 final size:21
Alignment explanation
Indices: 13433728--13433815 Score: 95
Period size: 21 Copynumber: 4.1 Consensus size: 21
13433718 TTGATCGACC
*
13433728 TTTGAACTTGTTTGAATAATT
1 TTTGAACTTGTTTGAATAGTT
*
13433749 TTTGAAGTTGTTTGAATGAGTT
1 TTTGAACTTGTTTGAAT-AGTT
* *
13433771 TTTGAACTTGTTGGAATAGCT
1 TTTGAACTTGTTTGAATAGTT
* * *
13433792 TTTAAACTTTTTTAAATAAGTT
1 TTTGAACTTGTTTGAAT-AGTT
13433814 TT
1 TT
13433816 AAAATGTCGA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 32 0.58
22 23 0.42
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (21 bp):
TTTGAACTTGTTTGAATAGTT
Found at i:13433814 original size:43 final size:43
Alignment explanation
Indices: 13433728--13433815 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
13433718 TTGATCGACC
* * * * * *
13433728 TTTGAACTTGTTTGAATAATTTTTGAAGTTGTTTGAATGAGTT
1 TTTGAACTTGTTGGAATAACTTTTAAACTTGTTTAAATAAGTT
* *
13433771 TTTGAACTTGTTGGAATAGCTTTTAAACTTTTTTAAATAAGTT
1 TTTGAACTTGTTGGAATAACTTTTAAACTTGTTTAAATAAGTT
13433814 TT
1 TT
13433816 AAAATGTCGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (43 bp):
TTTGAACTTGTTGGAATAACTTTTAAACTTGTTTAAATAAGTT
Found at i:13433874 original size:21 final size:21
Alignment explanation
Indices: 13433850--13433890 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13433840 AAAAGTTTCA
13433850 AAATTACTTGAATGATTTTTG
1 AAATTACTTGAATGATTTTTG
* *
13433871 AAATTGCTTTAATGATTTTT
1 AAATTACTTGAATGATTTTT
13433891 TAACTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
AAATTACTTGAATGATTTTTG
Found at i:13436466 original size:34 final size:34
Alignment explanation
Indices: 13436428--13436500 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
13436418 GAGCCTGGTA
* *
13436428 AAAAGTGA-TTATGAGGGTTTTGCTTGATCTCGTG
1 AAAAGT-ATTTATGAGGGTGTTGCTTGATCTCATG
*
13436462 AAAAGTATTTGTGAGGGTGTTGCTTGATCTCATG
1 AAAAGTATTTATGAGGGTGTTGCTTGATCTCATG
13436496 AAAAG
1 AAAAG
13436501 CACATTCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.36
Consensus pattern (34 bp):
AAAAGTATTTATGAGGGTGTTGCTTGATCTCATG
Found at i:13438062 original size:28 final size:28
Alignment explanation
Indices: 13438022--13438114 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 28
13438012 TTAAGACAAA
* * *
13438022 AATATATTATCTTGTCTAAATTGAGACT
1 AATATGTTTTCTTGTCTAAATTAAGACT
*
13438050 AATATGTTTTCTTGTCTAAATTCAGA-T
1 AATATGTTTTCTTGTCTAAATTAAGACT
* *
13438077 AAACAAGTTTTCTTGTCTAAATTAAGAC-
1 -AATATGTTTTCTTGTCTAAATTAAGACT
13438105 ATATATGTTT
1 A-ATATGTTT
13438115 AAGCTGTCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.04
28 52 0.96
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (28 bp):
AATATGTTTTCTTGTCTAAATTAAGACT
Found at i:13447092 original size:34 final size:35
Alignment explanation
Indices: 13447038--13447109 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
13447028 AAGTAATCAC
* * *
13447038 AACCCTTACAAATGCCTTTTAGTAAGAGCAAGCAT
1 AACCCTCACAAATGCATTTTAATAAGAGCAAGCAT
* *
13447073 AACCCTCAC-AATGCATTTTAATAGGAGTAAGCAT
1 AACCCTCACAAATGCATTTTAATAAGAGCAAGCAT
13447107 AAC
1 AAC
13447110 ACTTGCTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 24 0.75
35 8 0.25
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (35 bp):
AACCCTCACAAATGCATTTTAATAAGAGCAAGCAT
Found at i:13447158 original size:34 final size:34
Alignment explanation
Indices: 13447120--13447187 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
13447110 ACTTGCTATA
* *
13447120 CCTTTTACAGAGAGAAAGCATAACCCATATAATG
1 CCTTTTACAGAGAGAAAGCACAACCCATACAATG
** *
13447154 CCTTTTATGGAGAGTAAGCACAACCCATACAATG
1 CCTTTTACAGAGAGAAAGCACAACCCATACAATG
13447188 GTTTTTTCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (34 bp):
CCTTTTACAGAGAGAAAGCACAACCCATACAATG
Found at i:13456158 original size:20 final size:20
Alignment explanation
Indices: 13456135--13456177 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
13456125 TATTTTTAAA
* *
13456135 TTATCATTTTAAATTTTTAT
1 TTATCATTATAAATTTATAT
* *
13456155 TTATTATTATGAATTTATAT
1 TTATCATTATAAATTTATAT
13456175 TTA
1 TTA
13456178 ATGCACTACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATCATTATAAATTTATAT
Found at i:13456539 original size:2 final size:2
Alignment explanation
Indices: 13456532--13456560 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13456522 TTACTTTCAT
13456532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13456561 GCAAAAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13458931 original size:19 final size:21
Alignment explanation
Indices: 13458879--13458928 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
13458869 GCTATCCATT
13458879 GATAAATATAGAACATCTATC
1 GATAAATATAGAACATCTATC
13458900 GATAAATATAGAACATCTATC
1 GATAAATATAGAACATCTATC
13458921 GATAAATA
1 GATAAATA
13458929 GAAGATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (21 bp):
GATAAATATAGAACATCTATC
Found at i:13468226 original size:2 final size:2
Alignment explanation
Indices: 13468221--13468247 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13468211 AACACACATA
13468221 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
13468248 AGACTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13472660 original size:2 final size:2
Alignment explanation
Indices: 13472653--13472693 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13472643 GTCGTGGGAA
*
13472653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13472694 GTGTTACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13474638 original size:29 final size:28
Alignment explanation
Indices: 13474603--13474676 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
13474593 TATACTTGTC
*
13474603 CACGTACAGCCTTTTCTCTTGTACCTGTT
1 CACGTACAG-CTTTTCTCTTGTACCTATT
*
13474632 CATGTACAGCTTCCTT-TCTTGTACCTATT
1 CACGTACAGCTT--TTCTCTTGTACCTATT
*
13474661 CACGAACAGCTTTTCT
1 CACGTACAGCTTTTCT
13474677 TTATTAACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.05
28 4 0.11
29 30 0.79
30 2 0.05
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.41
Consensus pattern (28 bp):
CACGTACAGCTTTTCTCTTGTACCTATT
Found at i:13479105 original size:15 final size:15
Alignment explanation
Indices: 13479087--13479117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13479077 TAACTATTTT
*
13479087 TAAAATAATTTAAAA
1 TAAAATAATATAAAA
13479102 TAAAATAATATAAAA
1 TAAAATAATATAAAA
13479117 T
1 T
13479118 TAAACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAATAATATAAAA
Found at i:13479136 original size:21 final size:20
Alignment explanation
Indices: 13479091--13479140 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
13479081 TATTTTTAAA
*
13479091 ATAATTTAAAATAAAATAAT
1 ATAAATTAAAATAAAATAAT
*
13479111 ATAAAATTAAACTAAAATAACT
1 AT-AAATTAAAATAAAATAA-T
13479133 -TAAATTAA
1 ATAAATTAA
13479141 CTACTCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 16 0.62
22 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAATTAAAATAAAATAAT
Found at i:13488020 original size:17 final size:17
Alignment explanation
Indices: 13487989--13488022 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13487979 TGCGCGCAGG
**
13487989 TGGGCCACATGTGCTGC
1 TGGGCCACACATGCTGC
13488006 TGGGCCACACATGCTGC
1 TGGGCCACACATGCTGC
13488023 ACACCCTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (17 bp):
TGGGCCACACATGCTGC
Found at i:13488282 original size:58 final size:58
Alignment explanation
Indices: 13488192--13488315 Score: 248
Period size: 58 Copynumber: 2.1 Consensus size: 58
13488182 CACTAGGGCA
13488192 AGCCGCGCATCAGCGCACCACTTGTGCACTAGCAGGCTGAGCACCCAGCACACCTGCG
1 AGCCGCGCATCAGCGCACCACTTGTGCACTAGCAGGCTGAGCACCCAGCACACCTGCG
13488250 AGCCGCGCATCAGCGCACCACTTGTGCACTAGCAGGCTGAGCACCCAGCACACCTGCG
1 AGCCGCGCATCAGCGCACCACTTGTGCACTAGCAGGCTGAGCACCCAGCACACCTGCG
13488308 AGCCGCGC
1 AGCCGCGC
13488316 GCACCCTCTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.22, C:0.40, G:0.27, T:0.11
Consensus pattern (58 bp):
AGCCGCGCATCAGCGCACCACTTGTGCACTAGCAGGCTGAGCACCCAGCACACCTGCG
Found at i:13490760 original size:14 final size:14
Alignment explanation
Indices: 13490741--13490767 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13490731 TTTGGTAAAT
13490741 TTTTTTATAAGTTC
1 TTTTTTATAAGTTC
13490755 TTTTTTATAAGTT
1 TTTTTTATAAGTT
13490768 ATAATTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAGTTC
Found at i:13493147 original size:30 final size:30
Alignment explanation
Indices: 13493113--13493172 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
13493103 ATATCATCTT
13493113 GGACCTACATTTTTTCTTTAATATTAGTTA
1 GGACCTACATTTTTTCTTTAATATTAGTTA
*
13493143 GGACCTACGTTTTTTCTTTAATATTAGTTA
1 GGACCTACATTTTTTCTTTAATATTAGTTA
13493173 CCCTGGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (30 bp):
GGACCTACATTTTTTCTTTAATATTAGTTA
Found at i:13494849 original size:22 final size:22
Alignment explanation
Indices: 13494797--13494850 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
13494787 ATCAACTGTT
* *
13494797 TTTA-GAAACTTACCTATATTC
1 TTTAGGAAATTTACCTAAATTC
* * *
13494818 TTTTGAAAATTTACCTAAATTG
1 TTTAGGAAATTTACCTAAATTC
13494840 TTTAGGAAATT
1 TTTAGGAAATT
13494851 ATGCACCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTAGGAAATTTACCTAAATTC
Found at i:13504153 original size:50 final size:50
Alignment explanation
Indices: 13504089--13504223 Score: 234
Period size: 50 Copynumber: 2.7 Consensus size: 50
13504079 TGGATTATGT
*
13504089 GGGTTACCACTTGATCTTGAAAAAAGCAAGAATCTATTCGTGAATTGTAA
1 GGGTTACCATTTGATCTTGAAAAAAGCAAGAATCTATTCGTGAATTGTAA
13504139 GGGTTACCATTTGATCTTGAAAAAAGCAAGAATCTATTCGTGAATTGTAA
1 GGGTTACCATTTGATCTTGAAAAAAGCAAGAATCTATTCGTGAATTGTAA
* *
13504189 GGGTTACCATTTGATCTTGTGAAAAGGCAAGAATC
1 GGGTTACCATTTGATCTTG-AAAAAAGCAAGAATC
13504224 CTGTTGTGGA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 68 0.84
51 13 0.16
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (50 bp):
GGGTTACCATTTGATCTTGAAAAAAGCAAGAATCTATTCGTGAATTGTAA
Found at i:13513359 original size:34 final size:34
Alignment explanation
Indices: 13513321--13513439 Score: 91
Period size: 34 Copynumber: 3.5 Consensus size: 34
13513311 TATGGGTTAC
*
13513321 GCTTGAGCCCGTAAAAAGGCATAGTGAGTGTTGT
1 GCTTGAGCCCGTAAAAAGGCATTGTGAGTGTTGT
** * *
13513355 GCTTGAGGTTACG-AAAAA-ACATTGTGAATGTTGT
1 GCTTGA-G-CCCGTAAAAAGGCATTGTGAGTGTTGT
** *
13513389 GCTTGCTCTCC-TAAAAAGGCATTGTGAGGGTTGT
1 GCTTGAGC-CCGTAAAAAGGCATTGTGAGTGTTGT
* * *
13513423 TCTTGAGCTCGAAAAAA
1 GCTTGAGCCCGTAAAAA
13513440 ATTGTAAAGT
Statistics
Matches: 62, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
33 7 0.11
34 47 0.76
35 6 0.10
36 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (34 bp):
GCTTGAGCCCGTAAAAAGGCATTGTGAGTGTTGT
Found at i:13513407 original size:68 final size:64
Alignment explanation
Indices: 13513332--13513457 Score: 162
Period size: 68 Copynumber: 1.9 Consensus size: 64
13513322 CTTGAGCCCG
* * *
13513332 TAAAAAGGCATAGTGAGTGTTGTGCTTGAGGTTACGAAAAAACATTGTGAATGTTGTGCTTGCTC
1 TAAAAAGGCATAGTGAGGGTTGTGCTTGA-GCT-CGAAAAAA-ATTGT-AAAGTTGTGCTTGCTC
13513397 TCC
62 TCC
* * *
13513400 TAAAAAGGCATTGTGAGGGTTGTTCTTGAGCTCGAAAAAAATTGTAAAGTTTTGCTTG
1 TAAAAAGGCATAGTGAGGGTTGTGCTTGAGCTCGAAAAAAATTGTAAAGTTGTGCTTG
13513458 ATCTTATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 11 0.21
65 5 0.10
66 8 0.15
67 2 0.04
68 26 0.50
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.33
Consensus pattern (64 bp):
TAAAAAGGCATAGTGAGGGTTGTGCTTGAGCTCGAAAAAAATTGTAAAGTTGTGCTTGCTCTCC
Found at i:13515843 original size:54 final size:54
Alignment explanation
Indices: 13515780--13515892 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
13515770 CATCAATATA
** * * *
13515780 GTTTCAATTATCTTTTTGTTGAGTAAGAAGAGTAAACAAGATGCCATTAGTATG
1 GTTTCAATTATCCCTTTGCTGAGTAAGAAGAGTAAACAAGATGCCATTAGCAGG
* * * * *
13515834 GTTTCAATTATCCCTTTGCTGAGTAGGATGAGTGAGCACGATGCCATTAGCAGG
1 GTTTCAATTATCCCTTTGCTGAGTAAGAAGAGTAAACAAGATGCCATTAGCAGG
13515888 GTTTC
1 GTTTC
13515893 CATTTTGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (54 bp):
GTTTCAATTATCCCTTTGCTGAGTAAGAAGAGTAAACAAGATGCCATTAGCAGG
Found at i:13538118 original size:243 final size:244
Alignment explanation
Indices: 13537667--13538372 Score: 637
Period size: 243 Copynumber: 2.9 Consensus size: 244
13537657 AATTAAACAT
* * * * *
13537667 TTAAATTTTTATTCTTGAGTTTAAATTGTTTTGCGGCTTACAAATGTTAATCTATAAATGAATAA
1 TTAAACTTTTATTCTTGAGTTTAAAGTGTATTACGACTTACAAATGTTAATCTATAAATGAATAA
* **** *
13537732 TAGTAAAGATAGAAAGAATTATAGTGAAAATTAATAGTTGTAAAACCTTGACATAAAAGAGTAAG
66 TAGTAAAGATAGAAAGAATTATAGTAAAAATTAATAGACAAAAAACCTTAACATAAAAGAGTAAG
* *
13537797 AATTAACACAAAAAATTATAAAGGTGGAAAAAGAATTGTCGAAATATTGACATAAATGTGTGAGA
131 AATTAACACAAAAAATTATAAAGGTGGAAAAAGAATTGTCAAAATATTAACATAAATGTGTGAGA
* **
13537862 TTTAATATAACAAGTCAATTATATCAAATAAACATAAT-TTTGTAAAAA
196 ATTAATATAACAAGTCAATTATATCAAATAAACATAATATTTAAAAAAA
* * * * * *
13537910 TTAAACTTTTATTCTTGAGTTTAGAGTGTATTACGATTTACAATTTTTGATCTATACATGAATAA
1 TTAAACTTTTATTCTTGAGTTTAAAGTGTATTACGACTTACAAATGTTAATCTATAAATGAATAA
* * * * *
13537975 TAGTAAAGATATAAAGAATTATGGTAAAAATTAGTA-ACAAAAAAGCCTTAACGTAAAATAGTAA
66 TAGTAAAGATAGAAAGAATTATAGTAAAAATTAATAGACAAAAAA-CCTTAACATAAAAGAGTAA
* * * * * * * * *
13538039 GAATTAATATAAAAAATTATGACAGGTTGAACAA-CATTGTTAAAATATTAACATAAATTTTTGA
130 GAATTAACACAAAAAATTAT-AAAGGTGGAAAAAGAATTGTCAAAATATTAACATAAATGTGTGA
* *
13538103 GAATTAATTTAACAAGTCAATTATGTCAAATAAACATAATATTTAAAAAAA
194 GAATTAATATAACAAGTCAATTATATCAAATAAACATAATATTTAAAAAAA
* ** * * * * * * *
13538154 TTAAGCACTTTATTTTTTATTATCAAGTTTAAAGTATTTTGCGGCTTACAAGTTTTAATCTATGA
1 TTAA--AC------TTTTATTCTTGAGTTTAAAGTGTATTACGACTTACAAATGTTAATCTATAA
* * * * * * * * *** * *
13538219 ATAAATAATAATAAGGATAAAAATAATTATTGTGAAAGTTAATAGTTGAAAAACTTTAACCTAAA
58 ATGAATAATAGTAAAGATAGAAAGAATTATAGTAAAAATTAATAGACAAAAAACCTTAACATAAA
* * * * * * * * *
13538284 ACAGTAAGAATTAACA-TAAAACTTATGAAGATAGAACAAGTATTGTTAAAATATTAACATAAAT
123 AGAGTAAGAATTAACACAAAAAATTATAAAGGTGGAAAAAGAATTGTCAAAATATTAACATAAAT
* * *
13538348 GTGTGAGATTTAATGTAATAAGTCA
188 GTGTGAGAATTAATATAACAAGTCA
13538373 TAATAATAAT
Statistics
Matches: 371, Mismatches: 79, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
242 4 0.01
243 181 0.49
244 22 0.06
246 2 0.01
250 9 0.02
251 51 0.14
252 97 0.26
253 5 0.01
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (244 bp):
TTAAACTTTTATTCTTGAGTTTAAAGTGTATTACGACTTACAAATGTTAATCTATAAATGAATAA
TAGTAAAGATAGAAAGAATTATAGTAAAAATTAATAGACAAAAAACCTTAACATAAAAGAGTAAG
AATTAACACAAAAAATTATAAAGGTGGAAAAAGAATTGTCAAAATATTAACATAAATGTGTGAGA
ATTAATATAACAAGTCAATTATATCAAATAAACATAATATTTAAAAAAA
Found at i:13555479 original size:15 final size:15
Alignment explanation
Indices: 13555456--13555490 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13555446 GAGTAGTTAA
13555456 TTTAAGTTATTTTAG
1 TTTAAGTTATTTTAG
* *
13555471 TTTATGTTATTTTAT
1 TTTAAGTTATTTTAG
13555486 TTTAA
1 TTTAA
13555491 ATTACTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (15 bp):
TTTAAGTTATTTTAG
Found at i:13561838 original size:69 final size:69
Alignment explanation
Indices: 13561763--13561942 Score: 247
Period size: 69 Copynumber: 2.6 Consensus size: 69
13561753 ATTTATCATA
* * * *
13561763 TAATTTTAAGGATTTCTTTTAAAGTCGAAAACTATTTCCTATGAATTTTTTC-AATTCAAATGCT
1 TAATTTTAAGGATTTCTTTTAAAGTAGGAAACAATTTCCTAT-AAATTTTTCAAATTCAAATGCT
13561827 ATCCT
65 ATCCT
* * * *
13561832 TAATTTTAAGAATTTCTGTCAAAGTAGGAAACAATTTCCTATAAATTTTTCAAATTGAAATGCTA
1 TAATTTTAAGGATTTCTTTTAAAGTAGGAAACAATTTCCTATAAATTTTTCAAATTCAAATGCTA
*
13561897 TCTT
66 TCCT
13561901 TAATTTT-AGGAATTTCTTTTAAAGTAGGAAACAATTTCCTAT
1 TAATTTTAAGG-ATTTCTTTTAAAGTAGGAAACAATTTCCTAT
13561943 TCTTTATGAA
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
68 10 0.10
69 87 0.90
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (69 bp):
TAATTTTAAGGATTTCTTTTAAAGTAGGAAACAATTTCCTATAAATTTTTCAAATTCAAATGCTA
TCCT
Found at i:13562245 original size:15 final size:16
Alignment explanation
Indices: 13562209--13562245 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
13562199 TGACATGCAG
13562209 TAATTTAATTTTATAA
1 TAATTTAATTTTATAA
13562225 -AA-TTAATTTT-TAA
1 TAATTTAATTTTATAA
13562238 TAATTTAA
1 TAATTTAA
13562246 AACTACTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.16
14 10 0.53
15 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTTAATTTTATAA
Found at i:13562413 original size:20 final size:22
Alignment explanation
Indices: 13562371--13562413 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
13562361 TTCTGCAACT
**
13562371 AAACATGATTTTAAATGTTTTA
1 AAACATGATTTTAAATGAATTA
13562393 AAACATG-TTTT-AATGAATTA
1 AAACATGATTTTAAATGAATTA
13562413 A
1 A
13562414 TTACATGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (22 bp):
AAACATGATTTTAAATGAATTA
Found at i:13571383 original size:28 final size:28
Alignment explanation
Indices: 13571343--13571566 Score: 295
Period size: 28 Copynumber: 7.9 Consensus size: 28
13571333 TGAAGGCAAC
* * *
13571343 TCTTGCCTAAATTGAGACAAACATATTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
*
13571371 TCTTGTCTAAATTAAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* *
13571399 TTTTGCCTAAATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGAC-AAACATGTTT
* *
13571428 TCTTATCTGAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
13571456 TCTTGTCTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* *
13571484 TCTTGCCTAAATTAAGATAAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
* *
13571513 TCTTATCTGAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
13571541 TATTGTCTAAATTAAGATAAAAATGT
1 TCTTGTCTAAATTAAGACAAACATGT
13571567 AAAAGTTATC
Statistics
Matches: 170, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
28 123 0.72
29 47 0.28
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:13571441 original size:57 final size:56
Alignment explanation
Indices: 13571343--13571566 Score: 295
Period size: 57 Copynumber: 4.0 Consensus size: 56
13571333 TGAAGGCAAC
* * *
13571343 TCTTGCCTAAATTGAGACAAACATATTTTCTTGTCTAAATTAAGACAAATATGTTT
1 TCTTGCCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTT
* * *
13571399 TTTTGCCTAAATTAAGACAAAACATGTTTTCTTATCTGAATTAAGACAAACATGTTT
1 TCTTGCCTAAATTAAGAC-AAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTT
* * *
13571456 TCTTGTCTAAATTAAGACAAACATGTTTTCTTGCCTAAATTAAGATAAAACATGTTT
1 TCTTGCCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGA-CAAACATGTTT
** * * * *
13571513 TCTTATCTGAATTAAGACAAACATGTTTTATTGTCTAAATTAAGATAAAAATGT
1 TCTTGCCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAACATGT
13571567 AAAAGTTATC
Statistics
Matches: 148, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
56 47 0.32
57 101 0.68
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (56 bp):
TCTTGCCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTT
Found at i:13571500 original size:85 final size:85
Alignment explanation
Indices: 13571352--13571566 Score: 358
Period size: 85 Copynumber: 2.5 Consensus size: 85
13571342 CTCTTGCCTA
* * * *
13571352 AATTGAGACAAACATATTTTCTTGTCTAAATTAAGACAAATATGTTTTTTTGCCTAAATTAAGAC
1 AATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGCCTAAATTAAGAC
13571417 AAAACATGTTTTCTTATCTG
66 AAAACATGTTTTCTTATCTG
* *
13571437 AATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGCCTAAATTAAGAT
1 AATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGCCTAAATTAAGAC
13571502 AAAACATGTTTTCTTATCTG
66 AAAACATGTTTTCTTATCTG
* *
13571522 AATTAAGACAAACATGTTTTATTGTCTAAATTAAGATAAAAATGT
1 AATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGT
13571567 AAAAGTTATC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 122 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (85 bp):
AATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAAAATGTTTTCTTGCCTAAATTAAGAC
AAAACATGTTTTCTTATCTG
Found at i:13572481 original size:24 final size:24
Alignment explanation
Indices: 13572452--13572500 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13572442 ATGGCTGTGA
13572452 ATAATTTTTATATTCAATTAAAAT
1 ATAATTTTTATATTCAATTAAAAT
13572476 ATAATTTTTATATTCAATTAAAAT
1 ATAATTTTTATATTCAATTAAAAT
13572500 A
1 A
13572501 CATGTATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAATTTTTATATTCAATTAAAAT
Found at i:13586175 original size:21 final size:22
Alignment explanation
Indices: 13586140--13586183 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
13586130 CTCTTAAAGT
13586140 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
13586162 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
13586183 A
1 A
13586184 TTAATTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:13589047 original size:28 final size:27
Alignment explanation
Indices: 13589015--13589086 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
13589005 TTAAGATATC
*
13589015 TATCTACTTTTGGTGCGTTAAAAGTATT
1 TATCTACTTTTGGTG-GTTAAAAGTATA
*
13589043 TATCTA-TTTGTGGTAGGTTACAAGTATA
1 TATCTACTTT-TGGT-GGTTAAAAGTATA
* *
13589071 CATCCACTTTTGGTGG
1 TATCTACTTTTGGTGG
13589087 GTAATTCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 5 0.14
28 28 0.76
29 4 0.11
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (27 bp):
TATCTACTTTTGGTGGTTAAAAGTATA
Found at i:13590656 original size:31 final size:31
Alignment explanation
Indices: 13590634--13590718 Score: 161
Period size: 31 Copynumber: 2.7 Consensus size: 31
13590624 GTGGTTCCCC
13590634 GTAACCCATTGCCAGTCGTATGTGGGCTTCG
1 GTAACCCATTGCCAGTCGTATGTGGGCTTCG
13590665 GTAACCCATTGCCAGTCGTATGTGGGCTTCG
1 GTAACCCATTGCCAGTCGTATGTGGGCTTCG
*
13590696 GTAACCCATTGCCAATCGTATGT
1 GTAACCCATTGCCAGTCGTATGT
13590719 AACCTTCCCC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (31 bp):
GTAACCCATTGCCAGTCGTATGTGGGCTTCG
Found at i:13594810 original size:13 final size:13
Alignment explanation
Indices: 13594792--13594820 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13594782 TTAAATAATA
13594792 TATCATAAATAAG
1 TATCATAAATAAG
13594805 TATCATAAATAAG
1 TATCATAAATAAG
13594818 TAT
1 TAT
13594821 TATTCTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (13 bp):
TATCATAAATAAG
Found at i:13597489 original size:24 final size:24
Alignment explanation
Indices: 13597455--13597501 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13597445 GGGAAAATCA
*
13597455 GAGATAGAATATAGAAATCTAGAG
1 GAGATAAAATATAGAAATCTAGAG
13597479 GAGATAAAATATAGAAATCTAGA
1 GAGATAAAATATAGAAATCTAGA
13597502 AGGAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (24 bp):
GAGATAAAATATAGAAATCTAGAG
Found at i:13605162 original size:41 final size:41
Alignment explanation
Indices: 13605117--13605196 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
13605107 TTCTATTTGA
*
13605117 AATCTATTGATACAGCTAAGAAATGTATCAATAAATCAAAC
1 AATCTATCGATACAGCTAAGAAATGTATCAATAAATCAAAC
* * **
13605158 AATCTATCGATACATCTAAGCAATGTATTGATAAATCAA
1 AATCTATCGATACAGCTAAGAAATGTATCAATAAATCAA
13605197 GCTTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (41 bp):
AATCTATCGATACAGCTAAGAAATGTATCAATAAATCAAAC
Found at i:13605181 original size:21 final size:20
Alignment explanation
Indices: 13605142--13605198 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
13605132 CTAAGAAATG
* *
13605142 TATCAATAAATCAAACAATC
1 TATCGATAAATCAAGCAATC
* *
13605162 TATCGATACATCTAAGCAATG
1 TATCGATAAATC-AAGCAATC
*
13605183 TATTGATAAATCAAGC
1 TATCGATAAATCAAGC
13605199 TTATTTTTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.28
Consensus pattern (20 bp):
TATCGATAAATCAAGCAATC
Found at i:13614974 original size:138 final size:132
Alignment explanation
Indices: 13614723--13614991 Score: 457
Period size: 138 Copynumber: 2.0 Consensus size: 132
13614713 TTCTTGTTGA
13614723 GTCCAATGTCACTTGGTAGAATGTCTTGAGGTCTATTGTTGAGAACATTAGCTAATTGACCCAAT
1 GTCCAATGTCACTTGGTAGAATGTCTTGAGGTCTATTGTTGAGAACATTAGCTAATTGACCCAAT
** *
13614788 TGTGTCAAGATTTTTGAGGGATGTTGATTGGCTTTGGATTAATATAGATTGACTTTGAATGACAA
66 TGTGTCAAGAGATTTGAGAGATGTTGATTGGCTTTGGATTAATATAGATTGACTTTGAATGACAA
13614853 CG
131 CG
13614855 GTCCAATGTCACTTGGTAGAATGTCTTGAGGTCTATTGTTGAGAACATTAGCTAACTGAAACTGA
1 GTCCAATGTCACTTGGTAGAATGTCTTGAGGTCTATTGTTGAGAACATTAGCTAA-T-----TGA
13614920 CCCAATTGTGTCAAGAGATTTGAGAGATGTTGATTGGCTTTGGATTAATATAGATTGACTTTGAA
60 CCCAATTGTGTCAAGAGATTTGAGAGATGTTGATTGGCTTTGGATTAATATAGATTGACTTTGAA
13614985 TGACAAC
125 TGACAAC
13614992 ATCTAACATT
Statistics
Matches: 128, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
132 55 0.43
133 1 0.01
138 72 0.56
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (132 bp):
GTCCAATGTCACTTGGTAGAATGTCTTGAGGTCTATTGTTGAGAACATTAGCTAATTGACCCAAT
TGTGTCAAGAGATTTGAGAGATGTTGATTGGCTTTGGATTAATATAGATTGACTTTGAATGACAA
CG
Found at i:13618269 original size:30 final size:28
Alignment explanation
Indices: 13618236--13618359 Score: 122
Period size: 30 Copynumber: 4.2 Consensus size: 28
13618226 CTTTAATTTT
* *
13618236 GACAAAAATATTTTATCTTATTTAAATTAT
1 GACAAAAATATTTT-T-TTGTTTAAATTAA
* * *
13618266 GACAAATATATTTTTTTGTCTAGATTAA
1 GACAAAAATATTTTTTTGTTTAAATTAA
13618294 GACAAAAATATATTTTTGTTGTCTTAAATTAA
1 GAC-AAAA-ATATTTTT-TTGT-TTAAATTAA
* * *
13618326 CACAAAAATATTTTCTTGTCTAAATTAA
1 GACAAAAATATTTTTTTGTTTAAATTAA
13618354 GACAAA
1 GACAAA
13618360 CATGTTAAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
28 25 0.32
29 8 0.10
30 28 0.36
31 8 0.10
32 9 0.12
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (28 bp):
GACAAAAATATTTTTTTGTTTAAATTAA
Found at i:13618321 original size:60 final size:58
Alignment explanation
Indices: 13618236--13618359 Score: 158
Period size: 60 Copynumber: 2.1 Consensus size: 58
13618226 CTTTAATTTT
** * * *
13618236 GACAAAAATATTTTATCTTATTTAAATTATGACAAATATATTTTTTTGTCTAGATTAA
1 GACAAAAATATTTTATCTTATTTAAATTAACACAAAAATATTTTCTTGTCTAAATTAA
* * *
13618294 GACAAAAATATATTTTTGTTGTCTTAAATTAACACAAAAATATTTTCTTGTCTAAATTAA
1 GACAAAAATAT-TTTATCTTAT-TTAAATTAACACAAAAATATTTTCTTGTCTAAATTAA
13618354 GACAAA
1 GACAAA
13618360 CATGTTAAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 11 0.20
59 7 0.12
60 38 0.68
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (58 bp):
GACAAAAATATTTTATCTTATTTAAATTAACACAAAAATATTTTCTTGTCTAAATTAA
Found at i:13618331 original size:32 final size:30
Alignment explanation
Indices: 13618236--13618359 Score: 123
Period size: 28 Copynumber: 4.2 Consensus size: 30
13618226 CTTTAATTTT
* * * *
13618236 GACAAAAATAT-TTTATCTTATTTAAATTAT
1 GACAAAAATATATTT-TTTTGTCTAAATTAA
*
13618266 GAC--AAATATATTTTTTTGTCTAGATTAA
1 GACAAAAATATATTTTTTTGTCTAAATTAA
13618294 GACAAAAATATATTTTTGTTGTCTTAAATTAA
1 GACAAAAATATATTTTT-TTGTC-TAAATTAA
* *
13618326 CAC-AAAA-ATATTTTCTTGTCTAAATTAA
1 GACAAAAATATATTTTTTTGTCTAAATTAA
13618354 GACAAA
1 GACAAA
13618360 CATGTTAAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
28 29 0.37
29 10 0.13
30 22 0.28
31 9 0.11
32 9 0.11
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (30 bp):
GACAAAAATATATTTTTTTGTCTAAATTAA
Found at i:13620618 original size:42 final size:44
Alignment explanation
Indices: 13620434--13620725 Score: 248
Period size: 44 Copynumber: 6.5 Consensus size: 44
13620424 CCATAAGTGA
* * *
13620434 AGTTGAGTTCAACTAGATGAACAAATATCTATAGAACCTAAATGAGTCT
1 AGTTGAGATCAACTAGAT-AACAAA-A--TATA-TACCTAAATGAGCCT
* ** * *
13620483 AGTTGAGATAAACTAGATAACAAAATATATATGTATATGAGCTT
1 AGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGCCT
* * *
13620527 GGTTGAGATTAACTATAGATAACAAAATATATACCTAAATGAGCAT
1 AGTTGAGATCAAC--TAGATAACAAAATATATACCTAAATGAGCCT
* **
13620573 AGTTGAGATCAACTAGTTAATGAAATA-A-ACCTAAATGAGCCT
1 AGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGCCT
* * * * **
13620615 AGTTCAGTTCAACTAGATAGCAAAATATATACCTAAATAAGTTT
1 AGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGCCT
* * * *
13620659 AGTTAAGTTCAATTAGATAACAAAATATATAACTAAATGAGTCC-
1 AGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAG-CCT
* * *
13620703 AGTTTAGTTCAACTGGATAACAA
1 AGTTGAGATCAACTAGATAACAA
13620726 TATGTATATA
Statistics
Matches: 199, Mismatches: 39, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
42 34 0.17
43 2 0.01
44 98 0.49
45 4 0.02
46 38 0.19
47 1 0.01
48 6 0.03
49 16 0.08
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (44 bp):
AGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGCCT
Found at i:13620662 original size:86 final size:88
Alignment explanation
Indices: 13620434--13620725 Score: 227
Period size: 86 Copynumber: 3.3 Consensus size: 88
13620424 CCATAAGTGA
* * * * *
13620434 AGTTGAGTTCAACTAGATGAACAAATATCTATAGAACCTAAATGAGTC-TAGTTGAGATAAACTA
1 AGTTCAGTTCAACTAGAT-AACAAA-A--TATA-TACCTAAATAAG-CATAGTTAAGATCAACTA
** * *
13620498 GATAACAAAATATATATGTATATGAG-CTT
60 GATAACAAAATATATAACTAAATGAGTC-C
* * * * *
13620527 GGTTGAGATT-AACTATAGATAACAAAATATATACCTAAATGAGCATAGTTGAGATCAACTAGTT
1 AGTTCAG-TTCAAC--TAGATAACAAAATATATACCTAAATAAGCATAGTTAAGATCAACTAGAT
** *
13620591 AATGAAATA-A-ACCTAAATGAG-CC
63 AACAAAATATATAACTAAATGAGTCC
* ** * *
13620614 TAGTTCAGTTCAACTAGATAGCAAAATATATACCTAAATAAGTTTAGTTAAGTTCAATTAGATAA
1 -AGTTCAGTTCAACTAGATAACAAAATATATACCTAAATAAGCATAGTTAAGATCAACTAGATAA
13620679 CAAAATATATAACTAAATGAGTCC
65 CAAAATATATAACTAAATGAGTCC
* *
13620703 AGTTTAGTTCAACTGGATAACAA
1 AGTTCAGTTCAACTAGATAACAA
13620726 TATGTATATA
Statistics
Matches: 164, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
86 48 0.29
87 3 0.02
88 47 0.29
89 4 0.02
90 35 0.21
91 4 0.02
93 10 0.06
94 8 0.05
95 5 0.03
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (88 bp):
AGTTCAGTTCAACTAGATAACAAAATATATACCTAAATAAGCATAGTTAAGATCAACTAGATAAC
AAAATATATAACTAAATGAGTCC
Found at i:13637972 original size:35 final size:35
Alignment explanation
Indices: 13637849--13638004 Score: 152
Period size: 35 Copynumber: 4.5 Consensus size: 35
13637839 TTAAGTTGTA
* * * * **
13637849 CCTAATTTATTAAATTATTTAATTAGGCCATTGGG
1 CCTAATTGATTAAATTGTTTAATCAAGTTATTGGG
* * **** * *
13637884 TCTAATTAATTAAATTAAACAATTAAGTTATT-AG
1 CCTAATTGATTAAATTGTTTAATCAAGTTATTGGG
13637918 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
1 CCTAATTGATTAAA-TTGTTTAATCAAGTTATTGGG
* *
13637954 CCTAATTGGTTAAATTGTTTAATGAAGTTATTGGG
1 CCTAATTGATTAAATTGTTTAATCAAGTTATTGGG
13637989 CCTAATTGATTAAATT
1 CCTAATTGATTAAATT
13638005 AAACAATTAA
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
34 13 0.13
35 72 0.73
36 14 0.14
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (35 bp):
CCTAATTGATTAAATTGTTTAATCAAGTTATTGGG
Found at i:13651688 original size:74 final size:72
Alignment explanation
Indices: 13651582--13651770 Score: 195
Period size: 74 Copynumber: 2.6 Consensus size: 72
13651572 CTCTTAGTTG
* * * *
13651582 ACTAA-CATACTTCTTAGTCAACTAAGTCTTTTCTGTCTTCTACTCCTAGTTT-TTGACAGTGAG
1 ACTAACCATTCTTCTTGGTCAACTAAGTCTTTTCTGT-TTCTA-TCATAGTTTCTAG-CAGTGAG
*
13651645 CACTTAGTCA
63 CACTTAGCCA
* * * * *
13651655 ACTAACCATGT-TTCTTGGTCAACTAAGTTTTTTCTATTTTTTTATTATAGTTTCTAGTAGTGAG
1 ACTAACCAT-TCTTCTTGGTCAACTAAGTCTTTTC--TGTTTCTATCATAGTTTCTAGCAGTGAG
*
13651719 CACTTAGCCG
63 CACTTAGCCA
*
13651729 ACTAACCATTCTTCTTGGTCGACTAAGTCTTTTCTGTTTCTA
1 ACTAACCATTCTTCTTGGTCAACTAAGTCTTTTCTGTTTCTA
13651771 GATTGGCCAA
Statistics
Matches: 95, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
72 6 0.06
73 6 0.06
74 75 0.79
75 6 0.06
76 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (72 bp):
ACTAACCATTCTTCTTGGTCAACTAAGTCTTTTCTGTTTCTATCATAGTTTCTAGCAGTGAGCAC
TTAGCCA
Found at i:13652309 original size:25 final size:25
Alignment explanation
Indices: 13652275--13652329 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
13652265 ATATTAACAG
* *
13652275 TATTGTAAATAACTGTCATCAGCAT
1 TATTGCAAATAACTATCATCAGCAT
13652300 TATTGCAAATAACTATCATCAGCAT
1 TATTGCAAATAACTATCATCAGCAT
13652325 TATTG
1 TATTG
13652330 TCAACAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (25 bp):
TATTGCAAATAACTATCATCAGCAT
Found at i:13662157 original size:7 final size:7
Alignment explanation
Indices: 13662145--13662177 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
13662135 AGAAAAATTC
13662145 TTGAAGA
1 TTGAAGA
13662152 TTGAAGA
1 TTGAAGA
13662159 TTGAAGA
1 TTGAAGA
13662166 TTGAAGA
1 TTGAAGA
13662173 CTTGA
1 -TTGA
13662178 CAAATTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (7 bp):
TTGAAGA
Found at i:13668561 original size:27 final size:29
Alignment explanation
Indices: 13668518--13668581 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 29
13668508 ACTAACCCAA
* *
13668518 CCTTTCCTTTCTTTTTCTT-CTTT-CTCT
1 CCTTTCCTTCCTCTTTCTTCCTTTCCTCT
*
13668545 CTTTTCCTTCCTCTTTCTTCCTTTCCTCT
1 CCTTTCCTTCCTCTTTCTTCCTTTCCTCT
13668574 CCTTTCCT
1 CCTTTCCT
13668582 CTTTTCTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 16 0.52
28 4 0.13
29 11 0.35
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (29 bp):
CCTTTCCTTCCTCTTTCTTCCTTTCCTCT
Found at i:13668587 original size:18 final size:19
Alignment explanation
Indices: 13668536--13668587 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
13668526 TTCTTTTTCT
13668536 TCTTTCTCTCTTTTCCTTCC
1 TCTTTC-CTCTTTTCCTTCC
* *
13668556 TCTTTCTTCCTTTCC-T-C
1 TCTTTCCTCTTTTCCTTCC
13668573 TCCTTTCCTCTTTTC
1 T-CTTTCCTCTTTTC
13668588 TCCTTGGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
19 7 0.26
20 6 0.22
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (19 bp):
TCTTTCCTCTTTTCCTTCC
Found at i:13669548 original size:19 final size:18
Alignment explanation
Indices: 13669524--13669564 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13669514 TTTTAATTTT
13669524 TTTTATTAATAAAATATTA
1 TTTTATT-ATAAAATATTA
* *
13669543 TTTTATTCTAAAATATTC
1 TTTTATTATAAAATATTA
13669561 TTTT
1 TTTT
13669565 TAGACATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATTATAAAATATTA
Found at i:13669565 original size:19 final size:19
Alignment explanation
Indices: 13669521--13669566 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13669511 ATATTTTAAT
13669521 TTTTTTTATTAATAAAATA
1 TTTTTTTATTAATAAAATA
* *
13669540 TTATTTTATT-CTAAAATA
1 TTTTTTTATTAATAAAATA
13669558 TTCTTTTTA
1 TT-TTTTTA
13669567 GACATTACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTTATTAATAAAATA
Found at i:13673046 original size:63 final size:63
Alignment explanation
Indices: 13672944--13673065 Score: 208
Period size: 63 Copynumber: 1.9 Consensus size: 63
13672934 GAGGCTCTTG
*
13672944 ATATTGAGAACGATGCTTACGGGCAATATCTTGGTGATCATCAAAACGTGAACAAAGTTCCTA
1 ATATTGAGAACGATGCTTACGGGCAATATCTTGGAGATCATCAAAACGTGAACAAAGTTCCTA
** *
13673007 ATATTGAGAACGATGCTTGGGGGCAATATCTTGGAGATCATCAAAACTTGAACAAAGTT
1 ATATTGAGAACGATGCTTACGGGCAATATCTTGGAGATCATCAAAACGTGAACAAAGTT
13673066 ATCTTAATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (63 bp):
ATATTGAGAACGATGCTTACGGGCAATATCTTGGAGATCATCAAAACGTGAACAAAGTTCCTA
Found at i:13675040 original size:107 final size:107
Alignment explanation
Indices: 13674854--13675086 Score: 466
Period size: 107 Copynumber: 2.2 Consensus size: 107
13674844 ATATCATGTT
13674854 CGTATTTATATTCCTAGTTTTTTTCTATAATTGGGGGAAGGGAAATTAGAATCTTGCTCTTTAGG
1 CGTATTTATATTCCTAGTTTTTTTCTATAATTGGGGGAAGGGAAATTAGAATCTTGCTCTTTAGG
13674919 CAAGGGGATAATGCACTAACCAATAAGCCAAATACTTAGATG
66 CAAGGGGATAATGCACTAACCAATAAGCCAAATACTTAGATG
13674961 CGTATTTATATTCCTAGTTTTTTTCTATAATTGGGGGAAGGGAAATTAGAATCTTGCTCTTTAGG
1 CGTATTTATATTCCTAGTTTTTTTCTATAATTGGGGGAAGGGAAATTAGAATCTTGCTCTTTAGG
13675026 CAAGGGGATAATGCACTAACCAATAAGCCAAATACTTAGATG
66 CAAGGGGATAATGCACTAACCAATAAGCCAAATACTTAGATG
13675068 CGTATTTATATTCCTAGTT
1 CGTATTTATATTCCTAGTT
13675087 AATAATGTTT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 126 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (107 bp):
CGTATTTATATTCCTAGTTTTTTTCTATAATTGGGGGAAGGGAAATTAGAATCTTGCTCTTTAGG
CAAGGGGATAATGCACTAACCAATAAGCCAAATACTTAGATG
Found at i:13678002 original size:15 final size:14
Alignment explanation
Indices: 13677979--13678028 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
13677969 TTCTTTTAGC
*
13677979 TTTTTTTATTTATA
1 TTTTATTATTTATA
13677993 TTATTATTATTTATA
1 TT-TTATTATTTATA
* *
13678008 TTTTTTTATTTTTA
1 TTTTATTATTTATA
*
13678022 TTCTATT
1 TTTTATT
13678029 TGCTCATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTATTTATA
Found at i:13678191 original size:15 final size:16
Alignment explanation
Indices: 13678171--13678200 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13678161 CTGTTATGTG
13678171 AATTTTA-TTTTTAAT
1 AATTTTAGTTTTTAAT
13678186 AATTTTAGTTTTTAA
1 AATTTTAGTTTTTAA
13678201 ACAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
AATTTTAGTTTTTAAT
Found at i:13684954 original size:21 final size:21
Alignment explanation
Indices: 13684930--13684971 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13684920 AAAAATTCTT
*
13684930 CTTGATGAACAAGTATCGATA
1 CTTGATCAACAAGTATCGATA
* *
13684951 CTTGTTCATCAAGTATCGATA
1 CTTGATCAACAAGTATCGATA
13684972 TCTAGAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
CTTGATCAACAAGTATCGATA
Done.