Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 85 of 135
Found at i:28920760 original size:20 final size:20
Alignment explanation
Indices: 28920737--28920780 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
28920727 TAAAAATTTG
28920737 TTTTTTAA-AAAAGTTTAAA
1 TTTTTTAAGAAAAGTTTAAA
* *
28920756 -TTTTTAAGCAAAGTTTTAA
1 TTTTTTAAGAAAAGTTTAAA
28920775 TTTTTT
1 TTTTTT
28920781 TTAACTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTTTAAGAAAAGTTTAAA
Found at i:28920945 original size:149 final size:150
Alignment explanation
Indices: 28920602--28921127 Score: 542
Period size: 148 Copynumber: 3.6 Consensus size: 150
28920592 TATGTTTTTT
* * * * * *
28920602 AGAAAAG-TTTACATTTTTAAACAAAATTTTAATTTTTTTTAACTATTTCGAAATAAAAGCTT-G
1 AGAAAAGATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTTGAAATAAAAGTTTAG
* * * *
28920665 AATTTTTAAGTAAAATAGTGATTTT-TTGTAAAAAAAAAATAGAAAGTTTAGATTTTT-AGAAAT
65 -ATTTTTAAGTAAAATAGTGATTTTCAT-T-AAAAAATAA-AGAAAGTTTTGATTTTTAAAAAAT
*
28920728 -AAAA-A----TTT-GT--TTTTTA
126 AAAAATATGTTTTTAGTGATTTTAA
** * *
28920744 A-AAAAG-TTTAAATTTTTAAGCAAAGTTTTAATTTTTTTTAACTATTTCGAAATAAAAGTTTAG
1 AGAAAAGATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTTGAAATAAAAGTTTAG
* *
28920807 ATTTTTAAGTAAAATAGTGATTTTC-TTTAAAAA-AGAGAAAGTTTAT-ATTTTT-AAAAATAAA
65 ATTTTTAAGTAAAATAGTGATTTTCATTAAAAAATAAAGAAAGTTT-TGATTTTTAAAAAATAAA
*
28920868 AATCTAT-TTTTTAGTTATTTTAA
129 AA--TATGTTTTTAGTGATTTTAA
*
28920891 AGAAAAGATTTAAATATTTAAATAAAGTTTTGATTTTGTTTAACTATTTTGAAATAAAAGTTTAG
1 AGAAAAGATTTAAATTTTTAAATAAAGTTTTGATTTT-TTTAACTATTTTGAAATAAAAGTTTAG
*
28920956 ATTTTTAA--ATAA-AGTGATTTTCATTAAAAAATAAAGAAAGTTTTGATTTTTAAAAAATAAAA
65 ATTTTTAAGTAAAATAGTGATTTTCATTAAAAAATAAAGAAAGTTTTGATTTTTAAAAAATAAAA
*
28921018 ATATGTTTTTAGTGGTTTTAA
130 ATATGTTTTTAGTGATTTTAA
* * *
28921039 AGAAAA-ACTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAAACTATTCTAAAATAAAAGTTTT
1 AGAAAAGA-TTTAAATTTTTAAATAAAGTTTTGATTTTTTT-AACTATTTTGAAATAAAAGTTTA
* *
28921103 GATTTTGAAGTAAAGTAGTGATTTT
64 GATTTTTAAGTAAAATAGTGATTTT
28921128 GTTTTAATTA
Statistics
Matches: 332, Mismatches: 26, Indels: 43
0.83 0.06 0.11
Matches are distributed among these distances:
137 20 0.06
138 5 0.02
139 5 0.02
140 1 0.00
141 82 0.25
142 2 0.01
144 3 0.01
145 2 0.01
146 10 0.03
147 24 0.07
148 101 0.30
149 66 0.20
150 2 0.01
151 9 0.03
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (150 bp):
AGAAAAGATTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTAGA
TTTTTAAGTAAAATAGTGATTTTCATTAAAAAATAAAGAAAGTTTTGATTTTTAAAAAATAAAAA
TATGTTTTTAGTGATTTTAA
Found at i:28920963 original size:52 final size:50
Alignment explanation
Indices: 28920874--28921101 Score: 123
Period size: 52 Copynumber: 4.5 Consensus size: 50
28920864 TAAAAATCTA
** *
28920874 TTTTTTAGTTATTTTAAAGAAAAGATTTAAATATTTAAATAAAGTTTTGAT
1 TTTTTTAACTATTTTAAAGAAAAG-TTTAAATTTTTAAATAAAGTTTTGAT
* *
28920925 TTTGTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAAATAAAG---TGAT
1 TTT-TTTAACTATTTT-AAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGAT
* *** ** ****
28920974 TTTCATTAA--AAAATAAAG-AAAGTTTTGATTTTTAAA-AAA-TAAAAAT
1 TTT-TTTAACTATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGAT
* * *
28921020 ATGTTTTT-AGTGGTTTTAAAGAAAAACTTTAAATTTTTAAATAAAGTTTTGAT
1 -T-TTTTTAACT-ATTTTAAAG-AAAAGTTTAAATTTTTAAATAAAGTTTTGAT
* *
28921073 TTTTTTAAACTATTCTAAAATAAAAGTTT
1 TTTTTT-AACTATT-TTAAAGAAAAGTTT
28921102 TGATTTTGAA
Statistics
Matches: 129, Mismatches: 31, Indels: 33
0.67 0.16 0.17
Matches are distributed among these distances:
44 3 0.02
45 17 0.13
46 6 0.05
47 5 0.04
48 2 0.02
49 16 0.12
51 23 0.18
52 40 0.31
53 17 0.13
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (50 bp):
TTTTTTAACTATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGAT
Found at i:28921164 original size:24 final size:23
Alignment explanation
Indices: 28921124--28921169 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
28921114 AAAGTAGTGA
** *
28921124 TTTTGTTTTAATTAAAAGAAAAC
1 TTTTGTTTTAAAAAAAAAAAAAC
28921147 TTTTGATTTTAAAAAAAAAAAAA
1 TTTTG-TTTTAAAAAAAAAAAAA
28921170 TTCGACTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (23 bp):
TTTTGTTTTAAAAAAAAAAAAAC
Found at i:28921166 original size:148 final size:143
Alignment explanation
Indices: 28920489--28921168 Score: 543
Period size: 141 Copynumber: 4.7 Consensus size: 143
28920479 AAATTTGGGA
* *
28920489 AAAGTTTTGGTTTTTTTAAACAATTTCGAAATAAAAGCTTT-GATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGATTTTTTT-AACTATTT-GAAATAAAAG-TTTAGATTTTTAAGT-AAATAGTGATT
* * * *
28920553 TTCTTTAAAAAAG-AGAGTTTAGATTTTTAAAAATAAAAA-TA-----T-GT--TTTT-TAGAAA
62 TTATTTAAAAAAGAAAAGTTTTGATTTTTAAAAATAAAAACTATTTTTTAGTGATTTTAAAGAAA
* * *
28920607 AGTTTACATTTTTAAAC
127 AATTTAAATTTTTAAAT
* * *
28920624 AAAATTTTAATTTTTTTTAACTATTTCGAAATAAAAGCTT-GAATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGA-TTTTTTTAACTATTT-GAAATAAAAGTTTAG-ATTTTTAAGT-AAATAGTGATT
* * * *
28920688 TT-TTGTAAAAAAAAAATAGAAAGTTTAGATTTTTAGAAAT-AAAA--A---TTT-GT--TTTTT
62 TTATT-T----AAAAAAGA-AAAGTTTTGATTTTTAAAAATAAAAACTATTTTTTAGTGATTTTA
* **
28920743 AA-AAAAGTTTAAATTTTTAAGC
121 AAGAAAAATTTAAATTTTTAAAT
*
28920765 AAAGTTTTAATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTT
1 AAAGTTTTGA-TTTTTTTAACTATTT-GAAATAAAAGTTTAGATTTTTAAGT-AAATAGTGATTT
* *
28920830 TCTTTAAAAAAGAGAAAGTTTAT-ATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGA
63 TATTTAAAAAAGA-AAAGTTT-TGATTTTTAAAAATAAAAA-CTATTTTTTAGTGATTTTAAAGA
*
28920894 AAAGATTTAAATATTTAAAT
125 AAA-ATTTAAATTTTTAAAT
*
28920914 AAAGTTTTGATTTTGTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAAAT-AA-AGTGATTTT
1 AAAGTTTTGATTTT-TTTAACTA-TTTGAAATAAAAGTTTAGATTTTTAAGTAAATAGTGATTTT
* * *
28920977 CATTAAAAAATAAAGAAAGTTTTGATTTTTAAAAAATAAAAA-TATGTTTTTAGTGGTTTTAAAG
64 -ATTTAAAAA-AGA-AAAGTTTTGATTTTT-AAAAATAAAAACTAT-TTTTTAGTGATTTTAAAG
28921041 AAAAACTTTAAATTTTTAAAT
124 AAAAA-TTTAAATTTTTAAAT
* * *
28921062 AAAGTTTTGATTTTTTTAAACTATTCTAAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGATTT
1 AAAGTTTTGATTTTTTT-AACTATT-TGAAATAAAAGTTTAGATTTTTAAGTAAA-TAGTGATTT
* * * *
28921127 TGTTTTAATTAAAAGAAAACTTTTGATTTTAAAAAAAAAAAA
63 T-ATTTAA--AAAAGAAAAGTTTTGATTTTTAAAAATAAAAA
28921169 ATTCGACTAC
Statistics
Matches: 463, Mismatches: 40, Indels: 69
0.81 0.07 0.12
Matches are distributed among these distances:
134 5 0.01
135 50 0.11
136 7 0.02
137 26 0.06
138 4 0.01
139 7 0.02
140 4 0.01
141 108 0.23
142 4 0.01
144 3 0.01
145 2 0.00
146 9 0.02
147 25 0.05
148 99 0.21
149 66 0.14
150 13 0.03
151 26 0.06
152 2 0.00
153 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (143 bp):
AAAGTTTTGATTTTTTTAACTATTTGAAATAAAAGTTTAGATTTTTAAGTAAATAGTGATTTTAT
TTAAAAAAGAAAAGTTTTGATTTTTAAAAATAAAAACTATTTTTTAGTGATTTTAAAGAAAAATT
TAAATTTTTAAAT
Found at i:28922151 original size:3 final size:3
Alignment explanation
Indices: 28922143--28922174 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28922133 AATCTTTTAA
28922143 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28922175 AAGATCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28924801 original size:471 final size:471
Alignment explanation
Indices: 28923907--28924845 Score: 1312
Period size: 471 Copynumber: 2.0 Consensus size: 471
28923897 AACACTTGGT
*
28923907 AGTATTCCGAGGATCGTACCCAAAGGAGGCTTAAAGCAATAGTAAATCAAATCCCTGCAAAGAGT
1 AGTATTCCGAGGATCGTACCCAAAGAAGGCTTAAAGCAATAGTAAATCAAATCCCTGCAAAGAGT
* *
28923972 AAAATTAATTAGTGCTTATTTTAGGGTTTATAGTACAAAAAATAAAAGAGTGTTTTGAGTGCATA
66 AAAATTAATTAGTACTTATTTTAGGGTTTATAGTACAAAAAATAAAAGAGTGTTTTGAGAGCATA
* * ***
28924037 AAAATAAAAAGATAAAATAGAATAGAAAATAAAGGAAAAAGATTGAGTTTTAGAAATCTTATAAA
131 AAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAGAAGTAGAAATCTTATAAA
** * * * *
28924102 CGGCTTTGGGGATTTTAGGTCGCTTCCGTATGAGTTCTTTAATTGTTTGGTTTTGGGGATTTTCC
196 CGGCTTTGGGGAAATTAGGTCGCTTCCATATGAGTTCCTCAATTGTTGGGTTTTGGGGATTTTCC
* * * * *
28924167 TCCAATCAACTAGTCACTACCCCGGTTGGATCTCTCGATCTTCTGCCAGCATGGCATGTCGATAG
261 TCCAATCAACTAATCACTACCCCAGTTGGATATCTCGATCTTCTGCCAGCATAGCAAGTCGATAG
* * * *
28924232 AGATTACTTATCGCTAGATGTTACAATCTAAACTAGTTTGGGGAAAATGTGTTCATGGATGGGCA
326 AGATTACTTATCGCTAGATGTCACAATCTAAACTAGTTTAGGGAAAACGTGTTCAAGGATGGGCA
* *
28924297 ATACCAATTTTGGGTGCATCCCCACCTAGATGACTTTCTAGGGTTGTCAAGCCTAGTGTTTGTTC
391 ATACCAATTTTGGGTCCATCCCCACCAAGATGACTTTCTAGGGTTGTCAAGCCTAGTGTTTGTTC
*
28924362 AATGCTCTTCCTTGCA
456 AAAGCTCTTCCTTGCA
* * * ** *
28924378 AGTATTTCGAGGATCGTACCCAAAGAAGGCTTGAAGCGATAGTAAATTGAATCCCTGTAAAGAGT
1 AGTATTCCGAGGATCGTACCCAAAGAAGGCTTAAAGCAATAGTAAATCAAATCCCTGCAAAGAGT
* ** *
28924443 AAAATTAATTAGTACTTGTTTTAGGGTTTATAGTATGAGAAATAAAAGAGTTGTTTTGAGAGCAT
66 AAAATTAATTAGTACTTATTTTAGGGTTTATAGTACAAAAAATAAAAGAG-TGTTTTGAGAGCAT
* * * *
28924508 AAATAT-AAAAGAT-AAATAAAATAGGAAATAAAAGCAAAAGTTTGAGAAGTAGAAAATCTTATA
130 AAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAGAAGTAG-AAATCTTATA
* * ** *
28924571 AACGGCTTTGGGGAAATTAGGTTGTTTCCATATGCTTTCCTCGATTGTTGGGTTTTGGGGATTTT
194 AACGGCTTTGGGGAAATTAGGTCGCTTCCATATGAGTTCCTCAATTGTTGGGTTTTGGGGATTTT
* * * *
28924636 CCTTCAATCAACTAATCATTACCCCAGTTGGATATCTCGATCTTCCAT-CGA-CCTAGCAAGTCG
259 CCTCCAATCAACTAATCACTACCCCAGTTGGATATCTCGATCTT-C-TGCCAGCATAGCAAGTCG
* *
28924699 ATAGAGATTACTTATCGCTAGATGTCATAATCTAAA-TCGGTTTAGGGAAAACGTGTTCAAGGAT
322 ATAGAGATTACTTATCGCTAGATGTCACAATCTAAACT-AGTTTAGGGAAAACGTGTTCAAGGAT
* *
28924763 GGGCAATACCAATTTTGGGTCCATTCCCACCAAGATGACTTTCTAGGGTTGTCAGGCCTAGTGTT
386 GGGCAATACCAATTTTGGGTCCATCCCCACCAAGATGACTTTCTAGGGTTGTCAAGCCTAGTGTT
*
28924828 TGTTCAAAGTTCTTCCTT
451 TGTTCAAAGCTCTTCCTT
28924846 TCCCAAATAG
Statistics
Matches: 409, Mismatches: 54, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
470 32 0.08
471 355 0.87
472 21 0.05
473 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (471 bp):
AGTATTCCGAGGATCGTACCCAAAGAAGGCTTAAAGCAATAGTAAATCAAATCCCTGCAAAGAGT
AAAATTAATTAGTACTTATTTTAGGGTTTATAGTACAAAAAATAAAAGAGTGTTTTGAGAGCATA
AAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAGAAGTAGAAATCTTATAAA
CGGCTTTGGGGAAATTAGGTCGCTTCCATATGAGTTCCTCAATTGTTGGGTTTTGGGGATTTTCC
TCCAATCAACTAATCACTACCCCAGTTGGATATCTCGATCTTCTGCCAGCATAGCAAGTCGATAG
AGATTACTTATCGCTAGATGTCACAATCTAAACTAGTTTAGGGAAAACGTGTTCAAGGATGGGCA
ATACCAATTTTGGGTCCATCCCCACCAAGATGACTTTCTAGGGTTGTCAAGCCTAGTGTTTGTTC
AAAGCTCTTCCTTGCA
Found at i:28938694 original size:27 final size:27
Alignment explanation
Indices: 28938657--28938725 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
28938647 TTGTTCTCTT
*
28938657 CAGATTTCTTGTCATTCTCATCGGAAC
1 CAGATTTCTTGTCATTCTCATCCGAAC
* * *
28938684 CAGATTGCTTGTCAATCTCATCCGAAT
1 CAGATTTCTTGTCATTCTCATCCGAAC
28938711 CAGATTTCTTGTCAT
1 CAGATTTCTTGTCAT
28938726 CAGAATTCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (27 bp):
CAGATTTCTTGTCATTCTCATCCGAAC
Found at i:28941229 original size:16 final size:17
Alignment explanation
Indices: 28941208--28941239 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28941198 ATCTAGATAA
28941208 TAATTA-TTCATCCAAG
1 TAATTATTTCATCCAAG
28941224 TAATTATTTCATCCAA
1 TAATTATTTCATCCAA
28941240 CTATTACTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATTATTTCATCCAAG
Found at i:28943260 original size:40 final size:40
Alignment explanation
Indices: 28943204--28943454 Score: 209
Period size: 41 Copynumber: 6.2 Consensus size: 40
28943194 TTGGTATGGT
28943204 GGTGTATTTATCGGGCTTTGTGCCTAGCAGGCTTAGTGCC
1 GGTGTATTTATCGGGCTTTGTGCCTAGCAGGCTTAGTGCC
* * **
28943244 GGTGTATTTATGGGGCTTTGTACCTAGCAGGCTTAGTGTT
1 GGTGTATTTATCGGGCTTTGTGCCTAGCAGGCTTAGTGCC
* * * * * *
28943284 GGTGTATTTTATAGGGCTTTGTGCTTAACAGGCTCAATGCT
1 GGTGTA-TTTATCGGGCTTTGTGCCTAGCAGGCTTAGTGCC
** * *
28943325 GGTGTATTTGATCAAGCATTGTGCCTAGCAGGCTTAGTGTC
1 GGTGTATTT-ATCGGGCTTTGTGCCTAGCAGGCTTAGTGCC
* * * *
28943366 AGTGTATTATATCGGGCATTAG-GCCTAGCAGGCTTCGTGTC
1 GGTGTATT-TATCGGGC-TTTGTGCCTAGCAGGCTTAGTGCC
* * * * * * *
28943407 AGTATATCTTAACAGG-TCTTGAGCCTAGCAGTCTTCGTGCC
1 GGTGTAT-TTATCGGGCT-TTGTGCCTAGCAGGCTTAGTGCC
28943448 GGTGTAT
1 GGTGTAT
28943455 CAAATTAGTC
Statistics
Matches: 169, Mismatches: 35, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
39 1 0.01
40 47 0.28
41 117 0.69
42 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (40 bp):
GGTGTATTTATCGGGCTTTGTGCCTAGCAGGCTTAGTGCC
Found at i:28943599 original size:13 final size:13
Alignment explanation
Indices: 28943595--28943670 Score: 66
Period size: 13 Copynumber: 5.7 Consensus size: 13
28943585 TATGAATTGT
28943595 TTATATAGAAATAG
1 TTATAT-GAAATAG
* *
28943609 ATATATGAAACAG
1 TTATATGAAATAG
*
28943622 TTATATG-AATTG
1 TTATATGAAATAG
28943634 TTTATATGGAAATAG
1 -TTATAT-GAAATAG
*
28943649 ATATATGAAAT-G
1 TTATATGAAATAG
28943661 ATTATATGAA
1 -TTATATGAA
28943671 GTATTTTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
12 4 0.08
13 31 0.62
14 11 0.22
15 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.16, T:0.37
Consensus pattern (13 bp):
TTATATGAAATAG
Found at i:28943616 original size:40 final size:40
Alignment explanation
Indices: 28943572--28943670 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
28943562 CAAATGATTT
*
28943572 TATGAAACGACTATATGAATTGTTTATATAGAAATAGATA
1 TATGAAACGATTATATGAATTGTTTATATAGAAATAGATA
*
28943612 TATGAAAC-AGTTATATGAATTGTTTATATGGAAATAGATA
1 TATGAAACGA-TTATATGAATTGTTTATATAGAAATAGATA
*
28943652 TATGAAATGATTATATGAA
1 TATGAAACGATTATATGAA
28943671 GTATTTTTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
39 1 0.02
40 52 0.96
41 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.36
Consensus pattern (40 bp):
TATGAAACGATTATATGAATTGTTTATATAGAAATAGATA
Found at i:28943645 original size:27 final size:27
Alignment explanation
Indices: 28943596--28943668 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
28943586 ATGAATTGTT
*
28943596 TATATAGAAATAGA-TATAT-GAAACAGT
1 TATAT-GAAAT-GATTATATGGAAACAGA
* * *
28943623 TATATGAATTGTTTATATGGAAATAGA
1 TATATGAAATGATTATATGGAAACAGA
28943650 TATATGAAATGATTATATG
1 TATATGAAATGATTATATG
28943669 AAGTATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 1 0.03
26 9 0.24
27 28 0.74
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.37
Consensus pattern (27 bp):
TATATGAAATGATTATATGGAAACAGA
Found at i:28947343 original size:3 final size:3
Alignment explanation
Indices: 28947335--28947391 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
28947325 GTATTAAAGT
* * *
28947335 AGA AGA AG- AGA A-A AGA A-A AGA AGA TGA AAA ATA AG- AGA AGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
28947377 AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA
28947392 CATTGCCCCG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
2 8 0.18
3 33 0.75
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:28947357 original size:15 final size:15
Alignment explanation
Indices: 28947337--28947391 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
28947327 ATTAAAGTAG
28947337 AAGAAGAGAAAAGAA
1 AAGAAGAGAAAAGAA
28947352 AAGAAGATGAAAA-ATA
1 AAGAAGA-GAAAAGA-A
28947368 AGAGAAG-GAAGAAGAA
1 A-AGAAGAGAA-AAGAA
28947384 GAAGAAGA
1 -AAGAAGA
28947392 CATTGCCCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 11 0.33
16 15 0.45
17 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (15 bp):
AAGAAGAGAAAAGAA
Found at i:28947693 original size:3 final size:3
Alignment explanation
Indices: 28947680--28947762 Score: 102
Period size: 3 Copynumber: 28.7 Consensus size: 3
28947670 TGTGGGTATT
* * *
28947680 GAA GCA GAA GAA G-A GAA -AA GAA -AA GAA GAT GAA AAA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
28947724 GGAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
28947763 CGTTGCCCAG
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 8 0.12
3 58 0.84
4 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.33, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:28950817 original size:64 final size:64
Alignment explanation
Indices: 28950738--28950866 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
28950728 TAAGGGTAAA
28950738 TAGGTAAATTTAGTATTTAAGTGATAATAGGTAAAAATAATAGAATTTAGGTTGTCTTCTTCAT
1 TAGGTAAATTTAGTATTTAAGTGATAATAGGTAAAAATAATAGAATTTAGGTTGTCTTCTTCAT
28950802 TAGGTAAATTTAGTATTTAAGTGATAATAGGTAAAAATAATAGAATTTAGGTTGTCTTCTTCAT
1 TAGGTAAATTTAGTATTTAAGTGATAATAGGTAAAAATAATAGAATTTAGGTTGTCTTCTTCAT
28950866 T
1 T
28950867 TTGAAACAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (64 bp):
TAGGTAAATTTAGTATTTAAGTGATAATAGGTAAAAATAATAGAATTTAGGTTGTCTTCTTCAT
Found at i:28954066 original size:465 final size:466
Alignment explanation
Indices: 28953195--28954126 Score: 1839
Period size: 465 Copynumber: 2.0 Consensus size: 466
28953185 AAGAGTCCTG
28953195 AACGAGATGGCTTGTTCTCTAGAAGACTACCTGAGGTGTGCAGCTTTGTTATTGAAGGACGAGGC
1 AACGAGATGGCTTGTTCTCTAGAAGACTACCTGAGGTGTGCAGCTTTGTTATTGAAGGACGAGGC
28953260 TTACAATTGGTGGACGATGATTTTAGCAGCGATGCTTGAGAATGAAGTTACCTGGGAATTTTTCC
66 TTACAATTGGTGGACGATGATTTTAGCAGCGATGCTTGAGAATGAAGTTACCTGGGAATTTTTCC
28953325 AAGCAGAATTCAAAAAGAAATATGTCTACAAAAGGTACCTGGACAAGAGAAAGAGAGTTTTTAAA
131 AAGCAGAATTCAAAAAGAAATATGTCTACAAAAGGTACCTGGACAAGAGAAAGAGAGTTTTTAAA
28953390 TTTGAGACAAGGAAATAAAATAGTGGCAGAATATGAGCGGGAATTTGTACAACTTAGTAAGTATG
196 TTTGAGACAAGGAAATAAAATAGTGGCAGAATATGAGCGGGAATTTGTACAACTTAGTAAGTATG
28953455 CTCGTGAGATTGTACAGACAGATGAGGCAATGTACGTTCGTTTCAAAGACGGGCTGAATGACGAA
261 CTCGTGAGATTGTACAGACAGATGAGGCAATGTACGTTCGTTTCAAAGACGGGCTGAATGACGAA
28953520 ATCAAGATGATGGTAAGAGGATCCGAGCTGCGATCGTTTGTAGTTCTTGCGGATAGAGCTCAAAA
326 ATCAAGATGATGGTAAGAGGATCCGAGCTGCGATCGTTTGTAGTTCTTGCGGATAGAGCTCAAAA
28953585 GATGGAAGAAATTTACCACAATAAAAGGTAAAAAGA-AAGAGGTTTCGAGAATCGGGAAAGAAGA
391 GATGGAAGAAATTTACCACAATAAAAGGTAAAAAGAGAAGAGGTTTCGAGAATCGGGAAAGAAGA
28953649 GTATCACCAGA
456 GTATCACCAGA
28953660 AACGAGATGGCTTGTTCTCTAGAAGACTACCTGAGGTGTGCAGCTTTGTTATTGAAGGACGAGGC
1 AACGAGATGGCTTGTTCTCTAGAAGACTACCTGAGGTGTGCAGCTTTGTTATTGAAGGACGAGGC
*
28953725 TTATAATTGGTGGACGATGATTTTAGCAGCGATGCTTGAGAATGAAGTTACCTGGGAATTTTTCC
66 TTACAATTGGTGGACGATGATTTTAGCAGCGATGCTTGAGAATGAAGTTACCTGGGAATTTTTCC
28953790 AAGCAGAATTCAAAAAGAAATATGTCTACAAAAGGTACCTGGACAAGAGAAAGAGAGTTTTTAAA
131 AAGCAGAATTCAAAAAGAAATATGTCTACAAAAGGTACCTGGACAAGAGAAAGAGAGTTTTTAAA
28953855 TTTGAGACAAGGAAATAAAATAGTGGCAGAATATGAGCGGGAATTTGTACAACTTAGTAAGTATG
196 TTTGAGACAAGGAAATAAAATAGTGGCAGAATATGAGCGGGAATTTGTACAACTTAGTAAGTATG
*
28953920 CTCGTGAGATTGTACAGACAGATGAGGCAATGTACGTTCTTTTCAAAGACGGGCTGAATGACGAA
261 CTCGTGAGATTGTACAGACAGATGAGGCAATGTACGTTCGTTTCAAAGACGGGCTGAATGACGAA
28953985 ATCAAGATGATGGTAAGAGGATCCGAGCTGCGATCGTTTGTAGTTCTTGCGGATAGAGCTCAAAA
326 ATCAAGATGATGGTAAGAGGATCCGAGCTGCGATCGTTTGTAGTTCTTGCGGATAGAGCTCAAAA
28954050 GATGGAAGAAATTTACCACAATAAAAGGTAAAAAGAGAAGAGGTTTCGAGAATCGGGAAAGAAGA
391 GATGGAAGAAATTTACCACAATAAAAGGTAAAAAGAGAAGAGGTTTCGAGAATCGGGAAAGAAGA
28954115 GTATCACCAGA
456 GTATCACCAGA
28954126 A
1 A
28954127 TTTTTTTTAT
Statistics
Matches: 464, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
465 424 0.91
466 40 0.09
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.25
Consensus pattern (466 bp):
AACGAGATGGCTTGTTCTCTAGAAGACTACCTGAGGTGTGCAGCTTTGTTATTGAAGGACGAGGC
TTACAATTGGTGGACGATGATTTTAGCAGCGATGCTTGAGAATGAAGTTACCTGGGAATTTTTCC
AAGCAGAATTCAAAAAGAAATATGTCTACAAAAGGTACCTGGACAAGAGAAAGAGAGTTTTTAAA
TTTGAGACAAGGAAATAAAATAGTGGCAGAATATGAGCGGGAATTTGTACAACTTAGTAAGTATG
CTCGTGAGATTGTACAGACAGATGAGGCAATGTACGTTCGTTTCAAAGACGGGCTGAATGACGAA
ATCAAGATGATGGTAAGAGGATCCGAGCTGCGATCGTTTGTAGTTCTTGCGGATAGAGCTCAAAA
GATGGAAGAAATTTACCACAATAAAAGGTAAAAAGAGAAGAGGTTTCGAGAATCGGGAAAGAAGA
GTATCACCAGA
Found at i:28960008 original size:21 final size:21
Alignment explanation
Indices: 28959984--28960043 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
28959974 TAGTTGCATG
*
28959984 ACTTGTATCGGTAGAAATTAT
1 ACTTGTATCGGTAGAAATTAC
* *
28960005 ACTTGTATCGGTAGAACTTGC
1 ACTTGTATCGGTAGAAATTAC
**
28960026 ACAGGTATCGGTAGAAAT
1 ACTTGTATCGGTAGAAAT
28960044 CTGCACAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAATTAC
Found at i:28961667 original size:41 final size:41
Alignment explanation
Indices: 28961551--28961760 Score: 212
Period size: 41 Copynumber: 5.2 Consensus size: 41
28961541 TTGTTATGGT
* * * *
28961551 GGTGTA-TTTATCAAGCTTTGTGACTAGCATGCTTAGTGCT
1 GGTGTATTTTATCAGGCTTTGTGCCTAGCAAGCTTAGTGCC
* * *
28961591 AGTGTA-TTTATC-GAGCTTTGTGCCTAGAAAACTTAGTGCC
1 GGTGTATTTTATCAG-GCTTTGTGCCTAGCAAGCTTAGTGCC
* * * *
28961631 AGTGTATTTTATCGGGCTATT-TGCGTAGCAGGCTTAGTGCC
1 GGTGTATTTTATCAGGCT-TTGTGCCTAGCAAGCTTAGTGCC
* * * *
28961672 GGTGTATATTATCAGGATTTATGCCTAGCAAGCTTAGTGTC
1 GGTGTATTTTATCAGGCTTTGTGCCTAGCAAGCTTAGTGCC
* * *
28961713 GGTGTATTTTAGCAGGCTTTGTGCCTAGCAGGCTTCGTGCC
1 GGTGTATTTTATCAGGCTTTGTGCCTAGCAAGCTTAGTGCC
28961754 GGTGTAT
1 GGTGTAT
28961761 CTTAATAAGC
Statistics
Matches: 140, Mismatches: 25, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
40 40 0.29
41 97 0.69
42 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (41 bp):
GGTGTATTTTATCAGGCTTTGTGCCTAGCAAGCTTAGTGCC
Found at i:28961741 original size:16 final size:16
Alignment explanation
Indices: 28961722--28961753 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28961712 CGGTGTATTT
*
28961722 TAGCAGGCTTTGTGCC
1 TAGCAGGCTTCGTGCC
28961738 TAGCAGGCTTCGTGCC
1 TAGCAGGCTTCGTGCC
28961754 GGTGTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.28, G:0.31, T:0.28
Consensus pattern (16 bp):
TAGCAGGCTTCGTGCC
Found at i:28961780 original size:41 final size:41
Alignment explanation
Indices: 28961656--28961788 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
28961646 GCTATTTGCG
* * *
28961656 TAGCAGGCTTAGTGCCGGTGTATATT-ATCAGGATTTATGCC
1 TAGCAGGCTTAGTGCCGGTGTATATTAATAAGCATTGA-GCC
* * * ** * * *
28961697 TAGCAAGCTTAGTGTCGGTGTATTTTAGCAGGCTTTGTGCC
1 TAGCAGGCTTAGTGCCGGTGTATATTAATAAGCATTGAGCC
* * *
28961738 TAGCAGGCTTCGTGCCGGTGTATCTTAATAAGCCTTGAGCC
1 TAGCAGGCTTAGTGCCGGTGTATATTAATAAGCATTGAGCC
*
28961779 TAGTAGGCTT
1 TAGCAGGCTT
28961789 CATGTTGGTG
Statistics
Matches: 70, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
41 67 0.96
42 3 0.04
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (41 bp):
TAGCAGGCTTAGTGCCGGTGTATATTAATAAGCATTGAGCC
Found at i:28961801 original size:82 final size:82
Alignment explanation
Indices: 28961574--28961781 Score: 199
Period size: 82 Copynumber: 2.5 Consensus size: 82
28961564 AGCTTTGTGA
* ** * * * * * *
28961574 CTAGCATGCTTAGTGCTAGTGTAT-TTATCGAGCTTTG-TGCCTAGAAAACTTAGTGCCAGTGTA
1 CTAGCAGGCTTAGTGCCGGTGTATATTAT-AAGCATTGATGCCTAGCAAGCTTAGTGTCGGTGTA
* *
28961637 TTTTATCGGGCTATTTGC
65 TTTTAGCAGGCTATTTGC
* * * *
28961655 GTAGCAGGCTTAGTGCCGGTGTATATTATCAGGATTTATGCCTAGCAAGCTTAGTGTCGGTGTAT
1 CTAGCAGGCTTAGTGCCGGTGTATATTATAAGCATTGATGCCTAGCAAGCTTAGTGTCGGTGTAT
28961720 TTTAGCAGGCT-TTGTGC
66 TTTAGCAGGCTATT-TGC
* * *
28961737 CTAGCAGGCTTCGTGCCGGTGTATCTTAATAAGCCTTGA-GCCTAG
1 CTAGCAGGCTTAGTGCCGGTGTATATT-ATAAGCATTGATGCCTAG
28961782 TAGGCTTCAT
Statistics
Matches: 102, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
81 26 0.25
82 69 0.68
83 7 0.07
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (82 bp):
CTAGCAGGCTTAGTGCCGGTGTATATTATAAGCATTGATGCCTAGCAAGCTTAGTGTCGGTGTAT
TTTAGCAGGCTATTTGC
Found at i:28961947 original size:13 final size:13
Alignment explanation
Indices: 28961931--28961987 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
28961921 ATGAAACGAC
28961931 TATATGAAATGTT
1 TATATGAAATGTT
*
28961944 TATATGAAAATAG-A
1 TATATG-AAAT-GTT
*
28961958 TATATGAAATGGT
1 TATATGAAATGTT
*
28961971 TATATGAAGTGTT
1 TATATGAAATGTT
28961984 TATA
1 TATA
28961988 CGAAGTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 1 0.03
13 25 0.68
14 10 0.27
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (13 bp):
TATATGAAATGTT
Found at i:28982542 original size:25 final size:26
Alignment explanation
Indices: 28982490--28982545 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
28982480 ATTGCACCCA
*
28982490 AGAA-TGTCGCTGCATTAACATGTAC
1 AGAATTGTCGCTGCATGAACATGTAC
* *
28982515 AGAATTGTCGCT-CATGAACGTGTCC
1 AGAATTGTCGCTGCATGAACATGTAC
28982540 AGAATT
1 AGAATT
28982546 ACGCCCAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (26 bp):
AGAATTGTCGCTGCATGAACATGTAC
Found at i:28990390 original size:12 final size:12
Alignment explanation
Indices: 28990373--28990401 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28990363 AAATATAAAC
28990373 GCATTTTCATAA
1 GCATTTTCATAA
28990385 GCATTTTCATAA
1 GCATTTTCATAA
28990397 GCATT
1 GCATT
28990402 ATGTCGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (12 bp):
GCATTTTCATAA
Found at i:29007170 original size:17 final size:17
Alignment explanation
Indices: 29007150--29007182 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29007140 TTTAAGGACT
29007150 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
29007167 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
29007183 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:29007457 original size:50 final size:50
Alignment explanation
Indices: 29007377--29007532 Score: 140
Period size: 50 Copynumber: 3.1 Consensus size: 50
29007367 TGACATCCAT
* *
29007377 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAGTTCGCATCATAAATAAT-ATCATGCATTAAG
* ** *
29007428 TAACTTACATGTTAGTTAA-TTACGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAGTT-CGCATCATAAATAATATCATGCATTAAG
* * *
29007478 TAACTCCCATGTTAGTTAAAGTTTC-CATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGTTAGTT-AAG-TTCGCATCA-TAAAT-AATATCATGCATTAAG
29007530 TAA
1 TAA
29007533 TCCATTAGTT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
49 3 0.04
50 45 0.53
51 16 0.19
52 19 0.22
53 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAGTTCGCATCATAAATAATATCATGCATTAAG
Found at i:29010276 original size:14 final size:14
Alignment explanation
Indices: 29010248--29010282 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
29010238 TGTTTTGAAA
29010248 AAGAAAAGTAAAAG
1 AAGAAAAGTAAAAG
29010262 AAGTAAAAG-AAAAG
1 AAG-AAAAGTAAAAG
29010276 AAGAAAA
1 AAGAAAA
29010283 ATTTTAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
AAGAAAAGTAAAAG
Found at i:29022510 original size:47 final size:47
Alignment explanation
Indices: 29022409--29022533 Score: 160
Period size: 47 Copynumber: 2.7 Consensus size: 47
29022399 ATCACATTAA
**
29022409 TGTAGATAAACTACCACATAATCAAATTATGGACAAGCCACCAAAAT
1 TGTAGATAAACTACCACATAATCAAATCGTGGACAAGCCACCAAAAT
* * * * *
29022456 CGCAGATATACTACCACATAATCAAATCGTGGACAAGCCACCACATT
1 TGTAGATAAACTACCACATAATCAAATCGTGGACAAGCCACCAAAAT
* * *
29022503 TGTAGATAAACTGCTACATTATCAAATCGTG
1 TGTAGATAAACTACCACATAATCAAATCGTG
29022534 AACATTTTCA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (47 bp):
TGTAGATAAACTACCACATAATCAAATCGTGGACAAGCCACCAAAAT
Found at i:29027311 original size:71 final size:71
Alignment explanation
Indices: 29027220--29027595 Score: 441
Period size: 71 Copynumber: 5.3 Consensus size: 71
29027210 CATTCAAATT
* * *
29027220 TAAGACCATACCTGGGCTATGACAGTTATTCAGTCGTAAGACCATGGTTGAACCATGGCAGTGTA
1 TAAGACCATAGCTGGGCTATGACAGTTATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTA
29027285 TATACG
66 TATACG
* ** * **
29027291 AAAGACCATATTTGGGCTATGGA-AGTTATTCAGACATAAGACCATGGTTGGACCATAACAGTGT
1 TAAGACCATAGCTGGGCTAT-GACAGTTATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGT
29027355 ATATACG
65 ATATACG
* * * * *
29027362 TAAGACTATAGTTGGGCTATGACAATTATTCAGACGCAAGACCATGGTTGGACCATTGCAGTGTA
1 TAAGACCATAGCTGGGCTATGACAGTTATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTA
29027427 TATACG
66 TATACG
** * * * *
29027433 TAAGACCATAGCTACGCTATGGCAGTTTTTCAAAAGTAAGACCATGGTTGGACCATGGCAGTGTA
1 TAAGACCATAGCTGGGCTATGACAGTTATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTA
*
29027498 TAAACG
66 TATACG
* ** * * * *
29027504 TAAGACCATAGCTGGACTATGGTAGTTATTCAGGCGTAAGACCATGGTTGAACAATGACAGTGT-
1 TAAGACCATAGCTGGGCTATGACAGTTATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTA
*
29027568 TAATATG
66 T-ATACG
* *
29027575 TAAGACAATACCTGGGCTATG
1 TAAGACCATAGCTGGGCTATG
29027596 GCATTTTGAT
Statistics
Matches: 258, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
70 3 0.01
71 253 0.98
72 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (71 bp):
TAAGACCATAGCTGGGCTATGACAGTTATTCAGACGTAAGACCATGGTTGGACCATGGCAGTGTA
TATACG
Found at i:29027491 original size:36 final size:35
Alignment explanation
Indices: 29027254--29027580 Score: 180
Period size: 35 Copynumber: 9.2 Consensus size: 35
29027244 GTTATTCAGT
* *
29027254 CGTAAGACCATGGTTGAACCATGGCAGTGTATATA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTATAAA
* ** * * * *
29027289 CGAAAGACCATATTTGGGCTATGGAAGT-TATTCAGA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTA-T-AAA
* ** *
29027325 CATAAGACCATGGTTGGACCATAACAGTGTATATA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTATAAA
* * * * * * *
29027360 CGTAAGACTATAGTTGGGCTATGACAAT-TATTCAGA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTA-T-AAA
* * *
29027396 CGCAAGACCATGGTTGGACCATTGCAGTGTATATA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTATAAA
* * * *
29027431 CGTAAGACCATAGCT--ACGCTATGGCAGTTTTTCAAA
1 CGTAAGACCATGGTTGGAC-C-ATGGCAGTGTAT-AAA
*
29027467 AGTAAGACCATGGTTGGACCATGGCAGTGTATAAA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTATAAA
* * * * **
29027502 CGTAAGACCATAGCTGGACTATGGTAGT-TATTCAGG
1 CGTAAGACCATGGTTGGACCATGGCAGTGTA-T-AAA
* * *
29027538 CGTAAGACCATGGTTGAACAATGACAGTGT-TAATA
1 CGTAAGACCATGGTTGGACCATGGCAGTGTATAA-A
*
29027573 TGTAAGAC
1 CGTAAGAC
29027581 AATACCTGGG
Statistics
Matches: 214, Mismatches: 63, Indels: 30
0.70 0.21 0.10
Matches are distributed among these distances:
33 2 0.01
34 8 0.04
35 104 0.49
36 92 0.43
37 6 0.03
38 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (35 bp):
CGTAAGACCATGGTTGGACCATGGCAGTGTATAAA
Found at i:29031128 original size:38 final size:38
Alignment explanation
Indices: 29031079--29031161 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
29031069 TATGCAGGTA
* *
29031079 TTTATCAGGCTTTGTGCCTAGCAAGCTTTC-TGCCGATG
1 TTTATCGGGCTTAGTGCCTAGCAAGC-TTCGTGCCGATG
* *
29031117 TTTATCGGGCTTAGTGCCTAGTAGGCTTCGTGCCGATG
1 TTTATCGGGCTTAGTGCCTAGCAAGCTTCGTGCCGATG
*
29031155 GTTATCG
1 TTTATCG
29031162 ATCTTAATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (38 bp):
TTTATCGGGCTTAGTGCCTAGCAAGCTTCGTGCCGATG
Found at i:29039817 original size:37 final size:37
Alignment explanation
Indices: 29039767--29039841 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
29039757 CCGTTGGGCA
* *
29039767 AATTTTTACACCGAGTGAACTAAGAGCTAAGACGATT
1 AATTTTTACACCGAGTGAACTAAAAGCTAAGAAGATT
29039804 AATTTTTACACCGAGTGAACTAAAAGCTAAGAAGATT
1 AATTTTTACACCGAGTGAACTAAAAGCTAAGAAGATT
29039841 A
1 A
29039842 TACTTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (37 bp):
AATTTTTACACCGAGTGAACTAAAAGCTAAGAAGATT
Found at i:29043819 original size:7 final size:8
Alignment explanation
Indices: 29043806--29043830 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29043796 AGAAAATATG
29043806 AAAAAAAT
1 AAAAAAAT
29043814 AAAAAAAT
1 AAAAAAAT
29043822 AAAAAAAT
1 AAAAAAAT
29043830 A
1 A
29043831 TTATGTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:29052061 original size:19 final size:20
Alignment explanation
Indices: 29052021--29052066 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
29052011 ACGTTGTTGC
29052021 CGCACATCATCGTTATCGCTGT
1 CGCACATCATCGTTA-C-CTGT
29052043 CGCACATCATCGTTA-CTGT
1 CGCACATCATCGTTACCTGT
29052062 CGCAC
1 CGCAC
29052067 GCTATTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.38
22 15 0.62
ACGTcount: A:0.20, C:0.35, G:0.17, T:0.28
Consensus pattern (20 bp):
CGCACATCATCGTTACCTGT
Found at i:29055287 original size:23 final size:22
Alignment explanation
Indices: 29055261--29055304 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
29055251 AAAATATTTC
*
29055261 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
29055284 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
29055305 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:29081531 original size:9 final size:9
Alignment explanation
Indices: 29081519--29081561 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
29081509 ATTTCAACAA
29081519 TTTTTTCTT
1 TTTTTTCTT
29081528 TTTTTT-TT
1 TTTTTTCTT
29081536 TTTTTTCTT
1 TTTTTTCTT
*
29081545 TTCTTTCTT
1 TTTTTTCTT
*
29081554 CTTTTTCT
1 TTTTTTCT
29081562 CATTTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:29082656 original size:24 final size:25
Alignment explanation
Indices: 29082619--29082670 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
29082609 TAGGTTCTTT
*
29082619 TTCTTCTTTCTCTTCTTCCTT-TCC
1 TTCTTCTTTCTCTTCATCCTTCTCC
*
29082643 TTCTTC-TTCTTCTTGATCCTTCTCC
1 TTCTTCTTTC-TCTTCATCCTTCTCC
29082668 TTC
1 TTC
29082671 AACTGATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.62
25 6 0.25
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (25 bp):
TTCTTCTTTCTCTTCATCCTTCTCC
Found at i:29093945 original size:16 final size:16
Alignment explanation
Indices: 29093921--29093952 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29093911 TCCTTACAAA
*
29093921 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
29093937 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
29093953 AAAAATTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:29106912 original size:16 final size:16
Alignment explanation
Indices: 29106888--29106918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29106878 TTAAAAACTT
29106888 TAAAAAAATTAAAAAA
1 TAAAAAAATTAAAAAA
*
29106904 TAAACAAATTAAAAA
1 TAAAAAAATTAAAAA
29106919 TTCTTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAAATTAAAAAA
Found at i:29107064 original size:12 final size:12
Alignment explanation
Indices: 29107047--29107127 Score: 83
Period size: 12 Copynumber: 6.8 Consensus size: 12
29107037 ATAACATCCA
*
29107047 AACAACCAAAAT
1 AACAACAAAAAT
*
29107059 AACAACCAAAAT
1 AACAACAAAAAT
*
29107071 AGCAACAAAAAT
1 AACAACAAAAAT
*
29107083 AATAA-AAAAAT
1 AACAACAAAAAT
*
29107094 AGCAACAAAAAT
1 AACAACAAAAAT
* *
29107106 AACAATAAAAAC
1 AACAACAAAAAT
*
29107118 AACACCAAAA
1 AACAACAAAA
29107128 TAATAAAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
11 9 0.16
12 48 0.84
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:29107092 original size:23 final size:23
Alignment explanation
Indices: 29107066--29107150 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
29107056 AATAACAACC
29107066 AAAATAGCAACAAAAATAATAAA
1 AAAATAGCAACAAAAATAATAAA
* *
29107089 AAAATAGCAACAAAAATAACAAT
1 AAAATAGCAACAAAAATAATAAA
29107112 AAAA-A-CAACACCAAAATAATAAA
1 AAAATAGCAACA--AAAATAATAAA
*
29107135 AAAAGTAGCACCAAAA
1 AAAA-TAGCAACAAAA
29107151 CAGCAACCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
21 5 0.10
22 1 0.02
23 38 0.73
24 3 0.06
25 1 0.02
26 4 0.08
ACGTcount: A:0.71, C:0.14, G:0.05, T:0.11
Consensus pattern (23 bp):
AAAATAGCAACAAAAATAATAAA
Found at i:29107128 original size:35 final size:35
Alignment explanation
Indices: 29107051--29107164 Score: 88
Period size: 35 Copynumber: 3.3 Consensus size: 35
29107041 CATCCAAACA
* * * *
29107051 ACCAAAATAACAACCAAAATAGCAACAAAAATAAT
1 ACCAAAATAACAACAAAAATAACAACAAAAACAAC
** * *
29107086 AAAAAAATAGCAACAAAAATAACAATAAAAACAAC
1 ACCAAAATAACAACAAAAATAACAACAAAAACAAC
* * * *
29107121 ACCAAAATAATAA-AAAAAGTAGC-ACCAAAACAGC
1 ACCAAAATAACAACAAAAA-TAACAACAAAAACAAC
29107155 AACCAAAATA
1 -ACCAAAATA
29107165 GTAAAAAAAC
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
34 13 0.21
35 48 0.79
ACGTcount: A:0.68, C:0.18, G:0.04, T:0.10
Consensus pattern (35 bp):
ACCAAAATAACAACAAAAATAACAACAAAAACAAC
Found at i:29107202 original size:41 final size:41
Alignment explanation
Indices: 29107156--29107250 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
29107146 CAAAACAGCA
** *
29107156 ACCAAAATAGTAAAAA-AAC-ACCAAAACAGTAAAAACACAAC
1 ACCAAAATAACAAAAATAACAACCAAAACAGCAAAAA-A-AAC
* *
29107197 ACCAAAACAACAAAAATAGCAACCAAAACAGCAAAAAAAAC
1 ACCAAAATAACAAAAATAACAACCAAAACAGCAAAAAAAAC
29107238 ACCAAAATAACAA
1 ACCAAAATAACAA
29107251 TATAATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 28 0.61
42 3 0.07
43 15 0.33
ACGTcount: A:0.67, C:0.23, G:0.04, T:0.05
Consensus pattern (41 bp):
ACCAAAATAACAAAAATAACAACCAAAACAGCAAAAAAAAC
Found at i:29107221 original size:21 final size:20
Alignment explanation
Indices: 29107167--29107250 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 20
29107157 CCAAAATAGT
**
29107167 AAAAAAACACCAAAACAGTA
1 AAAAAAACACCAAAACAACA
29107187 AAAACACAACACCAAAACAACA
1 AAAA-A-AACACCAAAACAACA
* * *
29107209 AAAATAGCAACCAAAACAGCA
1 AAAAAAAC-ACCAAAACAACA
*
29107230 AAAAAAACACCAAAATAACA
1 AAAAAAACACCAAAACAACA
29107250 A
1 A
29107251 TATAATTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
20 17 0.33
21 18 0.35
22 17 0.33
ACGTcount: A:0.69, C:0.24, G:0.04, T:0.04
Consensus pattern (20 bp):
AAAAAAACACCAAAACAACA
Found at i:29108203 original size:26 final size:26
Alignment explanation
Indices: 29108163--29108310 Score: 160
Period size: 26 Copynumber: 5.7 Consensus size: 26
29108153 GTCTTCTAGA
29108163 AATTTAGCT-TATACGAGCCCAGACAG
1 AATTTAGCTCT-TACGAGCCCAGACAG
* *
29108189 AGTTTAGCCCTTACGAGCCCAGACAG
1 AATTTAGCTCTTACGAGCCCAGACAG
* * *
29108215 AATTTAGTTCTTATGAGCCCAGATAG
1 AATTTAGCTCTTACGAGCCCAGACAG
29108241 AATTTAGCTCTTACGAGCCCAGACAG
1 AATTTAGCTCTTACGAGCCCAGACAG
* * *
29108267 AA-TAACGCTCTTACAAG-CTAGACAG
1 AATTTA-GCTCTTACGAGCCCAGACAG
*
29108292 AA-TAACGCTCTTACGAGCC
1 AATTTA-GCTCTTACGAGCC
29108311 AGAGTTTAGA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
25 25 0.24
26 79 0.75
27 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (26 bp):
AATTTAGCTCTTACGAGCCCAGACAG
Found at i:29118442 original size:26 final size:26
Alignment explanation
Indices: 29118413--29118543 Score: 117
Period size: 26 Copynumber: 5.1 Consensus size: 26
29118403 GTCTTCTAGA
* *
29118413 AATTTAGCTCATATGAGCCCAAACAG
1 AATTTAGCTCTTATGAGCCCAGACAG
* *
29118439 AATTTAGCTCTTATGAGCTCAGATAG
1 AATTTAGCTCTTATGAGCCCAGACAG
*
29118465 AATTTAGCTCTTACGAGCCCAGACAG
1 AATTTAGCTCTTATGAGCCCAGACAG
* * *
29118491 AA-TAACACTCTTACGAG-CCAGACA-
1 AATTTA-GCTCTTATGAGCCCAGACAG
* * *
29118515 AAATAACGCTCTTACGAG-CCAGACAG
1 AATTTA-GCTCTTATGAGCCCAGACAG
29118541 AAT
1 AAT
29118544 AACGCTCTTA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
24 2 0.02
25 30 0.33
26 59 0.65
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (26 bp):
AATTTAGCTCTTATGAGCCCAGACAG
Found at i:29118502 original size:52 final size:51
Alignment explanation
Indices: 29118412--29118559 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 51
29118402 AGTCTTCTAG
* * * * * *
29118412 AAATTTAGCTCATATGAGCCCAAACAGAATTTA-GCTCTTATGAGCTCAGAT
1 AAATTTAGCTCTTACGAGCCCAGACAGAA-TAACGCTCTTACGAGCTCAGAC
*
29118463 AGAATTTAGCTCTTACGAGCCCAGACAGAATAACACTCTTACGAGC-CAGAC
1 A-AATTTAGCTCTTACGAGCCCAGACAGAATAACGCTCTTACGAGCTCAGAC
* *
29118514 AAAATAACGCTCTTACGAG-CCAGACAGAATAACGCTCTTACGAGCT
1 AAATTTA-GCTCTTACGAGCCCAGACAGAATAACGCTCTTACGAGCT
29118560 AGAGTTTAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
50 29 0.35
51 19 0.23
52 35 0.42
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (51 bp):
AAATTTAGCTCTTACGAGCCCAGACAGAATAACGCTCTTACGAGCTCAGAC
Found at i:29118519 original size:25 final size:25
Alignment explanation
Indices: 29118445--29118558 Score: 149
Period size: 25 Copynumber: 4.5 Consensus size: 25
29118435 ACAGAATTTA
* * *
29118445 GCTCTTATGAGCTCAGATAGAATTTA-
1 GCTCTTACGAGC-CAGACAGAA-TAAC
29118471 GCTCTTACGAGCCCAGACAGAATAAC
1 GCTCTTACGAG-CCAGACAGAATAAC
* *
29118497 ACTCTTACGAGCCAGACAAAATAAC
1 GCTCTTACGAGCCAGACAGAATAAC
29118522 GCTCTTACGAGCCAGACAGAATAAC
1 GCTCTTACGAGCCAGACAGAATAAC
29118547 GCTCTTACGAGC
1 GCTCTTACGAGC
29118559 TAGAGTTTAG
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
25 50 0.63
26 28 0.35
27 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAGAATAAC
Found at i:29126688 original size:21 final size:21
Alignment explanation
Indices: 29126642--29126738 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
29126632 ATAGTGCAAA
* *
29126642 CTTCTACCGATACAAGTGACA
1 CTTCTACCGATACAAGTGTCT
*
29126663 GTTCTACCGATACAAGTGTCT
1 CTTCTACCGATACAAGTGTCT
* *
29126684 CTTCTACTGAAACAAGTGTCT
1 CTTCTACCGATACAAGTGTCT
* * *
29126705 CTTCTATCGAAACAAGTCT-T
1 CTTCTACCGATACAAGTGTCT
*
29126725 ACTTCTACAGATAC
1 -CTTCTACCGATAC
29126739 TAAAAACTCC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
20 1 0.02
21 62 0.98
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (21 bp):
CTTCTACCGATACAAGTGTCT
Found at i:29133323 original size:18 final size:17
Alignment explanation
Indices: 29133282--29133324 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
29133272 TATCATAAGA
*
29133282 GGAGGTGGAGCCCTTAC
1 GGAGGTGGAGACCTTAC
29133299 GGAAGGTGGAGACCTTAC
1 GG-AGGTGGAGACCTTAC
29133317 TGGAGGTG
1 -GGAGGTG
29133325 CCTCAGGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.21, C:0.16, G:0.44, T:0.19
Consensus pattern (17 bp):
GGAGGTGGAGACCTTAC
Found at i:29140444 original size:21 final size:22
Alignment explanation
Indices: 29140420--29140462 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29140410 AGTATCTTCT
*
29140420 ATTTCTTCTAT-TATTTTCTTA
1 ATTTCATCTATCTATTTTCTTA
29140441 ATTTCATCTATCCTATTTTCTT
1 ATTTCATCTAT-CTATTTTCTT
29140463 CTCATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTCATCTATCTATTTTCTTA
Found at i:29141112 original size:23 final size:23
Alignment explanation
Indices: 29141086--29141153 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
29141076 CTACAAATTT
*
29141086 GGTGGTTCGTCCACAACCTACAA
1 GGTGGTTCATCCACAACCTACAA
* * *
29141109 GGTGATTCATCCATAATCTACAA
1 GGTGGTTCATCCACAACCTACAA
* *
29141132 GGTAGTTTATCCACAACCTACA
1 GGTGGTTCATCCACAACCTACA
29141154 TTTGTTAGCA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
GGTGGTTCATCCACAACCTACAA
Found at i:29144171 original size:13 final size:13
Alignment explanation
Indices: 29144153--29144179 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29144143 TTAGTGTAGC
29144153 AGATCAGATGGAG
1 AGATCAGATGGAG
29144166 AGATCAGATGGAG
1 AGATCAGATGGAG
29144179 A
1 A
29144180 CGAGTCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.37, T:0.15
Consensus pattern (13 bp):
AGATCAGATGGAG
Found at i:29149151 original size:68 final size:68
Alignment explanation
Indices: 29149039--29149179 Score: 237
Period size: 68 Copynumber: 2.1 Consensus size: 68
29149029 AGTTCGCCAA
* *
29149039 GACAGTAAACATGGGATCATATTGTGTAAGACCATAGCTTGGCTATGACAACAAATCGAGTCCAC
1 GACAGTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGCTATGACAACAAATCGAGTCCAC
29149104 CAG
66 CAG
* *
29149107 GACAGTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGCTATGACAACATATGGAGTCCAC
1 GACAGTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGCTATGACAACAAATCGAGTCCAC
*
29149172 TAG
66 CAG
29149175 GACAG
1 GACAG
29149180 CGAACCAGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (68 bp):
GACAGTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGCTATGACAACAAATCGAGTCCAC
CAG
Found at i:29151894 original size:80 final size:80
Alignment explanation
Indices: 29151761--29152081 Score: 453
Period size: 80 Copynumber: 4.0 Consensus size: 80
29151751 CCTAGAGGAT
* ** * * *
29151761 TTGGATTAACCAACAAATGTCCGTCAAATCCTATCACCCAGTGCTTAGGGGATAAACTGCAAAAG
1 TTGGATTAACCAACAAATATCCGTCAAATCCTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAG
*
29151826 TGAGCCCAGCTCTAG
66 TGAGCCCAACTCTAG
* * * * *
29151841 TTGGATTAACCAACAAATATTCATCAAATCCTGGCACCCAGTGCCTAGTGGATAAATCGTAAAAG
1 TTGGATTAACCAACAAATATCCGTCAAATCCTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAG
* *
29151906 TGAGCCTAGCTCTAG
66 TGAGCCCAACTCTAG
* *
29151921 TTGGATTAACCAACAAATATCCGTCAAATCTTGGCACCTAGTGCCTAGCGGATAAACCGCAAAAG
1 TTGGATTAACCAACAAATATCCGTCAAATCCTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAG
29151986 TGAGCCCAACTCTAG
66 TGAGCCCAACTCTAG
* * * * *
29152001 TTGGATTAACCAATAAATATTCGTCAAATCTTGACACCCAGTACCTAGCGGATAAACCGCAAAAG
1 TTGGATTAACCAACAAATATCCGTCAAATCCTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAG
29152066 TGAGCCCAACTCTAG
66 TGAGCCCAACTCTAG
29152081 T
1 T
29152082 CAGTTAAACT
Statistics
Matches: 216, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 216 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (80 bp):
TTGGATTAACCAACAAATATCCGTCAAATCCTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAG
TGAGCCCAACTCTAG
Found at i:29152181 original size:7 final size:7
Alignment explanation
Indices: 29152161--29152218 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
29152151 CAATAATGAC
29152161 TGGTCAA
1 TGGTCAA
**
29152168 TAATCAA
1 TGGTCAA
*
29152175 CGGTCAA
1 TGGTCAA
*
29152182 CGGTCAA
1 TGGTCAA
*
29152189 TGATCAA
1 TGGTCAA
29152196 TGGTCAA
1 TGGTCAA
*
29152203 -AGTCAA
1 TGGTCAA
29152209 TGGTCAA
1 TGGTCAA
29152216 TGG
1 TGG
29152219 GTCGGGTCGA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (7 bp):
TGGTCAA
Found at i:29152188 original size:21 final size:21
Alignment explanation
Indices: 29152162--29152202 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29152152 AATAATGACT
29152162 GGTCAATAATCAACGGTCAAC
1 GGTCAATAATCAACGGTCAAC
* *
29152183 GGTCAATGATCAATGGTCAA
1 GGTCAATAATCAACGGTCAA
29152203 AGTCAATGGT
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:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (21 bp):
GGTCAATAATCAACGGTCAAC
Found at i:29152210 original size:13 final size:13
Alignment explanation
Indices: 29152177--29152215 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
29152167 ATAATCAACG
* *
29152177 GTCAACGGTCAAT
1 GTCAATGGTCAAA
29152190 GATCAATGGTCAAA
1 G-TCAATGGTCAAA
29152204 GTCAATGGTCAA
1 GTCAATGGTCAA
29152216 TGGGTCGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (13 bp):
GTCAATGGTCAAA
Found at i:29165622 original size:62 final size:64
Alignment explanation
Indices: 29165534--29165705 Score: 253
Period size: 67 Copynumber: 2.7 Consensus size: 64
29165524 TTATTTATTT
* *
29165534 ATTTATCTATCTATATTCATAAAATAATAAATAAAT-AATAAAAA-AAA-TTAATATTATTTTAC
1 ATTTATTTATTTATATTCAT-AAATAATAAATAAATAAATAAAAACAAAGTTAATATTATTTTAC
29165596 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAGTTAATATTATTTT
1 ATTTATTTATTTATATTCATA-AATAATAAATAAATAAAT-A-AAAACAAAGTTAATATTATTTT
*
29165661 AT
63 AC
29165663 ATTTATTTATTTATATTCAT-AATAATAAATAAATAAATAAAAA
1 ATTTATTTATTTATATTCATAAATAATAAATAAATAAATAAAAA
29165706 TAATAAGAAA
Statistics
Matches: 101, Mismatches: 3, Indels: 11
0.88 0.03 0.10
Matches are distributed among these distances:
61 1 0.01
62 32 0.32
63 7 0.07
64 2 0.02
65 22 0.22
66 3 0.03
67 34 0.34
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (64 bp):
ATTTATTTATTTATATTCATAAATAATAAATAAATAAATAAAAACAAAGTTAATATTATTTTAC
Found at i:29166297 original size:40 final size:40
Alignment explanation
Indices: 29166233--29166580 Score: 321
Period size: 40 Copynumber: 8.8 Consensus size: 40
29166223 ATAGTTTTAA
* * *
29166233 GGGTAAAAGATTGGATTGT-TTCAATCTGCCTCATGGTCG
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCTCATGGTCG
* **
29166272 GGGTAAGAGATCGAATGGTCTTCAATCTGCCCTC-TGGTTA
1 GGGTAAGAGATCGGATGGTCTTCAATCTG-CCTCATGGTCG
* * * * * * *
29166312 GGGTAAAAGTTTGAATCG-CTTCAATCTACCCCATGGTCG
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCTCATGGTCG
** * **
29166351 GGGTAAGAGATCGGATGGTCTTCAATCTGCCTTTTAGTTA
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCTCATGGTCG
* * * * *
29166391 GGGTAAAAGATTGGATTG-CTTCAATCTACCCCATGGTCG
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCTCATGGTCG
* *
29166430 GGGTAAGAGATCGGATGGTCTTCAATCTTCCCTC-TGGTCA
1 GGGTAAGAGATCGGATGGTCTTCAATC-TGCCTCATGGTCG
* * * *
29166470 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATAGTCG
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCCTCATGGTCG
*
29166510 GGGTAAGAGATCGGATGGTCTTCAATCTACCCTC-TGGTCG
1 GGGTAAGAGATCGGATGGTCTTCAATCT-GCCTCATGGTCG
* ** *
29166550 GCGTAAGAGATCGGATAATCTTCAATTTGCC
1 GGGTAAGAGATCGGATGGTCTTCAATCTGCC
29166581 CATTTCAGTT
Statistics
Matches: 243, Mismatches: 58, Indels: 16
0.77 0.18 0.05
Matches are distributed among these distances:
38 3 0.01
39 76 0.31
40 153 0.63
41 11 0.05
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
GGGTAAGAGATCGGATGGTCTTCAATCTGCCTCATGGTCG
Found at i:29166363 original size:79 final size:79
Alignment explanation
Indices: 29166232--29166547 Score: 479
Period size: 79 Copynumber: 4.0 Consensus size: 79
29166222 TATAGTTTTA
* * * *
29166232 AGGGTAAAAGATTGGATTGTTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGAATGGTCTTCAA
1 AGGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
29166297 TCTGCCCTCTGGTT
66 TCTGCCCTCTGGTT
* * *
29166311 AGGGTAAAAGTTTGAATCGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
* * *
29166376 TCTGCCTTTTAGTT
66 TCTGCCCTCTGGTT
29166390 AGGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
* *
29166455 TCTTCCCTCTGGTC
66 TCTGCCCTCTGGTT
* * *
29166469 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATAGTCGGGGTAAGAGATCGGATGGTCTTCA
1 AGGGTAAAAGATTGGATTG-CTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCA
*
29166534 ATCTACCCTCTGGT
65 ATCTGCCCTCTGGT
29166548 CGGCGTAAGA
Statistics
Matches: 214, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
79 158 0.74
80 56 0.26
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (79 bp):
AGGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAA
TCTGCCCTCTGGTT
Found at i:29166746 original size:52 final size:50
Alignment explanation
Indices: 29166618--29166747 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 50
29166608 ATCCTTGCAA
* *
29166618 CTTCAATTTGCCCCTCTACAGCTTTAGGTGAATGACATTCACCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGACATTCACCATCGCGG
* ** *
29166668 CTTCAATCTGCCCCTCTACAGCTTTAGGT-ATATGAGATTTGCCATCGTGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGA-ATGACATTCACCATCGCGG
**
29166718 CTTCAATCTGTGTTCCTCTACAGCTTTAGG
1 CTTCAATC--TGCCCCTCTACAGCTTTAGG
29166748 GGTATAGGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 50 0.72
52 18 0.26
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGACATTCACCATCGCGG
Found at i:29171579 original size:31 final size:31
Alignment explanation
Indices: 29171533--29171605 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
29171523 CGTCTTTCTC
29171533 AAACTTT-T-AATGCATGAAAATGCGATGCA
1 AAACTTTATGAATGCATGAAAATGCGATGCA
29171562 AAACTTTATGAATGCATGAAAATGCGATGCA
1 AAACTTTATGAATGCATGAAAATGCGATGCA
*
29171593 AAATTTTATGAAT
1 AAACTTTATGAAT
29171606 ACATATGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 7 0.17
30 1 0.02
31 33 0.80
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATGCGATGCA
Found at i:29174175 original size:67 final size:69
Alignment explanation
Indices: 29174104--29174251 Score: 239
Period size: 67 Copynumber: 2.2 Consensus size: 69
29174094 ATCTATATTC
*
29174104 ATAAAATAAATATTATTTTACATTTATTTATTTATATTCAT-ACAATAATAAATAAATAAAT-AA
1 ATAAAATAAATATTATTTTACATTTATTTATTTATATTCATAAAAATAATAAATAAATAAATAAA
29174167 TAAA
66 TAAA
*
29174171 ATAAAATAAATATTATTTTATATTTATTTATTTATATTCATAAAAATAATAAATAAATAAATAAA
1 ATAAAATAAATATTATTTTACATTTATTTATTTATATTCATAAAAATAATAAATAAATAAATAAA
*
29174236 TATA
66 TAAA
29174240 ATAAGAA-AAATA
1 ATAA-AATAAATA
29174252 GAATTGGGTT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
67 40 0.53
68 19 0.25
69 14 0.19
70 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (69 bp):
ATAAAATAAATATTATTTTACATTTATTTATTTATATTCATAAAAATAATAAATAAATAAATAAA
TAAA
Found at i:29177133 original size:29 final size:29
Alignment explanation
Indices: 29177101--29177158 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
29177091 TTTCACACCT
* * *
29177101 TGTGTGATATTATTTTGTGTTGTGTTATC
1 TGTGTGATATTAATCTATGTTGTGTTATC
*
29177130 TGTGTGATTTTAATCTATGTTGTGTTATC
1 TGTGTGATATTAATCTATGTTGTGTTATC
29177159 ACATGCTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (29 bp):
TGTGTGATATTAATCTATGTTGTGTTATC
Found at i:29178712 original size:10 final size:10
Alignment explanation
Indices: 29178697--29178729 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
29178687 TTAATAAATT
29178697 GTGTAAAAAG
1 GTGTAAAAAG
29178707 GTGTAAAAAG
1 GTGTAAAAAG
29178717 GTGTAAAAAG
1 GTGTAAAAAG
29178727 GTG
1 GTG
29178730 CTCTTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (10 bp):
GTGTAAAAAG
Found at i:29178801 original size:12 final size:12
Alignment explanation
Indices: 29178784--29178809 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29178774 TGTACTTTAT
29178784 GAGTATGTAGGA
1 GAGTATGTAGGA
29178796 GAGTATGTAGGA
1 GAGTATGTAGGA
29178808 GA
1 GA
29178810 CCATTAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.42, T:0.23
Consensus pattern (12 bp):
GAGTATGTAGGA
Found at i:29180460 original size:51 final size:50
Alignment explanation
Indices: 29180389--29180728 Score: 387
Period size: 51 Copynumber: 6.6 Consensus size: 50
29180379 CTATAAACAA
* * * *
29180389 AAAGGTCCGACGACTAAGTGTAATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGT-CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* *
29180440 AAAGTTCAAATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
1 AAAGGTC-GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* *
29180491 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTC-GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
29180542 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
1 AAAGG-TCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* * ***
29180593 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATTTATT
1 AAAGGT-CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* ** * * * *
29180644 AAGGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAA-C
1 AAAGGT-CGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTA-CGAATT
29180696 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGT-CGATGACTA-AGTGTCATCGTGAGTA
29180729 TTAAATGAAA
Statistics
Matches: 250, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
50 2 0.01
51 213 0.85
52 8 0.03
53 27 0.11
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (50 bp):
AAAGGTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
Found at i:29180565 original size:102 final size:102
Alignment explanation
Indices: 29180389--29180728 Score: 452
Period size: 102 Copynumber: 3.3 Consensus size: 102
29180379 CTATAAACAA
* * * * *
29180389 AAAGGTCCGACGACTAAGTGTAATCATGAGTAAATGAATCCTTTACGGATTAAA-GTTCAAATGA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTTC-GATGA
29180453 CTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
65 CTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
*
29180491 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTTCGATGAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTTCGATGAC
29180556 TAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
66 TAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* * ** * *
29180593 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATTTATTAAGGGTCCGATGAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTTCGATGAC
** * * * *
29180658 TTTGTGTCATCGTGAGTATATGAATTCCTATATGGAA-C
66 TAAGTGTCATCGTGAGTAAATGAA-TCCTTTA-CGAATT
29180696 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
29180729 TTAAATGAAA
Statistics
Matches: 214, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
102 170 0.79
103 12 0.06
104 31 0.14
105 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (102 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTTCGATGAC
TAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
Found at i:29180595 original size:153 final size:154
Alignment explanation
Indices: 29180389--29180728 Score: 459
Period size: 153 Copynumber: 2.2 Consensus size: 154
29180379 CTATAAACAA
* * * * *
29180389 AAAGGTCCGACGACTAAGTGTAATCATGAGTAAATGAATCCTTTACGGATTAAAGTTCAAATGAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCAAATGAC
* * *
29180454 TAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCTGATGACTAAGTGTCATCGTG
66 TAAGTGTCATCGTGAGTAAATGAATCCATGACGAATTAAAGGTCCGATGACTAAGTGTCATCGTG
* **
29180519 AGTAAATGAA-TCCTTTATGGATT
131 AGTAAATGAATTCCTATATGGAAC
* **
29180542 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCCGATGAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCAAATGAC
*** * **
29180607 TAAGTGTCATCGTGAGTAAATGAATCCATGATTTATTAAGGGTCCGATGACTTTGTGTCATCGTG
66 TAAGTGTCATCGTGAGTAAATGAATCCATGACGAATTAAAGGTCCGATGACTAAGTGTCATCGTG
*
29180672 AGTATATGAATTCCTATATGGAAC
131 AGTAAATGAATTCCTATATGGAAC
29180696 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
29180729 TTAAATGAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
153 122 0.75
154 12 0.07
155 27 0.17
156 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (154 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGGTCAAATGAC
TAAGTGTCATCGTGAGTAAATGAATCCATGACGAATTAAAGGTCCGATGACTAAGTGTCATCGTG
AGTAAATGAATTCCTATATGGAAC
Found at i:29210687 original size:18 final size:17
Alignment explanation
Indices: 29210646--29210687 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
29210636 AAAAAGTGAT
29210646 AAAAAAGTAGAGAAAAA
1 AAAAAAGTAGAGAAAAA
29210663 AGAAAAA-TACGAGAAAAA
1 A-AAAAAGTA-GAGAAAAA
29210681 GAAAAAA
1 -AAAAAA
29210688 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAGTAGAGAAAAA
Found at i:29214781 original size:94 final size:94
Alignment explanation
Indices: 29214664--29214834 Score: 290
Period size: 94 Copynumber: 1.8 Consensus size: 94
29214654 AAAAAAGGGG
* * *
29214664 TTTGATATATTCTTTATCTGATAAAGAAATATAATTTAATTATTATTTAAAAGAGTTTTAGATAA
1 TTTGATATATTCCTTATCTGATAAAGAAATAGAATTTAAGTATTATTTAAAAGAGTTTTAGATAA
29214729 ATAATAATTAAATTTCAAAAACAAAAGGA
66 ATAATAATTAAATTTCAAAAACAAAAGGA
*
29214758 TTTGATATATTCCTTAT-TAGATAAGGAAATAGAATTTAAGTATTATTTAAAAGAGTTTTAGATA
1 TTTGATATATTCCTTATCT-GATAAAGAAATAGAATTTAAGTATTATTTAAAAGAGTTTTAGATA
29214822 AATAATAATTAAA
65 AATAATAATTAAA
29214835 ATAGAATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 1 0.01
94 71 0.99
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.40
Consensus pattern (94 bp):
TTTGATATATTCCTTATCTGATAAAGAAATAGAATTTAAGTATTATTTAAAAGAGTTTTAGATAA
ATAATAATTAAATTTCAAAAACAAAAGGA
Found at i:29214833 original size:26 final size:25
Alignment explanation
Indices: 29214804--29214886 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
29214794 TAAGTATTAT
29214804 TTAAAAGAGTTTTAGATAAATAATAA
1 TTAAAAGAGTTTTA-ATAAATAATAA
* * * * *
29214830 TTAAAATAGAATTTT-ATTATTATTAT
1 TT-AAA-AGAGTTTTAATAAATAATAA
*
29214856 TTAAAAGAGTTTTAAATAAAAAATAA
1 TTAAAAGAGTTTT-AATAAATAATAA
29214882 TTAAA
1 TTAAA
29214887 TAAAAATTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
24 7 0.17
25 3 0.07
26 22 0.52
27 3 0.07
28 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (25 bp):
TTAAAAGAGTTTTAATAAATAATAA
Found at i:29214885 original size:15 final size:16
Alignment explanation
Indices: 29214867--29214902 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
29214857 TAAAAGAGTT
29214867 TTAAATAAAAA-ATAA
1 TTAAATAAAAATATAA
*
29214882 TTAAATAAAAATTTAA
1 TTAAATAAAAATATAA
29214898 TTAAA
1 TTAAA
29214903 AGAGTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAATAAAAATATAA
Found at i:29214895 original size:52 final size:52
Alignment explanation
Indices: 29214798--29214900 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
29214788 AGAATTTAAG
* * * *
29214798 TATTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTTTATTAT
1 TATTATTTAAAAGAGTTTTAAATAAAAAATAATTAAAATAAAATTTAATTAT
29214850 TATTATTTAAAAGAGTTTTAAATAAAAAATAATT-AAATAAAAATTTAATTA
1 TATTATTTAAAAGAGTTTTAAATAAAAAATAATTAAAAT-AAAATTTAATTA
29214901 AAAGAGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.09
52 42 0.91
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (52 bp):
TATTATTTAAAAGAGTTTTAAATAAAAAATAATTAAAATAAAATTTAATTAT
Found at i:29214896 original size:38 final size:37
Alignment explanation
Indices: 29214854--29214976 Score: 104
Period size: 38 Copynumber: 3.2 Consensus size: 37
29214844 TATTATTATT
*
29214854 ATTTAAAAGAGTTTTAAATAAAAAATAATTAAATAAAA
1 ATTTAAAAGAGTTTTAGATAAAAAATAATTAAAT-AAA
* ***
29214892 ATTTAATTAAAAGAGTTTTAGATAAATAAA-AATTATATTGTT
1 A--T--TTAAAAGAGTTTTAGATAAA-AAATAATTA-AATAAA
* * *
29214934 ATTTAAAAGAGTTATAGATAAATAATAATTAAATAGA
1 ATTTAAAAGAGTTTTAGATAAAAAATAATTAAATAAA
29214971 ATTTAA
1 ATTTAA
29214977 TTATTAGTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
37 10 0.15
38 25 0.37
40 2 0.03
42 25 0.37
43 5 0.07
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (37 bp):
ATTTAAAAGAGTTTTAGATAAAAAATAATTAAATAAA
Found at i:29214989 original size:48 final size:47
Alignment explanation
Indices: 29214927--29215028 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 47
29214917 ATAAAAATTA
* * * *
29214927 TATTGTTATTTAAAAGAGTTATAGATAAATA-ATAATTAAATAGAATT
1 TATTATTAGTTAAAAGAGTTATAAATAAA-AGATAATTAAATAGAAAT
* *
29214974 TAATTATTAGTTAAAAGAGTTTTAAATAAAAGATAATTTAATAGAAAT
1 T-ATTATTAGTTAAAAGAGTTATAAATAAAAGATAATTAAATAGAAAT
29215022 TATTATT
1 TATTATT
29215029 GAAAAGAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 8 0.17
48 39 0.83
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (47 bp):
TATTATTAGTTAAAAGAGTTATAAATAAAAGATAATTAAATAGAAAT
Found at i:29215011 original size:128 final size:133
Alignment explanation
Indices: 29214800--29215040 Score: 384
Period size: 128 Copynumber: 1.8 Consensus size: 133
29214790 AATTTAAGTA
* *
29214800 TTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTTTATTATTATTATTTAAAAGAG
1 TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAATTTTA-TATTATTAGTTAAAAGAG
29214865 TTTTAAATAAAAAATAATTAAATAAAAATT-TAATT-AAAAGAGTTTTAGATAAATAAAAATTAT
65 TTTTAAATAAAAAATAATTAAATAAAAATTATAATTGAAAAGAGTTTTAGATAAATAAAAATTAT
29214928 ATTG
130 ATTG
29214932 TTATTTAAAAGAGTTATAGATAAATAATAATT-AAATAGAA-TTTA-ATTATTAGTTAAAAGAGT
1 TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAATTTTATATTATTAGTTAAAAGAGT
* * * *
29214994 TTTAAATAAAAGATAATTTAATAGAAATTATTATTGAAAAGAGTTTT
66 TTTAAATAAAAAATAATTAAATAAAAATTATAATTGAAAAGAGTTTT
29215041 TAAAATTCAA
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
128 43 0.43
129 4 0.04
130 15 0.15
131 8 0.08
132 31 0.31
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (133 bp):
TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAATTTTATATTATTAGTTAAAAGAGT
TTTAAATAAAAAATAATTAAATAAAAATTATAATTGAAAAGAGTTTTAGATAAATAAAAATTATA
TTG
Found at i:29215172 original size:2 final size:2
Alignment explanation
Indices: 29215167--29215206 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29215157 TATATATATA
29215167 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29215207 ATATATACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29215843 original size:25 final size:26
Alignment explanation
Indices: 29215799--29215858 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
29215789 ATATACGAAA
*
29215799 AAAATTGAAGAAAAAATAATACAGACT
1 AAAATTG-AGAAAAAATAATACAGACC
*
29215826 AAAATTGA-AAAAAATAATACGGACC
1 AAAATTGAGAAAAAATAATACAGACC
29215851 AAAATTGA
1 AAAATTGA
29215859 TTTACATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 23 0.74
26 1 0.03
27 7 0.23
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.18
Consensus pattern (26 bp):
AAAATTGAGAAAAAATAATACAGACC
Found at i:29215853 original size:108 final size:109
Alignment explanation
Indices: 29215715--29215942 Score: 325
Period size: 109 Copynumber: 2.1 Consensus size: 109
29215705 ACAAAAAATA
* * *
29215715 TAAAATTCGAAAAAAAATAATATGGACCAAAATTGATTTAGAGATTC-AAAAAATACGAACATTG
1 TAAAATT-G-AAAAAAATAATACGGACCAAAATTGATTTACAGATACAAAAAAATACGAACATTG
** *
29215779 TAGTCATTTGATATACGAAAAAAATT-GAAGAAAAAATAATACAGAC
64 TAGTCAACTAAT-TACGAAAAAAATTCGAAGAAAAAATAATACAGAC
*
29215825 TAAAATTGAAAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACGAACATTGTA
1 TAAAATTGAAAAAAATAATACGGACCAAAATTGATTTACAGATACAAAAAAATACGAACATTGTA
* *
29215890 GTCAACTAATTACGAAAAAAATTCGAAGAAAAATTAATACGGAC
66 GTCAACTAATTACGAAAAAAATTCGAAGAAAAAATAATACAGAC
*
29215934 CAAAATTGA
1 TAAAATTGA
29215943 TTTACGGATA
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
108 46 0.43
109 53 0.50
110 7 0.07
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.24
Consensus pattern (109 bp):
TAAAATTGAAAAAAATAATACGGACCAAAATTGATTTACAGATACAAAAAAATACGAACATTGTA
GTCAACTAATTACGAAAAAAATTCGAAGAAAAAATAATACAGAC
Found at i:29215922 original size:85 final size:85
Alignment explanation
Indices: 29215834--29216116 Score: 353
Period size: 84 Copynumber: 3.4 Consensus size: 85
29215824 CTAAAATTGA
*
29215834 AAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACGAACATTGTAGTCAACTAA
1 AAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
29215899 T-TACGAAAAAAATTCGAAG
66 TATACGAAAAAAATTCGAAG
* ** * * * *
29215918 AAAAATTAATACGGACCAAAATTGATTTACGGATACAAAAAAATAAAAATATCGTAGTCAACTTA
1 AAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
29215983 TATACG-AAAAAA-TCGAAG
66 TATACGAAAAAAATTCGAAG
* * *
29216001 AAAAATTAATATGGACCAGAATTGATTTACATATAC-AAAAAATACAAACATTGTAGT--ACTAA
1 AAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
* *
29216063 TATACCAAAAAACAATTTCGAAC
66 TATA-CGAAAAA-AA-TTCGAAG
* * *
29216086 AAAAAATAATAAGGAACAAAATTGAATTACA
1 AAAAAATAATACGGACCAAAATTGATTTACA
29216117 GAGATCAAAA
Statistics
Matches: 170, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
80 8 0.05
81 1 0.01
82 22 0.13
83 40 0.24
84 64 0.38
85 35 0.21
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.23
Consensus pattern (85 bp):
AAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
TATACGAAAAAAATTCGAAG
Found at i:29216031 original size:167 final size:167
Alignment explanation
Indices: 29215826--29216129 Score: 422
Period size: 168 Copynumber: 1.8 Consensus size: 167
29215816 AATACAGACT
* *
29215826 AAAATTGAAAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAAATACGAACATTGTAG
1 AAAATCGAAAAAAATAATACGGACCAAAATTGATTTACATATAC-AAAAAATACAAACATTGTAG
* * * * * *
29215891 TCAACTAAT-TA-CGAAAAA-AA-TTCGAAGAAAAATTAATACGGACCAAAATTGATTTAC-G-G
65 T--ACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAG
29215950 ATACAAAAAAATAAAAATATCGTAGTCAACTTATATACGAA
128 AT-CAAAAAAATAAAAATATCGTAGTCAACTTATATACGAA
* *
29215991 AAAATCGAAGAAAAATTAATATGGACCAGAATTGATTTACATATACAAAAAATACAAACATTGTA
1 AAAATCGAA-AAAAA-TAATACGGACCAAAATTGATTTACATATACAAAAAATACAAACATTGTA
29216056 GTACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAGA
64 GTACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAGA
29216121 TCAAAAAAA
129 TCAAAAAAA
29216130 ATGATTTATG
Statistics
Matches: 121, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
164 6 0.05
165 10 0.08
166 31 0.26
167 30 0.25
168 32 0.26
169 9 0.07
170 3 0.02
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.23
Consensus pattern (167 bp):
AAAATCGAAAAAAATAATACGGACCAAAATTGATTTACATATACAAAAAATACAAACATTGTAGT
ACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAGATC
AAAAAAATAAAAATATCGTAGTCAACTTATATACGAA
Found at i:29225337 original size:26 final size:25
Alignment explanation
Indices: 29225307--29225355 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
29225297 TTTTTTGTTA
29225307 ATATTTTAATATATATAAAA-ATAAAT
1 ATATTTTAA-ATAT-TAAAATATAAAT
29225333 ATATTTTAAATATTAAAATATAA
1 ATATTTTAAATATTAAAATATAA
29225356 CCAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
26 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTTAAATATTAAAATATAAAT
Found at i:29234346 original size:7 final size:7
Alignment explanation
Indices: 29234334--29234369 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
29234324 CTCGAACCCG
29234334 TTGACCA
1 TTGACCA
29234341 TTGACCA
1 TTGACCA
29234348 TTGACCA
1 TTGACCA
*
29234355 TTGA-CT
1 TTGACCA
29234361 TTGACCA
1 TTGACCA
29234368 TT
1 TT
29234370 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (7 bp):
TTGACCA
Found at i:29234366 original size:13 final size:13
Alignment explanation
Indices: 29234334--29234375 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29234324 CTCGAACCCG
*
29234334 TTGACCATTGACCA
1 TTGACCATTGA-CT
29234348 TTGACCATTGACT
1 TTGACCATTGACT
*
29234361 TTGACCATTAACT
1 TTGACCATTGACT
29234374 TT
1 TT
29234376 TTCTGAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:29242164 original size:58 final size:56
Alignment explanation
Indices: 29242102--29242340 Score: 198
Period size: 58 Copynumber: 4.1 Consensus size: 56
29242092 TAATTTTGGA
* * * *
29242102 AAGTTTTAGGGGCAAAAATGTCATTTTAGGAAAGTTCA-GGGCAAAATGT-GTTTTTTAG
1 AAGTTCTA-GGGCAAAAATGTGATTTT-GG-AAGTT-AGGGGCAAAATGTAATTTTTAAG
* ** *
29242160 AAGTTCGAGGGTTAAAATGTGATTTTTGCAAGTTAGGGGGCAAAATGTAATTTTTAAG
1 AAGTTCTAGGGCAAAAATGTGA-TTTTGGAAGTTA-GGGGCAAAATGTAATTTTTAAG
* * *
29242218 AAGTTCTAGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGAG
1 AAGTTCTAGGGCAAAAATGTGA-TTTTGGAAG-TTAGGGGCAAAATGTAATTTTTAAG
* * *
29242276 AAGTT-TAAGGGTC-AAAATGTAATTTTTAAGAAGTTTAGGGGTAAAATTGTAATTTTTAAG
1 AAGTTCT-AGGG-CAAAAATGTGA-TTTT-GGAAG-TTAGGGGCAAAA-TGTAATTTTTAAG
29242336 AAGTT
1 AAGTT
29242341 TTGGGGGGTC
Statistics
Matches: 155, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 24 0.15
58 88 0.57
59 20 0.13
60 17 0.11
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (56 bp):
AAGTTCTAGGGCAAAAATGTGATTTTGGAAGTTAGGGGCAAAATGTAATTTTTAAG
Found at i:29242404 original size:92 final size:90
Alignment explanation
Indices: 29242200--29242453 Score: 252
Period size: 92 Copynumber: 2.8 Consensus size: 90
29242190 AGTTAGGGGG
* * *
29242200 CAAAATGTAATTTTTAAGAAGTTCT-A-GGGTAAAAATGTGATTTTTG-GAAGTTTAGGGGT-AA
1 CAAAATGTAATTTTTAAGAAGTT-TAAGGGGT-AAAATGTAATTTTAGAAAAGTTTAGGGGTCAA
* ** * **
29242261 AATGTAATTTTTGAGAAGTTTAAGGGT
64 AATGTGATTTTAAAAAAGTTTAAAAGT
* *
29242288 CAAAATGTAATTTTTAAGAAGTTT-AGGGGTAAAATTGTAATTTTTA-AGAAGTTTTGGGGGGTC
1 CAAAATGTAATTTTTAAGAAGTTTAAGGGGTAAAA-TGTAA-TTTTAGAAAAG-TTT-AGGGGTC
29242351 AAAATGTGATTTTAAAAAAGTTTAAAAGT
62 AAAATGTGATTTTAAAAAAGTTTAAAAGT
* * * *
29242380 TAAAATGTGATTTTTGAA-ATGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAA
1 CAAAATGTAATTTTT-AAGAAGTTTAAGGGGTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAA
*
29242444 ATATGATTTT
65 ATGTGATTTT
29242454 TGGAAAGTTC
Statistics
Matches: 140, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
87 6 0.04
88 31 0.22
89 8 0.06
90 21 0.15
91 13 0.09
92 50 0.36
93 11 0.08
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.38
Consensus pattern (90 bp):
CAAAATGTAATTTTTAAGAAGTTTAAGGGGTAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAA
TGTGATTTTAAAAAAGTTTAAAAGT
Found at i:29242445 original size:30 final size:30
Alignment explanation
Indices: 29242075--29242445 Score: 200
Period size: 30 Copynumber: 12.6 Consensus size: 30
29242065 AGTTTCAGAG
* * *
29242075 AGTTTA-GGGTTAAAATATAATTTT-GGAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* *
29242103 AGTTTTAGGGG-CAAAAATGTCATTTTAGGAA
1 AG-TTTAGGGGTC-AAAATGTAATTTTAGAAA
* **
29242134 AGTTCA-GGG-CAAAATGTGTTTTTTAG--A
1 AGTTTAGGGGTCAAAATGT-AATTTTAGAAA
* * * * *
29242161 AG-TTCGAGGGTTAAAATGTGATTTTTG-CA
1 AGTTTAG-GGGTCAAAATGTAATTTTAGAAA
* *
29242190 AG-TTAGGGGGCAAAATGTAATTTTTA-AGA
1 AGTTTAGGGGTCAAAATGTAA-TTTTAGAAA
* * * *
29242219 AGTTCTA-GGGTAAAAATGTGATTTTTG-GA
1 AGTT-TAGGGGTCAAAATGTAATTTTAGAAA
* *
29242248 AGTTTAGGGGT-AAAATGTAATTTTTGAGA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* *
29242277 AGTTTAAGGGTCAAAATGTAATTTTTA-AGA
1 AGTTTAGGGGTCAAAATGTAA-TTTTAGAAA
*
29242307 AGTTTAGGGGT-AAAATTGTAATTTTTA-AGA
1 AGTTTAGGGGTCAAAA-TGTAA-TTTTAGAAA
* * *
29242337 AGTTTTGGGGGGTCAAAATGTGATTTTAAAAA
1 AG-TTT-AGGGGTCAAAATGTAATTTTAGAAA
*** * * *
29242369 AGTTTAAAAGTTAAAATGTGATTTTTGAAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
* * *
29242399 TGTTTAAGGGTTAAAATGTAATTTTAGAAA
1 AGTTTAGGGGTCAAAATGTAATTTTAGAAA
29242429 AGTTTAGGGGTCAAAAT
1 AGTTTAGGGGTCAAAAT
29242446 ATGATTTTTG
Statistics
Matches: 276, Mismatches: 44, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.00
27 3 0.01
28 44 0.16
29 64 0.23
30 124 0.45
31 23 0.08
32 13 0.05
33 4 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
AGTTTAGGGGTCAAAATGTAATTTTAGAAA
Found at i:29244128 original size:6 final size:6
Alignment explanation
Indices: 29244114--29244154 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
29244104 GGGACATTAA
* *
29244114 TAAATT TAAACT TAAATT TAAA-A TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
29244155 CTATTTGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:29244160 original size:17 final size:17
Alignment explanation
Indices: 29244120--29244152 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29244110 TTAATAAATT
*
29244120 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
29244137 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
29244153 TTCTATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:29244746 original size:39 final size:39
Alignment explanation
Indices: 29244706--29245168 Score: 325
Period size: 39 Copynumber: 11.6 Consensus size: 39
29244696 GGCTGCAATT
* * *
29244706 TGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGATGATT
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
*
29244745 TGCCCCAGGCTCAGGGTAAGAGATTGAATGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGA-T---TGGCTGATGGTGATC
* * * * * *
29244788 TGCCCTAAGATCGGGGTAAAATATCGAATGGCTGATGGTGATT
1 TGCCCCAGGCTCGGGGT--AAGA--GATTGGCTGATGGTGATC
29244831 TGCCCCAGGCTCGGGGTAAGAGA-T--C-GAGTGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGG-TG--ATC
* * * * *
29244870 TACCTCAAGCTCGGGATAAAAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* * * *
29244909 TACGCCAGGCTCGGGGTAAGAGATCAAATGGTTGATGGTGGTC
1 TGCCCCAGGCTCGGGGTAAGAGAT----TGGCTGATGGTGATC
* ***
29244952 TGCCCCAGGCTCGGGGTAAAAGA-TCAATGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* * * **
29244990 TGCCCTAAGCTCGGGGTAAAAGA-T--CAAATGGTTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGG-TG--ATC
29245029 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* * **** *
29245068 TGCCCCAAGCTCGGGGTAAAAGATCAAATGACT-GTAATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTGATC
* *
29245107 TG-CCCAGGTTCGGGGTAAGAGATTGACTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
* *
29245145 TGCCCCAAGCTTGGGGTAAGAGAT
1 TGCCCCAGGCTCGGGGTAAGAGAT
29245169 CGGAATCTTC
Statistics
Matches: 333, Mismatches: 62, Indels: 58
0.74 0.14 0.13
Matches are distributed among these distances:
35 2 0.01
36 8 0.02
37 5 0.02
38 63 0.19
39 142 0.43
40 4 0.01
41 7 0.02
42 9 0.03
43 88 0.26
45 3 0.01
47 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (39 bp):
TGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATC
Found at i:29244906 original size:78 final size:78
Alignment explanation
Indices: 29244659--29245169 Score: 463
Period size: 78 Copynumber: 6.4 Consensus size: 78
29244649 GATGGTGATC
* * * * * *
29244659 TGGTGATTTTCCCTAAGCTCGGGGTAAAAGACCAAATGGCTGCAATTTGCCCCAGGCTCGGGGTA
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
* *
29244724 AGAGATTGGCTAA
66 AAAGATTGGCTGA
* * * * ** * * *
29244737 TGATGATTTGCCCCAGGCTCAGGGTAAGAGATTGAATGGCTG-ATGGTGATCTGCCCTAAGATCG
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCA-----ATCTGCCCCAGGCTCG
*
29244801 GGGTAAAATATCGAATGGCTGA
61 GGGT-AAA-A--GATTGGCTGA
* * * * * * * *
29244823 TGGTGATTTGCCCCAGGCTCGGGGTAAGAGATCGAGTGGCTGCAATCTACCTCAAGCTCGGGATA
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
29244888 AAAGATTGGCTGA
66 AAAGATTGGCTGA
* * * * *
29244901 TGGTGATCTACGCCAGGCTCGGGGTAAGAGATCAAATGGTTG-ATGGTGGTCTGCCCCAGGCTCG
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCA-----ATCTGCCCCAGGCTCG
***
29244965 GGGTAAAAGA-TCAATGA
61 GGGTAAAAGATTGGCTGA
* * *
29244982 TGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCAAATGGTTGCAATCTGCCCCAGGCTCGGGGTA
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
*
29245047 AGAGATTGGCTGA
66 AAAGATTGGCTGA
* * * *
29245060 TGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGACTGTAATCTG-CCCAGGTTCGGGGTA
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
* *
29245124 AGAGATTGACTGA
66 AAAGATTGGCTGA
*
29245137 TGGTGATCTGCCCCAAGCTTGGGGTAAGAGATC
1 TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATC
29245170 GGAATCTTCA
Statistics
Matches: 358, Mismatches: 58, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
77 83 0.23
78 127 0.35
80 1 0.00
81 44 0.12
82 53 0.15
83 2 0.01
84 1 0.00
86 46 0.13
87 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (78 bp):
TGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
AAAGATTGGCTGA
Found at i:29244930 original size:164 final size:159
Alignment explanation
Indices: 29244659--29245169 Score: 555
Period size: 164 Copynumber: 3.2 Consensus size: 159
29244649 GATGGTGATC
* * *
29244659 TGGTGATTTTCCCTAAGCTCGGGGTAAAAGACCAAATGGCTGCAATTTGCCCCAGGCTCGGGGTA
1 TGGTGATTTGCCCTAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
* * * * **
29244724 AGAGATTGGCTAATGATGATTTGCCCCAGGCTCAGGGTAAGAGATTGAATGGCTGATGGTGATCT
66 AGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTGATGGTGATCT
* *
29244789 GCCCTAAGATCGGGGTAAAATATCGAATGGCTGA
131 GCCCCAAGATCGGGGTAAAAGATC-AA----TGA
* * * * * * * * *
29244823 TGGTGATTTGCCCCAGGCTCGGGGTAAGAGATCGAGTGGCTGCAATCTACCTCAAGCTCGGGATA
1 TGGTGATTTGCCCTAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
* * * * *
29244888 AAAGATTGGCTGATGGTGATCTACGCCAGGCTCGGGGTAAGAGATCAAATGGTTGATGGTGGTCT
66 AGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTGATGGTGATCT
* *
29244953 GCCCCAGGCTCGGGGTAAAAGATCAATGA
131 GCCCCAAGATCGGGGTAAAAGATCAATGA
* *
29244982 TGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCAAATGGTTGCAATCTGCCCCAGGCTCGGGGTA
1 TGGTGATTTGCCCTAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
* * * *
29245047 AGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGAC---T-GTAATCT
66 AGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTGATGGTGATCT
* * * * *
29245108 G-CCCAGGTTCGGGGTAAGAGATTGACTGA
131 GCCCCAAGATCGGGGTAAAAGA-TCAATGA
* * * *
29245137 TGGTGATCTGCCCCAAGCTTGGGGTAAGAGATC
1 TGGTGATTTGCCCTAAGCTCGGGGTAAAAGATC
29245170 GGAATCTTCA
Statistics
Matches: 292, Mismatches: 54, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
154 18 0.06
155 41 0.14
156 1 0.00
159 103 0.35
163 2 0.01
164 127 0.43
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (159 bp):
TGGTGATTTGCCCTAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGCCCCAGGCTCGGGGTA
AGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTGATGGTGATCT
GCCCCAAGATCGGGGTAAAAGATCAATGA
Found at i:29256998 original size:23 final size:21
Alignment explanation
Indices: 29256960--29257001 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
29256950 TTTTGGCAAG
*
29256960 GTATATTATTTTTTTATATGT
1 GTATATTATTTATTTATATGT
29256981 GTATATATATTATATTTATAT
1 GTATAT-TATT-TATTTATAT
29257002 CTTTTCGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
GTATATTATTTATTTATATGT
Found at i:29257768 original size:30 final size:29
Alignment explanation
Indices: 29257732--29257868 Score: 132
Period size: 29 Copynumber: 4.7 Consensus size: 29
29257722 TGTTTACCCA
*
29257732 AAAATCACTTTTTAACCCCCAAACTTTTCT
1 AAAATCACATTTTAA-CCCCAAACTTTTCT
* * *
29257762 AAAATCACATTTTGACCTCAAACTTTCCT
1 AAAATCACATTTTAACCCCAAACTTTTCT
* *
29257791 AAAATCACATTTTAACCCTAAAATTTTCT
1 AAAATCACATTTTAACCCCAAACTTTTCT
** ** *
29257820 AAAATTTCATTTTAAACCTTAAA-TTTTCC
1 AAAATCACATTTT-AACCCCAAACTTTTCT
*
29257849 ATAAATTACATTTTAACCCC
1 A-AAATCACATTTTAACCCC
29257869 TAAATTTCAC
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
29 57 0.64
30 32 0.36
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (29 bp):
AAAATCACATTTTAACCCCAAACTTTTCT
Found at i:29257873 original size:30 final size:29
Alignment explanation
Indices: 29257732--29257875 Score: 130
Period size: 30 Copynumber: 4.9 Consensus size: 29
29257722 TGTTTACCCA
* * *
29257732 AAAATCACTTTTTAACCCCCAAACTTTTCT
1 AAAATCACATTTTAACCCCTAAA-TTTTCC
* * *
29257762 AAAATCACATTTTGACCTC-AAACTTTCC
1 AAAATCACATTTTAACCCCTAAATTTTCC
*
29257790 TAAAATCACATTTTAA-CCCTAAAATTTTCT
1 -AAAATCACATTTTAACCCCT-AAATTTTCC
** * *
29257820 AAAATTTCATTTTAAACCTTAAATTTTCC
1 AAAATCACATTTTAACCCCTAAATTTTCC
*
29257849 ATAAATTACATTTTAACCCCTAAATTT
1 A-AAATCACATTTTAACCCCTAAATTT
29257876 CACAAATTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
28 6 0.06
29 39 0.42
30 48 0.52
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.39
Consensus pattern (29 bp):
AAAATCACATTTTAACCCCTAAATTTTCC
Found at i:29257874 original size:59 final size:58
Alignment explanation
Indices: 29257732--29257875 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 58
29257722 TGTTTACCCA
* * *
29257732 AAAATCACTTTTTAACCCCCAAACTTTTCTAAAATCACATTTTGACCTCAAACTTTCCT
1 AAAATCACATTTTAACCCCTAAA-TTTTCTAAAATCACATTTTAACCTCAAACTTTCCT
** * *
29257791 AAAATCACATTTTAA-CCCTAAAATTTTCTAAAATTTCATTTTAAACCTTAAATTTTCC-
1 AAAATCACATTTTAACCCCT-AAATTTTCTAAAATCACATTTT-AACCTCAAACTTTCCT
*
29257849 ATAAATTACATTTTAACCCCTAAATTT
1 A-AAATCACATTTTAACCCCTAAATTT
29257876 CACAAATTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
58 21 0.29
59 48 0.66
60 4 0.05
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.39
Consensus pattern (58 bp):
AAAATCACATTTTAACCCCTAAATTTTCTAAAATCACATTTTAACCTCAAACTTTCCT
Found at i:29258073 original size:15 final size:14
Alignment explanation
Indices: 29258041--29258081 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
29258031 TAACACAATG
29258041 AATAAATATACGAA
1 AATAAATATACGAA
29258055 AATAAATATGA-GAAA
1 AATAAATAT-ACG-AA
29258070 AATAAA-ATACGA
1 AATAAATATACGA
29258082 GTTATGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.08
14 13 0.54
15 9 0.38
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:29258237 original size:59 final size:59
Alignment explanation
Indices: 29258174--29258562 Score: 174
Period size: 59 Copynumber: 6.6 Consensus size: 59
29258164 GAAAAAAAAC
* * * *
29258174 GGGGTCGAAAATG-AAGTTTT-GGAGAGTTTGGGGTTAAAATGTAATTTTGAAAAGTTTTA
1 GGGGTC-AAAATGCAA-TTTTAGGAAAGTTTAGGGTAAAAATGTAATTTTGAAAAGTTTGA
* * * * *
29258233 GGGGTAAAAATGCCATTTTAGGAAAGTTTAGGGTAAAAATGTGATTTTTAGAAGTTTGA
1 GGGGTCAAAATGCAATTTTAGGAAAGTTTAGGGTAAAAATGTAATTTTGAAAAGTTTGA
** * * * * * *
29258292 -GGGTCAAAATGTTATTTT-TGAAAATTCAGGGGCAAAAATGTAATTTTTGAGAAGTTCGA
1 GGGGTCAAAATGCAATTTTAGGAAAGTTTA-GGGTAAAAATGTAA-TTTTGAAAAGTTTGA
* * * * *
29258351 -GGG-CAAAATGTAATTTTTAAG-AAGTTAAAAGGTCAAAATGTAAATTTT-AAGAAGTTT-A
1 GGGGTCAAAATGCAA-TTTTAGGAAAGTT-TAGGGTAAAAATGT-AATTTTGAA-AAGTTTGA
* * * * * * * * *
29258409 AGAGTAAAAATGTAATTTTTAAG-AAGTTCAAGGGGTTAAAATGTGATTTTAGAAAAATTT-A
1 GGGGTCAAAATGCAA-TTTTAGGAAAGTT-TA-GGGTAAAAATGTAATTTT-GAAAAGTTTGA
* ** * * * *
29258470 GGGGTTAAAATGTGATTAT-GAAAAAGTTTAGAGGTTAAAATGTAATTTTGGAAAAG-TTAA
1 GGGGTCAAAATGCAATTTTAG-GAAAGTTTAG-GGTAAAAATGTAATTTT-GAAAAGTTTGA
*** *
29258530 GGGGTCAAAATATGATTTTTGGAAAGTTTAGGG
1 GGGGTCAAAATGCAATTTTAGGAAAGTTTAGGG
29258563 ACCTTCTGGG
Statistics
Matches: 261, Mismatches: 50, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
57 7 0.03
58 48 0.18
59 87 0.33
60 84 0.32
61 33 0.13
62 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
GGGGTCAAAATGCAATTTTAGGAAAGTTTAGGGTAAAAATGTAATTTTGAAAAGTTTGA
Found at i:29258243 original size:30 final size:29
Alignment explanation
Indices: 29258181--29258562 Score: 224
Period size: 30 Copynumber: 12.9 Consensus size: 29
29258171 AACGGGGTCG
* * *
29258181 AAAATG-AAGTTTTGGAGAGTTT-GGGGTT
1 AAAATGTAA-TTTTGAAAAGTTTAGGGGTA
29258209 AAAATGTAATTTTGAAAAGTTTTAGGGGTA
1 AAAATGTAATTTTGAAAAG-TTTAGGGGTA
** *
29258239 AAAATGCCATTTTAGGAAAGTTTA-GGGTA
1 AAAATGTAATTTT-GAAAAGTTTAGGGGTA
* * * *
29258268 AAAATGTGATTTTTAGAAGTTT-GAGGGTC
1 AAAATGTAATTTTGAAAAGTTTAG-GGGTA
* * *
29258297 AAAATGTTATTTTTGAAAA-TTCAGGGGCA
1 AAAATG-TAATTTTGAAAAGTTTAGGGGTA
* * *
29258326 AAAATGTAATTTTTGAGAAG-TTCGAGGG-C
1 AAAATGTAA-TTTTGAAAAGTTTAG-GGGTA
* * ** *
29258355 AAAATGTAATTTTTAAGAAGTTAAAAGGTC
1 AAAATGTAATTTTGAA-AAGTTTAGGGGTA
* *
29258385 AAAATGTAAATTTT-AAGAAGTTTAAGAGTA
1 AAAATGT-AATTTTGAA-AAGTTTAGGGGTA
* * *
29258415 AAAATGTAATTTTTAAGAAGTTCAAGGGGTT
1 AAAATGTAATTTTGAA-AAGTT-TAGGGGTA
* * *
29258446 AAAATGTGATTTTAGAAAAATTTAGGGGTT
1 AAAATGTAATTTT-GAAAAGTTTAGGGGTA
* * * *
29258476 AAAATGTGATTATGAAAAAGTTTAGAGGTT
1 AAAATGTAATTTTG-AAAAGTTTAGGGGTA
*
29258506 AAAATGTAATTTTGGAAAAGTTAAGGGGTCA
1 AAAATGTAATTTT-GAAAAGTTTAGGGGT-A
* *
29258537 AAATATG-ATTTTTGGAAAGTTTAGGG
1 AAA-ATGTAATTTTGAAAAGTTTAGGG
29258563 ACCTTCTGGG
Statistics
Matches: 279, Mismatches: 53, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
28 27 0.10
29 73 0.26
30 134 0.48
31 40 0.14
32 5 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTGAAAAGTTTAGGGGTA
Found at i:29261469 original size:12 final size:12
Alignment explanation
Indices: 29261454--29261482 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
29261444 TCAAGACGAG
29261454 GAAGAGAAAGAA
1 GAAGAGAAAGAA
29261466 GAAGAGAAAGAA
1 GAAGAGAAAGAA
29261478 GAAGA
1 GAAGA
29261483 AGAACCTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAAGAGAAAGAA
Found at i:29266789 original size:20 final size:20
Alignment explanation
Indices: 29266764--29266811 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29266754 CCTGTTGACT
29266764 CGTTGACCCGTTGACCG-GTC
1 CGTTGACCCGTTGACCGAG-C
* *
29266784 CGTTGACCGGTTGATCGAGC
1 CGTTGACCCGTTGACCGAGC
29266804 CGTTGACC
1 CGTTGACC
29266812 ATTGACCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.25
Consensus pattern (20 bp):
CGTTGACCCGTTGACCGAGC
Found at i:29266828 original size:7 final size:7
Alignment explanation
Indices: 29266757--29266841 Score: 54
Period size: 7 Copynumber: 12.4 Consensus size: 7
29266747 ACCCGAACCT
29266757 GTTGACTC
1 GTTGAC-C
29266765 GTTGACCC
1 GTTGA-CC
29266773 GTTGACC
1 GTTGACC
*
29266780 G--GTCC
1 GTTGACC
29266785 GTTGACC
1 GTTGACC
*
29266792 GGTTGATC
1 -GTTGACC
*
29266800 G-AG-CC
1 GTTGACC
29266805 GTTGACC
1 GTTGACC
*
29266812 ATTGACC
1 GTTGACC
*
29266819 GTTGATC
1 GTTGACC
29266826 GTTGA-C
1 GTTGACC
*
29266832 TTTGACC
1 GTTGACC
29266839 GTT
1 GTT
29266842 AACTTTTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
5 6 0.10
6 7 0.12
7 28 0.47
8 17 0.29
9 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.32
Consensus pattern (7 bp):
GTTGACC
Found at i:29268261 original size:21 final size:21
Alignment explanation
Indices: 29268237--29268286 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
29268227 AACTTGATTA
29268237 GGTAGAAGAGTCACTTGTATC
1 GGTAGAAGAGTCACTTGTATC
**
29268258 GGTAGAACTGTCACTTGTATC
1 GGTAGAAGAGTCACTTGTATC
29268279 GGTAGAAG
1 GGTAGAAG
29268287 TTTGCACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (21 bp):
GGTAGAAGAGTCACTTGTATC
Found at i:29275040 original size:9 final size:9
Alignment explanation
Indices: 29275018--29275088 Score: 72
Period size: 9 Copynumber: 7.9 Consensus size: 9
29275008 GCAGAGTACA
29275018 GATGAAGA-
1 GATGAAGAT
*
29275026 GAATGAAGGT
1 G-ATGAAGAT
29275036 GATGAAGAT
1 GATGAAGAT
*
29275045 GATGATGAT
1 GATGAAGAT
*
29275054 GATGATGAT
1 GATGAAGAT
* *
29275063 AATGATGAT
1 GATGAAGAT
*
29275072 GATGATGAT
1 GATGAAGAT
29275081 GATGAAGA
1 GATGAAGA
29275089 CAACGATGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
8 1 0.02
9 53 0.96
10 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.25
Consensus pattern (9 bp):
GATGAAGAT
Found at i:29275050 original size:3 final size:3
Alignment explanation
Indices: 29275035--29275085 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
29275025 AGAATGAAGG
* *
29275035 TGA TGA AGA TGA TGA TGA TGA TGA TGA TAA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
29275083 TGA
1 TGA
29275086 AGACAACGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:29280901 original size:26 final size:25
Alignment explanation
Indices: 29280848--29280899 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
29280838 ATTATTTTAA
* *
29280848 TTAGAGTGATTAAATTAAAAAAAAT
1 TTAGAGTGAATAAAATAAAAAAAAT
*
29280873 TTAGAGTGAATAAAATAAAATAAAT
1 TTAGAGTGAATAAAATAAAAAAAAT
29280898 TT
1 TT
29280900 TATTTTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (25 bp):
TTAGAGTGAATAAAATAAAAAAAAT
Found at i:29282868 original size:20 final size:20
Alignment explanation
Indices: 29282843--29282880 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29282833 GAGATTAGAA
29282843 AATATTTATCAAATCATAAC
1 AATATTTATCAAATCATAAC
*
29282863 AATATTTATCACATCATA
1 AATATTTATCAAATCATA
29282881 TCATAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATTTATCAAATCATAAC
Found at i:29283479 original size:35 final size:35
Alignment explanation
Indices: 29283439--29283551 Score: 97
Period size: 35 Copynumber: 3.2 Consensus size: 35
29283429 GTAGAAGAAA
29283439 AGAAATAAAGTTTCTAAATGATGATAACAGAAAAT
1 AGAAATAAAGTTTCTAAATGATGATAACAGAAAAT
***** ** *
29283474 AGAAATAGAAGAGAAGAGAAATTTTGGTAGA-AG-AAA-
1 AGAAAT--AA-AGTTTCTAAATGATGATA-ACAGAAAAT
29283510 AGAAATAAAGTTTCTAAATGATGATAACAGAAAAT
1 AGAAATAAAGTTTCTAAATGATGATAACAGAAAAT
29283545 AGAAATA
1 AGAAATA
29283552 GAAGAGAAGA
Statistics
Matches: 55, Mismatches: 16, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
32 1 0.02
33 12 0.22
34 5 0.09
35 13 0.24
36 6 0.11
37 5 0.09
38 12 0.22
39 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.22
Consensus pattern (35 bp):
AGAAATAAAGTTTCTAAATGATGATAACAGAAAAT
Found at i:29283500 original size:71 final size:71
Alignment explanation
Indices: 29283420--29283561 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
29283410 AGAAGCACTT
29283420 GAAATTTTGGTAGAAGAAAAGAAATAAAGTTTCTAAATGATGATAACAGAAAATAGAAATAGAAG
1 GAAATTTTGGTAGAAGAAAAGAAATAAAGTTTCTAAATGATGATAACAGAAAATAGAAATAGAAG
29283485 AGAAGA
66 AGAAGA
29283491 GAAATTTTGGTAGAAGAAAAGAAATAAAGTTTCTAAATGATGATAACAGAAAATAGAAATAGAAG
1 GAAATTTTGGTAGAAGAAAAGAAATAAAGTTTCTAAATGATGATAACAGAAAATAGAAATAGAAG
29283556 AGAAGA
66 AGAAGA
29283562 AAAACAAGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (71 bp):
GAAATTTTGGTAGAAGAAAAGAAATAAAGTTTCTAAATGATGATAACAGAAAATAGAAATAGAAG
AGAAGA
Found at i:29283678 original size:25 final size:22
Alignment explanation
Indices: 29283617--29283674 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
29283607 TGATACGGTT
* *
29283617 TTGATGTGGTGATGTTATGATGG
1 TTGA-GTGGTGGTGTTATGAAGG
29283640 TTGAGTGGTGGTGTTATGAAGG
1 TTGAGTGGTGGTGTTATGAAGG
*
29283662 TTGAATGGTGGTG
1 TTGAGTGGTGGTG
29283675 GTGTGGTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (22 bp):
TTGAGTGGTGGTGTTATGAAGG
Found at i:29283685 original size:22 final size:22
Alignment explanation
Indices: 29283623--29283696 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
29283613 GGTTTTGATG
* * *
29283623 TGGTGATGTTATGATGGTTGAG
1 TGGTGGTGGTATGATGGTTGAA
* *
29283645 TGGTGGTGTTATGAAGGTTGAA
1 TGGTGGTGGTATGATGGTTGAA
* * *
29283667 TGGTGGTGGTGTGGTGGTTGTA
1 TGGTGGTGGTATGATGGTTGAA
29283689 TGGTGGTG
1 TGGTGGTG
29283697 AAAAGAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.14, C:0.00, G:0.47, T:0.39
Consensus pattern (22 bp):
TGGTGGTGGTATGATGGTTGAA
Found at i:29283979 original size:22 final size:24
Alignment explanation
Indices: 29283954--29283998 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
29283944 TTACTTACTA
29283954 AAAGATGGAC-AA-TTTTGCATGG
1 AAAGATGGACTAAGTTTTGCATGG
* *
29283976 AAAGGTTGACTAAGTTTTGCATG
1 AAAGATGGACTAAGTTTTGCATG
29283999 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (24 bp):
AAAGATGGACTAAGTTTTGCATGG
Found at i:29285658 original size:19 final size:19
Alignment explanation
Indices: 29285634--29285673 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
29285624 CATGAGGAAC
29285634 TAATCCTCTTTTGGGGGAT
1 TAATCCTCTTTTGGGGGAT
29285653 TAATCCTCTTTTGGGGGAT
1 TAATCCTCTTTTGGGGGAT
29285672 TA
1 TA
29285674 GCGAGTGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (19 bp):
TAATCCTCTTTTGGGGGAT
Found at i:29291243 original size:26 final size:26
Alignment explanation
Indices: 29291214--29291558 Score: 492
Period size: 26 Copynumber: 13.3 Consensus size: 26
29291204 CATTAATTTC
*
29291214 ACGTTTACGATCGTCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
29291240 ACGTTTACGCTCGTCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* *
29291266 ACATTTATGCTCGTCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* *
29291292 ACGTTTACTCTCGTCATCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* *
29291318 ACGTTTATGCTCGTTAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
29291344 ACGTTTACGCTCGTCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* * *
29291370 AAGTTTATGCTCGTCAGCATAAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* *
29291396 ACGTTTACGCTTGCCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
*
29291422 ACGTTTACGCTCATCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* *
29291448 ACGTTTATGCTCATCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* * *
29291474 ACATTCATGCTCGTCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
*
29291500 ACGTTTACGCTCGTCAACATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
* *
29291526 ACGTTAACGCTTGTCAGCATGAATAT
1 ACGTTTACGCTCGTCAGCATGAATAT
*
29291552 TCGTTTA
1 ACGTTTA
29291559 TATCACTAGA
Statistics
Matches: 282, Mismatches: 37, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 282 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (26 bp):
ACGTTTACGCTCGTCAGCATGAATAT
Found at i:29300487 original size:12 final size:12
Alignment explanation
Indices: 29300470--29300494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29300460 AAAGAATGGA
29300470 AAAACTAAAATT
1 AAAACTAAAATT
29300482 AAAACTAAAATT
1 AAAACTAAAATT
29300494 A
1 A
29300495 CAAAGAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAACTAAAATT
Found at i:29302512 original size:91 final size:91
Alignment explanation
Indices: 29302354--29302519 Score: 269
Period size: 91 Copynumber: 1.8 Consensus size: 91
29302344 GACGGTTCAA
* * * *
29302354 AATTCAAACAACAAGCACTCAAAACGGGTTCAAGCACTAGAAATGGTAAAGCACATGACATTTTT
1 AATTCAAACAACAAGCACTCAAAACGAGTTCAAGAACTAGAAATGGTAAAGCACATGACAATGTT
29302419 CCCTACTCGTCCTTAATATTGTTTAG
66 CCCTACTCGTCCTTAATATTGTTTAG
* * *
29302445 AATTCGAACAACAAGCACTCAAAACGATTTCAAGAACTAGAAATGGTTAAGCACATGACAATGTT
1 AATTCAAACAACAAGCACTCAAAACGAGTTCAAGAACTAGAAATGGTAAAGCACATGACAATGTT
29302510 CCCTACTCGT
66 CCCTACTCGT
29302520 TCCCAATTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 68 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (91 bp):
AATTCAAACAACAAGCACTCAAAACGAGTTCAAGAACTAGAAATGGTAAAGCACATGACAATGTT
CCCTACTCGTCCTTAATATTGTTTAG
Done.