Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013350.1 Corchorus olitorius cultivar O-4 contig13383, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 29101
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:58 original size:41 final size:41
Alignment explanation
Indices: 1--317 Score: 258
Period size: 40 Copynumber: 7.7 Consensus size: 41
*
1 TTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATTCCCAGT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTCCCAGT
* * *
42 TTGCCCTTCCTCATCGGAAGGTGTTG--TCAGCATTCCCCGT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTTA-AATTCCCAGT
* * *
82 TTGTCCTTCCTCATCGGAAGGTTTTG-TTTAAGTTCACCAGT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTC-CCAGT
* * * *
123 TTGTCCTTCCTCACCGGAAGGTGTTG-TTTAGATTTCCAGT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTCCCAGT
*
163 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATCCCATTCTTTCCAGT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTTAA----ATTC---CCAGT
* * * *
211 TTGCCCTTCCCCACCGGAAGGTGTTGATTT-CATTCCCA-T
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTCCCAGT
* * * *
250 TATGCCCTTCCCCACCGGAAGGTATTGATTTT--ATT-CCTGTT
1 T-TGCCCTTCCTCATCGGAAGGTGTTG-TTTTAAATTCCCAG-T
*
291 TTGCCCTTCC-CGGTCGGAAGGTGTTGT
1 TTGCCCTTCCTC-ATCGGAAGGTGTTGT
318 CTTCAATGAT
Statistics
Matches: 229, Mismatches: 31, Indels: 34
0.78 0.11 0.12
Matches are distributed among these distances:
39 8 0.03
40 114 0.50
41 69 0.30
43 4 0.02
45 3 0.01
48 31 0.14
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (41 bp):
TTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTCCCAGT
Found at i:141 original size:81 final size:80
Alignment explanation
Indices: 1--272 Score: 282
Period size: 81 Copynumber: 3.3 Consensus size: 80
* *
1 TTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
1 TTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
*
66 TG-TCAGCATTCCCCGT
65 TGTTCAG-ATTCCCAGT
* * * *
82 TTGTCCTTCCTCATCGGAAGGTTTTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGTGT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTC-CCAGTTTGCCCTTCCTCACCGGAAGGTGT
* *
147 TGTTTAGATTTCCAGT
65 TGTTCAGATTCCCAGT
*
163 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATCCCATTCTTTCCAGTTTGCCCTTCCCCACCGG
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTT-AA----ATTC---CCAGTTTGCCCTTCCTCACCGG
228 AAGGTGTTGATTTC--ATTCCCA-T
58 AAGGTGTTG--TTCAGATTCCCAGT
* *
250 TATGCCCTTCCCCACCGGAAGGT
1 T-TGCCCTTCCTCATCGGAAGGT
273 ATTGATTTTA
Statistics
Matches: 160, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
80 8 0.05
81 86 0.54
82 5 0.03
86 3 0.02
87 2 0.01
88 54 0.34
90 2 0.01
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (80 bp):
TTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTT
GTTCAGATTCCCAGT
Found at i:229 original size:48 final size:49
Alignment explanation
Indices: 155--250 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 49
145 GTTGTTTAGA
* *
155 TTTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATCCCATTC
1 TTTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTAAATCCCATTC
* *
203 TTTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCATT
1 TTTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTAAATCCCATT
251 ATGCCCTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 32 0.74
49 11 0.26
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.39
Consensus pattern (49 bp):
TTTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTAAATCCCATTC
Found at i:347 original size:48 final size:46
Alignment explanation
Indices: 279--767 Score: 582
Period size: 48 Copynumber: 10.2 Consensus size: 46
269 AGGTATTGAT
279 TTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGA
1 TTTATTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
* *
327 TTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGGTGTTTTCAATA
1 TTTATTC-CGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* * * *
374 TTTTATTCTAGTTTTGCCCTTCCCGGTCGAAAGGTGTTGTCTTACAGTGT
1 -TTTATTC-CGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTT-CAAT-A
*
424 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATT-CCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* * ** *
471 TTTTATTCTTGTTTTACCCTTCCCATTCGGAAGGTGTTGTCTTCAAAGA
1 -TTTATTC-CGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTC-AATA
*
520 TTTATTACCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATT-CCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* *
567 TTTTATTCCAGTTTTGCCCTTACCGGTCGGAAGGTGTTGTCTTCAATGT
1 -TTTATTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
* * * * *
616 TTTATACCCGTTTTGCGCTTCCCAGCCGGAAGGTGTTGTTTTCAATA
1 TTTAT-TCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
* *
663 TTTCATTCCTGTTTTGCCCTTCCCTGTCGGAAGGTGTTGTCTTCAATGT
1 TTT-ATTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-A
*
712 TTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA
1 TTTATT-CCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
759 TTTCATTCC
1 TTT-ATTCC
768 TGTCTTCAAT
Statistics
Matches: 379, Mismatches: 44, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
47 17 0.04
48 309 0.82
49 52 0.14
50 1 0.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (46 bp):
TTTATTCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATA
Found at i:566 original size:96 final size:96
Alignment explanation
Indices: 277--770 Score: 751
Period size: 96 Copynumber: 5.1 Consensus size: 96
267 GAAGGTATTG
*
277 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGATTTATT-CTCGTTTT
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTAC-CGTTTT
*
341 GCCCTTCCCGGTCGGAAGGTGGTGTTTTCAAT
65 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * *
373 ATTTTATT-CTAGTTTTGCCCTTCCCGGTCGAAAGGTGTTGTCTTACAGTGTTTTATTCCCGTTT
1 ATTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTT-CAATGTTTTATTACCGTTT
437 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
64 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * ** * *
470 ATTTTATTCTTGTTTTACCCTTCCCATTCGGAAGGTGTTGTCTTCAAAGATTTATTACCGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTACCGTTTTG
535 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* *
566 ATTTTATTCCAGTTTTGCCCTTACCGGTCGGAAGGTGTTGTCTTCAATGTTTTA-TACCCGTTTT
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTA-CCGTTTT
* * *
630 GCGCTTCCCAGCCGGAAGGTGTTGTTTTCAAT
65 GCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * *
662 ATTTCATTCCTGTTTTGCCCTTCCCTGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTG
1 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTACCGTTTTG
727 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
66 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
*
758 ATTTCATTCCTGT
1 ATTTTATTCCTGT
771 CTTCAATGTT
Statistics
Matches: 360, Mismatches: 32, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
95 4 0.01
96 269 0.75
97 85 0.24
98 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (96 bp):
ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTACCGTTTTG
CCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
Found at i:637 original size:144 final size:142
Alignment explanation
Indices: 277--978 Score: 706
Period size: 144 Copynumber: 4.7 Consensus size: 142
267 GAAGGTATTG
* *
277 ATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGATTTATTCTCGTTTTG
1 ATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTCGTTTTG
* * * * *
342 CCCTTCCCGGTCGGAAGGTGGTGTTTTCAATATTTTATTCTAGTTTTGCCCTTCCCGGTCGAAAG
66 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAA-AATTTATTC-CGTTTTGCCCTTCCCGGTCGGAAG
* *
407 GTGTTGTCTTACAGT
129 GTGTTGT-TTTCAAT
* * * * *
422 GTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCTTGTTTTA
1 ATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTCGTTTTG
* *
487 CCCTTCCCATTCGGAAGGTGTTGTCTTCAAAGATTTATTACCGTTTTGCCCTTCCCGGTCGGAAG
66 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAAA-ATTTATT-CCGTTTTGCCCTTCCCGGTCGGAAG
552 GTGTTGTTTTCAAT
129 GTGTTGTTTTCAAT
* * * *
566 ATTTTATTCCAGTTTTGCCCTTACCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCCGTTTTG
1 ATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTCGTTTTG
* * * *
631 CGCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCTGTCGGAAG
66 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAAAATTT-ATTCC-GTTTTGCCCTTCCCGGTCGGAAG
*
696 GTGTTGTCTTCAAT
129 GTGTTGTTTTCAAT
* * * *
710 GTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTCTTC
1 ATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAAT-GTT--TT-AT-TC-TC
* * * ** * * * *
775 AATGTTTTATTCTCGTTTTCCC-TTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCTAGTT
60 ---G-TTT-TGC-C--CTTCCCAGT--CGGAAGG-TGTTGTT---TTCAA-AATTTATTC-CGTT
*
839 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTTGAAT
109 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * *
873 ATTTTATTCCTGTTTTGCCATTCCCGGTTGGAAGGTGTTGTCTTCAATGTTTTATTC-CTGTTTT
1 ATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTC-GTTTT
* * *
937 GCCCTTCCCGGTCGGAAGGCGTTGTTTTCAATATTTCATTCC
65 GCCCTTCCCAGTCGGAAGGTGTTGTTTTCAAAATTT-ATTCC
979 TTTCTTCAAT
Statistics
Matches: 457, Mismatches: 72, Indels: 58
0.78 0.12 0.10
Matches are distributed among these distances:
143 9 0.02
144 179 0.39
145 121 0.26
146 1 0.00
147 7 0.02
148 6 0.01
149 6 0.01
150 2 0.00
151 1 0.00
152 2 0.00
153 4 0.01
154 5 0.01
155 2 0.00
156 1 0.00
158 7 0.02
159 6 0.01
160 7 0.02
162 2 0.00
163 86 0.19
164 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (142 bp):
ATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTCGTTTTG
CCCTTCCCAGTCGGAAGGTGTTGTTTTCAAAATTTATTCCGTTTTGCCCTTCCCGGTCGGAAGGT
GTTGTTTTCAAT
Found at i:818 original size:67 final size:68
Alignment explanation
Indices: 700--833 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 68
690 CGGAAGGTGT
700 TGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCAT
1 TGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCAT
765 TCC
66 TCC
* *
768 TGTCTTCAATGTTTTATTCTCGTTTT-CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCAT
832 TC
66 TC
834 TAGTTTTGCC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 39 0.61
68 25 0.39
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (68 bp):
TGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCAT
TCC
Found at i:824 original size:163 final size:164
Alignment explanation
Indices: 604--933 Score: 493
Period size: 163 Copynumber: 2.0 Consensus size: 164
594 CGGAAGGTGT
*
604 TGTCTTCAATGTTTTATACCCGTTTTGCGCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCAT
1 TGTCTTCAATGTTTTATACCCGTTTTGCCCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCAT
* * *
669 TCCT-GTTTTGCCCTTCCCTGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTTC
66 T-CTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGTTTTGCCATTC
*
733 CCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
130 CCGGTCGGAAGGTGTTGTCTTCAATATTTCATTCC
* * * * *
768 TGTCTTCAATGTTTTATTCTCGTTTT-CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTCTTCAATGTTTTATACCCGTTTTGCCCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCAT
* * *
832 TCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTGAATATTTTATTCCTGTTTTGCCATTCC
66 TCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGTTTTGCCATTCC
* * *
897 CGGTTGGAAGGTGTTGTCTTCAATGTTTTATTCC
131 CGGTCGGAAGGTGTTGTCTTCAATATTTCATTCC
931 TGT
1 TGT
934 TTTGCCCTTC
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
162 2 0.01
163 123 0.83
164 24 0.16
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (164 bp):
TGTCTTCAATGTTTTATACCCGTTTTGCCCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCAT
TCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGTTTTGCCATTCC
CGGTCGGAAGGTGTTGTCTTCAATATTTCATTCC
Found at i:882 original size:115 final size:116
Alignment explanation
Indices: 656--885 Score: 356
Period size: 115 Copynumber: 2.0 Consensus size: 116
646 AGGTGTTGTT
* * *
656 TTCAATATTTCATTCCTGTTTTGCCCTTCCCTGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCC
1 TTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCA
721 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
66 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
* * * *
772 TTCAATGTTTTATT-CTCGTTTT-CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCT
1 TTCAATATTTCATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCC
* *
835 AGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTGAATATTTTATTCCTGT
65 AGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGT
886 TTTGCCATTC
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
115 87 0.84
116 17 0.16
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (116 bp):
TTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCA
GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
Found at i:953 original size:211 final size:211
Alignment explanation
Indices: 560--1030 Score: 719
Period size: 211 Copynumber: 2.2 Consensus size: 211
550 AGGTGTTGTT
* * * * *
560 TTCAATATTTTATTCCAGTTTTGCCCTTACCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCC
1 TTCAATGTTTTATTCC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATACCA
* * *
625 GTTTTGCGCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCTGT
65 GTTTTGCCCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTTTTGCCATTCCCGGT
*
690 CGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
130 CGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTC
755 AATATTTCATTCCTGTC
195 AATATTTCATTCCTGTC
* *
772 TTCAATGTTTTATTCTCGTTTT-CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCTA
1 TTCAATGTTTTATTC-CGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATACCA
* * * *
836 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTGAATATTTTATTCCTGTTTTGCCATTCCCGGT
65 GTTTTGCCCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTTTTGCCATTCCCGGT
* *
901 TGGAAGGTGTTGTCTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTC
130 CGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTC
*
966 AATATTTCATTCCTTTC
195 AATATTTCATTCCTGTC
** *
983 TTCAATGTTTTATTCCCGTTTTGCCCTTCCCTATCGGAAGGAGTTGTT
1 TTCAATGTTTTATT-CCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
1031 CCTATTCTCT
Statistics
Matches: 235, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
211 192 0.82
212 42 0.18
213 1 0.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (211 bp):
TTCAATGTTTTATTCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATACCAG
TTTTGCCCTTCCCAGCCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTTTTGCCATTCCCGGTC
GGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGCGTTGTTTTCA
ATATTTCATTCCTGTC
Found at i:978 original size:48 final size:49
Alignment explanation
Indices: 772--979 Score: 300
Period size: 48 Copynumber: 4.3 Consensus size: 49
762 CATTCCTGTC
* *
772 TTCAATGTTTTATT-CTCGTTTT-CCCTTCCCGGTCGGAAGGTGTTGTT
1 TTCAATATTTTATTCCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
819 TTCAATATTTTATT-CTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
1 TTCAATATTTTATTCCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* * * *
867 TTGAATATTTTATTCCT-GTTTTGCCATTCCCGGTTGGAAGGTGTTGTC
1 TTCAATATTTTATTCCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* *
915 TTCAATGTTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGCGTTGTT
1 TTCAATATTTTATTCCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
*
963 TTCAATATTTCATTCCT
1 TTCAATATTTTATTCCT
980 TTCTTCAATG
Statistics
Matches: 145, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
47 20 0.14
48 123 0.85
49 2 0.01
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (49 bp):
TTCAATATTTTATTCCTAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
Found at i:1773 original size:30 final size:30
Alignment explanation
Indices: 1739--1842 Score: 199
Period size: 30 Copynumber: 3.5 Consensus size: 30
1729 TAAATACAAA
1739 TCAAGGGTCATTGTGGGTTATAATAGATTT
1 TCAAGGGTCATTGTGGGTTATAATAGATTT
1769 TCAAGGGTCATTGTGGGTTATAATAGATTT
1 TCAAGGGTCATTGTGGGTTATAATAGATTT
1799 TCAAGGGTCATTGTGGGTTATAATAGATTT
1 TCAAGGGTCATTGTGGGTTATAATAGATTT
*
1829 TCAAGGGTAATTGT
1 TCAAGGGTCATTGT
1843 TTTTAGAAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.39
Consensus pattern (30 bp):
TCAAGGGTCATTGTGGGTTATAATAGATTT
Found at i:4007 original size:21 final size:21
Alignment explanation
Indices: 3983--4053 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
3973 CTTAGGCAAT
*
3983 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4004 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4025 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
4046 TCCAATGA
1 TCCAATGA
4054 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:9072 original size:25 final size:24
Alignment explanation
Indices: 9035--9081 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
9025 TTAGAAAACT
9035 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
9061 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
9082 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:10017 original size:42 final size:42
Alignment explanation
Indices: 9928--10020 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
9918 TCTTAGGCAA
* *
9928 TTCCAATGAGCTTGAAACCTTCTCCAATGAGTTTGGAACCTT
1 TTCCAATGAGCTAGAAACCTTCTCCAATGAGCTTGGAACCTT
* *
9970 CTCCAATGAGCTAGGAACCTTCTCCAATGAGCTTGGAA-CTT
1 TTCCAATGAGCTAGAAACCTTCTCCAATGAGCTTGGAACCTT
10011 GTTCCAATGA
1 -TTCCAATGA
10021 TCTCCTAGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (42 bp):
TTCCAATGAGCTAGAAACCTTCTCCAATGAGCTTGGAACCTT
Found at i:10020 original size:21 final size:21
Alignment explanation
Indices: 9929--10008 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
9919 CTTAGGCAAT
*
9929 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
9950 TCCAATGAGTTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
9971 TCCAATGAGCTAGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
9992 TCCAATGAGCTTGGAAC
1 TCCAATGAGCTTGGAAC
10009 TTGTTCCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:13955 original size:33 final size:32
Alignment explanation
Indices: 13850--13959 Score: 104
Period size: 33 Copynumber: 3.5 Consensus size: 32
13840 CCATTTTTTA
*
13850 CTCTTTTTACTAATTACCATTTTTACTC-TCT
1 CTCTTTTTACTGATTACCATTTTTACTCTTCT
* * * *
13881 CTAATTAAATTACTGATCA-CATTTTT-CT-TACT
1 CT-CTT--TTTACTGATTACCATTTTTACTCTTCT
13913 CT-TTTTTACTGATTACCATTGTTTACTCTTCT
1 CTCTTTTTACTGATTACCATT-TTTACTCTTCT
13945 CTCTTTTTACTGATT
1 CTCTTTTTACTGATT
13960 TCATTGACTA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
28 9 0.15
29 4 0.06
30 5 0.08
31 4 0.06
32 13 0.21
33 19 0.31
34 8 0.13
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.54
Consensus pattern (32 bp):
CTCTTTTTACTGATTACCATTTTTACTCTTCT
Found at i:13972 original size:32 final size:33
Alignment explanation
Indices: 13906--13974 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
13896 ATCACATTTT
**
13906 TCTTACTCTTTTTTACTGATTACCATTGTTTAC
1 TCTTACTCTTTTTTACTGATTACCATTGACTAC
*
13939 TCTT-CTCTCTTTTTACTGATT-TCATTGACTAC
1 TCTTACTCT-TTTTTACTGATTACCATTGACTAC
13971 TCTT
1 TCTT
13975 TTTAACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.16, C:0.23, G:0.06, T:0.55
Consensus pattern (33 bp):
TCTTACTCTTTTTTACTGATTACCATTGACTAC
Found at i:14037 original size:26 final size:27
Alignment explanation
Indices: 13997--14059 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
13987 ATTGATTACC
* *
13997 CTTATTCTCTTTACTGA-TTACCATTTT
1 CTTACTCTTTTTACT-ATTTACCATTTT
14024 -TTACTCTTTTTACTATTTACCATTTT
1 CTTACTCTTTTTACTATTTACCATTTT
14050 CTTACTCTTT
1 CTTACTCTTT
14060 GAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.03
26 22 0.69
27 9 0.28
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.59
Consensus pattern (27 bp):
CTTACTCTTTTTACTATTTACCATTTT
Found at i:14066 original size:25 final size:26
Alignment explanation
Indices: 14014--14067 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
14004 TCTTTACTGA
* *
14014 TTACCATTTTTTACTCTTTTTACTAT
1 TTACCATTTTTTACTCTTTTGACAAT
14040 TTACCATTTTCTTACTC-TTTGA-AAT
1 TTACCATTTT-TTACTCTTTTGACAAT
14065 TTA
1 TTA
14068 AATACTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 14 0.56
27 6 0.24
ACGTcount: A:0.22, C:0.19, G:0.02, T:0.57
Consensus pattern (26 bp):
TTACCATTTTTTACTCTTTTGACAAT
Found at i:14094 original size:21 final size:21
Alignment explanation
Indices: 14070--14183 Score: 66
Period size: 21 Copynumber: 5.8 Consensus size: 21
14060 GAAATTTAAA
14070 TACTGATTACCATTACCATTT
1 TACTGATTACCATTACCATTT
* *
14091 TACTGATTACTCTTTACC-CTT
1 TACTGATTAC-CATTACCATTT
* * * *
14112 TACTAACTACTATGACCATTT
1 TACTGATTACCATTACCATTT
14133 TACT-A-T----TTACTC--TT
1 TACTGATTACCATTAC-CATTT
**
14147 TACTCTTTACCATTACCATTT
1 TACTGATTACCATTACCATTT
*
14168 TACTGATTACTATTAC
1 TACTGATTACCATTAC
14184 TCTTTCTTGA
Statistics
Matches: 69, Mismatches: 13, Indels: 22
0.66 0.12 0.21
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 2 0.03
19 2 0.03
20 9 0.13
21 41 0.59
22 6 0.09
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.46
Consensus pattern (21 bp):
TACTGATTACCATTACCATTT
Found at i:14148 original size:14 final size:14
Alignment explanation
Indices: 14131--14205 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
14121 CTATGACCAT
14131 TTTACTATTTACTC
1 TTTACTATTTACTC
*
14145 TTTACTCTTTAC-C
1 TTTACTATTTACTC
* * *
14158 ATTACCATTTTACTG
1 TTTACTA-TTTACTC
*
14173 ATTACTA-TTACTC
1 TTTACTATTTACTC
14186 TTT-CT-TGATTACTC
1 TTTACTAT--TTACTC
14200 TTTACT
1 TTTACT
14206 CTATACTGAC
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 12 0.26
14 25 0.53
15 8 0.17
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTACTATTTACTC
Found at i:14213 original size:41 final size:41
Alignment explanation
Indices: 14168--14253 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
14158 ATTACCATTT
*
14168 TACTGATTACTATTACTCTTTCTTGATTACTCTTTACTCTA
1 TACTGACTACTATTACTCTTTCTTGATTACTCTTTACTCTA
* * *
14209 TACTGACTATTATTATTCTTTCTTGATTACTCTTTACTCTT
1 TACTGACTACTATTACTCTTTCTTGATTACTCTTTACTCTA
14250 TACT
1 TACT
14254 TTTACCATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (41 bp):
TACTGACTACTATTACTCTTTCTTGATTACTCTTTACTCTA
Found at i:14408 original size:37 final size:36
Alignment explanation
Indices: 14289--14540 Score: 275
Period size: 37 Copynumber: 6.9 Consensus size: 36
14279 AAAAATGCTT
*
14289 TGGATGGGAACTTTCCCACTTTGAAAAC-T-AAAAC
1 TGGATGGGAACTTTCCCAATTTGAAAACTTAAAAAC
* *
14323 TGAAAATGACGGGAACTTTCCCTAAATTGAAAAC-T-AAAAC
1 TG-----GATGGGAACTTTCCC-AATTTGAAAACTTAAAAAC
* * *
14363 TTGATGGGAACTTTCCCAATTTAAAAACGTTGAAAAC
1 TGGATGGGAACTTTCCCAATTTGAAAAC-TTAAAAAC
14400 -GGAATGGGAACTTTCCCAATTTGAAAACTTAAAAAC
1 TGG-ATGGGAACTTTCCCAATTTGAAAACTTAAAAAC
*
14436 TGG-TGGGAACTTTCCCAATTTAAAAACTTTAAAAAC
1 TGGATGGGAACTTTCCCAATTTGAAAAC-TTAAAAAC
*
14472 TGAATGGGAACTTTCCCAATTTGAAAACTTAAAAAAC
1 TGGATGGGAACTTTCCCAATTTGAAAACTT-AAAAAC
* *
14509 TGG-TGGGGACTTTCCCAATTTGAAAATTTAAA
1 TGGATGGGAACTTTCCCAATTTGAAAACTTAAA
14541 CCTGATGGGA
Statistics
Matches: 188, Mismatches: 16, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
34 11 0.06
35 40 0.21
36 45 0.24
37 62 0.33
39 14 0.07
40 16 0.09
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (36 bp):
TGGATGGGAACTTTCCCAATTTGAAAACTTAAAAAC
Found at i:14539 original size:72 final size:72
Alignment explanation
Indices: 14333--14540 Score: 305
Period size: 72 Copynumber: 2.9 Consensus size: 72
14323 TGAAAATGAC
* * * *
14333 GGGAACTTTCCCTAAATTGAAAAC-T-AAAACTTGATGGGAACTTTCCCAATTTAAAAACGTTGA
1 GGGAACTTTCCC-AATTTGAAAACTTAAAAAC-TGGTGGGAACTTTCCCAATTTAAAAACTTTAA
14396 AAACGGAAT
64 AAACGGAAT
14405 GGGAACTTTCCCAATTTGAAAACTTAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTAAAA
1 GGGAACTTTCCCAATTTGAAAACTTAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTAAAA
*
14470 ACTGAAT
66 ACGGAAT
* *
14477 GGGAACTTTCCCAATTTGAAAACTTAAAAAACTGGTGGGGACTTTCCCAATTTGAAAA-TTTAAA
1 GGGAACTTTCCCAATTTGAAAACTT-AAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTAAA
14541 CCTGATGGGA
Statistics
Matches: 126, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
71 10 0.08
72 81 0.64
73 35 0.28
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (72 bp):
GGGAACTTTCCCAATTTGAAAACTTAAAAACTGGTGGGAACTTTCCCAATTTAAAAACTTTAAAA
ACGGAAT
Found at i:16295 original size:17 final size:18
Alignment explanation
Indices: 16268--16302 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
16258 CAAGGGTAAA
16268 TTTTCTTTTTTCTTTTTG
1 TTTTCTTTTTTCTTTTTG
16286 TTTT-TTTTTTCTTTTTG
1 TTTTCTTTTTTCTTTTTG
16303 ATTTACTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.86
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTTTG
Found at i:20953 original size:33 final size:33
Alignment explanation
Indices: 20866--21198 Score: 228
Period size: 31 Copynumber: 10.4 Consensus size: 33
20856 GTTGATTTTA
* * *
20866 AAAACTAAGAAAGACCTGTCTGAGGTCCAAAACT
1 AAAACTGAGAAAGACCTGTCTGAGGT-CGAAATT
* * *
20900 AAAA--GATAAAGACCTATCTGAGGTCGAATTT
1 AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
*
20931 AAAACTGAGGAAGACCTGTCTGAGGTCGAAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
* * * * *
20964 AAAACTGAGAAAGACATGTTTGAGCTCTGGAACTG
1 AAAACTGAGAAAGACCTGTCTGAGGTC--GAAATT
*
20999 AAAA---ATAAAGACCTGTCTGAGGTCGAAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
*
21029 AAAACTGAGAAAGACCTGTCTGAGGTTGAAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
* * * *
21062 AAAA--GATAAAGACTTGTCTGAGGTCTAAAACT
1 AAAACTGAGAAAGACCTGTCTGAGGTC-GAAATT
* * * * *
21094 GAAA--GATAGAGACCTGTCCGAGGTCGAATTT
1 AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
* * * * *
21125 GAAA--GATAGAGACCTGTCCGAGGTCGAATTT
1 AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
* * * *
21156 AAAA--G-GTAAAGACATGTTTGAAGTCGAAAAT
1 AAAACTGAG-AAAGACCTGTCTGAGGTCGAAATT
21187 -AAACTGAGAAAG
1 AAAACTGAGAAAG
21199 GATGACCTGT
Statistics
Matches: 242, Mismatches: 45, Indels: 26
0.77 0.14 0.08
Matches are distributed among these distances:
30 11 0.05
31 81 0.33
32 63 0.26
33 75 0.31
34 4 0.02
35 8 0.03
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (33 bp):
AAAACTGAGAAAGACCTGTCTGAGGTCGAAATT
Found at i:20953 original size:65 final size:65
Alignment explanation
Indices: 20805--21149 Score: 223
Period size: 65 Copynumber: 5.4 Consensus size: 65
20795 GTCAACTCTA
* ** * * * * *
20805 AAAACTAAGAAAGACCTGTCTGAGGTCTGAACT--GA--AG-AAGACCAGTCTGTGGTTGATTTT
1 AAAACTGAGAAAGACCTGTCTGAGGTCAAAACTAAAACGAGAAAGACCTGTCTGAGGTCGAATTT
* * *
20865 AAAAACTAAGAAAGACCTGTCTGAGGTCCAAAACTAAAA-GATAAAGACCTATCTGAGGTCGAAT
1 -AAAACTGAGAAAGACCTGTCTGAGGT-CAAAACTAAAACGAGAAAGACCTGTCTGAGGTCGAAT
20929 TT
64 TT
* * * * * *
20931 AAAACTGAGGAAGACCTGTCTGAGGTCGAAATTAAAACTGAGAAAGACATGTTTGAGCTCTGGAA
1 AAAACTGAGAAAGACCTGTCTGAGGTCAAAACTAAAAC-GAGAAAGACCTGTCTGAGGTC--GAA
* *
20996 CTG
63 TTT
* * * * *
20999 AAAA---ATAAAGACCTGTCTGAGGTCGAAATTAAAACTGAGAAAGACCTGTCTGAGGTTGAAAT
1 AAAACTGAGAAAGACCTGTCTGAGGTCAAAACTAAAAC-GAGAAAGACCTGTCTGAGGTCGAATT
21061 T
65 T
* * * * * *
21062 AAAA--GATAAAGACTTGTCTGAGGTCTAAAACTGAAA-GATAGAGACCTGTCCGAGGTCGAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTC-AAAACTAAAACGAGAAAGACCTGTCTGAGGTCGAATT
21124 T
65 T
* * * *
21125 GAAA--GATAGAGACCTGTCCGAGGTC
1 AAAACTGAGAAAGACCTGTCTGAGGTC
21150 GAATTTAAAA
Statistics
Matches: 232, Mismatches: 41, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
61 26 0.11
62 5 0.02
63 51 0.22
64 29 0.12
65 79 0.34
66 34 0.15
68 8 0.03
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (65 bp):
AAAACTGAGAAAGACCTGTCTGAGGTCAAAACTAAAACGAGAAAGACCTGTCTGAGGTCGAATTT
Found at i:21012 original size:98 final size:96
Alignment explanation
Indices: 20873--21176 Score: 341
Period size: 98 Copynumber: 3.2 Consensus size: 96
20863 TTAAAAACTA
* * * * *
20873 AGAAAGACCTGTCTGAGGTCCAAAACT-AAAAGATAAAGACCTATCTGAGGTCGAATTTAAAACT
1 AGAAAGACATGTTTGAGCTCTAAAACTGAAAA-ATAAAGACCTGTCTGAGGTCGAATTTAAAACT
20937 GAGGAAGACCTGTCTGAGGTCGAAATTAAAACTG
65 GAGGAAGACCTGTCTGAGGTCGAAATTAAAA--G
** *
20971 AGAAAGACATGTTTGAGCTCTGGAACTGAAAAATAAAGACCTGTCTGAGGTCGAAATTAAAACTG
1 AGAAAGACATGTTTGAGCTCTAAAACTGAAAAATAAAGACCTGTCTGAGGTCGAATTTAAAACTG
* *
21036 AGAAAGACCTGTCTGAGGTTGAAATTAAAAG
66 AGGAAGACCTGTCTGAGGTCGAAATTAAAAG
* * * * * * *
21067 ATAAAGACTTGTCTGAGGTCTAAAACTGAAAGATAGAGACCTGTCCGAGGTCGAATTTGAAAGA-
1 AGAAAGACATGTTTGAGCTCTAAAACTGAAAAATAAAGACCTGTCTGAGGTCGAATTT-AAA-AC
* *
21131 T-A-G-AGACCTGTCCGAGGTCGAATTTAAAAG
64 TGAGGAAGACCTGTCTGAGGTCGAAATTAAAAG
21161 -GTAAAGACATGTTTGA
1 AG-AAAGACATGTTTGA
21177 AGTCGAAAAT
Statistics
Matches: 175, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
94 36 0.21
96 50 0.29
97 4 0.02
98 81 0.46
99 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (96 bp):
AGAAAGACATGTTTGAGCTCTAAAACTGAAAAATAAAGACCTGTCTGAGGTCGAATTTAAAACTG
AGGAAGACCTGTCTGAGGTCGAAATTAAAAG
Found at i:21245 original size:39 final size:39
Alignment explanation
Indices: 21194--21556 Score: 550
Period size: 39 Copynumber: 9.3 Consensus size: 39
21184 AATAAACTGA
* * * * *
21194 GAAAGGATGACCTGTTTCCAGTCAACCTTGGTAACTACT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * *
21233 GAAAAGACGACCTATTTCCAGTCAACTTTGATAACTGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
21272 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
21311 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* *
21350 GAAAAGATGACCTGTTTCTAGTCAATTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* *
21389 GAAAAGATGACCTTTTTCCAGTCAACTTTGATAAATGTT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
21428 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGC-T
* *
21468 G-AAAGATGACCTGTTTCTAGTCAACTTTGATAATTGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * *
21506 GAAAAGATGACCTGTTTCCAGTCAACTTTGATGACTACT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
21545 G-AAAGATGACCT
1 GAAAAGATGACCT
21557 AAAGCATTGA
Statistics
Matches: 299, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
38 13 0.04
39 284 0.95
40 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (39 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
Found at i:21583 original size:16 final size:16
Alignment explanation
Indices: 21562--21594 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21552 GACCTAAAGC
*
21562 ATTGAAGGATTGAAGA
1 ATTGAAGCATTGAAGA
21578 ATTGAAGCATTGAAGA
1 ATTGAAGCATTGAAGA
21594 A
1 A
21595 AAACCACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.27, T:0.24
Consensus pattern (16 bp):
ATTGAAGCATTGAAGA
Found at i:21685 original size:22 final size:22
Alignment explanation
Indices: 21618--21904 Score: 103
Period size: 22 Copynumber: 13.2 Consensus size: 22
21608 TCGTTGAAGT
* *
21618 AAATTGATGCATTGAAGAATTG
1 AAATTGAAGAATTGAAGAATTG
* *
21640 ACAATTTAAGAATTTGAAGTATTG
1 A-AATTGAAGAA-TTGAAGAATTG
*
21664 AAATTGAA-ACATTGAAGGATTG
1 AAATTGAAGA-ATTGAAGAATTG
*
21686 AATTTGAAGAATTG-A-AATTG
1 AAATTGAAGAATTGAAGAATTG
*
21706 AACCATTGAA-ATATT-CA-AATTG
1 AA--ATTGAAGA-ATTGAAGAATTG
21728 AACCATTGAAGAATT---GAATTG
1 AA--ATTGAAGAATTGAAGAATTG
* *
21749 AAATTGAAGCATTCAA-ATATTG
1 AAATTGAAGAATTGAAGA-ATTG
* *
21771 TAATTGAAGAATTGGAA-TATTG
1 AAATTGAAGAATT-GAAGAATTG
* *
21793 AATTTGAAGAGTTG-A-AATTG
1 AAATTGAAGAATTGAAGAATTG
* *
21813 AAACGTTGAAGGATT-AA-ATTTG
1 AAA--TTGAAGAATTGAAGAATTG
*
21835 AAGAATTG-A-AATTGAAGCATTG
1 -A-AATTGAAGAATTGAAGAATTG
*
21857 AAATATTG-A-AATTGAAGCATTG
1 -AA-ATTGAAGAATTGAAGAATTG
*
21879 AAATATTG-A-AATTGAAGCATTG
1 -AA-ATTGAAGAATTGAAGAATTG
21901 AAAT
1 AAAT
21905 ATTGAAATTG
Statistics
Matches: 217, Mismatches: 25, Indels: 48
0.75 0.09 0.17
Matches are distributed among these distances:
19 10 0.05
20 18 0.08
21 17 0.08
22 140 0.65
23 19 0.09
24 13 0.06
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (22 bp):
AAATTGAAGAATTGAAGAATTG
Found at i:21692 original size:14 final size:14
Alignment explanation
Indices: 21628--21985 Score: 135
Period size: 14 Copynumber: 24.6 Consensus size: 14
21618 AAATTGATGC
21628 ATTGAAGAATTGACA
1 ATTGAAGAATTGA-A
*
21643 ATTTAAGAATTTGAA
1 ATTGAAGAA-TTGAA
21658 GTATTG-A-AATTGAAA
1 --ATTGAAGAATTG-AA
*
21673 CATTGAAGGATTGAA
1 -ATTGAAGAATTGAA
*
21688 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
**
21702 ATTGAACCATTGAA
1 ATTGAAGAATTGAA
**
21716 ATATTCA-AATTGAA
1 AT-TGAAGAATTGAA
21730 CCATTGAAGAATTG-A
1 --ATTGAAGAATTGAA
21745 ATTG-A-AATTGAA
1 ATTGAAGAATTGAA
* *
21757 GCATTCAA-ATATTGTA
1 --ATTGAAGA-ATTGAA
21773 ATTGAAGAATTGGAA
1 ATTGAAGAATT-GAA
*
21788 TATTG-A-ATTTGAA
1 -ATTGAAGAATTGAA
21801 GAGTTG-A-AATTGAA
1 -A-TTGAAGAATTGAA
*
21815 ACGTTGAAGGATT-AA
1 A--TTGAAGAATTGAA
21830 ATTTGAAGAATTGAA
1 A-TTGAAGAATTGAA
*
21845 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
21860 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
21873 GCATTGAA-ATATTGAA
1 --ATTGAAGA-ATTGAA
*
21889 ATTGAAGCATTGAAA
1 ATTGAAGAATTG-AA
21904 TATTG-A-AATTGAA
1 -ATTGAAGAATTGAA
*
21917 GCATTGAATAATTGAA
1 --ATTGAAGAATTGAA
*
21933 GTTGAA-ACATTGACA
1 ATTGAAGA-ATTGA-A
21948 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
*
21962 CATTGAAGGATTGAA
1 -ATTGAAGAATTGAA
21977 ATTGAAGAA
1 ATTGAAGAA
21986 AGACCACACT
Statistics
Matches: 268, Mismatches: 35, Indels: 81
0.70 0.09 0.21
Matches are distributed among these distances:
11 5 0.02
12 2 0.01
13 14 0.05
14 138 0.51
15 50 0.19
16 56 0.21
17 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:21700 original size:36 final size:36
Alignment explanation
Indices: 21653--21985 Score: 205
Period size: 36 Copynumber: 9.2 Consensus size: 36
21643 ATTTAAGAAT
* *
21653 TTGAAGTATTGAAATTGAAACATTGAAGGATTGAAT
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAA
* ** *
21689 TTGAAGAATTGAAATTGAACCATTGAAATATTCAAA
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAA
**
21725 TTGAACCATTGAAGAATTG--A-ATTGAA--ATTGAAGCA
1 TTGAAGAATTG-A-AATTGAAACATTGAAGGATTGAA--A
* * * *
21760 TTCAA-ATATTGTAATTGAAGA-ATTGGAA-TATTGAAT
1 TTGAAGA-ATTGAAATTGAA-ACATT-GAAGGATTGAAA
* *
21796 TTGAAGAGTTGAAATTGAAACGTTGAAGGATT-AAA
1 TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAA
* **
21831 TTTGAAGAATTGAAATTGAAGCATTGAAATATTGAAA
1 -TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAA
* *
21868 TTGAAGCATTGAAATATTG-AA-ATTGAAGCATTGAAATA
1 TTGAAGAATTG-AA-ATTGAAACATTGAAGGATTG-AA-A
21906 TTG-A-AATTGAAGCATTGAATA-ATTGAA-G-TTGAAACA
1 TTGAAGAATTGAA--ATTGAA-ACATTGAAGGATTG-AA-A
*
21942 TTGACA-TATTGAAATTGAAACATTGAAGGATTGAAA
1 TTGA-AGAATTGAAATTGAAACATTGAAGGATTGAAA
21978 TTGAAGAA
1 TTGAAGAA
21986 AGACCACACT
Statistics
Matches: 234, Mismatches: 35, Indels: 56
0.72 0.11 0.17
Matches are distributed among these distances:
33 10 0.04
35 25 0.11
36 145 0.62
37 18 0.08
38 36 0.15
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAACATTGAAGGATTGAAA
Found at i:21905 original size:22 final size:22
Alignment explanation
Indices: 21839--21983 Score: 220
Period size: 22 Copynumber: 6.6 Consensus size: 22
21829 AATTTGAAGA
21839 ATTGAAATTGAAGCATTGAAAT
1 ATTGAAATTGAAGCATTGAAAT
21861 ATTGAAATTGAAGCATTGAAAT
1 ATTGAAATTGAAGCATTGAAAT
21883 ATTGAAATTGAAGCATTGAAAT
1 ATTGAAATTGAAGCATTGAAAT
21905 ATTGAAATTGAAGCATTG-AAT
1 ATTGAAATTGAAGCATTGAAAT
* * *
21926 AATTGAAGTTGAAACATTGACAT
1 -ATTGAAATTGAAGCATTGAAAT
* **
21949 ATTGAAATTGAAACATTGAAGG
1 ATTGAAATTGAAGCATTGAAAT
21971 ATTGAAATTGAAG
1 ATTGAAATTGAAG
21984 AAAGACCACA
Statistics
Matches: 113, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.03
22 108 0.96
23 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (22 bp):
ATTGAAATTGAAGCATTGAAAT
Found at i:21945 original size:8 final size:7
Alignment explanation
Indices: 21628--21982 Score: 89
Period size: 8 Copynumber: 48.9 Consensus size: 7
21618 AAATTGATGC
21628 ATTGAAGA
1 ATTGAA-A
*
21636 ATTGACA
1 ATTGAAA
*
21643 ATTTAAGA
1 ATTGAA-A
*
21651 ATTTGAAGT
1 A-TTGAA-A
21660 ATTG-AA
1 ATTGAAA
21666 ATTGAAA
1 ATTGAAA
*
21673 CATTGAAGG
1 -ATTGAA-A
21682 ATTG-AA
1 ATTGAAA
*
21688 TTTGAAGA
1 ATTGAA-A
21696 ATTG-AA
1 ATTGAAA
*
21702 ATTGAACC
1 ATTGAA-A
21710 ATTGAAA
1 ATTGAAA
*
21717 TATT-CAA
1 -ATTGAAA
*
21724 ATTGAACC
1 ATTGAA-A
21732 ATTGAAGA
1 ATTGAA-A
21740 ATTG--A
1 ATTGAAA
21745 ATTG-AA
1 ATTGAAA
*
21751 ATTGAAGC
1 ATTGAA-A
*
21759 ATTCAAA
1 ATTGAAA
*
21766 TATTG-TA
1 -ATTGAAA
21773 ATTGAAGA
1 ATTGAA-A
*
21781 ATTGGAAT
1 ATT-GAAA
21789 ATTG-AA
1 ATTGAAA
*
21795 TTTGAAGA
1 ATTGAA-A
*
21803 GTTG-AA
1 ATTGAAA
21809 ATTGAAA
1 ATTGAAA
* *
21816 CGTTGAAGG
1 -ATTGAA-A
21825 ATT-AAA
1 ATTGAAA
*
21831 TTTGAAGA
1 ATTGAA-A
21839 ATTG-AA
1 ATTGAAA
*
21845 ATTGAAGC
1 ATTGAA-A
21853 ATTGAAA
1 ATTGAAA
21860 TATTG-AA
1 -ATTGAAA
*
21867 ATTGAAGC
1 ATTGAA-A
21875 ATTGAAA
1 ATTGAAA
21882 TATTG-AA
1 -ATTGAAA
*
21889 ATTGAAGC
1 ATTGAA-A
21897 ATTGAAA
1 ATTGAAA
21904 TATTG-AA
1 -ATTGAAA
*
21911 ATTGAAGC
1 ATTGAA-A
21919 ATTGAATA
1 ATTGAA-A
21927 ATTG-AA
1 ATTGAAA
*
21933 GTTGAAA
1 ATTGAAA
*
21940 CATTGACAT
1 -ATTGA-AA
21949 ATTG-AA
1 ATTGAAA
21955 ATTGAAA
1 ATTGAAA
*
21962 CATTGAAGG
1 -ATTGAA-A
21971 ATTG-AA
1 ATTGAAA
21977 ATTGAA
1 ATTGAA
21983 GAAAGACCAC
Statistics
Matches: 254, Mismatches: 49, Indels: 89
0.65 0.12 0.23
Matches are distributed among these distances:
5 5 0.02
6 64 0.25
7 44 0.17
8 131 0.52
9 10 0.04
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (7 bp):
ATTGAAA
Found at i:22022 original size:56 final size:56
Alignment explanation
Indices: 21953--22368 Score: 546
Period size: 56 Copynumber: 7.6 Consensus size: 56
21943 TGACATATTG
** * *
21953 AAATTGAAACATTGAAGGATTGAAATTGAAGAAAGACCACACTGAATCGTTGAAGT
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
* * *
22009 AAATTGATGCATTGAATATTTGAAATTGAAGAAAGACCACACTGGATTGTTGAAGT
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
** *
22065 AAATTGATGTTTTGAAGAATTGAAATTGAAGAAAGACCACACTGGATTGTTGAAGT
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
22121 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
* *
22177 AAATTGATGCATTGAATAATTGAAATCGAAGAAAGACCACACTGGATCGTTGAAGT
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
* **
22233 AAATTGATGTATTGAAGAATTGAAATTGAAGAAAGACCACGTTGGATC------G-
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
* * * *
22282 ---TTGATGCATTGAAGAATTTAAATTAAAGAAAAACCACACTGGATCGTGGAAGT
1 AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
** * *
22335 AAACCGATGCATTGTATAATTGAAAATTGAAGAA
1 AAATTGATGCATTGAAGAATTG-AAATTGAAGAA
22369 TTTGAAGTAT
Statistics
Matches: 316, Mismatches: 33, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
46 39 0.12
50 1 0.00
52 1 0.00
56 265 0.84
57 10 0.03
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (56 bp):
AAATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTGAAGT
Found at i:22293 original size:46 final size:46
Alignment explanation
Indices: 22236--22328 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
22226 TTGAAGTAAA
* * * **
22236 TTGATGTATTGAAGAATTGAAATTGAAGAAAGACCACGTTGGATCG
1 TTGATGCATTGAAGAATTGAAATTAAAGAAAAACCACACTGGATCG
*
22282 TTGATGCATTGAAGAATTTAAATTAAAGAAAAACCACACTGGATCG
1 TTGATGCATTGAAGAATTGAAATTAAAGAAAAACCACACTGGATCG
22328 T
1 T
22329 GGAAGTAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (46 bp):
TTGATGCATTGAAGAATTGAAATTAAAGAAAAACCACACTGGATCG
Found at i:22402 original size:22 final size:22
Alignment explanation
Indices: 22353--22463 Score: 132
Period size: 22 Copynumber: 5.0 Consensus size: 22
22343 GCATTGTATA
*
22353 ATTGAAAATTGAAGAATTTGAAGT
1 ATTG-AAATTGAAGAA-TTGAAGG
*
22377 ATTGAAATTGAAGTATTGAAGG
1 ATTGAAATTGAAGAATTGAAGG
* *
22399 ATTGAATTTGAAGAATTGAAGT
1 ATTGAAATTGAAGAATTGAAGG
** *
22421 ATCAAAATTGAAGCATTGAAGG
1 ATTGAAATTGAAGAATTGAAGG
*
22443 ATTGAATTTGAAGAATTGAAG
1 ATTGAAATTGAAGAATTGAAG
22464 AAAGATGATC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
22 59 0.81
23 10 0.14
24 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (22 bp):
ATTGAAATTGAAGAATTGAAGG
Found at i:22429 original size:44 final size:44
Alignment explanation
Indices: 22361--22463 Score: 170
Period size: 44 Copynumber: 2.3 Consensus size: 44
22351 TAATTGAAAA
** *
22361 TTGAAGAATTTGAAGTATTGAAATTGAAGTATTGAAGGATTGAAT
1 TTGAAGAA-TTGAAGTATCAAAATTGAAGCATTGAAGGATTGAAT
22406 TTGAAGAATTGAAGTATCAAAATTGAAGCATTGAAGGATTGAAT
1 TTGAAGAATTGAAGTATCAAAATTGAAGCATTGAAGGATTGAAT
22450 TTGAAGAATTGAAG
1 TTGAAGAATTGAAG
22464 AAAGATGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 47 0.85
45 8 0.15
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.32
Consensus pattern (44 bp):
TTGAAGAATTGAAGTATCAAAATTGAAGCATTGAAGGATTGAAT
Found at i:22455 original size:14 final size:15
Alignment explanation
Indices: 22361--22463 Score: 90
Period size: 14 Copynumber: 6.9 Consensus size: 15
22351 TAATTGAAAA
22361 TTGAAGAATTTGAAGT
1 TTGAAGAA-TTGAAGT
22377 ATTG-A-AATTGAAGT
1 -TTGAAGAATTGAAGT
*
22391 ATTGAAGGATTGAA-T
1 -TTGAAGAATTGAAGT
22406 TTGAAGAATTGAAGT
1 TTGAAGAATTGAAGT
* * *
22421 ATCAA-AATTGAAGCA
1 TTGAAGAATTGAAG-T
*
22436 TTGAAGGATTGAA-T
1 TTGAAGAATTGAAGT
22450 TTGAAGAATTGAAG
1 TTGAAGAATTGAAG
22464 AAAGATGATC
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 43 0.61
15 11 0.16
16 13 0.19
17 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.32
Consensus pattern (15 bp):
TTGAAGAATTGAAGT
Done.