Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004878.1 Hibiscus syriacus cultivar Beakdansim tig00010992_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 161712
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:10037 original size:15 final size:16
Alignment explanation
Indices: 10017--10058 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
10007 AATTAAACAT
10017 AGTATAATAAATT-CA
1 AGTATAATAAATTGCA
*
10032 AGTATATTAAATTGCA
1 AGTATAATAAATTGCA
10048 AG-ATAGATAAA
1 AGTATA-ATAAA
10059 AATACATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (16 bp):
AGTATAATAAATTGCA
Found at i:15768 original size:14 final size:13
Alignment explanation
Indices: 15734--15886 Score: 71
Period size: 14 Copynumber: 10.9 Consensus size: 13
15724 AACCATAAAT
15734 TATATTATATTT-A
1 TATA-TATATTTAA
15747 TATATATATTTAA
1 TATATATATTTAA
*
15760 TACTATATATTTAT
1 TA-TATATATTTAA
* *
15774 TTTCAAACTATGTTATA
1 TAT-ATA-TAT-TTA-A
15791 TATATATATATTCCAA
1 TATATATAT-TT--AA
15807 GCTATATAT-TTTAA
1 --TATATATATTTAA
* *
15821 AATTATATATATATA
1 TA-TATATATTTA-A
*
15836 TATATATATATATA
1 TATATATATTTA-A
*
15850 TATATATATATATA
1 TATATATATTTA-A
*
15864 TATATATATCTAA
1 TATATATATTTAA
15877 -AT-TATATTTA
1 TATATATATTTA
15887 TTTTCAAAAC
Statistics
Matches: 115, Mismatches: 12, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
11 7 0.06
12 10 0.09
13 14 0.12
14 55 0.48
15 10 0.09
16 8 0.07
17 4 0.03
18 7 0.06
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (13 bp):
TATATATATTTAA
Found at i:15829 original size:2 final size:2
Alignment explanation
Indices: 15824--15921 Score: 112
Period size: 2 Copynumber: 49.5 Consensus size: 2
15814 ATTTTAAAAT
15824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
15866 TA TA TA TC TA AA T- TA TA TT TA T- TT TCA -A AA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA
15907 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
15922 TTCAAAACTA
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
1 3 0.04
2 79 0.95
3 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15939 original size:51 final size:51
Alignment explanation
Indices: 15846--15960 Score: 185
Period size: 51 Copynumber: 2.2 Consensus size: 51
15836 TATATATATA
* * *
15846 TATATATATATATATATATATATATATCTAAATTATATTTATTTTCAAAAC
1 TATATATATATATATATATATATATATCAAAACTATACTTATTTTCAAAAC
*
15897 TATATATATATATATATATATATATTTCAAAACTATACTTATTTTCAAAAC
1 TATATATATATATATATATATATATATCAAAACTATACTTATTTTCAAAAC
15948 TATACTATATATA
1 TATA-TATATATA
15961 ACCAAAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 51 0.86
52 8 0.14
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (51 bp):
TATATATATATATATATATATATATATCAAAACTATACTTATTTTCAAAAC
Found at i:15981 original size:15 final size:15
Alignment explanation
Indices: 15964--15997 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
15954 ATATATAACC
15964 AAAATATAACAAAACA
1 AAAATA-AACAAAACA
*
15980 AAAATAAACTAAACA
1 AAAATAAACAAAACA
15995 AAA
1 AAA
15998 GGAAACTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAATAAACAAAACA
Found at i:16498 original size:182 final size:181
Alignment explanation
Indices: 16212--16622 Score: 601
Period size: 182 Copynumber: 2.3 Consensus size: 181
16202 TTCACTTCAA
* *
16212 TGCTCTTCTGGGAAGATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAAGATCAAATCTG
1 TGCTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAAGATCAAATATG
** * *
16277 GAAAATGATGATCTTCTCTGCTACTCTTTAGGAGAGATCATATCTAAGGGAAGAC-GGATCTGCT
66 GAAAATGACAATCTGCTCTGCTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACTGG-TCTGCT
* * * *
16341 CCACTATTCTTTAGGGGAGATCATATTCGATAAAAAATTTTGATCCACTTTGC
130 CCACTACTCTTTAGGGGAGATCAGACTCGA-AAAAAATTTTGACCCACTTTGC
* * *
16394 TGCTCTTCAGGGAAAATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAATATTAAATATG
1 TGCTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAAGATCAAATATG
*
16459 GAAAATGACAATCTGCTTTGCTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACTGGTCTGCTC
66 GAAAATGACAATCTGCTCTGCTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACTGGTCTGCTC
* * *
16524 CACTACTCTTTAGGGGATATCAGACTCGAGAAAAATTTTGACCCACTTTGT
131 CACTACTCTTTAGGGGAGATCAGACTCGAAAAAAATTTTGACCCACTTTGC
* * *
16575 TGATCTTCAGGGAAGATTGAATCGAA-CTTGATTTGCTTCACTGCTCTT
1 TGCTCTTCAGGGAAGATTGAATC-AAGATTGATTTGCTTCACTACTCTT
16623 TATGAATACC
Statistics
Matches: 206, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 60 0.29
182 144 0.70
183 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (181 bp):
TGCTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAAGATCAAATATG
GAAAATGACAATCTGCTCTGCTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACTGGTCTGCTC
CACTACTCTTTAGGGGAGATCAGACTCGAAAAAAATTTTGACCCACTTTGC
Found at i:16668 original size:182 final size:182
Alignment explanation
Indices: 16215--16682 Score: 541
Period size: 182 Copynumber: 2.6 Consensus size: 182
16205 ACTTCAATGC
* * * * *
16215 TCTTCTGGGAAGATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAAGATCAAATCTGGAA
1 TCTTCAGGGAAAATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAATACCAAATATGGAA
* ** * ** *
16280 AATGATGATCTTCTCTGCTACTCTTTAGGAGAGATCATATCTAAGGGAAGACGGATCTGCTCCAC
66 AATAACAATCTGCTCCACTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACGGATCTGCTCCAC
* * * * *
16345 TATTCTTTAGGGGAGATCATATTCGATAAAAAATTTTGATCCACTTTGCTGC
131 TACTCTTTAGGGGAGATCAGACTCGATAAAAAATTTTGACCCACTTTGCTGA
**
16397 TCTTCAGGGAAAATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAATATTAAATATGGAA
1 TCTTCAGGGAAAATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAATACCAAATATGGAA
* ***
16462 AATGACAATCTGCTTTGCTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACTGG-TCTGCTCCA
66 AATAACAATCTGCTCCACTACTCTTTAGGAGAGATCAGATCTAAGGGAAGAC-GGATCTGCTCCA
* * *
16526 CTACTCTTTAGGGGATATCAGACTCGA-GAAAAATTTTGACCCACTTTGTTGA
130 CTACTCTTTAGGGGAGATCAGACTCGATAAAAAATTTTGACCCACTTTGCTGA
* * * * * *
16578 TCTTCAGGGAAGATTGAATCGAA-CTTGATTTGCTTCACTGCTCTTTATGAATACCAAATTTGAA
1 TCTTCAGGGAAAATTGAATC-AAGATTGATTTGCTTCACTACTCTTCAGGAATACCAAATATG--
* * *
16642 AGAAAA-AAC-GTCTGCTCCATTACTCTTTAGGGGAGATCAGA
63 -GAAAATAACAATCTGCTCCACTACTCTTTAGGAGAGATCAGA
16683 CTTGAGATAC
Statistics
Matches: 248, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
181 72 0.29
182 167 0.67
183 4 0.02
184 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (182 bp):
TCTTCAGGGAAAATTGAATCAAGATTGATTTGCTTCACTACTCTTCAGGAATACCAAATATGGAA
AATAACAATCTGCTCCACTACTCTTTAGGAGAGATCAGATCTAAGGGAAGACGGATCTGCTCCAC
TACTCTTTAGGGGAGATCAGACTCGATAAAAAATTTTGACCCACTTTGCTGA
Found at i:16770 original size:134 final size:135
Alignment explanation
Indices: 16516--16776 Score: 321
Period size: 134 Copynumber: 1.9 Consensus size: 135
16506 GGGAAGACTG
* * *
16516 GTCTGCTCCACTACTCTTTAGGGGATATCAGACTCGAGAAAAATTTTGACCCACTTTGTTGATCT
1 GTCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGACCCACTTCGCTGATCT
* * * * *
16581 TCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTTATGAATACCAAATTTGAAAGAA
66 TCAAGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAA
16646 AAAAC
131 AAAAC
* * * * ** *
16651 GTCTGCTCCATTACTCTTTAGGGGAGATCAGACTTGAG-ATACTTTTGATTCACTTCGCTGCTCT
1 GTCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGACCCACTTCGCTGATCT
* * *
16715 TCAAGGAAGATTGAATC-AGATTTGATTTGCTTCTCTTG-TCTTCAAGAAGATCAAATCTGAAA
66 TCAAGGAAGATTGAATCGA-ACTTGATTTGCTTCAC-TGCTCTTCAAGAAGACCAAATCTGAAA
16777 ATTAAACATT
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
133 1 0.01
134 68 0.64
135 37 0.35
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (135 bp):
GTCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGACCCACTTCGCTGATCT
TCAAGGAAGATTGAATCGAACTTGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAA
AAAAC
Found at i:17405 original size:45 final size:44
Alignment explanation
Indices: 17338--17452 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
17328 TACTGAAAAG
* * *
17338 TTGACTCCTCTACGCGAAAAAGTCAAAAAAGACAACA-CTAAGACA
1 TTGACTCCTCTTCGCGAGAAAGTCAAAAAAG-CAACAGCGAA-ACA
* * ** *
17383 TTGACTCCTCTTCACGAGAAAGTCTAGGAAGCAACAGCGAAAGA
1 TTGACTCCTCTTCGCGAGAAAGTCAAAAAAGCAACAGCGAAACA
*
17427 TTGACTCCTCTTCGTGAGAAAGTCAA
1 TTGACTCCTCTTCGCGAGAAAGTCAA
17453 GAATAACATT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 30 0.52
45 28 0.48
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (44 bp):
TTGACTCCTCTTCGCGAGAAAGTCAAAAAAGCAACAGCGAAACA
Found at i:17480 original size:42 final size:40
Alignment explanation
Indices: 17382--17776 Score: 306
Period size: 38 Copynumber: 10.1 Consensus size: 40
17372 ACACTAAGAC
* *
17382 ATTGACTCCTCTTCACGAGAAAGTCTAGGAAGCAACAGCGAAAG
1 ATTGACTCCTCTTCACGAGAAAGTC-AAGAA-TAACA--GAAAG
**
17426 ATTGACTCCTCTTCGTGAGAAAGTCAAGAATAACATTGAAAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACA--GAAAG
* *
17468 ATTGACTCCTCTTTACGAGGAAGTCAAGAATAAC--AAAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAGAAAG
* * * * *
17506 ATTAACTTCTCTTCATGA-AGAGGTCAAAAATAAC--AAAG
1 ATTGACTCCTCTTCACGAGA-AAGTCAAGAATAACAGAAAG
* *
17544 ATTGTCTTCTCTTCACGAGAAAGTCAAGAAT-A-AGAAAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAGAAAG
*
17582 ATTGACTTCTCTTCACGATG-AAGTCAAGAATAA-A-AAAG
1 ATTGACTCCTCTTCACGA-GAAAGTCAAGAATAACAGAAAG
** * * *
17620 ATCAACTTCTATTCACGACG-AAGTCAAGAATAAC--AAAT
1 ATTGACTCCTCTTCACGA-GAAAGTCAAGAATAACAGAAAG
* *
17658 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC--AAAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAGAAAG
* * * *
17696 ATTGACTTCTCTTAATGAGGAAGTCAAGAATAAC-G-AAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAGAAAG
** * * *
17734 ATCAACTTCTCTTCACGAGGAAGCCAAGAATAAC--AAAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAGAAAG
17772 ATTGA
1 ATTGA
17777 TTGAAATTTC
Statistics
Matches: 300, Mismatches: 41, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
37 2 0.01
38 228 0.76
39 4 0.01
42 39 0.13
43 4 0.01
44 23 0.08
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (40 bp):
ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAGAAAG
Found at i:17518 original size:38 final size:38
Alignment explanation
Indices: 17422--17776 Score: 431
Period size: 38 Copynumber: 9.2 Consensus size: 38
17412 AGCAACAGCG
* ** *
17422 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
17460 ATTGAAAGATTGACTCCTCTTTACGAGGAAGTCAAGAATAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
17502 AAAGATTAACTTCTCTTCATGAAGAGGTCAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
17540 AAAGATTGTCTTCTCTTCACGAGAAAGTCAAGAATAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
17578 AAAGATTGACTTCTCTTCACGATGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * *
17616 AAAGATCAACTTCTATTCACGACGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
17654 AAATATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
17692 AAAGATTGACTTCTCTTAATGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** *
17730 GAAGATCAACTTCTCTTCACGAGGAAGCCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
17768 AAAGATTGA
1 AAAGATTGA
17777 TTGAAATTTC
Statistics
Matches: 268, Mismatches: 45, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
38 234 0.87
42 34 0.13
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:17627 original size:114 final size:114
Alignment explanation
Indices: 17422--17776 Score: 476
Period size: 114 Copynumber: 3.1 Consensus size: 114
17412 AGCAACAGCG
* ** * *
17422 AAAGATTGACTCCTCTTCGTGAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTTACGAG
1 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT-A-A--GAAAGATTGACTTCTCTTAACGAG
* * * *
17487 GAAGTCAAGAATAACAAAGATTAACTTCTCTTCATGAAGAGGTCAAAAATAAC
62 GAAGTCAAGAATAACAAAGATCAACTTCTCTTCACGAAGAAGTCAAGAATAAC
* * *
17540 AAAGATTGTCTTCTCTTCACGAGAAAGTCAAGAATAAGAAAGATTGACTTCTCTTCACGATGAAG
1 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAAGAAAGATTGACTTCTCTTAACGAGGAAG
* * *
17605 TCAAGAATAAAAAAGATCAACTTCTATTCACGACGAAGTCAAGAATAAC
66 TCAAGAATAACAAAGATCAACTTCTCTTCACGAAGAAGTCAAGAATAAC
* * * *
17654 AAATATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTAATGAGGAAG
1 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAAGAAAGATTGACTTCTCTTAACGAGGAAG
* * *
17719 TCAAGAATAACGAAGATCAACTTCTCTTCACGAGGAAGCCAAGAATAAC
66 TCAAGAATAACAAAGATCAACTTCTCTTCACGAAGAAGTCAAGAATAAC
17768 AAAGATTGA
1 AAAGATTGA
17777 TTGAAATTTC
Statistics
Matches: 210, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
114 177 0.84
116 1 0.00
117 1 0.00
118 31 0.15
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (114 bp):
AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAAGAAAGATTGACTTCTCTTAACGAGGAAG
TCAAGAATAACAAAGATCAACTTCTCTTCACGAAGAAGTCAAGAATAAC
Found at i:18660 original size:257 final size:255
Alignment explanation
Indices: 18129--19021 Score: 1105
Period size: 257 Copynumber: 3.5 Consensus size: 255
18119 AACTGATAGT
* * **
18129 CCAATTTGGGAAATTGTTTATTAGGTAAGAAACTTTAGAAATTACTTTCTTACTTTTCAAAAATT
1 CCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTAGAAATCGCTTTCTTACTTTTCAAAAATT
* * * * * * *
18194 TCATTTTCTGAAAATATTAAATGTGATACTTTGAAAATCGCTTTCTCATTTTTTAAAAAAATCAT
66 TCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCA-TTTTT--CAAATTCAT
* * * * * *
18259 GTGAAAAAATTCTTCCCGAAGGTATTATA-GATGGCCTAAAGGACTTAACATCTTACTCGAAAGA
128 GTGAAAACA-TCCTACCGAAGGTATTA-AGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGA
* * * * *
18323 CTGACAGATGATCCAAAGGATTTAATCATCATGCTTGAAAGA-TATACTGAGAGCCCGAAGGACT
191 TTGACAGATGACCCAAAAGATTTAATCATCATGCTCGAAAGACT-TACTGTGA-CCCGAAGGACT
18387 TA
254 TA
* *
18389 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTGAAATCGCTTTCTTACTTTTCAAAAATT
1 CCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTAGAAATCGCTTTCTTACTTTTCAAAAATT
* * * *
18454 TCATTTTCTGAAAAATACTAAATGAGAAATTTTGGAAATCGCTTTCTCAATTTTCAAATTTATAT
66 TCATTTTCT-AAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGT
* * *
18519 GAAAACATCCTACCTGAAGGTCTTAAGGATGGCCCGAAGGA-TTATCATCTTGCTCAAAAGATTG
130 GAAAACATCCTACC-GAAGGTATTAAGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGATTG
* * * * *
18583 ACAGATGACCCGAACGATTTAATCATCATGCTCGAAATACTTATTGTTGACCCAAAGGACTTA
194 ACAGATGACCCAAAAGATTTAATCATCATGCTCGAAAGACTTACTG-TGACCCGAAGGACTTA
* * * *
18646 CCAATTTGGGAAATAATTTATTGGGTAAGAAACTTTGGAAAT-GACTTTCTTACTTTTCAAAAAT
1 CCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTAGAAATCG-CTTTCTTACTTTTCAAAAAT
* * * *
18710 TTCATTTTCTAAAAACATTAAATGAGAAACTTTTGAAATCGCTTTCTCCTTTTTCAAATTCATGT
65 TTCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGT
* * *
18775 GAAAACATCCTATCCGAAGGTATTACGAATGGCCTGAAGGACTTATCATCTTGCTTGAAAGACTT
130 GAAAACATCCTA-CCGAAGGTATTAAGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGA-TT
* *
18840 -ACATATGACCCAAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
193 GACAGATGACCCAAAAGATTTAATCATCATGCTCGAAAGACTTACTG-TGACCCGAAGGACTTA
* * *
18903 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTAAAAACCGCTTTCTTACTTTTCAAAAATT
1 CCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTAGAAATCGCTTTCTTACTTTTCAAAAATT
* * *
18968 TCATTTTC-ATAAAAGACTTAAATTAGAAACTTTGGAAATTGCTTTCTCATTTTT
66 TCATTTTCTA-AAAATAC-TAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTT
19022 TGAAAATCAA
Statistics
Matches: 546, Mismatches: 75, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
256 83 0.15
257 286 0.52
258 72 0.13
260 72 0.13
261 33 0.06
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (255 bp):
CCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTAGAAATCGCTTTCTTACTTTTCAAAAATT
TCATTTTCTAAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTG
AAAACATCCTACCGAAGGTATTAAGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGATTGAC
AGATGACCCAAAAGATTTAATCATCATGCTCGAAAGACTTACTGTGACCCGAAGGACTTA
Found at i:20799 original size:15 final size:14
Alignment explanation
Indices: 20761--20855 Score: 76
Period size: 14 Copynumber: 6.9 Consensus size: 14
20751 TTGATTTATT
20761 TTTTCTT-TTTTTC
1 TTTTCTTCTTTTTC
*
20774 -TCTCTGT-TTTTTC
1 TTTTCT-TCTTTTTC
20787 TTTTCTATC-TTTTC
1 TTTTCT-TCTTTTTC
20801 TCTTTC-TCTTTTTCC
1 T-TTTCTTCTTTTT-C
*
20816 TTTTCTTCTTTTTT
1 TTTTCTTCTTTTTC
*
20830 TTTTC-TCTTCTTTT
1 TTTTCTTCTT-TTTC
20844 TTTTCTTCTTTT
1 TTTTCTTCTTTT
20856 ATCTCTATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
12 4 0.06
13 13 0.19
14 35 0.51
15 17 0.25
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:20834 original size:28 final size:27
Alignment explanation
Indices: 20759--20855 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 27
20749 ACTTGATTTA
* *
20759 TTTT-TTCTTTTTTTCTCTCTGTTTTTTC
1 TTTTCTTCTTTTTTT-TTTCT-CTTTTTC
* *
20787 TTTTCTATCTTTTCTCTTTCTCTTTTTCC
1 TTTTCT-TCTTTTTTTTTTCTCTTTTT-C
*
20816 TTTTCTTCTTTTTTTTTTCTCTTCTTTT
1 TTTTCTTCTTTTTTTTTTCTCTT-TTTC
20844 TTTTCTTCTTTT
1 TTTTCTTCTTTT
20856 ATCTCTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
28 36 0.62
29 15 0.26
30 7 0.12
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (27 bp):
TTTTCTTCTTTTTTTTTTCTCTTTTTC
Found at i:26526 original size:19 final size:19
Alignment explanation
Indices: 26502--26591 Score: 162
Period size: 19 Copynumber: 4.7 Consensus size: 19
26492 CCCTAAACCC
*
26502 CTATTTCCTCATTTGTTCT
1 CTATTTCTTCATTTGTTCT
*
26521 CTATTTCTGCATTTGTTCT
1 CTATTTCTTCATTTGTTCT
26540 CTATTTCTTCATTTGTTCT
1 CTATTTCTTCATTTGTTCT
26559 CTATTTCTTCATTTGTTCT
1 CTATTTCTTCATTTGTTCT
26578 CTATTTCTTCATTT
1 CTATTTCTTCATTT
26592 TAAAGAGAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.11, C:0.22, G:0.06, T:0.61
Consensus pattern (19 bp):
CTATTTCTTCATTTGTTCT
Found at i:26992 original size:21 final size:19
Alignment explanation
Indices: 26966--27008 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
26956 GTTTCAGTTT
26966 TTGGTTCCTCTGCTTTGGTTA
1 TTGGTTCCTCTG-TTT-GTTA
* *
26987 TTGGTTTCTTTGTTTGTTA
1 TTGGTTCCTCTGTTTGTTA
27006 TTG
1 TTG
27009 TTATTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.05, C:0.12, G:0.23, T:0.60
Consensus pattern (19 bp):
TTGGTTCCTCTGTTTGTTA
Found at i:27816 original size:21 final size:21
Alignment explanation
Indices: 27791--27843 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 21
27781 ATAAAACTAT
*
27791 ACTATATATATATTTTTCACA
1 ACTATATATATATTTTTCAAA
*
27812 GCTATAT-T-TA-TTTTCAAA
1 ACTATATATATATTTTTCAAA
27830 ACTATACTATATAT
1 ACTATA-TATATAT
27844 AAAAAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
18 12 0.48
19 3 0.12
20 2 0.08
21 8 0.32
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (21 bp):
ACTATATATATATTTTTCAAA
Found at i:27841 original size:42 final size:45
Alignment explanation
Indices: 27727--27844 Score: 147
Period size: 44 Copynumber: 2.7 Consensus size: 45
27717 TAATAATTTA
*
27727 TATATTTATTTTC-AAACTATATTATATATATATATATTCCAAGC
1 TATATTTATTTTCAAAACTATACTATATATATATATATTCCAAGC
* * *
27771 TTTATGTT-TTAT-AAAACTATACTATATATATAT-T-TTTCACAGC
1 TATAT-TTATTTTCAAAACTATACTATATATATATATATTCCA-AGC
27814 TATATTTATTTTCAAAACTATACTATATATA
1 TATATTTATTTTCAAAACTATACTATATATA
27845 AAAAAACTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
42 6 0.10
43 11 0.17
44 44 0.70
45 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (45 bp):
TATATTTATTTTCAAAACTATACTATATATATATATATTCCAAGC
Found at i:27871 original size:22 final size:20
Alignment explanation
Indices: 27827--27865 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27817 ATTTATTTTC
27827 AAAACTATACTATATATAAA
1 AAAACTATACTATATATAAA
27847 AAAACTATACTATATATAA
1 AAAACTATACTATATATAA
27866 CCAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAACTATACTATATATAAA
Found at i:27892 original size:15 final size:16
Alignment explanation
Indices: 27868--27901 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
27858 ATATATAACC
27868 AAAATAAAACAAAACA
1 AAAATAAAACAAAACA
*
27884 AAAAT-AAACTAAACA
1 AAAATAAAACAAAACA
27899 AAA
1 AAA
27902 GGAAACTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAATAAAACAAAACA
Found at i:33433 original size:28 final size:28
Alignment explanation
Indices: 33393--33457 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
33383 CTCAACGGTG
* *
33393 GACTGGGTCAGACATGCAAGTTGGGTTA
1 GACTGGGTCAGACAGGCAAATTGGGTTA
33421 GACTGGGTCAGACAGGCAAATTGGGTTA
1 GACTGGGTCAGACAGGCAAATTGGGTTA
33449 GACTGGGTC
1 GACTGGGTC
33458 GGGTCGAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (28 bp):
GACTGGGTCAGACAGGCAAATTGGGTTA
Found at i:36565 original size:24 final size:24
Alignment explanation
Indices: 36533--36601 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
36523 CTACAGAGGT
36533 TTGTGCTTTTGCAGTC-GATGAAGC
1 TTGTGCTTTTGCAG-CAGATGAAGC
*
36557 TTGTGCTTTTGTAGCAGATGAAGC
1 TTGTGCTTTTGCAGCAGATGAAGC
* *
36581 TTGTGCTTTTACAGAAGATGA
1 TTGTGCTTTTGCAGCAGATGA
36602 GCCTTCTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.38
Consensus pattern (24 bp):
TTGTGCTTTTGCAGCAGATGAAGC
Found at i:39390 original size:24 final size:24
Alignment explanation
Indices: 39357--39411 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
39347 TAGTTAATGC
* *
39357 ATCGAAGCACATATTACAGAGTGT
1 ATCGATGCACATACTACAGAGTGT
*
39381 ATCGATGCACATACTACATAGTGT
1 ATCGATGCACATACTACAGAGTGT
*
39405 ACCGATG
1 ATCGATG
39412 TACTACAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (24 bp):
ATCGATGCACATACTACAGAGTGT
Found at i:40142 original size:22 final size:22
Alignment explanation
Indices: 40112--40155 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40102 AGTCGAGGGT
*
40112 TATATAGTGGTCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
40134 TATACAGTGGTCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
40156 AATTTCATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (22 bp):
TATACAGTGGTCCTTCGGGACA
Found at i:47682 original size:23 final size:24
Alignment explanation
Indices: 47639--47686 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
47629 TAATAACAAT
47639 ACAATATAATATAATAAATATATA
1 ACAATATAATATAATAAATATATA
47663 ACAA-ATAATA-AATAATATATATA
1 ACAATATAATATAATAA-ATATATA
47686 A
1 A
47687 ATAATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
ACAATATAATATAATAAATATATA
Found at i:47692 original size:23 final size:23
Alignment explanation
Indices: 47639--47693 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 23
47629 TAATAACAAT
47639 ACAATATAATATAATAAATATATA
1 ACAA-ATAATATAATAAATATATA
47663 ACAAATAATA-AAT-AATATAT-
1 ACAAATAATATAATAAATATATA
*
47683 ATAAATAATAT
1 ACAAATAATAT
47694 GTATACTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.31
21 7 0.24
22 3 0.10
23 6 0.21
24 4 0.14
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
ACAAATAATATAATAAATATATA
Found at i:47803 original size:37 final size:36
Alignment explanation
Indices: 47736--48139 Score: 339
Period size: 37 Copynumber: 10.6 Consensus size: 36
47726 ATACATTATA
*
47736 TTTTCAAAAACCA-TTTTAAAAACTATATATTATATG
1 TTTTCAAAAA-TATTTTTAAAAACTATATATTATATG
47772 TTTTCAAAAATATTTTTAAAAAACTATATATTATATG
1 TTTTCAAAAATATTTTT-AAAAACTATATATTATATG
* * * *
47809 TTTCCAAAATTACGTTTTCAAAAATTATATTATATATAAT-
1 TTTTCAAAAATA--TTTTTAAAAACTATA-TAT-TAT-ATG
* *
47849 TTTTCAAAAATA-TTTCAAAAATTATATATTATATG
1 TTTTCAAAAATATTTTTAAAAACTATATATTATATG
* *
47884 TTTTCAAAAATGTGTTTTCAAAACTATATATTATATG
1 TTTTCAAAAATAT-TTTTAAAAACTATATATTATATG
**
47921 TTTTCCAAAACCGATTTTTAAAAAACTATATATTATATACG
1 TTTT-CAAAA-ATATTTTT-AAAAACTATATATTATAT--G
* * **
47962 TTTTCAAAAATATGTTTTCAAAACTATATATCATAAA
1 TTTTCAAAAATAT-TTTTAAAAACTATATATTATATG
* * *
47999 TTTTCAAAAACT-TGTTTTCAAAACCATATTATATATATA
1 TTTTCAAAAA-TAT-TTTTAAAAACTATA-TAT-TATATG
* * *
48038 TTTTCAAAAACCGATTTTTTTAAAAAATATATATTATATTT
1 TTTTC-AAAA---ATATTTTTAAAAACTATATATTATA-TG
*
48079 TTTTCAAAAATCATTTTCTAAAAACTATATATTATCTG
1 TTTTCAAAAAT-ATTTT-TAAAAACTATATATTATATG
*
48117 TTTTTCAAAAATATTTTCAAAAA
1 -TTTTCAAAAATATTTTTAAAAA
48140 TTATGCTATA
Statistics
Matches: 307, Mismatches: 33, Indels: 55
0.78 0.08 0.14
Matches are distributed among these distances:
34 2 0.01
35 15 0.05
36 17 0.06
37 99 0.32
38 32 0.10
39 78 0.25
40 34 0.11
41 16 0.05
42 12 0.04
43 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (36 bp):
TTTTCAAAAATATTTTTAAAAACTATATATTATATG
Found at i:53940 original size:34 final size:34
Alignment explanation
Indices: 53890--53956 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
53880 AGCAATAAGA
*
53890 ACTCCAGCTGCTATCATCAAAAATAGAAATATGT
1 ACTCCAGCTGCAATCATCAAAAATAGAAATATGT
* * * *
53924 ACTCCAGGTGCAATCATCAGATATAGAATTATG
1 ACTCCAGCTGCAATCATCAAAAATAGAAATATG
53957 CACTTTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (34 bp):
ACTCCAGCTGCAATCATCAAAAATAGAAATATGT
Found at i:58438 original size:20 final size:21
Alignment explanation
Indices: 58413--58454 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
58403 CGATTACACC
*
58413 TTCTAATATCAAATT-CAACA
1 TTCTAACATCAAATTCCAACA
*
58433 TTCTAACATTAAATTCCAACA
1 TTCTAACATCAAATTCCAACA
58454 T
1 T
58455 AATACATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (21 bp):
TTCTAACATCAAATTCCAACA
Found at i:60745 original size:34 final size:34
Alignment explanation
Indices: 60702--60802 Score: 130
Period size: 34 Copynumber: 3.0 Consensus size: 34
60692 GCGCAATAAG
* * *
60702 CACTCTAGGTGCTATCATCAGAAACATAAATTTA
1 CACTCTAGGTGCAATCATCAGATACATAAATATA
* *
60736 CACTCTAGGTGCAATCATCAGATACAGAAATATG
1 CACTCTAGGTGCAATCATCAGATACATAAATATA
* **
60770 CACTCCAAATGCAATCATCAGATACATAAATAT
1 CACTCTAGGTGCAATCATCAGATACATAAATAT
60803 GAACTCCAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.26
Consensus pattern (34 bp):
CACTCTAGGTGCAATCATCAGATACATAAATATA
Found at i:60821 original size:34 final size:35
Alignment explanation
Indices: 60715--60821 Score: 98
Period size: 34 Copynumber: 3.1 Consensus size: 35
60705 TCTAGGTGCT
* * * *
60715 ATCATCAGAAACATAAAT-TTACACTCTAGGT-GCA
1 ATCATCAGATACATAAATATGA-ACTCCAGGTATCA
* * *
60749 ATCATCAGATACAGAAATATGCACTCCA--AATGCA
1 ATCATCAGATACATAAATATGAACTCCAGGTAT-CA
60783 ATCATCAGATACATAAATATGAACTCCAGGTATC-
1 ATCATCAGATACATAAATATGAACTCCAGGTATCA
60817 ATCAT
1 ATCAT
60822 ATAATGTACA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
34 54 0.93
35 2 0.03
36 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.25
Consensus pattern (35 bp):
ATCATCAGATACATAAATATGAACTCCAGGTATCA
Found at i:68729 original size:206 final size:207
Alignment explanation
Indices: 68345--68872 Score: 660
Period size: 206 Copynumber: 2.5 Consensus size: 207
68335 TTTGACGCAC
* *** *
68345 TTTCAATTTCTTAGTTGTTTTCTTCTTTTGAATGCACAAAAAATTCTGGGAAATCTGCA-TTTTT
1 TTTCAATTT-GTAGTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTT
* * *
68409 CTATTTGGGATTGAGGAAAAGTTTTAACTTGGATATCAATTAGCTTGAATCACAATATGTTGCTG
65 CTGTTTGGGATTGAGGAAAAG---TAACTTGGATATCAATTAGCTTGAAACACAATATATTGCTG
* * *
68474 ATTTAGTTGTGTTGTTTTCTTTTGCACGAGCAAAGTTATTGATTTATAAGTTTAAGTCTCAAGCT
127 ATTTAGTTGTGTTGTTTTCTTTTACACGAGCAAAGTTATTGACTTATAAGTTTAAGTCCCAAGCT
* *
68539 TGTGTGTG-TTGTGGT
192 TGTGTGTGTTTCTGAT
*
68554 TTTCAATTTGTAGGTTGTTTTCTTCTTTTGAATGTATGCAAAATTCTGGGGAATCTGCATTATTT
1 TTTCAATTTGTA-GTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATT-TTT
* ** * *
68619 TCTGTTTGGGATTGAGGGAAAGT-A-TT-GACTATCAATTTTCTTGAAACATAATATATTGTTGA
64 TCTGTTTGGGATTGAGGAAAAGTAACTTGGA-TATCAATTAGCTTGAAACACAATATATTGCTGA
** * *
68681 TTTAGTTGTGTTGTTTTCTTTTACGTGAGCAAAGTTATT-AGCTTATAAGTTTTAGTCCCATGCT
128 TTTAGTTGTGTTGTTTTCTTTTACACGAGCAAAGTTATTGA-CTTATAAGTTTAAGTCCCAAGCT
68745 TGTGTGTGTTTCTGAT
192 TGTGTGTGTTTCTGAT
*
68761 TTTCAATTTGTTTGTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTT
1 TTTCAATTTG-TAGTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTT
68826 -TGTTT-GGATTGAGGAAAAGTCTTAACTT-GACTATCAATTAGCTTGAA
65 CTGTTTGGGATTGAGGAAAAG---TAACTTGGA-TATCAATTAGCTTGAA
68873 TCCAACTTAT
Statistics
Matches: 279, Mismatches: 28, Indels: 24
0.84 0.08 0.07
Matches are distributed among these distances:
204 13 0.05
205 8 0.03
206 96 0.34
207 64 0.23
208 5 0.02
209 69 0.25
210 1 0.00
211 23 0.08
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.46
Consensus pattern (207 bp):
TTTCAATTTGTAGTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTTC
TGTTTGGGATTGAGGAAAAGTAACTTGGATATCAATTAGCTTGAAACACAATATATTGCTGATTT
AGTTGTGTTGTTTTCTTTTACACGAGCAAAGTTATTGACTTATAAGTTTAAGTCCCAAGCTTGTG
TGTGTTTCTGAT
Found at i:71593 original size:2 final size:2
Alignment explanation
Indices: 71586--71610 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71576 TCAATATACA
71586 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
71611 ACAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71784 original size:85 final size:85
Alignment explanation
Indices: 71639--71801 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
71629 CAATCACGAC
* * * * *
71639 ACACGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCATACAT
1 ACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAAT
*
71704 GCGTGTCATAAATTTATGAA
66 GCGCGTCATAAATTTATGAA
* * *
71724 ACACAAATGTGTGTCATCTTAATTT-ATGATGGGGGCTTCAATGACGCGCAATG-AGCGTCATAA
1 ACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGTA-AGTCATAA
71787 ATGCGCGTCATAAAT
64 ATGCGCGTCATAAAT
71802 GCGTGTCATA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 63 0.94
86 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (85 bp):
ACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAAT
GCGCGTCATAAATTTATGAA
Found at i:71794 original size:13 final size:13
Alignment explanation
Indices: 71773--71840 Score: 109
Period size: 13 Copynumber: 5.2 Consensus size: 13
71763 AATGACGCGC
*
71773 AATGAGCGTCATA
1 AATGCGCGTCATA
71786 AATGCGCGTCATA
1 AATGCGCGTCATA
*
71799 AATGCGTGTCATA
1 AATGCGCGTCATA
*
71812 AATGCGTGTCATA
1 AATGCGCGTCATA
71825 AATGCGCGTCATA
1 AATGCGCGTCATA
71838 AAT
1 AAT
71841 TCATGATGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:76780 original size:33 final size:33
Alignment explanation
Indices: 76729--76795 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
76719 AATAACAATG
* *
76729 TTCCAAAGTTCAACTAAGAAGACAATCTAACCA
1 TTCCAAAGTCCAAATAAGAAGACAATCTAACCA
*
76762 TTCCAAAGTCCAAATAAGAAGACAATCTGACCA
1 TTCCAAAGTCCAAATAAGAAGACAATCTAACCA
76795 T
1 T
76796 GGAAGATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (33 bp):
TTCCAAAGTCCAAATAAGAAGACAATCTAACCA
Found at i:90959 original size:87 final size:87
Alignment explanation
Indices: 90812--91543 Score: 351
Period size: 87 Copynumber: 8.5 Consensus size: 87
90802 TAATTAAATG
* * * **
90812 TTATCCAAAGA--GAGAACAAGTTAATAATAAGAAGAACTTGTTCCACCTATTT-CTCAAATCCA
1 TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCTACCT-TTTGCTTGAATCCA
* *
90874 TCATAGAAAAAGATGTATCACCA
65 TCATAGAAAAAGATGAATCAACA
* * * *
90897 TTGTCCAAAGAGGGAGAAGAAGTTCATAACAAGAAGAATTTGTTTTACCTTTTGCTTGAATCCAT
1 TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCTACCTTTTGCTTGAATCCAT
* *
90962 CACAAAAAAAGATGAATCAACA
66 CATAGAAAAAGATGAATCAACA
* * * * *
90984 TTATACAGAGGGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCTACCTTTTGCTTGAGTCCAT
1 TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCTACCTTTTGCTTGAATCCAT
* * * **
91049 TATAG--AAGGTAT-AGACCAGTA
66 CATAGAAAAAG-ATGA-ATCAACA
* * * * * * * * *
91070 TTGTTC-AAGAAGGACAAGAAGTTCGTAATGAGAAGAACTCGTTCGA-CTTATTTCTTGAATCCA
1 TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCTACCTT-TTGCTTGAATCCA
** * * *
91133 TCATAGAAGGAGGTGGATAAACA
65 TCATAGAAAAAGATGAATCAACA
* * * * * *
91156 CTT-TCTCAATAGA--GAGAATAAGTTCATACTGAGAAGTACTTGTT-TGGCCTATTGCTTGAAT
1 -TTATC-CAA-AGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCT-ACCTTTTGCTTGAAT
* ** *** *
91217 GCATTGTAGAAGGTGGTGAATCAACA
62 CCATCATAGAAAAAGATGAATCAACA
* * * * * ** * *
91243 GTGTCCAAAGAGGGATAAGAAGTTCATAATGAGAAGAACTTGTTCAATGTTTTTCTCGAATCCAT
1 TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCTACCTTTTGCTTGAATCCAT
* * * *
91308 CACAGAAGGACG-TGGATCAACA
66 CATAGAA-AAAGATGAATCAACA
* ** * * * * **
91330 TTTTCTTAAGAGGGAGAATAAGTTCATAATGAA-AATAACTTATT-TGATCTTTCT-CTCAAATC
1 TTATCCAAAGAGGGAGAAGAAGTTCATAAT-AAGAAGAACTTGTTCT-ACCTTT-TGCTTGAATC
* * * *
91392 CATCACAGAAGAAGGTTG-ATCAACT
63 CATCATAGAA-AAAGATGAATCAACA
* * * *
91417 TTGTCCAAAGAGGGAGAAGAAGTTCATAATAAGAA-CA-TAT-TT-GACCTTTTG-TTCGAATCT
1 TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACT-TGTTCTACCTTTTGCTT-GAATCC
* * *
91477 A-CATAGAAGAAGATGGATCATCA
64 ATCATAGAAAAAGATGAATCAACA
* ** * * *
91500 TTGTCCAAAGAGCAATAAAAAGTTCATAATGAA-AAGAACATGTT
1 TTATCCAAAGAGGGAGAAGAAGTTCATAAT-AAGAAGAACTTGTT
91544 TGACATTCGG
Statistics
Matches: 491, Mismatches: 123, Indels: 66
0.72 0.18 0.10
Matches are distributed among these distances:
82 4 0.01
83 41 0.08
84 17 0.03
85 71 0.14
86 26 0.05
87 320 0.65
88 9 0.02
89 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (87 bp):
TTATCCAAAGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCTACCTTTTGCTTGAATCCAT
CATAGAAAAAGATGAATCAACA
Found at i:91181 original size:172 final size:174
Alignment explanation
Indices: 90997--91376 Score: 419
Period size: 174 Copynumber: 2.2 Consensus size: 174
90987 TACAGAGGGG
* * *
90997 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCT-ACCTTTTGCTTGAGTCCATTATAGAAGGT-A
1 GAGAATAAGTTCATAATGAGAAGAACTTGTT-TGACCTATTGCTTGAATCCATTATAGAAGGTGA
** * * * *
91060 T-AGACCAGTATTGTTC-AAGAAGGACAAGAAGTTCGTAATGAGAAGAACTCGTTCGACT-TATT
65 TGA-ACCAACAGTGTCCAAAGAAGGACAAGAAGTTCATAATGAGAAGAACTCGTTC-AATGTATT
* * * *
91122 TCTTGAATCCATCATAGAAGGAGGTGGATAAACACTTTCTCAATAGA
128 TCTCGAATCCATCACAGAAGGACGTGGATAAACACTTTCTCAAGAGA
* * * * * *
91169 GAGAATAAGTTCATACTGAGAAGTACTTGTTTGGCCTATTGCTTGAATGCATTGTAGAAGGTGGT
1 GAGAATAAGTTCATAATGAGAAGAACTTGTTTGACCTATTGCTTGAATCCATTATAGAAGGTGAT
* * * * *
91234 GAATCAACAGTGTCCAAAGAGGGATAAGAAGTTCATAATGAGAAGAACTTGTTCAATGTTTTTCT
66 GAACCAACAGTGTCCAAAGAAGGACAAGAAGTTCATAATGAGAAGAACTCGTTCAATGTATTTCT
* * * *
91299 CGAATCCATCACAGAAGGACGTGGATCAACATTTTCTTAAGAGG
131 CGAATCCATCACAGAAGGACGTGGATAAACACTTTCTCAAGAGA
* * *
91343 GAGAATAAGTTCATAATGAAAATAACTTATTTGA
1 GAGAATAAGTTCATAATGAGAAGAACTTGTTTGA
91377 TCTTTCTCTC
Statistics
Matches: 169, Mismatches: 34, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
171 1 0.01
172 52 0.31
173 11 0.07
174 105 0.62
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (174 bp):
GAGAATAAGTTCATAATGAGAAGAACTTGTTTGACCTATTGCTTGAATCCATTATAGAAGGTGAT
GAACCAACAGTGTCCAAAGAAGGACAAGAAGTTCATAATGAGAAGAACTCGTTCAATGTATTTCT
CGAATCCATCACAGAAGGACGTGGATAAACACTTTCTCAAGAGA
Found at i:91424 original size:174 final size:174
Alignment explanation
Indices: 91076--91451 Score: 402
Period size: 174 Copynumber: 2.2 Consensus size: 174
91066 AGTATTGTTC
* * * * *
91076 AAGAAGGACAAGAAGTTCGTAATGAGAAGAACTCGTTCGACTTATTTCTTGAATCCATCATAGAA
1 AAGAGGGACAAGAAGTTCATAATGAGAAGAACTCGTTCGAATTATTTCTCGAATCCATCACAGAA
* * * * * *
91141 GGAGGTGGATAAACACTTTCTCAATAGAGAGAATAAGTTCATACTGAGAAGTACTTGTTTGGCCT
66 GGACGTGGATAAACACTTTCTCAAGAGAGAGAATAAGTTCATAATGAGAAATACTTATTTGACCT
* * *** **
91206 ATTGCTTGAATGCATTGTAGAAGGTGGTGAATCAACAGTGTCCA
131 ATTGCTTAAATCCATCACAGAAGAAGGTGAATCAACAGTGTCCA
* * *
91250 AAGAGGGATAAGAAGTTCATAATGAGAAGAACTTGTTC-AATGTTTTTCTCGAATCCATCACAGA
1 AAGAGGGACAAGAAGTTCATAATGAGAAGAACTCGTTCGAAT-TATTTCTCGAATCCATCACAGA
* * * * *
91314 AGGACGTGGATCAACATTTTCTTAAGAGGGAGAATAAGTTCATAATGA-AAATAACTTATTTGAT
65 AGGACGTGGATAAACACTTTCTCAAGAGAGAGAATAAGTTCATAATGAGAAAT-ACTTATTTGAC
**
91378 CT-TT-CTCTCAAATCCATCACAGAAGAAGGTTG-ATCAACTTTGTCCA
129 CTATTGCT-T-AAATCCATCACAGAAGAAGG-TGAATCAACAGTGTCCA
* *
91424 AAGAGGGAGAAGAAGTTCATAATAAGAA
1 AAGAGGGACAAGAAGTTCATAATGAGAA
91452 CATATTTGAC
Statistics
Matches: 167, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
172 2 0.01
173 8 0.05
174 155 0.93
175 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (174 bp):
AAGAGGGACAAGAAGTTCATAATGAGAAGAACTCGTTCGAATTATTTCTCGAATCCATCACAGAA
GGACGTGGATAAACACTTTCTCAAGAGAGAGAATAAGTTCATAATGAGAAATACTTATTTGACCT
ATTGCTTAAATCCATCACAGAAGAAGGTGAATCAACAGTGTCCA
Found at i:93677 original size:13 final size:15
Alignment explanation
Indices: 93647--93680 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
93637 CAGCTTCATT
93647 TCTCTATTTTTCCTC
1 TCTCTATTTTTCCTC
93662 TCTCTATTTTTCCTC
1 TCTCTATTTTTCCTC
93677 TCTC
1 TCTC
93681 ACTCTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (15 bp):
TCTCTATTTTTCCTC
Found at i:94517 original size:3 final size:3
Alignment explanation
Indices: 94509--94586 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
94499 TTAATATATT
*
94509 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
94557 TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
94587 ATCAATATGG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:95044 original size:113 final size:113
Alignment explanation
Indices: 94846--95619 Score: 1062
Period size: 113 Copynumber: 6.8 Consensus size: 113
94836 TCTTGATGAG
*
94846 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
94910 AGAAGAGTTGATCCATCAAGTGATGGATTTGA-GCAAAA-ATCTGAACAAA
65 GGAAAAGCTGATCCATCAAGTGAT-GATTTGAGGCAAAAGGT-TGAACAAA
* * ***
94959 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
95024 GAAAAGCTAATCTATCAAGTGATAGATTTGA-GCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GATTTGAGGCAAAAGGTTGAACAAA
95072 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
* *
95136 GGAAAAGATAATCCATCAAGTGATAGATTTGA-GCAAAAGGTTGAACAAA
65 GGAAAAGCTGATCCATCAAGTGAT-GATTTGAGGCAAAAGGTTGAACAAA
* * * *
95185 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTATTTTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
95250 GAAAGGCTGATCCATCAATTGATGAATTT-AGGTAAAAGGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATG-ATTTGAGGCAAAAGGTTGAACAAA
95298 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
95363 GAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATGATTTGAGGCAAAAGGTTGAACAAA
95411 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
95476 GAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAG
66 GAAAAGCTGATCCATCAAGTGATGATTTGAGGCAAAAGGTTGAACAAA
*
95524 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACTTTCTCT-
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
95588 GAAAATG-TCAATCCATCAACTGATAGATTTGA
66 GAAAA-GCT-GATCCATCAAGTGAT-GATTTGA
95620 ATCTTTGCTA
Statistics
Matches: 614, Mismatches: 37, Indels: 19
0.92 0.06 0.03
Matches are distributed among these distances:
112 15 0.02
113 592 0.96
114 7 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGATTTGAGGCAAAAGGTTGAACAAA
Found at i:96552 original size:83 final size:83
Alignment explanation
Indices: 96408--96997 Score: 1126
Period size: 83 Copynumber: 7.1 Consensus size: 83
96398 CTTATTTCTA
96408 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96473 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
96491 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96556 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
96574 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96639 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
96657 CTATGAGCATATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96722 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
96740 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96805 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
96823 CTATGAGCATATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96888 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
96906 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
96971 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
96989 CTATGAGCA
1 CTATGAGCA
96998 CATTGCATTT
Statistics
Matches: 497, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 497 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:98162 original size:7 final size:7
Alignment explanation
Indices: 98150--98205 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
98140 TGACCCCCCT
98150 TTTTTTC
1 TTTTTTC
98157 TTTTTTC
1 TTTTTTC
* *
98164 TCTCTTC
1 TTTTTTC
98171 TTTTTT-
1 TTTTTTC
98177 TTTCTTT-
1 TTT-TTTC
*
98184 TTCTTT-
1 TTTTTTC
98190 TTTTTTC
1 TTTTTTC
98197 TTTTTTC
1 TTTTTTC
98204 TT
1 TT
98206 CAAGTATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 11 0.27
7 30 0.73
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:98184 original size:23 final size:22
Alignment explanation
Indices: 98149--98205 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
98139 TTGACCCCCC
98149 TTTTTTTCTTTTTTCTCTCTTCTT
1 TTTTTTTC-TTTTTCT-TCTTCTT
* *
98173 TTTTTTTCTTTTTCTTTTTTTT
1 TTTTTTTCTTTTTCTTCTTCTT
98195 TCTTTTTTCTT
1 T-TTTTTTCTT
98206 CAAGTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 6 0.20
23 16 0.53
24 8 0.27
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTCTTTTTCTTCTTCTT
Found at i:98199 original size:16 final size:16
Alignment explanation
Indices: 98148--98201 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
98138 CTTGACCCCC
*
98148 CTTTTT-TTCTTTTTT
1 CTTTTTCTTTTTTTTT
*
98163 CTCTCTTCTTTTTTTTT
1 CT-TTTTCTTTTTTTTT
98180 CTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
98196 CTTTTT
1 CTTTTT
98202 TCTTCAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 2 0.06
16 22 0.65
17 10 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:98201 original size:17 final size:17
Alignment explanation
Indices: 98157--98205 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
98147 CCTTTTTTTC
* *
98157 TTTTTTCTCTCTTCTTT
1 TTTTTTCTTTTTTCTTT
98174 TTTTTTC-TTTTTCTTT
1 TTTTTTCTTTTTTCTTT
98190 TTTTTTCTTTTTTCTT
1 TTTTTTCTTTTTTCTT
98206 CAAGTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTTTTTCTTT
Found at i:108814 original size:28 final size:29
Alignment explanation
Indices: 108783--108855 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
108773 AAAATAAAAC
* *
108783 ATATAAATATTATGAAAA-TAATAAGTAA
1 ATATAAATATTATGAAAAGAAAGAAGTAA
* * *
108811 ATATAAAAATTTTGAAAAGAAAGAATTAA
1 ATATAAATATTATGAAAAGAAAGAAGTAA
108840 ATATTAAATA-TATGAA
1 ATA-TAAATATTATGAA
108856 CTTTTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 16 0.44
29 15 0.42
30 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (29 bp):
ATATAAATATTATGAAAAGAAAGAAGTAA
Found at i:109515 original size:13 final size:13
Alignment explanation
Indices: 109478--109517 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
109468 TTGATATTGA
109478 AAAATAAATA-TT
1 AAAATAAATATTT
*
109490 AAAATAATTTATTT
1 AAAATAA-ATATTT
109504 AAAATAAATATTT
1 AAAATAAATATTT
109517 A
1 A
109518 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:109531 original size:17 final size:17
Alignment explanation
Indices: 109491--109539 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
109481 ATAAATATTA
*
109491 AAATAATTTATTTAAAAT
1 AAAT-ATTTATTTATAAT
*
109509 AAATATTTATTTATTAT
1 AAATATTTATTTATAAT
* *
109526 ATATATATATTTAT
1 AAATATTTATTTAT
109540 GACTACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTATTTATAAT
Found at i:110403 original size:15 final size:14
Alignment explanation
Indices: 110379--110420 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
110369 CCTCGGTAAG
*
110379 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
110394 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
110408 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
110421 GCTGCTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:110411 original size:20 final size:20
Alignment explanation
Indices: 110379--110420 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
110369 CCTCGGTAAG
*
110379 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
110399 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
110419 TT
1 TT
110421 GCTGCTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:110937 original size:3 final size:3
Alignment explanation
Indices: 110929--110985 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
110919 TTAATATATT
* *
110929 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
110977 TAA TAA TAA
1 TAA TAA TAA
110986 ATCAATATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:114998 original size:29 final size:26
Alignment explanation
Indices: 114952--115019 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 26
114942 AGAAAATAAA
*
114952 AAAATAAGGATAATAATA-ATAAGATGGAC
1 AAAAT-AGGATAAGAATAGATAA-A--GAC
114981 AAAATAGTGATAAGAATAGATAAAGAC
1 AAAATAG-GATAAGAATAGATAAAGAC
115008 AAAATAGAGATA
1 AAAATAG-GATA
115020 TATAATGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 14 0.40
28 2 0.06
29 15 0.43
30 4 0.11
ACGTcount: A:0.60, C:0.03, G:0.18, T:0.19
Consensus pattern (26 bp):
AAAATAGGATAAGAATAGATAAAGAC
Found at i:124038 original size:17 final size:17
Alignment explanation
Indices: 124016--124052 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
124006 GGCCATGCCA
**
124016 GTATCGGTACCCTATGT
1 GTATCGGTACAATATGT
124033 GTATCGGTACAATATGT
1 GTATCGGTACAATATGT
124050 GTA
1 GTA
124053 CATTGTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (17 bp):
GTATCGGTACAATATGT
Found at i:124807 original size:2 final size:2
Alignment explanation
Indices: 124800--124835 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
124790 TACTAACTTC
124800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124836 ATGTTATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127396 original size:21 final size:21
Alignment explanation
Indices: 127370--127409 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
127360 AAGTCCATAC
127370 TAGTATCTGTATCGATACCTA
1 TAGTATCTGTATCGATACCTA
* *
127391 TAGTATGTGTATCGGTACC
1 TAGTATCTGTATCGATACC
127410 CTGTTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (21 bp):
TAGTATCTGTATCGATACCTA
Found at i:128937 original size:138 final size:138
Alignment explanation
Indices: 128679--128947 Score: 430
Period size: 138 Copynumber: 1.9 Consensus size: 138
128669 TATTAATAGT
* * * *
128679 GTTATTACCATAGAGTCTTATCTCATGGGGAATACATTTTTGCTAAACACTGAAATTATTGTCAA
1 GTTACTACCATAGAGTCTTATCTCATGGGGAAGACATTTCTGCTAAACACTGAAATTATTGCCAA
* * *
128744 CCATCTAGGTCTAGAAAATAAGGGTATTGATACTGAGGATGAATTTATTCCTGGTTCTATAAACC
66 CCATCTAGGTCCAGAAAATAAGGGTATAGATACTGAGGATGAATTTATTCATGGTTCTATAAACC
128809 CCGATTTG
131 CCGATTTG
* * *
128817 GTTACTACCCTAGAGTCTTATCTCATGGGGAAGACATTTCTGCTAGACGCTGAAATTATTGCCAA
1 GTTACTACCATAGAGTCTTATCTCATGGGGAAGACATTTCTGCTAAACACTGAAATTATTGCCAA
* *
128882 CCATCTAGGTCCAGAAAATAGGGGTATAGATACTGAGGATGAATTTATTCATGGTTCTCTAAACC
66 CCATCTAGGTCCAGAAAATAAGGGTATAGATACTGAGGATGAATTTATTCATGGTTCTATAAACC
128947 C
131 C
128948 TGACTCTATT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 119 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (138 bp):
GTTACTACCATAGAGTCTTATCTCATGGGGAAGACATTTCTGCTAAACACTGAAATTATTGCCAA
CCATCTAGGTCCAGAAAATAAGGGTATAGATACTGAGGATGAATTTATTCATGGTTCTATAAACC
CCGATTTG
Found at i:133018 original size:11 final size:9
Alignment explanation
Indices: 132985--133023 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
132975 TACAAAAAAC
132985 TTTAATCCA
1 TTTAATCCA
132994 -TTAATCCA
1 TTTAATCCA
133002 TTTAATCCA
1 TTTAATCCA
133011 CGTTTAATCCA
1 --TTTAATCCA
133022 TT
1 TT
133024 GAATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.30
9 10 0.37
11 9 0.33
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.44
Consensus pattern (9 bp):
TTTAATCCA
Found at i:134425 original size:15 final size:15
Alignment explanation
Indices: 134407--134442 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
134397 CAGCAACGGC
134407 GGCAGTGATATCGGT
1 GGCAGTGATATCGGT
* *
134422 GGCAGTGATGTTGGT
1 GGCAGTGATATCGGT
134437 GGCAGT
1 GGCAGT
134443 AACGTCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.44, T:0.28
Consensus pattern (15 bp):
GGCAGTGATATCGGT
Found at i:138446 original size:2 final size:2
Alignment explanation
Indices: 138439--138468 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
138429 GCCTTATAGT
138439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
138469 GTTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:148005 original size:18 final size:18
Alignment explanation
Indices: 147979--148030 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
147969 TGTAGTATGA
*
147979 GATTTAAATAGTAAAAGC
1 GATTTAAATAATAAAAGC
*
147997 GATTAAAATAAATAAAAGC
1 GATTTAAAT-AATAAAAGC
*
148016 AATTTAAATAA-AAAA
1 GATTTAAATAATAAAA
148031 TAAGAGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 15 0.52
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.25
Consensus pattern (18 bp):
GATTTAAATAATAAAAGC
Found at i:149697 original size:13 final size:13
Alignment explanation
Indices: 149681--149705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
149671 TTTTCATGTA
149681 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
149694 TTTTTTCTTTTT
1 TTTTTTCTTTTT
149706 TTCGAACAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:149722 original size:25 final size:25
Alignment explanation
Indices: 149694--149749 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
149684 TTTCTTTTTC
149694 TTTTTTCTTTTTTTCGAACAG-TAT
1 TTTTTTCTTTTTTTCGAACAGTTAT
* *
149718 TTTTTTCTTCTTTTTCGAACTGTTGT
1 TTTTTTCTT-TTTTTCGAACAGTTAT
149744 TTTTTT
1 TTTTTT
149750 TCCCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 9 0.32
25 11 0.39
26 8 0.29
ACGTcount: A:0.11, C:0.12, G:0.09, T:0.68
Consensus pattern (25 bp):
TTTTTTCTTTTTTTCGAACAGTTAT
Found at i:149746 original size:24 final size:24
Alignment explanation
Indices: 149695--149747 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
149685 TTCTTTTTCT
*
149695 TTTTTCTTTTTTTCGAACAGTATT
1 TTTTTCTTTTTTTCGAACAGTATG
*
149719 TTTTTCTTCTTTTTCGAACTGT-TG
1 TTTTTCTT-TTTTTCGAACAGTATG
149743 TTTTT
1 TTTTT
149748 TTTCCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.66
Consensus pattern (24 bp):
TTTTTCTTTTTTTCGAACAGTATG
Found at i:153960 original size:23 final size:23
Alignment explanation
Indices: 153929--153984 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
153919 CTGAATTCGA
*
153929 TTCTTCTTCTGGATTTGTTTGTT
1 TTCTCCTTCTGGATTTGTTTGTT
153952 TTCTCCTTCTGGATTTGTTTGTT
1 TTCTCCTTCTGGATTTGTTTGTT
153975 TTCTCCTTCT
1 TTCTCCTTCT
153985 TTCCCGAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.04, C:0.20, G:0.14, T:0.62
Consensus pattern (23 bp):
TTCTCCTTCTGGATTTGTTTGTT
Found at i:154349 original size:19 final size:19
Alignment explanation
Indices: 154303--154354 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
154293 ATAGTATCAG
* *
154303 ATTTAAAT-AGTAAAAGCG
1 ATTTAAATAAATAAAAGCA
154321 A-TTAAGATAAATAAAAGCA
1 ATTTAA-ATAAATAAAAGCA
154340 ATTTAAATAAA-AAAA
1 ATTTAAATAAATAAAA
154355 ATAAGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 7 0.24
19 14 0.48
20 4 0.14
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.25
Consensus pattern (19 bp):
ATTTAAATAAATAAAAGCA
Found at i:158564 original size:17 final size:17
Alignment explanation
Indices: 158542--158576 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
158532 GATCCTGTGT
158542 TTCATAGAACCATATGA
1 TTCATAGAACCATATGA
158559 TTCATAGAACCATATGA
1 TTCATAGAACCATATGA
158576 T
1 T
158577 GTACTCGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (17 bp):
TTCATAGAACCATATGA
Found at i:161227 original size:83 final size:81
Alignment explanation
Indices: 161140--161296 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
161130 TAGTGAACTT
161140 TTTTTACTTTTTTATATT-TTTTCATTT-ATGTTCTTTTTTAATTTAGCCATATTTTATATTTAT
1 TTTTTACTTTTTTATATTCTTTT--TTTCAT-TT-TTTTTTAATTTAGCCAT-TTTTATATTTAT
161203 T-TTCTATT-TTTAGGTGACCA
61 TATT-TATTATTTAGGTGACCA
161223 TTTTTACTTTTTTATATTCTTTTTTTCATTTTTTTTTAATTTAGCCATTTTTATATTTATTATTT
1 TTTTTACTTTTTTATATTCTTTTTTTCATTTTTTTTTAATTTAGCCATTTTTATATTTATTATTT
161288 ATTATTTAG
66 ATTATTTAG
161297 TTTTTTAGGG
Statistics
Matches: 70, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
80 17 0.24
81 24 0.34
82 5 0.07
83 20 0.29
84 4 0.06
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.67
Consensus pattern (81 bp):
TTTTTACTTTTTTATATTCTTTTTTTCATTTTTTTTTAATTTAGCCATTTTTATATTTATTATTT
ATTATTTAGGTGACCA
Done.